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commit/galaxy-central: greg: Add the ability to deactivate / activate installed tool shed repositories. When a repository is deactivated, it's contained tools are eliminated from the tool panel on the fly. Similarly, if a deactivated repository is activated, it's contained tools are loaded into the tool panel on the fly. This works for tools contained in sections or outside sections in the tool panel.
by Bitbucket 13 Jan '12

13 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3d9f0ce7bb61/ changeset: 3d9f0ce7bb61 user: greg date: 2012-01-13 21:29:04 summary: Add the ability to deactivate / activate installed tool shed repositories. When a repository is deactivated, it's contained tools are eliminated from the tool panel on the fly. Similarly, if a deactivated repository is activated, it's contained tools are loaded into the tool panel on the fly. This works for tools contained in sections or outside sections in the tool panel. Also fix a bug which resulted in a server error when installing a tool shed repository that includs a .loc.sample file. affected #: 10 files diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -38,13 +38,13 @@ self.install_section( elem ) def install_repository( self, elem, section_name='', section_id='' ): # Install a single repository into the tool config. If outside of any sections, the entry looks something like: - # <repository name="cut_wrapper" description="Galaxy wrapper for the Cut tool" changeset_revision="f3ed6cfe6402"> + # <repository name="cut_wrapper" description="Galaxy wrapper for the Cut tool" installed_changeset_revision="f3ed6cfe6402"> # <tool id="Cut1" version="1.0.1" /> # </repository> name = elem.get( 'name' ) description = elem.get( 'description' ) changeset_revision = elem.get( 'changeset_revision' ) - # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<changeset revision> + # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos', self.repository_owner, name, changeset_revision ) if self.__isinstalled( elem, clone_dir ): log.debug( "Skipping automatic install of repository '%s' because it has already been installed in location '%s'" % ( name, clone_dir ) ) @@ -61,6 +61,7 @@ new_section_elem = Element( 'section' ) new_section_elem.attrib[ 'name' ] = section_name new_section_elem.attrib[ 'id' ] = section_id + new_section_elem.attrib[ 'version' ] = '' tool_section = ToolSection( new_section_elem ) self.app.toolbox.tool_panel[ section_key ] = tool_section else: @@ -74,7 +75,7 @@ returncode, tmp_name = update_repository( current_working_dir, relative_install_dir, changeset_revision ) if returncode == 0: metadata_dict = load_repository_contents( app=self.app, - name=name, + repository_name=name, description=description, owner=self.repository_owner, changeset_revision=changeset_revision, @@ -124,7 +125,7 @@ def install_section( self, elem ): # Install 1 or more repositories into a section in the tool config. An entry looks something like: # <section name="EMBOSS" id="EMBOSSLite"> - # <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="bdd88ae5d0ac"> + # <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" installed_changeset_revision="bdd88ae5d0ac"> # <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" /> # ... # </repository> diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -24,6 +24,7 @@ from galaxy.tools.actions import DefaultToolAction from galaxy.tools.deps import DependencyManager from galaxy.model import directory_hash_id +from galaxy.model.orm import * from galaxy.util.none_like import NoneDataset from galaxy.datatypes import sniff from cgi import FieldStorage @@ -37,15 +38,11 @@ pass class ToolBox( object ): - """ - Container for a collection of tools - """ - + """Container for a collection of tools""" def __init__( self, config_filenames, tool_root_dir, app ): """ - Create a toolbox from the config file names by `config_filename`, - using `tool_root_directory` as the base directory for finding - individual tool config files. + Create a toolbox from the config files named by `config_filenames`, using + `tool_root_dir` as the base directory for finding individual tool config files. """ # The shed_tool_confs dictionary contains shed_conf_filename : tool_path pairs. self.shed_tool_confs = {} @@ -62,7 +59,7 @@ try: self.init_tools( config_filename ) except: - log.exception( "ToolBox error reading %s", config_filename ) + log.exception( "Error loading tools defined in config %s", config_filename ) def init_tools( self, config_filename ): """ Read the configuration file and load each tool. @@ -82,7 +79,7 @@ log.info("removing all tool tag associations (" + str( self.sa_session.query( self.app.model.ToolTagAssociation ).count() ) + ")") self.sa_session.query( self.app.model.ToolTagAssociation ).delete() self.sa_session.flush() - log.info( "parsing the tool configuration %s" % config_filename ) + log.info( "Parsing the tool configuration %s" % config_filename ) tree = util.parse_xml( config_filename ) root = tree.getroot() tool_path = root.get( 'tool_path' ) @@ -94,53 +91,107 @@ tool_path = self.tool_root_dir for elem in root: if elem.tag == 'tool': - self.load_tool_tag_set( elem, self.tool_panel, tool_path, guid=elem.get( 'guid' ) ) + self.load_tool_tag_set( elem, self.tool_panel, tool_path, guid=elem.get( 'guid' ), section=None ) elif elem.tag == 'workflow': self.load_workflow_tag_set( elem, self.tool_panel ) - elif elem.tag == 'section' : + elif elem.tag == 'section': self.load_section_tag_set( elem, self.tool_panel, tool_path ) elif elem.tag == 'label': self.load_label_tag_set( elem, self.tool_panel ) - def load_tool_tag_set( self, elem, panel_dict, tool_path, guid=None ): + def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): + return self.sa_session.query( self.app.model.ToolShedRepository ) \ + .filter( and_( self.app.model.ToolShedRepository.table.c.tool_shed == tool_shed, + self.app.model.ToolShedRepository.table.c.name == name, + self.app.model.ToolShedRepository.table.c.owner == owner, + self.app.model.ToolShedRepository.table.c.installed_changeset_revision == installed_changeset_revision ) ) \ + .first() + def load_tool_tag_set( self, elem, panel_dict, tool_path, guid=None, section=None ): try: path = elem.get( "file" ) - tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) if guid is not None: - # Tool was installed from a Galaxy tool shed. - tool.tool_shed = elem.find( "tool_shed" ).text - tool.repository_name = elem.find( "repository_name" ).text - tool.repository_owner = elem.find( "repository_owner" ).text - tool.changeset_revision = elem.find( "changeset_revision" ).text - tool.old_id = elem.find( "id" ).text - tool.version = elem.find( "version" ).text - if self.app.config.get_bool( 'enable_tool_tags', False ): - tag_names = elem.get( "tags", "" ).split( "," ) - for tag_name in tag_names: - if tag_name == '': - continue - tag = self.sa_session.query( self.app.model.Tag ).filter_by( name=tag_name ).first() - if not tag: - tag = self.app.model.Tag( name=tag_name ) - self.sa_session.add( tag ) - self.sa_session.flush() - tta = self.app.model.ToolTagAssociation( tool_id=tool.id, tag_id=tag.id ) - self.sa_session.add( tta ) - self.sa_session.flush() - else: - for tagged_tool in tag.tagged_tools: - if tagged_tool.tool_id == tool.id: - break + # The tool is contained in an installed tool shed repository, so load + # the tool only if the repository has not been marked deleted. + tool_shed = elem.find( "tool_shed" ).text + repository_name = elem.find( "repository_name" ).text + repository_owner = elem.find( "repository_owner" ).text + installed_changeset_revision_elem = elem.find( "installed_changeset_revision" ) + if installed_changeset_revision_elem is None: + # Backward compatibility issue - the tag used to be named 'changeset_revision'. + installed_changeset_revision_elem = elem.find( "changeset_revision" ) + installed_changeset_revision = installed_changeset_revision_elem.text + tool_shed_repository = self.__get_tool_shed_repository( tool_shed, repository_name, repository_owner, installed_changeset_revision ) + if tool_shed_repository: + # Only load tools if the repository is not deactivated or uninstalled. + can_load = not tool_shed_repository.deleted + if can_load: + metadata = tool_shed_repository.metadata + update_needed = False + if 'tool_panel_section' in metadata: + if section: + # If the tool_panel_section dictionary is included in the metadata, update it if necessary. + tool_panel_section = metadata[ 'tool_panel_section' ] + if tool_panel_section [ 'id' ] != section.id or \ + tool_panel_section [ 'version' ] != section.version or \ + tool_panel_section [ 'name' ] != section.name: + tool_panel_section [ 'id' ] = section.id + tool_panel_section [ 'version' ] = section.version + tool_panel_section [ 'name' ] = section.name + update_needed = True else: + # The tool_panel_section was introduced late, so set it's value if its missing in the metadata. + if section: + tool_panel_section = dict( id=section.id, version=section.version, name=section.name ) + update_needed = True + else: + tool_panel_section = dict( id='', version='', name='' ) + update_needed = True + if update_needed: + metadata[ 'tool_panel_section' ] = tool_panel_section + tool_shed_repository.metadata = metadata + self.sa_session.add( tool_shed_repository ) + self.sa_session.flush() + else: + # If there is not yet a tool_shed_repository record, we're in the process of installing + # a new repository, so any included tools can be loaded into the tool panel. + can_load = True + else: + can_load = True + if can_load: + tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) + if guid is not None: + tool.tool_shed = tool_shed + tool.repository_name = repository_name + tool.repository_owner = repository_owner + tool.installed_changeset_revision = installed_changeset_revision + tool.old_id = elem.find( "id" ).text + tool.version = elem.find( "version" ).text + if self.app.config.get_bool( 'enable_tool_tags', False ): + tag_names = elem.get( "tags", "" ).split( "," ) + for tag_name in tag_names: + if tag_name == '': + continue + tag = self.sa_session.query( self.app.model.Tag ).filter_by( name=tag_name ).first() + if not tag: + tag = self.app.model.Tag( name=tag_name ) + self.sa_session.add( tag ) + self.sa_session.flush() tta = self.app.model.ToolTagAssociation( tool_id=tool.id, tag_id=tag.id ) self.sa_session.add( tta ) self.sa_session.flush() - if tool.id not in self.tools_by_id: - # Allow for the same tool to be loaded into multiple places in the - # tool panel. - self.tools_by_id[ tool.id ] = tool - key = 'tool_' + tool.id - panel_dict[ key ] = tool - log.debug( "Loaded tool: %s %s" % ( tool.id, tool.version ) ) + else: + for tagged_tool in tag.tagged_tools: + if tagged_tool.tool_id == tool.id: + break + else: + tta = self.app.model.ToolTagAssociation( tool_id=tool.id, tag_id=tag.id ) + self.sa_session.add( tta ) + self.sa_session.flush() + if tool.id not in self.tools_by_id: + # Allow for the same tool to be loaded into multiple places in the tool panel. + self.tools_by_id[ tool.id ] = tool + key = 'tool_' + tool.id + panel_dict[ key ] = tool + log.debug( "Loaded tool: %s %s" % ( tool.id, tool.version ) ) except: log.exception( "error reading tool from path: %s" % path ) def load_workflow_tag_set( self, elem, panel_dict ): @@ -161,22 +212,23 @@ def load_section_tag_set( self, elem, panel_dict, tool_path ): key = 'section_' + elem.get( "id" ) if key in panel_dict: - # Appending a tool to an existing section in self.tool_panel - elems = panel_dict[ key ].elems - log.debug( "Appending to section: %s" % elem.get( "name" ) ) + # Loading an existing section in self.tool_panel + section = panel_dict[ key ] + elems = section.elems + log.debug( "Reloading section: %s" % elem.get( "name" ) ) else: - # Appending a new section to self.tool_panel + # Adding a new section to self.tool_panel section = ToolSection( elem ) elems = section.elems log.debug( "Loading section: %s" % section.name ) - for section_elem in elem: - if section_elem.tag == 'tool': - self.load_tool_tag_set( section_elem, elems, tool_path, guid=section_elem.get( 'guid' ) ) - elif section_elem.tag == 'workflow': - self.load_workflow_tag_set( section_elem, elems ) - elif section_elem.tag == 'label': - self.load_label_tag_set( section_elem, elems ) - if key not in panel_dict: + for sub_elem in elem: + if sub_elem.tag == 'tool': + self.load_tool_tag_set( sub_elem, elems, tool_path, guid=sub_elem.get( 'guid' ), section=section ) + elif sub_elem.tag == 'workflow': + self.load_workflow_tag_set( sub_elem, elems ) + elif sub_elem.tag == 'label': + self.load_label_tag_set( sub_elem, elems ) + if key not in panel_dict and section.elems: panel_dict[ key ] = section def load_tool( self, config_file, guid=None ): """ @@ -409,7 +461,7 @@ self.tool_shed = None self.repository_name = None self.repository_owner = None - self.changeset_revision = None + self.installed_changeset_revision = None self.old_id = None self.version = None # Parse XML element containing configuration diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -3,7 +3,6 @@ from time import strftime from galaxy import util from galaxy.util.json import * -from galaxy.tools import ToolSection from galaxy.tools.search import ToolBoxSearch from galaxy.model.orm import * @@ -78,6 +77,17 @@ os.chdir( current_working_dir ) tmp_stderr.close() return returncode, tmp_name +def copy_sample_loc_file( app, filename ): + """Copy xxx.loc.sample to ~/tool-data/xxx.loc.sample and ~/tool-data/xxx.loc""" + head, sample_loc_file = os.path.split( filename ) + loc_file = sample_loc_file.replace( '.sample', '' ) + tool_data_path = os.path.abspath( app.config.tool_data_path ) + # It's ok to overwrite the .sample version of the file. + shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) + # Only create the .loc file if it does not yet exist. We don't + # overwrite it in case it contains stuff proprietary to the local instance. + if not os.path.exists( os.path.join( tool_data_path, loc_file ) ): + shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) ) def create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict, owner='' ): # This method is used by the InstallManager, which does not have access to trans. sa_session = app.model.context.current @@ -149,7 +159,7 @@ if datatypes: metadata_dict[ 'datatypes' ] = datatypes return metadata_dict -def generate_metadata( toolbox, relative_install_dir, repository_clone_url ): +def generate_metadata( toolbox, relative_install_dir, repository_clone_url, tool_section_dict=None ): """ Browse the repository files on disk to generate metadata. Since we are using disk files, it is imperative that the repository is updated to the desired change set revision before metadata @@ -158,6 +168,11 @@ metadata_dict = {} sample_files = [] datatypes_config = None + # Keep track of the section in the tool panel in which this repository's tools will be contained. + if tool_section_dict: + metadata_dict[ 'tool_panel_section' ] = tool_section_dict + else: + metadata_dict[ 'tool_panel_section' ] = dict( id='', version='', name='' ) # Find datatypes_conf.xml if it exists. for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0: @@ -264,6 +279,7 @@ def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, repository_tools_tups, tool_section=None, owner='' ): """Generate a list of ElementTree Element objects for each section or list of tools.""" elem_list = [] + tool_elem = None tmp_url = clean_repository_clone_url( repository_clone_url ) if not owner: owner = get_repository_owner( tmp_url ) @@ -271,6 +287,7 @@ root_elem = Element( 'section' ) root_elem.attrib[ 'name' ] = tool_section.name root_elem.attrib[ 'id' ] = tool_section.id + root_elem.attrib[ 'version' ] = tool_section.version for repository_tool_tup in repository_tools_tups: tool_file_path, guid, tool = repository_tool_tup if tool_section: @@ -285,7 +302,7 @@ repository_name_elem.text = repository_name repository_owner_elem = SubElement( tool_elem, 'repository_owner' ) repository_owner_elem.text = owner - changeset_revision_elem = SubElement( tool_elem, 'changeset_revision' ) + changeset_revision_elem = SubElement( tool_elem, 'installed_changeset_revision' ) changeset_revision_elem.text = changeset_revision id_elem = SubElement( tool_elem, 'id' ) id_elem.text = tool.id @@ -293,7 +310,7 @@ version_elem.text = tool.version if tool_section: elem_list.append( root_elem ) - else: + elif tool_elem: elem_list.append( tool_elem ) return elem_list def generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ): @@ -324,6 +341,15 @@ if repo_path.startswith( '/' ): repo_path = repo_path.replace( '/', '', 1 ) return repo_path.lstrip( '/' ).split( '/' )[ 0 ] +def get_repository_tools_tups( app, metadata_dict ): + repository_tools_tups = [] + if 'tools' in metadata_dict: + for tool_dict in metadata_dict[ 'tools' ]: + relative_path = tool_dict[ 'tool_config' ] + guid = tool_dict[ 'guid' ] + tool = app.toolbox.load_tool( os.path.abspath( relative_path ) ) + repository_tools_tups.append( ( relative_path, guid, tool ) ) + return repository_tools_tups def get_tool_id_guid_map( app, tool_id, version, tool_shed, repository_owner, repository_name ): # This method is used by the InstallManager, which does not have access to trans. sa_session = app.model.context.current @@ -545,7 +571,7 @@ # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules ) return converter_path, display_path -def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, +def load_repository_contents( app, repository_name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): # This method is used by the InstallManager, which does not have access to trans. # Generate the metadata for the installed tool shed repository. It is imperative that @@ -556,7 +582,16 @@ # and when updates have been pulled to previously installed repositories (in which case the # default value None is set for tool_section and shed_tool_conf, and the value of new_install # is passed as False). - metadata_dict = generate_metadata( app.toolbox, relative_install_dir, repository_clone_url ) + if tool_section: + section_id = tool_section.id + section_version = tool_section.version + section_name = tool_section.name + else: + section_id = '' + section_version = '' + section_name = '' + tool_section_dict = dict( id=section_id, version=section_version, name=section_name ) + metadata_dict = generate_metadata( app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) if 'datatypes_config' in metadata_dict: datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] ) # Load data types required by tools. @@ -568,12 +603,7 @@ # Load proprietary datatype display applications app.datatypes_registry.load_display_applications( display_path=display_path ) if 'tools' in metadata_dict: - repository_tools_tups = [] - for tool_dict in metadata_dict[ 'tools' ]: - relative_path = tool_dict[ 'tool_config' ] - guid = tool_dict[ 'guid' ] - tool = app.toolbox.load_tool( os.path.abspath( relative_path ) ) - repository_tools_tups.append( ( relative_path, guid, tool ) ) + repository_tools_tups = get_repository_tools_tups( app, metadata_dict ) if repository_tools_tups: sample_files = metadata_dict.get( 'sample_files', [] ) # Handle missing data table entries for tool parameters that are dynamically generated select lists. @@ -583,28 +613,20 @@ # Handle tools that use fabric scripts to install dependencies. handle_tool_dependencies( current_working_dir, relative_install_dir, repository_tools_tups ) if new_install: - # Generate a new entry for the tool config. - elem_list = generate_tool_panel_elem_list( name, - repository_clone_url, - changeset_revision, - repository_tools_tups, - tool_section=tool_section, - owner=owner ) - if tool_section: - for section_elem in elem_list: - # Load the section into the tool panel. - app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path ) - else: - # Load the tools into the tool panel outside of any sections. - for tool_elem in elem_list: - guid = tool_elem.get( 'guid' ) - app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid ) - for elem_entry in elem_list: - # Append the new entry (either section or list of tools) to the shed_tool_config file. - add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry ) - if app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. - app.toolbox_search = ToolBoxSearch( app.toolbox ) + load_altered_part_of_tool_panel( app=app, + repository_name=repository_name, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + repository_tools_tups=repository_tools_tups, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + tool_path=tool_path, + owner=owner, + add_to_config=True ) + else: + if app.toolbox_search.enabled: + # If search support for tools is enabled, index the new installed tools. + app.toolbox_search = ToolBoxSearch( app.toolbox ) # Remove the temporary file try: os.unlink( tmp_name ) @@ -612,9 +634,34 @@ pass # Add a new record to the tool_shed_repository table if one doesn't # already exist. If one exists but is marked deleted, undelete it. - log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name ) - create_or_update_tool_shed_repository( app, name, description, changeset_revision, repository_clone_url, metadata_dict ) + log.debug( "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % repository_name ) + create_or_update_tool_shed_repository( app, repository_name, description, changeset_revision, repository_clone_url, metadata_dict ) return metadata_dict +def load_altered_part_of_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, + tool_section, shed_tool_conf, tool_path, owner, add_to_config=True ): + # Generate a new entry for the tool config. + elem_list = generate_tool_panel_elem_list( repository_name, + repository_clone_url, + changeset_revision, + repository_tools_tups, + tool_section=tool_section, + owner=owner ) + if tool_section: + for section_elem in elem_list: + # Load the section into the tool panel. + app.toolbox.load_section_tag_set( section_elem, app.toolbox.tool_panel, tool_path ) + else: + # Load the tools into the tool panel outside of any sections. + for tool_elem in elem_list: + guid = tool_elem.get( 'guid' ) + app.toolbox.load_tool_tag_set( tool_elem, app.toolbox.tool_panel, tool_path=tool_path, guid=guid ) + if add_to_config: + # Append the new entry (either section or list of tools) to the shed_tool_config file. + for elem_entry in elem_list: + add_shed_tool_conf_entry( app, shed_tool_conf, elem_entry ) + if app.toolbox_search.enabled: + # If search support for tools is enabled, index the new installed tools. + app.toolbox_search = ToolBoxSearch( app.toolbox ) def pull_repository( current_working_dir, repo_files_dir, name ): # Pull the latest possible contents to the repository. log.debug( "Pulling latest updates to the repository named '%s'" % name ) diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1323,7 +1323,6 @@ status = kwd.get( 'status', 'done' ) if webapp == 'galaxy': cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ - .filter( trans.model.ToolShedRepository.deleted == False ) \ .first() return trans.fill_template( '/webapps/galaxy/admin/index.mako', webapp=webapp, @@ -2422,17 +2421,6 @@ ## ---- Utility methods ------------------------------------------------------- -def copy_sample_loc_file( app, filename ): - """Copy xxx.loc.sample to ~/tool-data/xxx.loc.sample and ~/tool-data/xxx.loc""" - head, sample_loc_file = os.path.split( filename ) - loc_file = sample_loc_file.replace( '.sample', '' ) - tool_data_path = os.path.abspath( app.config.tool_data_path ) - # It's ok to overwrite the .sample version of the file. - shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) - # Only create the .loc file if it does not yet exist. We don't - # overwrite it in case it contains stuff proprietary to the local instance. - if not os.path.exists( os.path.join( tool_data_path, loc_file ) ): - shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, loc_file ) ) def get_user( trans, user_id ): """Get a User from the database by id.""" user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1,5 +1,6 @@ from galaxy.web.controllers.admin import * from galaxy.util.shed_util import * +from galaxy import tools log = logging.getLogger( __name__ ) @@ -101,6 +102,14 @@ operations = [ grids.GridOperation( "Get updates", allow_multiple=False, condition=( lambda item: not item.deleted ), + async_compatible=False ), + grids.GridOperation( "Deactivate or uninstall", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ), + grids.GridOperation( "Activate or reinstall", + allow_multiple=False, + condition=( lambda item: item.deleted ), async_compatible=False ) ] standard_filters = [] default_filter = dict( deleted="False" ) @@ -108,8 +117,7 @@ preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) \ - .filter( self.model_class.table.c.deleted == False ) + return trans.sa_session.query( self.model_class ) class AdminToolshed( AdminGalaxy ): @@ -140,7 +148,12 @@ return self.manage_repository( trans, **kwd ) if operation == "get updates": return self.check_for_updates( trans, **kwd ) - kwd[ 'message' ] = 'Names of repositories for which updates are available are highlighted in red.' + if operation == "activate or reinstall": + return self.activate_or_reinstall_repository( trans, **kwd ) + if operation == "deactivate or uninstall": + return self.deactivate_or_uninstall_repository( trans, **kwd ) + if 'message' not in kwd or not kwd[ 'message' ]: + kwd[ 'message' ] = 'Names of repositories for which updates are available are highlighted in red.' return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin @@ -218,7 +231,8 @@ elem = Element( 'section' ) elem.attrib[ 'name' ] = new_tool_panel_section elem.attrib[ 'id' ] = section_id - tool_section = ToolSection( elem ) + elem.attrib[ 'version' ] = '' + tool_section = tools.ToolSection( elem ) trans.app.toolbox.tool_panel[ new_section_key ] = tool_section else: section_key = 'section_%s' % tool_panel_section @@ -245,7 +259,7 @@ if returncode == 0: owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) ) metadata_dict = load_repository_contents( app=trans.app, - name=name, + repository_name=name, description=description, owner=owner, changeset_revision=changeset_revision, @@ -305,13 +319,180 @@ status=status ) @web.expose @web.require_admin + def deactivate_or_uninstall_repository( self, trans, **kwd ): + # TODO: handle elimination of workflows loaded into the tool panel that are in the repository being deactivated. + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + remove_from_disk = params.get( 'remove_from_disk', '' ) + remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) + repository = get_repository( trans, kwd[ 'id' ] ) + if params.get( 'deactivate_or_uninstall_repository_button', False ): + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) + metadata = repository.metadata + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + # Generate the list of tool panel keys derived from the tools included in the repository. + repository_tool_panel_keys = [] + if repository_tools_tups: + repository_tool_panel_keys = [ 'tool_%s' % repository_tools_tup[ 1 ] for repository_tools_tup in repository_tools_tups ] + tool_panel_section = metadata[ 'tool_panel_section' ] + section_id = tool_panel_section[ 'id' ] + if section_id in [ '' ]: + # If the repository includes tools, they were loaded into the tool panel outside of any sections. + tool_section = None + self.__deactivate( trans, repository_tool_panel_keys ) + else: + # If the repository includes tools, they were loaded into the tool panel inside a section. + section_key = 'section_%s' % str( section_id ) + if section_key in trans.app.toolbox.tool_panel: + tool_section = trans.app.toolbox.tool_panel[ section_key ] + self.__deactivate( trans, repository_tool_panel_keys, tool_section=tool_section, section_key=section_key ) + else: + # The tool panel section could not be found, so handle deactivating tools + # as if they were loaded into the tool panel outside of any sections. + tool_section = None + self.__deactivate( trans, repository_tool_panel_keys ) + repository.deleted = True + trans.sa_session.add( repository ) + trans.sa_session.flush() + repository_clone_url = self.__generate_clone_url( trans, repository ) + load_altered_part_of_tool_panel( app=trans.app, + repository_name=repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + tool_section=tool_section, + shed_tool_conf=shed_tool_conf, + tool_path=tool_path, + owner=repository.owner, + add_to_config=False ) + if remove_from_disk_checked: + # TODO: Remove repository from disk and alter the shed tool config. + message = 'The repository named <b>%s</b> has been uninstalled.' % repository.name + else: + message = 'The repository named <b>%s</b> has been deactivated.' % repository.name + status = 'done' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=message, + status=status ) ) + remove_from_disk_check_box = CheckboxField( 'remove_from_disk', checked=remove_from_disk_checked ) + return trans.fill_template( '/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako', + repository=repository, + remove_from_disk_check_box=remove_from_disk_check_box, + message=message, + status=status ) + def __deactivate( self, trans, repository_tool_panel_keys, tool_section=None, section_key=None ): + # Delete tools loaded into the tool panel. If the tool_panel is received, + # the tools were loaded into the tool panel outside of any sections. If + # the tool_section is received, all tools were loaded into that section. + if tool_section: + # The tool_section.elems dictionary looks something like: + # {'tool_gvk.bx.psu.edu:9009/repos/test/filter/Filter1/1.0.1': <galaxy.tools.Tool instance at 0x10769ae60>} + for item_id, item in tool_section.elems.items(): + if item_id in repository_tool_panel_keys: + del tool_section.elems[ item_id ] + if not tool_section.elems: + del trans.app.toolbox.tool_panel[ section_key ] + else: + # The tool panel looks something like: + # {'tool_gvk.bx.psu.edu:9009/repos/test/blast2go/blast2go/0.0.2': <galaxy.tools.Tool instance at 0x1076a5f80>} + for item_id, item in trans.app.toolbox.tool_panel.items(): + if item_id in repository_tool_panel_keys: + del trans.app.toolbox.tool_panel[ item_id ] + @web.expose + @web.require_admin + def activate_or_reinstall_repository( self, trans, **kwd ): + # TODO: handle re-introduction of workflows loaded into the tool panel that are in the repository being activated. + repository = get_repository( trans, kwd[ 'id' ] ) + repository.deleted = False + trans.sa_session.add( repository ) + trans.sa_session.flush() + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) + metadata = repository.metadata + repository_tools_tups = get_repository_tools_tups( trans.app, metadata ) + tool_panel_section = metadata[ 'tool_panel_section' ] + section_id = tool_panel_section[ 'id' ] + # Generate the list of tool panel keys derived from the tools included in the repository. + #repository_tool_panel_keys = [] + #if repository_tools_tups: + # repository_tool_panel_keys = [ 'tool_%s' % repository_tools_tup[ 1 ] for repository_tools_tup in repository_tools_tups ] + if section_id in [ '' ]: + # If the repository includes tools, reload them into the tool panel outside of any sections. + self.__activate( trans, repository, repository_tools_tups, tool_section=None, section_key=None ) + else: + # If the repository includes tools, reload them into the appropriate tool panel section. + section_key = 'section_%s' % str( section_id ) + if section_key in trans.app.toolbox.tool_panel: + # Load the repository tools into a section that still exists in the tool panel. + tool_section = trans.app.toolbox.tool_panel[ section_key ] + self.__activate( trans, repository, repository_tools_tups, tool_section=tool_section, section_key=section_key ) + else: + # Load the repository tools into a section that no longer exists in the tool panel. + # We first see if the section exists in the tool config, which will be the case if + # the repository was only deactivated and not uninstalled. + section_loaded = False + for tcf in trans.app.config.tool_configs: + # Only inspect tool configs that contain installed tool shed repositories. + if tcf not in [ 'tool_conf.xml' ]: + log.info( "Parsing the tool configuration %s" % tcf ) + tree = util.parse_xml( tcf ) + root = tree.getroot() + tool_path = root.get( 'tool_path' ) + if tool_path is not None: + # Tool configs that contain tools installed from tool shed repositories + # must have a tool_path attribute. + for elem in root: + if elem.tag == 'section': + id_attr = elem.get( 'id' ) + if id_attr == section_id: + tool_section = elem + trans.app.toolbox.load_section_tag_set( tool_section, trans.app.toolbox.tool_panel, tool_path ) + section_loaded = True + break + if section_loaded: + break + message = 'The repository named <b>%s</b> has been activated.' % repository.name + status = 'done' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=message, + status=status ) ) + def __activate( self, trans, repository, repository_tools_tups, tool_section=None, section_key=None ): + if tool_section: + elems = tool_section.elems + for repository_tools_tup in repository_tools_tups: + relative_path, guid, tool = repository_tools_tup + tool.tool_shed = repository.tool_shed + tool.repository_name = repository.name + tool.repository_owner = repository.owner + tool.installed_changeset_revision = repository.installed_changeset_revision + # Set the tool's old_id to the id used before the tool shed existed. + tool.old_id = tool.id + # Set the tool's id to the tool shed guid. + tool.id = guid + if tool_section: + if tool.id not in elems: + elems[ 'tool_%s' % tool.id ] = tool + log.debug( "Reactivated tool: %s %s" % ( tool.id, tool.version ) ) + else: + if tool.id not in trans.app.toolbox.tools_by_id: + # Allow for the same tool to be loaded into multiple places in the tool panel. + trans.app.toolbox.tools_by_id[ tool.id ] = tool + trans.app.toolbox.tool_panel[ 'tool_%s' % tool.id ] = tool + log.debug( "Reactivated tool: %s %s" % ( tool.id, tool.version ) ) + if tool_section: + trans.app.toolbox.tool_panel[ section_key ] = tool_section + log.debug( "Appended reactivated tool to section: %s" % tool_section.name ) + @web.expose + @web.require_admin def manage_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, kwd[ 'id' ] ) description = util.restore_text( params.get( 'description', repository.description ) ) - tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) if params.get( 'edit_repository_button', False ): if description != repository.description: @@ -321,7 +502,12 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = self.__generate_clone_url( trans, repository ) - metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url ) + # In case metadata was previously generated for this repository, we'll + # check to see if it has information needed for the tool_section_dict. + metadata = repository.metadata + if 'tool_panel_section' in metadata: + tool_section_dict = metadata[ 'tool_panel_section' ] + metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url, tool_section_dict=tool_section_dict ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -360,7 +546,7 @@ message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name else: current_working_dir = os.getcwd() - tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) + shed_tool_conf, tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository ) if relative_install_dir: repo_files_dir = os.path.join( relative_install_dir, name ) returncode, tmp_name = pull_repository( current_working_dir, repo_files_dir, name ) @@ -440,17 +626,17 @@ # Get the relative tool installation paths from each of the shed tool configs. shed_tool_confs = trans.app.toolbox.shed_tool_confs relative_install_dir = None - # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs. - for shed_conf_filename, tool_path in shed_tool_confs.items(): + # The shed_tool_confs dictionary contains { shed_tool_conf : tool_path } pairs. + for shed_tool_conf, tool_path in shed_tool_confs.items(): relative_install_dir = os.path.join( tool_path, partial_install_dir ) if os.path.isdir( relative_install_dir ): break - return tool_path, relative_install_dir + return shed_tool_conf, tool_path, relative_install_dir def __generate_tool_path( self, repository_clone_url, changeset_revision ): """ Generate a tool path that guarantees repositories with the same name will always be installed in different directories. The tool path will be of the form: - <tool shed url>/repos/<repository owner>/<repository name>/<changeset revision> + <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision> http://test@bx.psu.edu:9009/repos/test/filter """ tmp_url = clean_repository_clone_url( repository_clone_url ) diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -4,7 +4,7 @@ from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * -from galaxy.util.shed_util import generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata +from galaxy.util.shed_util import copy_sample_loc_file, generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -10,6 +10,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div></ul> diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -0,0 +1,77 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <form name="uninstall_repository" id="uninstall_repository" action="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <div class="form-row"> + <label>Description:</label> + ${repository.description} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Revision:</label> + ${repository.changeset_revision}</a> + </div> + <div class="form-row"> + <label>Tool shed:</label> + ${repository.tool_shed} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Owner:</label> + ${repository.owner} + </div> + <div class="form-row"> + <label>Deleted:</label> + ${repository.deleted} + </div> + <div class="form-row"> + ${remove_from_disk_check_box.get_html( disabled=True )} + <label for="repository" style="display: inline;font-weight:normal;">Check to uninstall (not yet implemented) or leave blank to deactivate</label> + <br/><br/> + <label>Deactivating this repository will result in the following:</label> + <div class="toolParamHelp" style="clear: both;"> + 1. This repository record's deleted column in the tool_shed_repository database table will be set to True. + </div> + <div class="toolParamHelp" style="clear: both;"> + 2. The repository and all of it's contents will remain on disk. + </div> + <div class="toolParamHelp" style="clear: both;"> + 3. If this repository includes tools, they will not be loaded into the tool panel, but the tool config file in which they are defined will not be altered. + </div> + <br/> + <label>Uninstalling (not yet implemented) this repository will result in the following:</label> + <div class="toolParamHelp" style="clear: both;"> + 1. This repository record's deleted column in the tool_shed_repository database table will be set to True. + </div> + <div class="toolParamHelp" style="clear: both;"> + 2. The repository and all of it's contents will be removed from disk. + </div> + <div class="toolParamHelp" style="clear: both;"> + 3. If this repository includes tools, they will be removed from the tool config file in which they are defined and they will not be loaded into the tool panel. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="deactivate_or_uninstall_repository_button" value="Deactivate or Uninstall"/> + </div> + </form> + </div> +</div> diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -8,6 +8,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div></ul> diff -r 4a130280e6142f2c241e33a2bacc6d52e566047c -r 3d9f0ce7bb6138b20c200203014e60a4e9342160 templates/admin/tool_shed_repository/view_tool_metadata.mako --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -8,6 +8,7 @@ <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div></ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: fix reference track display bug.
by Bitbucket 13 Jan '12

13 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a130280e614/ changeset: 4a130280e614 user: jgoecks date: 2012-01-13 17:47:32 summary: Trackster: fix reference track display bug. affected #: 2 files diff -r da1c34c70e254fa559830342c9fa2b5752375e77 -r 4a130280e6142f2c241e33a2bacc6d52e566047c static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. 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S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: 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P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.feature_mapper=aq;this.has_icons=false;if(this.message||!ag){this.has_icons=true;var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(this.message){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(ai,aj,al,af){var ah=this;var ak=false;for(var ag=0;ag<ai.length;ag++){if(ai[ag].has_icons){ak=true;break}}if(ak){for(var ag=0;ag<ai.length;ag++){tile=ai[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af+ai.left_offset,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,ap);new_data_available.resolve(ap)});return new_data_available},get:function(af,ag){return c.prototype.get.call(this,this.gen_key(af,ag))},set_data:function(ag,ah,af){return this.set(this.gen_key(ag,ah),af)},gen_key:function(af,ah){var ag=af+"_"+ah;return ag},split_key:function(af){return af.split("_")}});var G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.feature_mapper=aq;this.has_icons=false;if(this.message||!ag){this.has_icons=true;var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(this.message){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(ai,aj,al,af){var ah=this;var ak=false;for(var ag=0;ag<ai.length;ag++){if(ai[ag].has_icons){ak=true;break}}if(ak){for(var ag=0;ag<ai.length;ag++){tile=ai[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var 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C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r da1c34c70e254fa559830342c9fa2b5752375e77 -r 4a130280e6142f2c241e33a2bacc6d52e566047c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3699,7 +3699,7 @@ seq = seq.data; for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.round(c * w_scale); - ctx.fillText(seq[c], c_start + track.left_offset, 10); + ctx.fillText(seq[c], c_start, 10); } return new Tile(track, tile_index, resolution, canvas, seq); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Bugfix for distributed object store that prevented certain kwargs from being passed to certain methods in the backend store.
by Bitbucket 13 Jan '12

13 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/da1c34c70e25/ changeset: da1c34c70e25 user: natefoo date: 2012-01-13 17:17:25 summary: Bugfix for distributed object store that prevented certain kwargs from being passed to certain methods in the backend store. affected #: 1 file diff -r 6cbf38099b7102b3547595d9949df24b4c699a3c -r da1c34c70e254fa559830342c9fa2b5752375e77 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -306,8 +306,8 @@ shutil.rmtree(path) return True if self.exists(obj, **kwargs): - os.remove(path) - return True + os.remove(path) + return True except OSError, ex: log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex)) return False @@ -909,20 +909,16 @@ def size(self, obj, **kwargs): return self.__call_method('size', obj, 0, False, **kwargs) - def delete(self, obj, entire_dir=False, **kwargs): + def delete(self, obj, **kwargs): return self.__call_method('delete', obj, False, False, **kwargs) - def get_data(self, obj, start=0, count=-1, **kwargs): + def get_data(self, obj, **kwargs): return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs) def get_filename(self, obj, **kwargs): return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) - def update_from_file(self, obj, file_name=None, create=False, **kwargs): - # can raise ObjectLocationMismatch - # TODO: handling create=True here? probably not since create() is called from w/in, so a store will be selected there - #if create and not self.exists(obj, **kwargs): - # store_id = random.choice(self.weighted_backend_names) + def update_from_file(self, obj, **kwargs): return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) def get_object_url(self, obj, **kwargs): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Add missing distributed object store config file option to the sample universe_wsgi.ini.
by Bitbucket 12 Jan '12

12 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6cbf38099b71/ changeset: 6cbf38099b71 user: natefoo date: 2012-01-12 22:30:27 summary: Add missing distributed object store config file option to the sample universe_wsgi.ini. affected #: 1 file diff -r 0cc2440265bd85f95eab3f05b81dc60a5478543d -r 6cbf38099b7102b3547595d9949df24b4c699a3c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -446,16 +446,21 @@ # -- Beta features # Object store mode (valid options are: disk, s3, distributed, hierarchical) -#object_store = s3 +#object_store = disk #aws_access_key = <AWS access key> #aws_secret_key = <AWS secret key> #s3_bucket = <name of an existing S3 bucket> #use_reduced_redundancy = True + # Size (in GB) that the cache used by object store should be limited to. # If the value is not specified, the cache size will be limited only by the file # system size. #object_store_cache_size = 100 +# Configuration file for the distributed object store, if object_store = +# distributed. See the sample at distributed_object_store_conf.xml.sample +#distributed_object_store_config_file = None + # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Fix jQuery 1.7 compatibility bug so that multi-selects are not replaced by search+select and pack scripts.
by Bitbucket 12 Jan '12

12 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0cc2440265bd/ changeset: 0cc2440265bd user: jgoecks date: 2012-01-12 19:26:58 summary: Fix jQuery 1.7 compatibility bug so that multi-selects are not replaced by search+select and pack scripts. affected #: 3 files diff -r 831237b1a55211232eff0daf19501933748f0523 -r 0cc2440265bd85f95eab3f05b81dc60a5478543d static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -204,7 +204,7 @@ } // Skip multi-select because widget cannot handle multi-select. - if (select_elt.attr('multiple') === true) { + if (select_elt.attr('multiple') === 'multiple') { return; } diff -r 831237b1a55211232eff0daf19501933748f0523 -r 0cc2440265bd85f95eab3f05b81dc60a5478543d static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){$("<li/>").html(j).click(i).appendTo(g)}else{$("<li class='head'/>").html(j).appendTo(g)}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'>");h.append(g).append("<div 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both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.message=au;this.feature_mapper=aq;if(this.message||!ag){var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(this.message){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af+ai.left_offset,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,ap);new_data_available.resolve(ap)});return new_data_available},get:function(af,ag){return c.prototype.get.call(this,this.gen_key(af,ag))},set_data:function(ag,ah,af){return this.set(this.gen_key(ag,ah),af)},gen_key:function(af,ah){var ag=af+"_"+ah;return ag},split_key:function(af){return af.split("_")}});var G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.feature_mapper=aq;this.has_icons=false;if(this.message||!ag){this.has_icons=true;var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(this.message){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(ai,aj,al,af){var ah=this;var ak=false;for(var ag=0;ag<ai.length;ag++){if(ai[ag].has_icons){ak=true;break}}if(ak){for(var ag=0;ag<ai.length;ag++){tile=ai[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af+ai.left_offset,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var 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X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: bug fix when padding tiles for display.
by Bitbucket 11 Jan '12

11 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/831237b1a552/ changeset: 831237b1a552 user: jgoecks date: 2012-01-11 20:19:27 summary: Trackster: bug fix when padding tiles for display. affected #: 1 file diff -r b716dc5d0e0eea1f8414cc75743852c02800b0d6 -r 831237b1a55211232eff0daf19501933748f0523 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2511,11 +2511,13 @@ // Attribute init. Tile.call(this, track, index, resolution, canvas, data); this.mode = mode; - this.message = message; this.feature_mapper = feature_mapper; + this.has_icons = false; // Add message + action icons to tile's html. if (this.message || !all_slotted) { + this.has_icons = true; + var tile = this; canvas = this.html_elt.children()[0], @@ -3145,21 +3147,20 @@ var track = this; // - // If some tiles have messages, set padding of tiles without messages - // so features and rows align. + // If some tiles have icons, set padding of tiles without icons so features and rows align. // - var messages_to_show = false; + var icons_present = false; for (var tile_index = 0; tile_index < tiles.length; tile_index++) { - if (tiles[tile_index].message) { - messages_to_show = true; + if (tiles[tile_index].has_icons) { + icons_present = true; break; } } - if (messages_to_show) { + if (icons_present) { for (var tile_index = 0; tile_index < tiles.length; tile_index++) { tile = tiles[tile_index]; - if (!tile.message) { - // Need to align with other tile(s) that have message(s). + if (!tile.has_icons) { + // Need to align with other tile(s) that have icons. tile.html_elt.css("padding-top", ERROR_PADDING); } } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Pack trackster script.
by Bitbucket 11 Jan '12

11 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c3f76217c9fc/ changeset: c3f76217c9fc user: jgoecks date: 2012-01-11 16:00:14 summary: Pack trackster script. affected #: 1 file diff -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 -r c3f76217c9fc95e1acc07fd9cd3d897115d22b4e static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: 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G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var af=true,ah=this.drawables[0].get_type();for(var ag=0;ag<this.drawables.length;ag++){if(this.drawables[ag].get_type()!==ah){af=false;break}}if(af){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(am,aj){for(var ao=0;ao<am.length;ao++){ah=am[ao];if(ah.hidden){continue}var ak="param_"+ao;var at=ai.values[ah.key];var av=$("<div class='form-row' />").appendTo(aj);av.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",at))}else{if(ah.type==="text"){av.append($('<input type="text"/>').attr("id",ak).val(at).click(function(){$(this).select()}))}else{if(ah.type=="select"){var aq=$("<select />").attr("id",ak);for(var an=0;an<ah.options.length;an++){$("<option/>").text(ah.options[an].label).attr("value",ah.options[an].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ah.type==="color"){var ap=$("<input />").attr("id",ak).attr("name",ak).val(at);var ar=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ar);var au=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:ap,color:at});$("<div />").append(ap).append(ar).appendTo(av).bind("click",function(aw){ar.css({left:$(this).position().left+$(ap).width()+5,top:$(this).position().top-($(ar).height()/2)+($(ap).height()/2)}).show();$(document).bind("click.color-picker",function(){ar.hide();$(document).unbind("click.color-picker")});aw.stopPropagation()})}else{av.append($("<input />").attr("id",ak).attr("name",ak).val(at))}}}}if(ah.help){av.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ah,am,ai,ag,ak,al,aq,ao){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.message=aq;this.feature_mapper=ao;if(this.message){var ag=this.html_elt.children()[0],ap=$("<div/>").addClass("tile-message").text(this.message).css({height:C-1,width:ag.width}).prependTo(this.html_elt),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);var an=this;aj.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(ar){ar.stopPropagation()});af.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,at,aw,au,ak,al,an){var ar=this,az=this._gen_tile_cache_key(at,al,aw),ax=aw*Q*au,ag=ax+Q*au;var ay=(af?undefined:ar.tile_cache.get(az));if(ay){ar.show_tile(ay,ak,al);return ay}var ap=true;var av=ar.data_manager.get_data(ax,ag,ar.mode,au,ar.data_url_extra_params);if(is_deferred(av)){ap=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ax,ag,ar.mode,au,view.reference_track.data_url_extra_params);if(is_deferred(am)){ap=false}}if(ap){p(av,an);var ao=ar.mode;if(ao==="Auto"){ao=ar.get_mode(av);ar.update_auto_mode(ao)}var ah=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(aw,au),ax=ai[0],ag=ai[1],at=Math.ceil((ag-ax)*al)+ar.left_offset,aq=ar.get_canvas_height(av,ao,al,at);ah.width=at;ah.height=aq;var ay=ar.draw_tile(av,ah,ao,au,aw,al,am);if(ay!==undefined){ar.tile_cache.set(az,ay);ar.show_tile(ay,ak,al)}return ay}var aj=$.Deferred();$.when(av,am).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,aj,ak,ai,ag,al,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=["Histogram","Line","Filled","Intensity"];M.call(this,ai,ah,ag);this.drawables=[];if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy()}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(af,at,ax,au,ak,am,ao){var ar=this,aB=this._gen_tile_cache_key(at,am,ax),ay=ax*Q*au,ag=ay+Q*au;var aA=(af?undefined:ar.tile_cache.get(aB));if(aA){ar.show_tile(aA,ak,am);return aA}var al=[],ar,ap=true,av,an;for(var aw=0;aw<this.drawables.length;aw++){ar=this.drawables[aw];av=ar.data_manager.get_data(ay,ag,ar.mode,au,ar.data_url_extra_params);if(is_deferred(av)){ap=false}al.push(av);an=null;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=view.reference_track.data_manager.get_data(ay,ag,ar.mode,au,view.reference_track.data_url_extra_params);if(is_deferred(an)){ap=false}}al.push(an)}if(ap){p(av,ao);var ah=ar.view.canvas_manager.new_canvas(),ai=ar._get_tile_bounds(ax,au),ay=ai[0],ag=ai[1],at=Math.ceil((ag-ay)*am),aq=ar.get_canvas_height(av,mode,am,at);ah.width=at;ah.height=aq;var az=0;for(var aw=0;aw<this.drawables.length;aw++,az+=2){ar=this.drawables[aw];av=al[az];an=al[az+1];aA=ar.draw_tile(av,ah,ar.mode,au,ax,am,an)}ar.tile_cache.set(aB,aA);ar.show_tile(aA,ak,am);return aA}var aj=$.Deferred(),ar=this;$.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar);aj.resolve()});return aj}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ah,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ao=ah.getContext("2d");ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af+ai.left_offset,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,ah,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var an=ah.getContext("2d"),af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);an.globalCompositeOperation="darker";al.draw(an,ah.width,ah.height);return new b(this.track,ag,ai,ah,ap.data)},data_and_mode_compatible:function(af,ag){return true},});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{max:ag})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",y,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,ah,at,aw,aA,an,ai){var au=this,ak=this._get_tile_bounds(aA,aw),aD=ak[0],ag=ak[1],aI=25,aj=this.left_offset;if(at==="summary_tree"||at==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aD,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aF=new L.SummaryTreePainter(ar,aD,ag,this.prefs);var av=ah.getContext("2d");av.translate(aj,T);aF.draw(av,ah.width,ah.height);return new k(au,aA,aw,ah,ar.data,ar.max)}var am=[];if(ar.data){var ap=this.filters_manager.filters;for(var ax=0,az=ar.data.length;ax<az;ax++){var al=ar.data[ax];var ay=false;var aq;for(var aC=0,aH=ap.length;aC<aH;aC++){aq=ap[aC];aq.update_attrs(al);if(!aq.keep(al)){ay=true;break}}if(!ay){am.push(al)}}}var aG=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aE=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aF=new (this.painter)(am,aD,ag,this.prefs,at,aG,aE,ai);var aB=null;var av=ah.getContext("2d");av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){slots=this.inc_slots[an].slots;av.translate(aj,0);aB=aF.draw(av,ah.width,ah.height,slots);aB.translation=-aj}return new O(au,aA,aw,ah,ar.data,at,ar.message,aB)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,D=Q/P,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var 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d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented 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am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var 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N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var 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requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,ap);new_data_available.resolve(ap)});return new_data_available},get:function(af,ag){return c.prototype.get.call(this,this.gen_key(af,ag))},set_data:function(ag,ah,af){return this.set(this.gen_key(ag,ah),af)},gen_key:function(af,ah){var ag=af+"_"+ah;return ag},split_key:function(af){return af.split("_")}});var G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view);aj.container.replace_drawable(aj,ai,true);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.message=au;this.feature_mapper=aq;if(this.message||!ag){var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(this.message){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af+ai.left_offset,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var 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N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Standardize code and error messages on 'public name' rather than 'username'
by Bitbucket 11 Jan '12

11 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0d1d62b8be2e/ changeset: 0d1d62b8be2e user: jgoecks date: 2012-01-11 15:44:39 summary: Standardize code and error messages on 'public name' rather than 'username' affected #: 3 files diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/security/validate_user_input.py --- a/lib/galaxy/security/validate_user_input.py +++ b/lib/galaxy/security/validate_user_input.py @@ -1,6 +1,6 @@ import re -VALID_USERNAME_RE = re.compile( "^[a-z0-9\-]+$" ) +VALID_PUBLICNAME_RE = re.compile( "^[a-z0-9\-]+$" ) def validate_email( trans, email, user=None, check_dup=True ): message = '' @@ -14,21 +14,21 @@ message = "User with that email already exists" return message -def validate_username( trans, username, user=None ): +def validate_publicname( trans, publicname, user=None ): # User names must be at least four characters in length and contain only lower-case # letters, numbers, and the '-' character. - if username in [ 'None', None, '' ]: + if publicname in [ 'None', None, '' ]: return '' - if user and user.username == username: + if user and user.username == publicname: return '' - if len( username ) < 4: - return "User name must be at least 4 characters in length" - if len( username ) > 255: - return "User name cannot be more than 255 characters in length" - if not( VALID_USERNAME_RE.match( username ) ): - return "User name must contain only lower-case letters, numbers and '-'" - if trans.sa_session.query( trans.app.model.User ).filter_by( username=username ).first(): - return "This user name is not available" + if len( publicname ) < 4: + return "Public name must be at least 4 characters in length" + if len( publicname ) > 255: + return "Public name cannot be more than 255 characters in length" + if not( VALID_PUBLICNAME_RE.match( publicname ) ): + return "Public name must contain only lower-case letters, numbers and '-'" + if trans.sa_session.query( trans.app.model.User ).filter_by( username=publicname ).first(): + return "Public name is taken; please choose another" return '' def validate_password( trans, password, confirm ): diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -16,7 +16,7 @@ from galaxy.web.form_builder import WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field from galaxy.visualization.tracks.data_providers import get_data_provider from galaxy.visualization.tracks.visual_analytics import get_tool_def -from galaxy.security.validate_user_input import validate_username +from galaxy.security.validate_user_input import validate_publicname from paste.httpexceptions import * from galaxy.exceptions import * @@ -1222,7 +1222,7 @@ def set_public_username( self, trans, id, username, **kwargs ): """ Set user's public username and delegate to sharing() """ user = trans.get_user() - message = validate_username( trans, username, user ) + message = validate_publicname( trans, username, user ) if message: return trans.fill_template( '/sharing_base.mako', item=self.get_item( trans, id ), message=message, status='error' ) user.username = username diff -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 -r 0d1d62b8be2e574f0050a801eedfa59eba2b7563 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -10,7 +10,7 @@ from galaxy.web.form_builder import * from galaxy.util.json import from_json_string, to_json_string from galaxy.web.framework.helpers import iff -from galaxy.security.validate_user_input import validate_email, validate_username, validate_password +from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password log = logging.getLogger( __name__ ) @@ -698,7 +698,7 @@ if user and params.get( 'change_username_button', False ): username = kwd.get( 'username', '' ) if username: - message = validate_username( trans, username, user ) + message = validate_publicname( trans, username, user ) if message: status = 'error' else: @@ -736,7 +736,7 @@ # Validate the new values for email and username message = validate_email( trans, email, user ) if not message and username: - message = validate_username( trans, username, user ) + message = validate_publicname( trans, username, user ) if message: status = 'error' else: @@ -878,7 +878,7 @@ if not message: message = validate_password( trans, password, confirm ) if not message and username: - message = validate_username( trans, username ) + message = validate_publicname( trans, username ) if not message: if webapp == 'galaxy': if self.get_all_forms( trans, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Fix for Dan's issues with the GATK tools not behaving properly in 'set at runtime' mode in workflows.
by Bitbucket 11 Jan '12

11 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/67a8349ff9b9/ changeset: 67a8349ff9b9 user: dannon date: 2012-01-11 15:04:42 summary: Fix for Dan's issues with the GATK tools not behaving properly in 'set at runtime' mode in workflows. affected #: 1 file diff -r 4ce50b22cabaf7257c774eb5ae4bb171a731bb7f -r 67a8349ff9b9e3a37b8fadf96ac2e3ae64d3ea24 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -757,7 +757,15 @@ # If we got this far, we can actually look at the dependencies # to see if their values will not be available until runtime. for dep_name in self.get_dependencies(): - dep_value = context[ dep_name ] + if dep_name in context: + dep_value = context[ dep_name ] + else: + # Quick hack to check deeper in the context. + # TODO: Context should really be scoped and the correct subset passed along. + # This happens specifically in all the GATK tools, the way the reference genome is handled. + for layer in context.itervalues(): + if isinstance( layer, dict ) and self.name in layer and dep_name in layer: + dep_value = layer[dep_name] # Dependency on a dataset that does not yet exist if isinstance( dep_value, DummyDataset ): return True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Better handling of JexlExpressions in stratification expressions for GATK VariantEval.
by Bitbucket 11 Jan '12

11 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4ce50b22caba/ changeset: 4ce50b22caba user: dan date: 2012-01-11 14:33:48 summary: Better handling of JexlExpressions in stratification expressions for GATK VariantEval. affected #: 2 files diff -r 82115950072cf4114619fe1e9c693c83d8e4c9ed -r 4ce50b22cabaf7257c774eb5ae4bb171a731bb7f tools/gatk/gatk_wrapper.py --- a/tools/gatk/gatk_wrapper.py +++ b/tools/gatk/gatk_wrapper.py @@ -6,6 +6,7 @@ """ import sys, optparse, os, tempfile, subprocess, shutil +from binascii import unhexlify from string import Template GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is @@ -46,6 +47,7 @@ #Parse Command Line parser = optparse.OptionParser() parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' ) + parser.add_option( '-o', '--pass_through_options', dest='pass_through_options_encoded', action='append', type="string", help='These options are passed through directly to GATK, with decoding from binascii.unhexlify.' ) parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' ) parser.add_option( '', '--max_jvm_heap', dest='max_jvm_heap', action='store', type="string", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value.' ) parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' ) @@ -59,6 +61,8 @@ cmd = ' '.join( options.pass_through_options ) else: cmd = '' + if options.pass_through_options_encoded: + cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) ) if options.max_jvm_heap is not None: cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) elif options.max_jvm_heap_fraction is not None: diff -r 82115950072cf4114619fe1e9c693c83d8e4c9ed -r 4ce50b22cabaf7257c774eb5ae4bb171a731bb7f tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -1,9 +1,10 @@ -<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.3"> +<tool id="gatk_variant_eval" name="Eval Variants" version="0.0.4"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement></requirements><command interpreter="python">gatk_wrapper.py + #from binascii import hexlify --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $var_count, $variant in enumerate( $reference_source.variants ): @@ -95,10 +96,11 @@ ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": + #for $stratification in $analysis_param_type.stratifications: + #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) ) + -o '${ hexlify( $select_string ) }' + #end for -p ' - #for $stratification in $analysis_param_type.stratifications: - --select_exps "${stratification.select_exps}" --select_names "${stratification.select_name}" - #end for #for $sample in $analysis_param_type.samples: --sample "${sample.sample}" @@ -326,7 +328,13 @@ </when><when value="advanced"><repeat name="stratifications" title="Stratification"> - <param name="select_exps" value="" type="text" label="Stratification Expression"/> + <param name="select_exps" value="" type="text" label="Stratification Expression"> + <sanitizer> + <valid> + <add value="""/> + </valid> + </sanitizer> + </param><param name="select_name" value="" type="text" label="Name"/></repeat> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in saving visualizations.
by Bitbucket 10 Jan '12

10 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/82115950072c/ changeset: 82115950072c user: jgoecks date: 2012-01-10 23:47:18 summary: Fix bug in saving visualizations. affected #: 1 file diff -r 2ef6a78863f1ab7e1364762eb114e5f8442f9687 -r 82115950072cf4114619fe1e9c693c83d8e4c9ed lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -692,7 +692,7 @@ session.add( vis_rev ) session.flush() encoded_id = trans.security.encode_id(vis.id) - return { "id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } + return { "vis_id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } @web.expose @web.require_login( "see all available libraries" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: gentler compositing and refactoring so that compositing operations are at appropriate level.
by Bitbucket 10 Jan '12

10 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2ef6a78863f1/ changeset: 2ef6a78863f1 user: jgoecks date: 2012-01-10 23:36:55 summary: Trackster: gentler compositing and refactoring so that compositing operations are at appropriate level. affected #: 1 file diff -r 1bc51ec0c5befabc6e0d7ab9ac30def126c6bf92 -r 2ef6a78863f1ab7e1364762eb114e5f8442f9687 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3576,6 +3576,8 @@ all_data_index = 0; var ctx = canvas.getContext('2d'); ctx.translate(this.left_offset, 0); + ctx.globalAlpha = 0.5; + ctx.globalCompositeOperation = "source-over"; for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { track = this.drawables[i]; tile_data = all_data[ all_data_index ]; @@ -3842,9 +3844,6 @@ tile_low = tile_bounds[0], tile_high = tile_bounds[1], painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode); - // HACK: this is needed for compositing tracks. This should be a config setting somewhere; also, - // "darker" may not be included in future canvas implementations. - ctx.globalCompositeOperation = "darker"; painter.draw(ctx, canvas.width, canvas.height, w_scale); return new Tile(this.track, tile_index, resolution, canvas, result.data); @@ -4201,7 +4200,6 @@ var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); // FIXME: it shouldn't be necessary to build in padding. ctx.translate(0, SUMMARY_TREE_TOP_PADDING); - ctx.globalCompositeOperation = "darker"; painter.draw(ctx, canvas.width, canvas.height, w_scale); return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); } @@ -4246,7 +4244,6 @@ var feature_mapper = null; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - ctx.globalCompositeOperation = "darker"; ctx.fillStyle = this.prefs.block_color; ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "right"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: User check when fetching visualization chrom information.
by Bitbucket 10 Jan '12

10 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8288ad7d6676/ changeset: 8288ad7d6676 user: jgoecks date: 2012-01-10 18:39:59 summary: User check when fetching visualization chrom information. affected #: 1 file diff -r 55c537958418c66afad2ad79690a98589816f644 -r 8288ad7d66762867c6a9f3d0e1e3891e68142ad2 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -336,7 +336,7 @@ len_file = None len_ds = None user_keys = {} - if 'dbkeys' in dbkey_user.preferences: + if dbkey_user and 'dbkeys' in dbkey_user.preferences: user_keys = from_json_string( dbkey_user.preferences['dbkeys'] ) if dbkey in user_keys: dbkey_attributes = user_keys[ dbkey ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Make paths to metadata temp files absolute.
by Bitbucket 09 Jan '12

09 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/46169ca11f43/ changeset: 46169ca11f43 user: natefoo date: 2012-01-09 19:19:56 summary: Make paths to metadata temp files absolute. affected #: 4 files diff -r 2acedad2ef87c907975dd5afab5eef9ccde31987 -r 46169ca11f432651d3ff08281dfaf896ff4f5b8c lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -1,6 +1,7 @@ import sys, logging, copy, shutil, weakref, cPickle, tempfile, os +from os.path import abspath -from galaxy.util import string_as_bool, relpath, stringify_dictionary_keys, listify +from galaxy.util import string_as_bool, stringify_dictionary_keys, listify from galaxy.util.odict import odict from galaxy.web import form_builder import galaxy.model @@ -476,7 +477,7 @@ def file_name( self ): if self._filename is None: #we need to create a tmp file, accessable across all nodes/heads, save the name, and return it - self._filename = relpath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) + self._filename = abspath( tempfile.NamedTemporaryFile( dir = self.tmp_dir, prefix = "metadata_temp_file_" ).name ) open( self._filename, 'wb+' ) #create an empty file, so it can't be reused using tempfile return self._filename def to_JSON( self ): @@ -563,7 +564,7 @@ #is located differently, i.e. on a cluster node with a different filesystem structure #file to store existing dataset - metadata_files.filename_in = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_in_%s_" % key ).name ) + metadata_files.filename_in = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_in_%s_" % key ).name ) #FIXME: HACK #sqlalchemy introduced 'expire_on_commit' flag for sessionmaker at version 0.5x @@ -574,17 +575,17 @@ cPickle.dump( dataset, open( metadata_files.filename_in, 'wb+' ) ) #file to store metadata results of set_meta() - metadata_files.filename_out = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name ) + metadata_files.filename_out = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name ) open( metadata_files.filename_out, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) #file to store a 'return code' indicating the results of the set_meta() call #results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure ) - metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name ) + metadata_files.filename_results_code = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name ) simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) #file to store kwds passed to set_meta() - metadata_files.filename_kwds = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name ) + metadata_files.filename_kwds = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name ) simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True ) #existing metadata file parameters need to be overridden with cluster-writable file locations - metadata_files.filename_override_metadata = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name ) + metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name ) open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) override_metadata = [] for meta_key, spec_value in dataset.metadata.spec.iteritems(): diff -r 2acedad2ef87c907975dd5afab5eef9ccde31987 -r 46169ca11f432651d3ff08281dfaf896ff4f5b8c lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -709,11 +709,11 @@ try: for fname in self.extra_filenames: os.remove( fname ) - self.app.object_store.delete(self.get_job(), base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) + self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, extra_dir=str(self.job_id)) except: log.exception( "Unable to cleanup job %d" % self.job_id ) diff -r 2acedad2ef87c907975dd5afab5eef9ccde31987 -r 46169ca11f432651d3ff08281dfaf896ff4f5b8c lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -31,7 +31,7 @@ commands += "; cd %s; " % os.path.abspath( os.getcwd() ) commands += job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), - tmp_dir = self.app.config.new_file_path, + tmp_dir = job_wrapper.working_directory, dataset_files_path = self.app.model.Dataset.file_path, output_fnames = job_wrapper.get_output_fnames(), set_extension = False, diff -r 2acedad2ef87c907975dd5afab5eef9ccde31987 -r 46169ca11f432651d3ff08281dfaf896ff4f5b8c lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -110,6 +110,7 @@ if job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] and self.app.config.set_metadata_externally and job_wrapper.output_paths: external_metadata_script = job_wrapper.setup_external_metadata( output_fnames = job_wrapper.get_output_fnames(), set_extension = True, + tmp_dir = job_wrapper.working_directory, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args = external_metadata_script, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 09 Jan '12

09 Jan '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/05f017e906b3/ changeset: 05f017e906b3 user: jgoecks date: 2012-01-09 18:12:32 summary: Trackster: add icon that shows more features by increasing the number of rows shown. Update tipsy text in 'get more data' icons' to include message. affected #: 4 files diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa static/images/fugue/exclamation.png Binary file static/images/fugue/exclamation.png has changed diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -57,6 +57,7 @@ .layer-transparent.active{background:transparent url(../images/fugue/layer-transparent.png) no-repeat;} .arrow-resize-090{background:transparent url(../images/fugue/arrow-resize-090-bw.png) no-repeat;} .arrow-resize-090.active{background:transparent url(../images/fugue/arrow-resize-090.png) no-repeat;} +.exclamation{background:transparent url(../images/fugue/exclamation.png) no-repeat;} .layers-stack{background:transparent url(../images/fugue/layers-stack-bw.png) no-repeat;} .layers-stack:hover{background:transparent url(../images/fugue/layers-stack.png) no-repeat;} .chevron-expand{background:transparent url(../images/fugue/chevron-expand-bw.png) no-repeat;} diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -297,6 +297,9 @@ .menu-button { margin: 0px 4px 0px 4px; } +.exclamation{ + background: transparent url(../images/fugue/exclamation.png) no-repeat; +} .layer-transparent { background: transparent url(../images/fugue/layer-transparent-bw.png) no-repeat; } diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2507,7 +2507,7 @@ }; extend(SummaryTreeTile.prototype, Tile.prototype); -var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, message, feature_mapper) { +var FeatureTrackTile = function(track, index, resolution, canvas, data, w_scale, mode, message, all_slotted, feature_mapper) { // Attribute init. Tile.call(this, track, index, resolution, canvas, data); this.mode = mode; @@ -2515,40 +2515,60 @@ this.feature_mapper = feature_mapper; // Add message + action icons to tile's html. - if (this.message) { + if (this.message || !all_slotted) { var + tile = this; canvas = this.html_elt.children()[0], - message_div = $("<div/>").addClass("tile-message").text(this.message) + message_div = $("<div/>").addClass("tile-message") // -1 to account for border. - .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt), - more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down") - .attr("title", "Get more data including depth").tipsy( {gravity: 's'} ).appendTo(message_div), - more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across") - .attr("title", "Get more data excluding depth").tipsy( {gravity: 's'} ).appendTo(message_div); + .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt); + + // Handle when not all elements are slotted. + if (!all_slotted) { + var icon = $("<a href='javascript:void(0);'/>").addClass("icon exclamation") + .attr("title", "To minimize track height, not all features in this region are displayed. Click to display more.") + .tipsy( {gravity: 's'} ).appendTo(message_div) + .click(function () { + $(".tipsy").hide(); + tile.track.slotters[w_scale].max_rows *= 2; + tile.track.request_draw(true); + }); + } + + // Handle message; only message currently is that only the first N elements are displayed. + if (this.message) { + var + num_features = data.length, + more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down") + .attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data including depth") + .tipsy( {gravity: 's'} ).appendTo(message_div), + more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across") + .attr("title", "For speed, only the first " + num_features + " features in this region were obtained from server. Click to get more data excluding depth") + .tipsy( {gravity: 's'} ).appendTo(message_div); - // Set up actions for icons. - var tile = this; - more_down_icon.click(function() { - // Mark tile as stale, request more data, and redraw track. - tile.stale = true; - track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); - $(".tipsy").hide(); - track.request_draw(); - }).dblclick(function(e) { - // Do not propogate as this would normally zoom in. - e.stopPropagation(); - }); + // Set up actions for icons. + more_down_icon.click(function() { + // Mark tile as stale, request more data, and redraw track. + tile.stale = true; + track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); + $(".tipsy").hide(); + track.request_draw(); + }).dblclick(function(e) { + // Do not propogate as this would normally zoom in. + e.stopPropagation(); + }); - more_across_icon.click(function() { - // Mark tile as stale, request more data, and redraw track. - tile.stale = true; - track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); - $(".tipsy").hide(); - track.request_draw(); - }).dblclick(function(e) { - // Do not propogate as this would normally zoom in. - e.stopPropagation(); - }); + more_across_icon.click(function() { + // Mark tile as stale, request more data, and redraw track. + tile.stale = true; + track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); + $(".tipsy").hide(); + track.request_draw(); + }).dblclick(function(e) { + // Do not propogate as this would normally zoom in. + e.stopPropagation(); + }); + } } }; extend(FeatureTrackTile.prototype, Tile.prototype); @@ -4003,7 +4023,7 @@ var dummy_context = this.view.canvas_manager.dummy_context, slotter = this.slotters[level]; if (!slotter || (slotter.mode !== mode)) { - slotter = new (slotting.FeatureSlotter)( level, mode === "Pack", MAX_FEATURE_DEPTH, function ( x ) { return dummy_context.measureText( x ) } ); + slotter = new (slotting.FeatureSlotter)( level, mode, MAX_FEATURE_DEPTH, function ( x ) { return dummy_context.measureText( x ) } ); this.slotters[level] = slotter; } @@ -4188,8 +4208,11 @@ // Handle row-by-row tracks - // Filter features. - var filtered = []; + // Preprocessing: filter features and determine whether all unfiltered features have been slotted. + var + filtered = [], + slots = this.slotters[w_scale].slots; + all_slotted = true; if ( result.data ) { var filters = this.filters_manager.filters; for (var i = 0, len = result.data.length; i < len; i++) { @@ -4205,7 +4228,12 @@ } } if (!hide_feature) { + // Feature visible. filtered.push(feature); + // Set flag if not slotted. + if ( !(feature[0] in slots) ) { + all_slotted = false; + } } } } @@ -4226,12 +4254,11 @@ if (result.data) { // Draw features. - slots = this.slotters[w_scale].slots; feature_mapper = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots); feature_mapper.translation = -left_offset; } - return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, mode, result.message, feature_mapper); + return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper); }, /** * Returns true if data is compatible with a given mode. @@ -4342,11 +4369,12 @@ * This implementation is incremental, any feature assigned a slot will be * retained for slotting future features. */ -exports.FeatureSlotter = function (w_scale, include_label, max_rows, measureText) { +exports.FeatureSlotter = function (w_scale, mode, max_rows, measureText) { this.slots = {}; this.start_end_dct = {}; this.w_scale = w_scale; - this.include_label = include_label; + this.mode = mode; + this.include_label = (mode === "Pack"); this.max_rows = max_rows; this.measureText = measureText; }; https://bitbucket.org/galaxy/galaxy-central/changeset/2acedad2ef87/ changeset: 2acedad2ef87 user: jgoecks date: 2012-01-09 18:12:49 summary: Merge. affected #: 4 files diff -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa -r 2acedad2ef87c907975dd5afab5eef9ccde31987 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -70,6 +70,8 @@ self.update_manager = update_manager.UpdateManager( self ) # Manage installed tool shed repositories self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) + # Load datatype display applications defined in local datatypes_conf.xml + self.datatypes_registry.load_display_applications() # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load history import/export tools diff -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa -r 2acedad2ef87c907975dd5afab5eef9ccde31987 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -28,19 +28,28 @@ self.set_external_metadata_tool = None self.sniff_order = [] self.upload_file_formats = [] + # Datatype elements defined in local datatypes_conf.xml + # that contain display applications + self.display_app_containers = [] + # Datatype elements in datatypes_conf.xml included in installed + # tool shed repositories that contain display applications + self.proprietary_display_app_containers = [] # Map a display application id to a display application self.display_applications = odict() + # The following 2 attributes are used in the to_xml_file() + # method to persist the current state into an xml file. + self.display_path_attr = None self.converters_path_attr = None # The 'default' converters_path defined in local datatypes_conf.xml - self.datatype_converters_path = None + self.converters_path = None # The 'default' display_path defined in local datatypes_conf.xml self.display_applications_path = None + self.inherit_display_application_by_class = [] self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None def load_datatypes( self, root_dir=None, config=None, imported_modules=None ): if root_dir and config: - inherit_display_application_by_class = [] # Parse datatypes_conf.xml tree = galaxy.util.parse_xml( config ) root = tree.getroot() @@ -48,11 +57,11 @@ self.log.debug( 'Loading datatypes from %s' % config ) registration = root.find( 'registration' ) # Set default paths defined in local datatypes_conf.xml. - if not self.datatype_converters_path: + if not self.converters_path: self.converters_path_attr = registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) - self.datatype_converters_path = os.path.join( root_dir, self.converters_path_attr ) - if not os.path.isdir( self.datatype_converters_path ): - raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path ) + self.converters_path = os.path.join( root_dir, self.converters_path_attr ) + if not os.path.isdir( self.converters_path ): + raise ConfigurationError( "Directory does not exist: %s" % self.converters_path ) if not self.display_applications_path: self.display_path_attr = registration.get( 'display_path', 'display_applications' ) self.display_applications_path = os.path.join( root_dir, self.display_path_attr ) @@ -60,7 +69,7 @@ # Keep an in-memory list of datatype elems to enable persistence. self.datatype_elems.append( elem ) try: - extension = elem.get( 'extension', None ) + extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) @@ -128,30 +137,14 @@ mimetype = composite_file.get( 'mimetype', None ) self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) for display_app in elem.findall( 'display' ): - display_file = os.path.join( self.display_applications_path, display_app.get( 'file', None ) ) - try: - inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) - display_app = DisplayApplication.from_file( display_file, self ) - if display_app: - if display_app.id in self.display_applications: - #if we already loaded this display application, we'll use the first one again - display_app = self.display_applications[ display_app.id ] - self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) - self.display_applications[ display_app.id ] = display_app #Display app by id - self.datatypes_by_extension[ extension ].add_display_application( display_app ) - if inherit and ( self.datatypes_by_extension[extension], display_app ) not in inherit_display_application_by_class: - #subclass inheritance will need to wait until all datatypes have been loaded - inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) - except: - self.log.exception( "error reading display application from path: %s" % display_file ) + if imported_modules: + if elem not in self.proprietary_display_app_containers: + self.proprietary_display_app_containers.append( elem ) + else: + if elem not in self.display_app_containers: + self.display_app_containers.append( elem ) except Exception, e: self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) - # Handle display_application subclass inheritance here: - for ext, d_type1 in self.datatypes_by_extension.iteritems(): - for d_type2, display_app in inherit_display_application_by_class: - current_app = d_type1.get_display_application( display_app.id, None ) - if current_app is None and isinstance( d_type1, type( d_type2 ) ): - d_type1.add_display_application( display_app ) # Load datatype sniffers from the config sniffers = root.find( 'sniffers' ) if sniffers: @@ -339,7 +332,7 @@ if converter_path: config_path = os.path.join( converter_path, tool_config ) else: - config_path = os.path.join( self.datatype_converters_path, tool_config ) + config_path = os.path.join( self.converters_path, tool_config ) try: converter = toolbox.load_tool( config_path ) toolbox.tools_by_id[ converter.id ] = converter @@ -348,7 +341,44 @@ self.datatype_converters[ source_datatype ][ target_datatype ] = converter self.log.debug( "Loaded converter: %s", converter.id ) except Exception, e: - self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) ) + self.log.exception( "Error loading converter (%s): %s" % ( config_path, str( e ) ) ) + def load_display_applications( self, display_path=None ): + if display_path: + # Load display applications defined by datatypes_conf.xml + # included in installed tool shed repository. + datatype_elems = self.proprietary_display_app_containers + else: + # Load display applications defined by local datatypes_conf.xml. + datatype_elems = self.display_app_containers + for elem in datatype_elems: + extension = elem.get( 'extension', None ) + for display_app in elem.findall( 'display' ): + display_file = display_app.get( 'file', None ) + if display_path: + config_path = os.path.join( display_path, display_file ) + else: + config_path = os.path.join( self.display_applications_path, display_file ) + try: + inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) + display_app = DisplayApplication.from_file( config_path, self ) + if display_app: + if display_app.id in self.display_applications: + # If we already loaded this display application, we'll use the first one loaded. + display_app = self.display_applications[ display_app.id ] + self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) + self.display_applications[ display_app.id ] = display_app + self.datatypes_by_extension[ extension ].add_display_application( display_app ) + if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class: + self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) + except Exception, e: + self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) ) + # Handle display_application subclass inheritance. + for extension, d_type1 in self.datatypes_by_extension.iteritems(): + for d_type2, display_app in self.inherit_display_application_by_class: + current_app = d_type1.get_display_application( display_app.id, None ) + if current_app is None and isinstance( d_type1, type( d_type2 ) ): + self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) ) + d_type1.add_display_application( display_app ) def load_external_metadata_tool( self, toolbox ): """Adds a tool which is used to set external metadata""" #we need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated tool. diff -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa -r 2acedad2ef87c907975dd5afab5eef9ccde31987 lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -23,9 +23,11 @@ path_items = datatypes_config.split( 'repos' ) relative_install_dir = '%srepos/%s/%s/%s' % \ ( path_items[0], tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) - converter_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) + converter_path, display_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, converter_path=converter_path ) - # TODO: handle display_applications - \ No newline at end of file + if display_path: + # Load proprietary datatype display applications + app.datatypes_registry.load_display_applications( display_path=display_path ) + \ No newline at end of file diff -r 05f017e906b33847b0d8ce50fcc3157ffa6ca0aa -r 2acedad2ef87c907975dd5afab5eef9ccde31987 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -449,7 +449,10 @@ # Parse datatypes_config. tree = util.parse_xml( datatypes_config ) datatypes_config_root = tree.getroot() + # Path to datatype converters converter_path = None + # Path to datatype display applications + display_path = None relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) datatype_class_modules = [] @@ -500,14 +503,13 @@ log.debug( "Exception importing datatypes code file %s: %s" % ( str( relative_path_to_datatype_file_name ), str( e ) ) ) finally: lock.release() - # Handle data type converters. + # Handle data type converters and display applications. for elem in registration.findall( 'datatype' ): if not converter_path: # If any of the <datatype> tag sets contain <converter> tags, set the converter_path - # if it is not already set. This requires repsitories to place all converters in the + # if it is not already set. This requires developers to place all converters in the # same subdirectory within the repository hierarchy. for converter in elem.findall( 'converter' ): - converter_path = None converter_config = converter.get( 'file', None ) if converter_config: for root, dirs, files in os.walk( relative_install_dir ): @@ -518,9 +520,23 @@ break if converter_path: break - else: + if not display_path: + # If any of the <datatype> tag sets contain <display> tags, set the display_path + # if it is not already set. This requires developers to place all display acpplications + # in the same subdirectory within the repository hierarchy. + for display_app in elem.findall( 'display' ): + display_config = display_app.get( 'file', None ) + if display_config: + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == display_config: + display_path = root + break + if display_path: + break + if converter_path and display_path: break - # TODO: handle display_applications else: # The repository includes a dataypes_conf.xml file, but no code file that # contains data type classes. This implies that the data types in datayptes_conf.xml @@ -528,7 +544,7 @@ imported_modules = [] # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules ) - return converter_path + return converter_path, display_path def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): # This method is used by the InstallManager, which does not have access to trans. @@ -544,11 +560,13 @@ if 'datatypes_config' in metadata_dict: datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] ) # Load data types required by tools. - converter_path = load_datatypes( app, datatypes_config, relative_install_dir ) + converter_path, display_path = load_datatypes( app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters app.datatypes_registry.load_datatype_converters( app.toolbox, converter_path=converter_path ) - # TODO: handle display_applications + if display_path: + # Load proprietary datatype display applications + app.datatypes_registry.load_display_applications( display_path=display_path ) if 'tools' in metadata_dict: repository_tools_tups = [] for tool_dict in metadata_dict[ 'tools' ]: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add support for handling datatype display applications in datatypes_conf.xml files included in installed tool shed repositories.
by Bitbucket 09 Jan '12

09 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4b7209d64451/ changeset: 4b7209d64451 user: greg date: 2012-01-09 18:12:19 summary: Add support for handling datatype display applications in datatypes_conf.xml files included in installed tool shed repositories. affected #: 4 files diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 4b7209d64451695eb86ea32d3dff0c999f81d977 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -70,6 +70,8 @@ self.update_manager = update_manager.UpdateManager( self ) # Manage installed tool shed repositories self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) + # Load datatype display applications defined in local datatypes_conf.xml + self.datatypes_registry.load_display_applications() # Load datatype converters defined in local datatypes_conf.xml self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load history import/export tools diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 4b7209d64451695eb86ea32d3dff0c999f81d977 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -28,19 +28,28 @@ self.set_external_metadata_tool = None self.sniff_order = [] self.upload_file_formats = [] + # Datatype elements defined in local datatypes_conf.xml + # that contain display applications + self.display_app_containers = [] + # Datatype elements in datatypes_conf.xml included in installed + # tool shed repositories that contain display applications + self.proprietary_display_app_containers = [] # Map a display application id to a display application self.display_applications = odict() + # The following 2 attributes are used in the to_xml_file() + # method to persist the current state into an xml file. + self.display_path_attr = None self.converters_path_attr = None # The 'default' converters_path defined in local datatypes_conf.xml - self.datatype_converters_path = None + self.converters_path = None # The 'default' display_path defined in local datatypes_conf.xml self.display_applications_path = None + self.inherit_display_application_by_class = [] self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None def load_datatypes( self, root_dir=None, config=None, imported_modules=None ): if root_dir and config: - inherit_display_application_by_class = [] # Parse datatypes_conf.xml tree = galaxy.util.parse_xml( config ) root = tree.getroot() @@ -48,11 +57,11 @@ self.log.debug( 'Loading datatypes from %s' % config ) registration = root.find( 'registration' ) # Set default paths defined in local datatypes_conf.xml. - if not self.datatype_converters_path: + if not self.converters_path: self.converters_path_attr = registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) - self.datatype_converters_path = os.path.join( root_dir, self.converters_path_attr ) - if not os.path.isdir( self.datatype_converters_path ): - raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path ) + self.converters_path = os.path.join( root_dir, self.converters_path_attr ) + if not os.path.isdir( self.converters_path ): + raise ConfigurationError( "Directory does not exist: %s" % self.converters_path ) if not self.display_applications_path: self.display_path_attr = registration.get( 'display_path', 'display_applications' ) self.display_applications_path = os.path.join( root_dir, self.display_path_attr ) @@ -60,7 +69,7 @@ # Keep an in-memory list of datatype elems to enable persistence. self.datatype_elems.append( elem ) try: - extension = elem.get( 'extension', None ) + extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) @@ -128,30 +137,14 @@ mimetype = composite_file.get( 'mimetype', None ) self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) for display_app in elem.findall( 'display' ): - display_file = os.path.join( self.display_applications_path, display_app.get( 'file', None ) ) - try: - inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) - display_app = DisplayApplication.from_file( display_file, self ) - if display_app: - if display_app.id in self.display_applications: - #if we already loaded this display application, we'll use the first one again - display_app = self.display_applications[ display_app.id ] - self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) - self.display_applications[ display_app.id ] = display_app #Display app by id - self.datatypes_by_extension[ extension ].add_display_application( display_app ) - if inherit and ( self.datatypes_by_extension[extension], display_app ) not in inherit_display_application_by_class: - #subclass inheritance will need to wait until all datatypes have been loaded - inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) - except: - self.log.exception( "error reading display application from path: %s" % display_file ) + if imported_modules: + if elem not in self.proprietary_display_app_containers: + self.proprietary_display_app_containers.append( elem ) + else: + if elem not in self.display_app_containers: + self.display_app_containers.append( elem ) except Exception, e: self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) - # Handle display_application subclass inheritance here: - for ext, d_type1 in self.datatypes_by_extension.iteritems(): - for d_type2, display_app in inherit_display_application_by_class: - current_app = d_type1.get_display_application( display_app.id, None ) - if current_app is None and isinstance( d_type1, type( d_type2 ) ): - d_type1.add_display_application( display_app ) # Load datatype sniffers from the config sniffers = root.find( 'sniffers' ) if sniffers: @@ -339,7 +332,7 @@ if converter_path: config_path = os.path.join( converter_path, tool_config ) else: - config_path = os.path.join( self.datatype_converters_path, tool_config ) + config_path = os.path.join( self.converters_path, tool_config ) try: converter = toolbox.load_tool( config_path ) toolbox.tools_by_id[ converter.id ] = converter @@ -348,7 +341,44 @@ self.datatype_converters[ source_datatype ][ target_datatype ] = converter self.log.debug( "Loaded converter: %s", converter.id ) except Exception, e: - self.log.exception( "Error loading converter (%s): %s" % ( converter_path, str( e ) ) ) + self.log.exception( "Error loading converter (%s): %s" % ( config_path, str( e ) ) ) + def load_display_applications( self, display_path=None ): + if display_path: + # Load display applications defined by datatypes_conf.xml + # included in installed tool shed repository. + datatype_elems = self.proprietary_display_app_containers + else: + # Load display applications defined by local datatypes_conf.xml. + datatype_elems = self.display_app_containers + for elem in datatype_elems: + extension = elem.get( 'extension', None ) + for display_app in elem.findall( 'display' ): + display_file = display_app.get( 'file', None ) + if display_path: + config_path = os.path.join( display_path, display_file ) + else: + config_path = os.path.join( self.display_applications_path, display_file ) + try: + inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) + display_app = DisplayApplication.from_file( config_path, self ) + if display_app: + if display_app.id in self.display_applications: + # If we already loaded this display application, we'll use the first one loaded. + display_app = self.display_applications[ display_app.id ] + self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) + self.display_applications[ display_app.id ] = display_app + self.datatypes_by_extension[ extension ].add_display_application( display_app ) + if inherit and ( self.datatypes_by_extension[ extension ], display_app ) not in self.inherit_display_application_by_class: + self.inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) + except Exception, e: + self.log.exception( "Error loading display application (%s): %s" % ( config_path, str( e ) ) ) + # Handle display_application subclass inheritance. + for extension, d_type1 in self.datatypes_by_extension.iteritems(): + for d_type2, display_app in self.inherit_display_application_by_class: + current_app = d_type1.get_display_application( display_app.id, None ) + if current_app is None and isinstance( d_type1, type( d_type2 ) ): + self.log.debug( "Adding inherited display application '%s' to datatype '%s'" % ( display_app.id, extension ) ) + d_type1.add_display_application( display_app ) def load_external_metadata_tool( self, toolbox ): """Adds a tool which is used to set external metadata""" #we need to be able to add a job to the queue to set metadata. The queue will currently only accept jobs with an associated tool. diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 4b7209d64451695eb86ea32d3dff0c999f81d977 lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -23,9 +23,11 @@ path_items = datatypes_config.split( 'repos' ) relative_install_dir = '%srepos/%s/%s/%s' % \ ( path_items[0], tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) - converter_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) + converter_path, display_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, converter_path=converter_path ) - # TODO: handle display_applications - \ No newline at end of file + if display_path: + # Load proprietary datatype display applications + app.datatypes_registry.load_display_applications( display_path=display_path ) + \ No newline at end of file diff -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e -r 4b7209d64451695eb86ea32d3dff0c999f81d977 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -449,7 +449,10 @@ # Parse datatypes_config. tree = util.parse_xml( datatypes_config ) datatypes_config_root = tree.getroot() + # Path to datatype converters converter_path = None + # Path to datatype display applications + display_path = None relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) datatype_class_modules = [] @@ -500,14 +503,13 @@ log.debug( "Exception importing datatypes code file %s: %s" % ( str( relative_path_to_datatype_file_name ), str( e ) ) ) finally: lock.release() - # Handle data type converters. + # Handle data type converters and display applications. for elem in registration.findall( 'datatype' ): if not converter_path: # If any of the <datatype> tag sets contain <converter> tags, set the converter_path - # if it is not already set. This requires repsitories to place all converters in the + # if it is not already set. This requires developers to place all converters in the # same subdirectory within the repository hierarchy. for converter in elem.findall( 'converter' ): - converter_path = None converter_config = converter.get( 'file', None ) if converter_config: for root, dirs, files in os.walk( relative_install_dir ): @@ -518,9 +520,23 @@ break if converter_path: break - else: + if not display_path: + # If any of the <datatype> tag sets contain <display> tags, set the display_path + # if it is not already set. This requires developers to place all display acpplications + # in the same subdirectory within the repository hierarchy. + for display_app in elem.findall( 'display' ): + display_config = display_app.get( 'file', None ) + if display_config: + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == display_config: + display_path = root + break + if display_path: + break + if converter_path and display_path: break - # TODO: handle display_applications else: # The repository includes a dataypes_conf.xml file, but no code file that # contains data type classes. This implies that the data types in datayptes_conf.xml @@ -528,7 +544,7 @@ imported_modules = [] # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules ) - return converter_path + return converter_path, display_path def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): # This method is used by the InstallManager, which does not have access to trans. @@ -544,11 +560,13 @@ if 'datatypes_config' in metadata_dict: datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] ) # Load data types required by tools. - converter_path = load_datatypes( app, datatypes_config, relative_install_dir ) + converter_path, display_path = load_datatypes( app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters app.datatypes_registry.load_datatype_converters( app.toolbox, converter_path=converter_path ) - # TODO: handle display_applications + if display_path: + # Load proprietary datatype display applications + app.datatypes_registry.load_display_applications( display_path=display_path ) if 'tools' in metadata_dict: repository_tools_tups = [] for tool_dict in metadata_dict[ 'tools' ]: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by Bitbucket 09 Jan '12

09 Jan '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aa2d3c5f577b/ changeset: aa2d3c5f577b user: jgoecks date: 2012-01-09 15:48:42 summary: Trackster: organization and variable renaming in slotter code. affected #: 1 file diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r aa2d3c5f577b9b26ef6765a9f7928c1ee948ce92 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3871,7 +3871,7 @@ this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; - this.inc_slots = {}; + this.slotters = {}; this.start_end_dct = {}; this.left_offset = 200; @@ -3988,10 +3988,8 @@ }, /** * Place features in slots for drawing (i.e. pack features). - * this.inc_slots[level] is created in this method. this.inc_slots[level] - * is a dictionary of slotted features; key is feature uid, value is a dictionary - * with keys 'slot' and 'text'. - * Returns the number of slots used to pack features. + * this.slotters[level] is created in this method. this.slotters[level] + * is a Slotter object. Returns the number of slots used to pack features. */ incremental_slots: function(level, features, mode) { @@ -3999,14 +3997,13 @@ // need to create new slots. var dummy_context = this.view.canvas_manager.dummy_context, - inc_slots = this.inc_slots[level]; - if (!inc_slots || (inc_slots.mode !== mode)) { - inc_slots = new (slotting.FeatureSlotter)( level, mode === "Pack", MAX_FEATURE_DEPTH, function ( x ) { return dummy_context.measureText( x ) } ); - inc_slots.mode = mode; - this.inc_slots[level] = inc_slots; + slotter = this.slotters[level]; + if (!slotter || (slotter.mode !== mode)) { + slotter = new (slotting.FeatureSlotter)( level, mode === "Pack", MAX_FEATURE_DEPTH, function ( x ) { return dummy_context.measureText( x ) } ); + this.slotters[level] = slotter; } - return inc_slots.slot_features( features ); + return slotter.slot_features( features ); }, /** * Given feature data, returns summary tree data. Feature data must be sorted by start @@ -4225,7 +4222,7 @@ if (result.data) { // Draw features. - slots = this.inc_slots[w_scale].slots; + slots = this.slotters[w_scale].slots; feature_mapper = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots); feature_mapper.translation = -left_offset; } @@ -4341,7 +4338,7 @@ * This implementation is incremental, any feature assigned a slot will be * retained for slotting future features. */ -exports.FeatureSlotter = function ( w_scale, include_label, max_rows, measureText ) { +exports.FeatureSlotter = function (w_scale, include_label, max_rows, measureText) { this.slots = {}; this.start_end_dct = {}; this.w_scale = w_scale; @@ -4356,8 +4353,12 @@ */ extend( exports.FeatureSlotter.prototype, { slot_features: function( features ) { - var w_scale = this.w_scale, inc_slots = this.slots, start_end_dct = this.start_end_dct, - undone = [], slotted = [], highest_slot = 0, max_rows = this.max_rows; + var w_scale = this.w_scale, + start_end_dct = this.start_end_dct, + undone = [], + slotted = [], + highest_slot = 0, + max_rows = this.max_rows; // If feature already exists in slots (from previously seen tiles), use the same slot, // otherwise if not seen, add to "undone" list for slot calculation. @@ -4368,9 +4369,9 @@ for (var i = 0, len = features.length; i < len; i++) { var feature = features[i], feature_uid = feature[0]; - if (inc_slots[feature_uid] !== undefined) { - highest_slot = Math.max(highest_slot, inc_slots[feature_uid]); - slotted.push(inc_slots[feature_uid]); + if (this.slots[feature_uid] !== undefined) { + highest_slot = Math.max(highest_slot, this.slots[feature_uid]); + slotted.push(this.slots[feature_uid]); } else { undone.push(i); } @@ -4462,7 +4463,7 @@ start_end_dct[slot_num] = []; } start_end_dct[slot_num].push([f_start, f_end]); - inc_slots[feature_uid] = slot_num; + this.slots[feature_uid] = slot_num; highest_slot = Math.max(highest_slot, slot_num); } else { https://bitbucket.org/galaxy/galaxy-central/changeset/38c1df19946e/ changeset: 38c1df19946e user: jgoecks date: 2012-01-09 16:10:17 summary: Trackster: add tipsy for icons used to get more data. affected #: 1 file diff -r aa2d3c5f577b9b26ef6765a9f7928c1ee948ce92 -r 38c1df19946ece9670d6cfd8df6baef73655dded static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2518,11 +2518,13 @@ if (this.message) { var canvas = this.html_elt.children()[0], - message_div = $("<div/>").addClass("tile-message").text(this.message). + message_div = $("<div/>").addClass("tile-message").text(this.message) // -1 to account for border. - css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt), - more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(message_div), - more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(message_div); + .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt), + more_down_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-down") + .attr("title", "Get more data including depth").tipsy( {gravity: 's'} ).appendTo(message_div), + more_across_icon = $("<a href='javascript:void(0);'/>").addClass("icon more-across") + .attr("title", "Get more data excluding depth").tipsy( {gravity: 's'} ).appendTo(message_div); // Set up actions for icons. var tile = this; @@ -2530,6 +2532,7 @@ // Mark tile as stale, request more data, and redraw track. tile.stale = true; track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); + $(".tipsy").hide(); track.request_draw(); }).dblclick(function(e) { // Do not propogate as this would normally zoom in. @@ -2540,6 +2543,7 @@ // Mark tile as stale, request more data, and redraw track. tile.stale = true; track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); + $(".tipsy").hide(); track.request_draw(); }).dblclick(function(e) { // Do not propogate as this would normally zoom in. https://bitbucket.org/galaxy/galaxy-central/changeset/4a9f7ff4e2c0/ changeset: 4a9f7ff4e2c0 user: jgoecks date: 2012-01-09 16:13:42 summary: Merge. affected #: 14 files diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e distributed_object_store_conf.xml.sample --- a/distributed_object_store_conf.xml.sample +++ b/distributed_object_store_conf.xml.sample @@ -1,11 +1,11 @@ <?xml version="1.0"?><backends> - <backend name="files1" type="disk" weight="1"> + <backend id="files1" type="disk" weight="1"><files_dir path="database/files1"/><extra_dir type="temp" path="database/tmp1"/><extra_dir type="job_work" path="database/job_working_directory1"/></backend> - <backend name="files2" type="disk" weight="1"> + <backend id="files2" type="disk" weight="1"><files_dir path="database/files2"/><extra_dir type="temp" path="database/tmp2"/><extra_dir type="job_work" path="database/job_working_directory2"/> diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -439,7 +439,7 @@ if mf is None: mf = self.new_file( dataset = parent, **value.kwds ) # Ensure the metadata file gets updated with content - parent.dataset.object_store.update_from_file( parent.dataset.id, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) + parent.dataset.object_store.update_from_file( parent.dataset, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) os.unlink( value.file_name ) value = mf.id return value diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -22,3 +22,7 @@ class ObjectNotFound( Exception ): """ Accessed object was not found """ pass + +class ObjectInvalid( Exception ): + """ Accessed object store ID is invalid """ + pass diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -320,19 +320,9 @@ # With job outputs in the working directory, we need the working # directory to be set before prepare is run, or else premature deletion # and job recovery fail. - # Attempt to put the working directory in the same store as the output dataset(s) - store_name = None - da = None - if job.output_datasets: - da = job.output_datasets[0] - elif job.output_library_datasets: - da = job.output_library_datasets[0] - if da is not None: - store_name = self.app.object_store.store_name(da.dataset.id) # Create the working dir if necessary - if not self.app.object_store.exists(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)): - self.app.object_store.create(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id), store_name=store_name) - self.working_directory = self.app.object_store.get_filename(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) + self.app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) + self.working_directory = self.app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) log.debug('(%s) Working directory for job is: %s' % (self.job_id, self.working_directory)) self.output_paths = None self.output_dataset_paths = None @@ -482,7 +472,7 @@ dataset.extension = 'data' # Update (non-library) job output datasets through the object store if dataset not in job.output_library_datasets: - self.app.object_store.update_from_file(dataset.id, create=True) + self.app.object_store.update_from_file(dataset.dataset, create=True) self.sa_session.add( dataset ) self.sa_session.flush() job.state = job.states.ERROR @@ -606,7 +596,7 @@ dataset.set_size() # Update (non-library) job output datasets through the object store if dataset not in job.output_library_datasets: - self.app.object_store.update_from_file(dataset.id, create=True) + self.app.object_store.update_from_file(dataset.dataset, create=True) if context['stderr']: dataset.blurb = "error" elif dataset.has_data(): @@ -719,8 +709,7 @@ try: for fname in self.extra_filenames: os.remove( fname ) - if self.working_directory is not None and os.path.isdir( self.working_directory ): - shutil.rmtree( self.working_directory ) + self.app.object_store.delete(self.get_job(), base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -16,7 +16,6 @@ from galaxy.util.hash_util import * from galaxy.web.form_builder import * from galaxy.model.item_attrs import UsesAnnotations, APIItem -from galaxy.exceptions import ObjectNotFound from sqlalchemy.orm import object_session from sqlalchemy.sql.expression import func import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil @@ -650,12 +649,7 @@ if not self.external_filename: assert self.id is not None, "ID must be set before filename used (commit the object)" assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id - try: - filename = self.object_store.get_filename( self.id ) - except ObjectNotFound, e: - # Create file if it does not exist - self.object_store.create( self.id ) - filename = self.object_store.get_filename( self.id ) + filename = self.object_store.get_filename( self ) return filename else: filename = self.external_filename @@ -669,7 +663,7 @@ file_name = property( get_file_name, set_file_name ) @property def extra_files_path( self ): - return self.object_store.get_filename( self.id, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id) + return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) def get_size( self, nice_size=False ): """Returns the size of the data on disk""" if self.file_size: @@ -679,16 +673,16 @@ return self.file_size else: if nice_size: - return galaxy.datatypes.data.nice_size( self.object_store.size(self.id) ) + return galaxy.datatypes.data.nice_size( self.object_store.size(self) ) else: - return self.object_store.size(self.id) + return self.object_store.size(self) def set_size( self ): """Returns the size of the data on disk""" if not self.file_size: if self.external_filename: self.file_size = os.path.getsize(self.external_filename) else: - self.file_size = self.object_store.size(self.id) + self.file_size = self.object_store.size(self) def get_total_size( self ): if self.total_size is not None: return self.total_size @@ -703,7 +697,7 @@ if self.file_size is None: self.set_size() self.total_size = self.file_size or 0 - if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): + if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): for root, dirs, files in os.walk( self.extra_files_path ): self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] ) def has_data( self ): @@ -721,7 +715,7 @@ # FIXME: sqlalchemy will replace this def _delete(self): """Remove the file that corresponds to this data""" - self.object_store.delete(self.id) + self.object_store.delete(self) @property def user_can_purge( self ): return self.purged == False \ @@ -730,9 +724,9 @@ def full_delete( self ): """Remove the file and extra files, marks deleted and purged""" # os.unlink( self.file_name ) - self.object_store.delete(self.id) - if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): - self.object_store.delete(self.id, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True) + self.object_store.delete(self) + if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): + self.object_store.delete(self, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True) # if os.path.exists( self.extra_files_path ): # shutil.rmtree( self.extra_files_path ) # TODO: purge metadata files @@ -1798,8 +1792,11 @@ assert self.id is not None, "ID must be set before filename used (commit the object)" # Ensure the directory structure and the metadata file object exist try: - self.history_dataset.dataset.object_store.create( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) - path = self.history_dataset.dataset.object_store.get_filename( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) + da = self.history_dataset or self.library_dataset + if self.object_store_id is None and da is not None: + self.object_store_id = da.dataset.object_store_id + da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) + path = da.dataset.object_store.get_filename( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) return path except AttributeError: # In case we're not working with the history_dataset diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -130,6 +130,7 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), Column( "purgable", Boolean, default=True ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "external_filename" , TEXT ), Column( "_extra_files_path", TEXT ), Column( 'file_size', Numeric( 15, 0 ) ), @@ -410,6 +411,7 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), Column( "job_runner_name", String( 255 ) ), Column( "job_runner_external_id", String( 255 ) ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "imported", Boolean, default=False, index=True ) ) JobParameter.table = Table( "job_parameter", metadata, @@ -641,6 +643,7 @@ Column( "lda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py @@ -0,0 +1,38 @@ +""" +Migration script to add 'object_store_id' column to various tables +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) +from galaxy.model.custom_types import TrimmedString + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + for t_name in ( 'dataset', 'job', 'metadata_file' ): + t = Table( t_name, metadata, autoload=True ) + c = Column( "object_store_id", TrimmedString( 255 ), index=True ) + try: + c.create( t ) + assert c is t.c.object_store_id + except Exception, e: + print "Adding object_store_id column to %s table failed: %s" % ( t_name, str( e ) ) + log.debug( "Adding object_store_id column to %s table failed: %s" % ( t_name, str( e ) ) ) + +def downgrade(): + metadata.reflect() + for t_name in ( 'dataset', 'job', 'metadata_file' ): + t = Table( t_name, metadata, autoload=True ) + try: + t.c.object_store_id.drop() + except Exception, e: + print "Dropping object_store_id column from %s table failed: %s" % ( t_name, str( e ) ) + log.debug( "Dropping object_store_id column from %s table failed: %s" % ( t_name, str( e ) ) ) diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -18,7 +18,9 @@ from galaxy.jobs import Sleeper from galaxy.model import directory_hash_id from galaxy.objectstore.s3_multipart_upload import multipart_upload -from galaxy.exceptions import ObjectNotFound +from galaxy.exceptions import ObjectNotFound, ObjectInvalid + +from sqlalchemy.orm import object_session from boto.s3.key import Key from boto.s3.connection import S3Connection @@ -40,14 +42,15 @@ self.running = False self.extra_dirs = {} - def exists(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Returns True if the object identified by `dataset_id` exists in this - file store, False otherwise. + Returns True if the object identified by `obj` exists in this file + store, False otherwise. FIELD DESCRIPTIONS (these apply to all the methods in this class): - :type dataset_id: int - :param dataset_id: Galaxy-assigned database ID of the dataset to be checked. + :type obj: object + :param obj: A Galaxy object with an assigned database ID accessible via + the .id attribute. :type base_dir: string :param base_dir: A key in self.extra_dirs corresponding to the base @@ -56,21 +59,21 @@ :type dir_only: bool :param dir_only: If True, check only the path where the file - identified by `dataset_id` should be located, not the - dataset itself. This option applies to `extra_dir` - argument as well. + identified by `obj` should be located, not the dataset + itself. This option applies to `extra_dir` argument as + well. :type extra_dir: string :param extra_dir: Append `extra_dir` to the directory structure where - the dataset identified by `dataset_id` should be located. - (e.g., 000/extra_dir/dataset_id) + the dataset identified by `obj` should be located. + (e.g., 000/extra_dir/obj.id) :type extra_dir_at_root: bool :param extra_dir_at_root: Applicable only if `extra_dir` is set. If True, the `extra_dir` argument is placed at root of the created directory structure rather - than at the end (e.g., extra_dir/000/dataset_id - vs. 000/extra_dir/dataset_id) + than at the end (e.g., extra_dir/000/obj.id + vs. 000/extra_dir/obj.id) :type alt_name: string :param alt_name: Use this name as the alternative name for the created @@ -78,53 +81,39 @@ """ raise NotImplementedError() - def store_name(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): - """ - Returns the name of the store in which the object identified by - `dataset_id` exists, or None if it does not exist or the store is the - default store. - """ - return None - - def file_ready(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return True if so, False otherwise.""" return True - def create(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, store_name=None): + def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Mark the object identified by `dataset_id` as existing in the store, but - with no content. This method will create a proper directory structure for + Mark the object identified by `obj` as existing in the store, but with + no content. This method will create a proper directory structure for the file if the directory does not already exist. See `exists` method for the description of other fields. - - :type store_name: string - :param store_name: Backend store in which to create the dataset, if - this store contains more than one backend. If the - named backend does not exist, a backend will be - chosen by the store. """ raise NotImplementedError() - - def empty(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + + def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Test if the object identified by `dataset_id` has content. + Test if the object identified by `obj` has content. If the object does not exist raises `ObjectNotFound`. See `exists` method for the description of the fields. """ raise NotImplementedError() - def size(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Return size of the object identified by `dataset_id`. + Return size of the object identified by `obj`. If the object does not exist, return 0. See `exists` method for the description of the fields. """ raise NotImplementedError() - def delete(self, dataset_id, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Deletes the object identified by `dataset_id`. + Deletes the object identified by `obj`. See `exists` method for the description of other fields. :type entire_dir: bool :param entire_dir: If True, delete the entire directory pointed to by @@ -133,10 +122,10 @@ """ raise NotImplementedError() - def get_data(self, dataset_id, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Fetch `count` bytes of data starting at offset `start` from the - object identified uniquely by `dataset_id`. + object identified uniquely by `obj`. If the object does not exist raises `ObjectNotFound`. See `exists` method for the description of other fields. @@ -148,15 +137,15 @@ """ raise NotImplementedError() - def get_filename(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Get the expected filename (including the absolute path) which can be used - to access the contents of the object uniquely identified by `dataset_id`. + to access the contents of the object uniquely identified by `obj`. See `exists` method for the description of the fields. """ raise NotImplementedError() - def update_from_file(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False): + def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False): """ Inform the store that the file associated with the object has been updated. If `file_name` is provided, update from that file instead @@ -166,14 +155,14 @@ :type file_name: string :param file_name: Use file pointed to by `file_name` as the source for - updating the dataset identified by `dataset_id` + updating the dataset identified by `obj` :type create: bool :param create: If True and the default dataset does not exist, create it first. """ raise NotImplementedError() - def get_object_url(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ If the store supports direct URL access, return a URL. Otherwise return None. @@ -210,22 +199,24 @@ super(DiskObjectStore, self).__init__() self.file_path = file_path or config.file_path self.config = config + self.extra_dirs['job_work'] = config.job_working_directory + self.extra_dirs['temp'] = config.new_file_path if extra_dirs is not None: - self.extra_dirs = extra_dirs + self.extra_dirs.update( extra_dirs ) - def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """Class method that returns the absolute path for the file corresponding - to the `dataset_id` regardless of whether the file exists. + to the `obj`.id regardless of whether the file exists. """ - path = self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, old_style=True) + path = self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, old_style=True) # For backward compatibility, check the old style root path first; otherwise, # construct hashed path if not os.path.exists(path): - return self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) + return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) - def _construct_path(self, dataset_id, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Construct the expected absolute path for accessing the object - identified by `dataset_id`. + identified by `obj`.id. :type base_dir: string :param base_dir: A key in self.extra_dirs corresponding to the base @@ -234,13 +225,13 @@ :type dir_only: bool :param dir_only: If True, check only the path where the file - identified by `dataset_id` should be located, not the + identified by `obj` should be located, not the dataset itself. This option applies to `extra_dir` argument as well. :type extra_dir: string :param extra_dir: Append the value of this parameter to the expected path - used to access the object identified by `dataset_id` + used to access the object identified by `obj` (e.g., /files/000/<extra_dir>/dataset_10.dat). :type alt_name: string @@ -252,16 +243,16 @@ the composed directory structure does not include a hash id (e.g., /files/dataset_10.dat (old) vs. /files/000/dataset_10.dat (new)) """ - base = self.file_path - if base_dir in self.extra_dirs: - base = self.extra_dirs.get(base_dir) + base = self.extra_dirs.get(base_dir, self.file_path) if old_style: if extra_dir is not None: path = os.path.join(base, extra_dir) else: path = base else: - rel_path = os.path.join(*directory_hash_id(dataset_id)) + # Construct hashed path + rel_path = os.path.join(*directory_hash_id(obj.id)) + # Optionally append extra_dir if extra_dir is not None: if extra_dir_at_root: rel_path = os.path.join(extra_dir, rel_path) @@ -269,103 +260,86 @@ rel_path = os.path.join(rel_path, extra_dir) path = os.path.join(base, rel_path) if not dir_only: - path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return os.path.abspath(path) - def exists(self, dataset_id, **kwargs): - path = self._construct_path(dataset_id, old_style=True, **kwargs) + def exists(self, obj, **kwargs): + path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility, check root path first; otherwise, construct # and check hashed path - if not os.path.exists(path): - path = self._construct_path(dataset_id, **kwargs) - return os.path.exists(path) + if os.path.exists(path): + return True + else: + path = self._construct_path(obj, **kwargs) + return os.path.exists(path) - def create(self, dataset_id, **kwargs): - kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): - # Pull out locally used fields - extra_dir = kwargs.get('extra_dir', None) - extra_dir_at_root = kwargs.get('extra_dir_at_root', False) + def create(self, obj, **kwargs): + if not self.exists(obj, **kwargs): + path = self._construct_path(obj, **kwargs) dir_only = kwargs.get('dir_only', False) - alt_name = kwargs.get('alt_name', None) - base_dir_key = kwargs.get('base_dir', None) - # Construct hashed path - path = os.path.join(*directory_hash_id(dataset_id)) - # Optionally append extra_dir - if extra_dir is not None: - if extra_dir_at_root: - path = os.path.join(extra_dir, path) - else: - path = os.path.join(path, extra_dir) - # Combine the constructted path with the root dir for all files - base_dir = self.extra_dirs.get(base_dir_key, self.file_path) - path = os.path.join(base_dir, path) # Create directory if it does not exist - if not os.path.exists(path): - os.makedirs(path) + dir = path if dir_only else os.path.dirname(path) + if not os.path.exists(dir): + os.makedirs(dir) + # Create the file if it does not exist if not dir_only: - path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) open(path, 'w').close() - util.umask_fix_perms( path, self.config.umask, 0666 ) + util.umask_fix_perms(path, self.config.umask, 0666) - def empty(self, dataset_id, **kwargs): - return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0 + def empty(self, obj, **kwargs): + return os.path.getsize(self.get_filename(obj, **kwargs)) > 0 - def size(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): + def size(self, obj, **kwargs): + if self.exists(obj, **kwargs): try: - return os.path.getsize(self.get_filename(dataset_id, **kwargs)) + return os.path.getsize(self.get_filename(obj, **kwargs)) except OSError: return 0 else: return 0 - def delete(self, dataset_id, entire_dir=False, **kwargs): - path = self.get_filename(dataset_id, **kwargs) + def delete(self, obj, entire_dir=False, **kwargs): + path = self.get_filename(obj, **kwargs) extra_dir = kwargs.get('extra_dir', None) try: if entire_dir and extra_dir: shutil.rmtree(path) return True - if self.exists(dataset_id, **kwargs): + if self.exists(obj, **kwargs): os.remove(path) return True except OSError, ex: - log.critical('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex)) + log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex)) return False - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - data_file = open(self.get_filename(dataset_id, **kwargs), 'r') + def get_data(self, obj, start=0, count=-1, **kwargs): + data_file = open(self.get_filename(obj, **kwargs), 'r') data_file.seek(start) content = data_file.read(count) data_file.close() return content - def get_filename(self, dataset_id, **kwargs): - path = self._construct_path(dataset_id, old_style=True, **kwargs) + def get_filename(self, obj, **kwargs): + path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility, check root path first; otherwise, construct - # and check hashed path + # and return hashed path if os.path.exists(path): return path else: - path = self._construct_path(dataset_id, **kwargs) - if os.path.exists(path): - return path - else: - raise ObjectNotFound() + return self._construct_path(obj, **kwargs) - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): + def update_from_file(self, obj, file_name=None, create=False, **kwargs): """ `create` parameter is not used in this implementation """ if create: - self.create(dataset_id, **kwargs) - if file_name and self.exists(dataset_id, **kwargs): + self.create(obj, **kwargs) + if file_name and self.exists(obj, **kwargs): try: - shutil.copy(file_name, self.get_filename(dataset_id, **kwargs)) + shutil.copy(file_name, self.get_filename(obj, **kwargs)) except IOError, ex: log.critical('Error copying %s to %s: %s' % (file_name, - self._get_filename(dataset_id, **kwargs), ex)) + self._get_filename(obj, **kwargs), ex)) - def get_object_url(self, dataset_id, **kwargs): + def get_object_url(self, obj, **kwargs): return None @@ -494,8 +468,8 @@ continue util.umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) - def _construct_path(self, dataset_id, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): - rel_path = os.path.join(*directory_hash_id(dataset_id)) + def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + rel_path = os.path.join(*directory_hash_id(obj.id)) if extra_dir is not None: if extra_dir_at_root: rel_path = os.path.join(extra_dir, rel_path) @@ -504,7 +478,7 @@ # S3 folders are marked by having trailing '/' so add it now rel_path = '%s/' % rel_path if not dir_only: - rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return rel_path def _get_cache_path(self, rel_path): @@ -665,18 +639,18 @@ log.error("Trouble pushing S3 key '%s' from file '%s': %s" % (rel_path, source_file, ex)) return False - def file_ready(self, dataset_id, **kwargs): + def file_ready(self, obj, **kwargs): """ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return True if so, False otherwise.""" - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) # Make sure the size in cache is available in its entirety if self._in_cache(rel_path) and os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path): return True return False - def exists(self, dataset_id, **kwargs): + def exists(self, obj, **kwargs): in_cache = in_s3 = False - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) # Check cache if self._in_cache(rel_path): in_cache = True @@ -699,9 +673,8 @@ else: return False - def create(self, dataset_id, **kwargs): - kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): + def create(self, obj, **kwargs): + if not self.exists(obj, **kwargs): #print "S3 OS creating a dataset with ID %s" % dataset_id # Pull out locally used fields extra_dir = kwargs.get('extra_dir', None) @@ -710,7 +683,7 @@ alt_name = kwargs.get('alt_name', None) # print "---- Processing: %s; %s" % (alt_name, locals()) # Construct hashed path - rel_path = os.path.join(*directory_hash_id(dataset_id)) + rel_path = os.path.join(*directory_hash_id(obj)) # Optionally append extra_dir if extra_dir is not None: if extra_dir_at_root: @@ -728,30 +701,30 @@ # self._push_to_s3(s3_dir, from_string='') # If instructed, create the dataset in cache & in S3 if not dir_only: - rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) open(os.path.join(self.staging_path, rel_path), 'w').close() self._push_to_s3(rel_path, from_string='') - def empty(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): - return bool(self.size(dataset_id, **kwargs) > 0) + def empty(self, obj, **kwargs): + if self.exists(obj, **kwargs): + return bool(self.size(obj, **kwargs) > 0) else: raise ObjectNotFound() - def size(self, dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def size(self, obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) if self._in_cache(rel_path): try: return os.path.getsize(self._get_cache_path(rel_path)) except OSError, ex: log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s" % (rel_path, ex)) - elif self.exists(dataset_id, **kwargs): + elif self.exists(obj, **kwargs): return self._get_size_in_s3(rel_path) log.warning("Did not find dataset '%s', returning 0 for size" % rel_path) return 0 - def delete(self, dataset_id, entire_dir=False, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def delete(self, obj, entire_dir=False, **kwargs): + rel_path = self._construct_path(obj, **kwargs) extra_dir = kwargs.get('extra_dir', None) try: # For the case of extra_files, because we don't have a reference to @@ -777,11 +750,11 @@ except S3ResponseError, ex: log.error("Could not delete key '%s' from S3: %s" % (rel_path, ex)) except OSError, ex: - log.error('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex)) + log.error('%s delete error %s' % (self._get_filename(obj, **kwargs), ex)) return False - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def get_data(self, obj, start=0, count=-1, **kwargs): + rel_path = self._construct_path(obj, **kwargs) # Check cache first and get file if not there if not self._in_cache(rel_path): self._pull_into_cache(rel_path) @@ -794,10 +767,10 @@ data_file.close() return content - def get_filename(self, dataset_id, **kwargs): + def get_filename(self, obj, **kwargs): #print "S3 get_filename for dataset: %s" % dataset_id dir_only = kwargs.get('dir_only', False) - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) cache_path = self._get_cache_path(rel_path) # S3 does not recognize directories as files so cannot check if those exist. # So, if checking dir only, ensure given dir exists in cache and return @@ -811,7 +784,7 @@ if self._in_cache(rel_path): return cache_path # Check if the file exists in persistent storage and, if it does, pull it into cache - elif self.exists(dataset_id, **kwargs): + elif self.exists(obj, **kwargs): if dir_only: # Directories do not get pulled into cache return cache_path else: @@ -824,11 +797,11 @@ raise ObjectNotFound() # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): + def update_from_file(self, obj, file_name=None, create=False, **kwargs): if create: - self.create(dataset_id, **kwargs) - if self.exists(dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + self.create(obj, **kwargs) + if self.exists(obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) # Chose whether to use the dataset file itself or an alternate file if file_name: source_file = os.path.abspath(file_name) @@ -848,9 +821,9 @@ else: raise ObjectNotFound() - def get_object_url(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def get_object_url(self, obj, **kwargs): + if self.exists(obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) try: key = Key(self.bucket, rel_path) return key.generate_url(expires_in = 86400) # 24hrs @@ -873,7 +846,7 @@ "requires a config file, please set one in " \ "'distributed_object_store_config_file')" self.backends = {} - self.weighted_backend_names = [] + self.weighted_backend_ids = [] random.seed() @@ -884,7 +857,7 @@ root = tree.getroot() log.debug('Loading backends for distributed object store from %s' % self.distributed_config) for elem in [ e for e in root if e.tag == 'backend' ]: - name = elem.get('name') + id = elem.get('id') weight = int(elem.get('weight', 1)) if elem.get('type', 'disk'): path = None @@ -895,94 +868,90 @@ elif sub.tag == 'extra_dir': type = sub.get('type') extra_dirs[type] = sub.get('path') - self.backends[name] = DiskObjectStore(config, file_path=path, extra_dirs=extra_dirs) - log.debug("Loaded disk backend '%s' with weight %s and file_path: %s" % (name, weight, path)) + self.backends[id] = DiskObjectStore(config, file_path=path, extra_dirs=extra_dirs) + log.debug("Loaded disk backend '%s' with weight %s and file_path: %s" % (id, weight, path)) if extra_dirs: log.debug(" Extra directories:") for type, dir in extra_dirs.items(): log.debug(" %s: %s" % (type, dir)) for i in range(0, weight): - # The simplest way to do weighting: add backend names to a + # The simplest way to do weighting: add backend ids to a # sequence the number of times equalling weight, then randomly # choose a backend from that sequence at creation - self.weighted_backend_names.append(name) + self.weighted_backend_ids.append(id) - def exists(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - return store is not None + def exists(self, obj, **kwargs): + return self.__call_method('exists', obj, False, False, **kwargs) - def store_name(self, dataset_id, **kwargs): - for name, store in self.backends.items(): - if store.exists(dataset_id, **kwargs): - return name - return None + #def store_id(self, obj, **kwargs): + # return self.__get_store_id_for(obj, **kwargs)[0] - def file_ready(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.file_ready(dataset_id, **kwargs) - return False + def file_ready(self, obj, **kwargs): + return self.__call_method('file_ready', obj, False, False, **kwargs) - def create(self, dataset_id, **kwargs): - store_name = kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): - if store_name is None or store_name not in self.backends: - store_name = random.choice(self.weighted_backend_names) - log.debug("Selected backend '%s' for creation of dataset %s" % (store_name, dataset_id)) + def create(self, obj, **kwargs): + """ + create() is the only method in which obj.object_store_id may be None + """ + if obj.object_store_id is None or not self.exists(obj, **kwargs): + if obj.object_store_id is None or obj.object_store_id not in self.backends: + obj.object_store_id = random.choice(self.weighted_backend_ids) + object_session( obj ).add( obj ) + object_session( obj ).flush() + log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) else: - log.debug("Using preferred backend '%s' for creation of dataset %s" % (store_name, dataset_id)) - return self.backends[store_name].create(dataset_id, **kwargs) + log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) + self.backends[obj.object_store_id].create(obj, **kwargs) - def empty(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.empty(dataset_id, **kwargs) - return True + def empty(self, obj, **kwargs): + return self.__call_method('empty', obj, True, False, **kwargs) - def size(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.size(dataset_id, **kwargs) - return 0 + def size(self, obj, **kwargs): + return self.__call_method('size', obj, 0, False, **kwargs) - def delete(self, dataset_id, entire_dir=False, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.delete(dataset_id, entire_dir=entire_dir, **kwargs) - return False + def delete(self, obj, entire_dir=False, **kwargs): + return self.__call_method('delete', obj, False, False, **kwargs) - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_data(dataset_id, start=0, count=-1, **kwargs) - raise ObjectNotFound() + def get_data(self, obj, start=0, count=-1, **kwargs): + return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs) - def get_filename(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_filename(dataset_id, **kwargs) - raise ObjectNotFound() + def get_filename(self, obj, **kwargs): + return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.update_from_file(dataset_id, file_name=file_name, create=create, **kwargs) - if create: - store_name = random.choice(self.weighted_backend_names) - return self.backends[store_name].update_from_file(dataset_id, file_name=file_name, create=create, **kwargs) - raise ObjectNotFound() + def update_from_file(self, obj, file_name=None, create=False, **kwargs): + # can raise ObjectLocationMismatch + # TODO: handling create=True here? probably not since create() is called from w/in, so a store will be selected there + #if create and not self.exists(obj, **kwargs): + # store_id = random.choice(self.weighted_backend_names) + return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) - def get_object_url(self, dataset_id, **kwargs): - # FIXME: dir_only - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_object_url(dataset_id, **kwargs) - return None + def get_object_url(self, obj, **kwargs): + return self.__call_method('get_object_url', obj, None, False, **kwargs) - def __get_store_for(self, dataset_id, **kwargs): - for store in self.backends.values(): - if store.exists(dataset_id, **kwargs): - return store + def __call_method(self, method, obj, default, default_is_exception, **kwargs): + object_store_id = self.__get_store_id_for(obj, **kwargs) + if object_store_id is not None: + return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs) + if default_is_exception: + raise default() + else: + return default + + def __get_store_id_for(self, obj, **kwargs): + if obj.object_store_id is not None and obj.object_store_id in self.backends: + return obj.object_store_id + else: + # if this instance has been switched from a non-distributed to a + # distributed object store, or if the object's store id is invalid, + # try to locate the object + log.warning('The backend object store ID (%s) for %s object with ID %s is invalid' % (obj.object_store_id, obj.__class__.__name__, obj.id)) + for id, store in self.backends.items(): + if store.exists(obj, **kwargs): + log.warning('%s object with ID %s found in backend object store with ID %s' % (obj.__class__.__name__, obj.id, id)) + obj.object_store_id = id + object_session( obj ).add( obj ) + object_session( obj ).flush() + return id return None class HierarchicalObjectStore(ObjectStore): diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1859,7 +1859,7 @@ a_files = os.listdir( temp_file_path ) if len( a_files ) > 0: for f in a_files: - self.app.object_store.update_from_file(hda.dataset.id, + self.app.object_store.update_from_file(hda.dataset, extra_dir="dataset_%d_files" % hda.dataset.id, alt_name = f, file_name = os.path.join(temp_file_path, f), @@ -1899,7 +1899,7 @@ sa_session=self.sa_session ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset ) # Move data from temp location to dataset location - self.app.object_store.update_from_file(child_dataset.dataset.id, filename, create=True) + self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True) self.sa_session.add( child_dataset ) self.sa_session.flush() child_dataset.set_size() @@ -1967,7 +1967,7 @@ self.sa_session.add( primary_data ) self.sa_session.flush() # Move data from temp location to dataset location - self.app.object_store.update_from_file(primary_data.dataset.id, filename, create=True) + self.app.object_store.update_from_file(primary_data.dataset, filename, create=True) primary_data.set_size() primary_data.name = "%s (%s)" % ( outdata.name, designation ) primary_data.info = outdata.info diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -228,8 +228,7 @@ # datasets first, then create the associations parent_to_child_pairs = [] child_dataset_names = set() - store_name = None - store_name_set = False # this is needed since None is a valid value for store_name + object_store_id = None for name, output in tool.outputs.items(): for filter in output.filters: try: @@ -292,12 +291,12 @@ trans.sa_session.add( data ) trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) - # Create an empty file immediately - trans.app.object_store.create( data.id, store_name=store_name ) - if not store_name_set: - # Ensure all other datasets in this job are created in the same store - store_name = trans.app.object_store.store_name( data.id ) - store_name_set = True + # Create an empty file immediately. The first dataset will be + # created in the "default" store, all others will be created in + # the same store as the first. + data.dataset.object_store_id = object_store_id + trans.app.object_store.create( data.dataset ) + object_store_id = data.dataset.object_store_id # these will be the same thing after the first output # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. @@ -382,6 +381,7 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) + job.object_store_id = object_store_id trans.sa_session.add( job ) trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -319,8 +319,7 @@ for name, value in tool.params_to_strings( params, trans.app ).iteritems(): job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) - store_name = None - store_name_set = False # this is needed since None is a valid value for store_name + object_store_id = None for i, dataset in enumerate( data_list ): if folder: job.add_output_library_dataset( 'output%i' % i, dataset ) @@ -328,11 +327,12 @@ job.add_output_dataset( 'output%i' % i, dataset ) # Create an empty file immediately if not dataset.dataset.external_filename: - trans.app.object_store.create( dataset.dataset.id, store_name=store_name ) + dataset.dataset.object_store_id = object_store_id + trans.app.object_store.create( dataset.dataset ) + object_store_id = dataset.dataset.object_store_id + trans.sa_session.add( dataset ) # open( dataset.file_name, "w" ).close() - if not store_name_set: - store_name = trans.app.object_store.store_name( dataset.dataset.id ) - store_name_set = True + job.object_store_id = object_store_id job.state = job.states.NEW trans.sa_session.add( job ) trans.sa_session.flush() diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -360,16 +360,16 @@ data = self._check_dataset(trans, dataset_id) if isinstance( data, basestring ): return data - log.debug( "dataset.py -> transfer_status: Checking transfer status for dataset %s..." % data.id ) + log.debug( "Checking transfer status for dataset %s..." % data.dataset.id ) # Pulling files in extra_files_path into cache is not handled via this # method but that's primarily because those files are typically linked to # through tool's output page anyhow so tying a JavaScript event that will # call this method does not seem doable? - if trans.app.object_store.file_ready(data.id): + if data.dataset.external_filename: return True else: - return False + return trans.app.object_store.file_ready(data.dataset) @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): @@ -382,7 +382,7 @@ if filename and filename != "index": # For files in extra_files_path - file_path = trans.app.object_store.get_filename(data.dataset.id, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) + file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) if os.path.exists( file_path ): if os.path.isdir( file_path ): return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories? diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -663,7 +663,7 @@ trans.response.set_content_type( 'application/x-gzip' ) else: trans.response.set_content_type( 'application/x-tar' ) - return trans.app.object_store.get_data(jeha.dataset.id) + return trans.app.object_store.get_data(jeha.dataset) elif jeha.job.state in [ model.Job.states.RUNNING, model.Job.states.QUEUED, model.Job.states.WAITING ]: return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \ % ( { 'n' : history.name, 's' : url_for( action="export_archive", id=id, qualified=True ) } ) ) diff -r 38c1df19946ece9670d6cfd8df6baef73655dded -r 4a9f7ff4e2c02bf87d33590061e09ef4e70fb84e lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1647,6 +1647,7 @@ for ldda_id in ldda_ids: try: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + assert not ldda.dataset.purged lddas.append( ldda ) except: ldda = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Object Store: Store the backend object store's ID in the database when using the distributed object store.
by Bitbucket 09 Jan '12

09 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ff576e7f989c/ changeset: ff576e7f989c user: natefoo date: 2012-01-09 16:06:23 summary: Object Store: Store the backend object store's ID in the database when using the distributed object store. affected #: 14 files diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf distributed_object_store_conf.xml.sample --- a/distributed_object_store_conf.xml.sample +++ b/distributed_object_store_conf.xml.sample @@ -1,11 +1,11 @@ <?xml version="1.0"?><backends> - <backend name="files1" type="disk" weight="1"> + <backend id="files1" type="disk" weight="1"><files_dir path="database/files1"/><extra_dir type="temp" path="database/tmp1"/><extra_dir type="job_work" path="database/job_working_directory1"/></backend> - <backend name="files2" type="disk" weight="1"> + <backend id="files2" type="disk" weight="1"><files_dir path="database/files2"/><extra_dir type="temp" path="database/tmp2"/><extra_dir type="job_work" path="database/job_working_directory2"/> diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -439,7 +439,7 @@ if mf is None: mf = self.new_file( dataset = parent, **value.kwds ) # Ensure the metadata file gets updated with content - parent.dataset.object_store.update_from_file( parent.dataset.id, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) + parent.dataset.object_store.update_from_file( parent.dataset, file_name=value.file_name, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name=os.path.basename(mf.file_name) ) os.unlink( value.file_name ) value = mf.id return value diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -22,3 +22,7 @@ class ObjectNotFound( Exception ): """ Accessed object was not found """ pass + +class ObjectInvalid( Exception ): + """ Accessed object store ID is invalid """ + pass diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -320,19 +320,9 @@ # With job outputs in the working directory, we need the working # directory to be set before prepare is run, or else premature deletion # and job recovery fail. - # Attempt to put the working directory in the same store as the output dataset(s) - store_name = None - da = None - if job.output_datasets: - da = job.output_datasets[0] - elif job.output_library_datasets: - da = job.output_library_datasets[0] - if da is not None: - store_name = self.app.object_store.store_name(da.dataset.id) # Create the working dir if necessary - if not self.app.object_store.exists(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)): - self.app.object_store.create(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id), store_name=store_name) - self.working_directory = self.app.object_store.get_filename(self.job_id, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) + self.app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) + self.working_directory = self.app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) log.debug('(%s) Working directory for job is: %s' % (self.job_id, self.working_directory)) self.output_paths = None self.output_dataset_paths = None @@ -482,7 +472,7 @@ dataset.extension = 'data' # Update (non-library) job output datasets through the object store if dataset not in job.output_library_datasets: - self.app.object_store.update_from_file(dataset.id, create=True) + self.app.object_store.update_from_file(dataset.dataset, create=True) self.sa_session.add( dataset ) self.sa_session.flush() job.state = job.states.ERROR @@ -606,7 +596,7 @@ dataset.set_size() # Update (non-library) job output datasets through the object store if dataset not in job.output_library_datasets: - self.app.object_store.update_from_file(dataset.id, create=True) + self.app.object_store.update_from_file(dataset.dataset, create=True) if context['stderr']: dataset.blurb = "error" elif dataset.has_data(): @@ -719,8 +709,7 @@ try: for fname in self.extra_filenames: os.remove( fname ) - if self.working_directory is not None and os.path.isdir( self.working_directory ): - shutil.rmtree( self.working_directory ) + self.app.object_store.delete(self.get_job(), base_dir='job_work', dir_only=True, extra_dir=str(self.job_id)) if self.app.config.set_metadata_externally: self.external_output_metadata.cleanup_external_metadata( self.sa_session ) galaxy.tools.imp_exp.JobExportHistoryArchiveWrapper( self.job_id ).cleanup_after_job( self.sa_session ) diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -16,7 +16,6 @@ from galaxy.util.hash_util import * from galaxy.web.form_builder import * from galaxy.model.item_attrs import UsesAnnotations, APIItem -from galaxy.exceptions import ObjectNotFound from sqlalchemy.orm import object_session from sqlalchemy.sql.expression import func import os.path, os, errno, codecs, operator, socket, pexpect, logging, time, shutil @@ -650,12 +649,7 @@ if not self.external_filename: assert self.id is not None, "ID must be set before filename used (commit the object)" assert self.object_store is not None, "Object Store has not been initialized for dataset %s" % self.id - try: - filename = self.object_store.get_filename( self.id ) - except ObjectNotFound, e: - # Create file if it does not exist - self.object_store.create( self.id ) - filename = self.object_store.get_filename( self.id ) + filename = self.object_store.get_filename( self ) return filename else: filename = self.external_filename @@ -669,7 +663,7 @@ file_name = property( get_file_name, set_file_name ) @property def extra_files_path( self ): - return self.object_store.get_filename( self.id, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id) + return self.object_store.get_filename( self, dir_only=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id ) def get_size( self, nice_size=False ): """Returns the size of the data on disk""" if self.file_size: @@ -679,16 +673,16 @@ return self.file_size else: if nice_size: - return galaxy.datatypes.data.nice_size( self.object_store.size(self.id) ) + return galaxy.datatypes.data.nice_size( self.object_store.size(self) ) else: - return self.object_store.size(self.id) + return self.object_store.size(self) def set_size( self ): """Returns the size of the data on disk""" if not self.file_size: if self.external_filename: self.file_size = os.path.getsize(self.external_filename) else: - self.file_size = self.object_store.size(self.id) + self.file_size = self.object_store.size(self) def get_total_size( self ): if self.total_size is not None: return self.total_size @@ -703,7 +697,7 @@ if self.file_size is None: self.set_size() self.total_size = self.file_size or 0 - if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): + if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): for root, dirs, files in os.walk( self.extra_files_path ): self.total_size += sum( [ os.path.getsize( os.path.join( root, file ) ) for file in files ] ) def has_data( self ): @@ -721,7 +715,7 @@ # FIXME: sqlalchemy will replace this def _delete(self): """Remove the file that corresponds to this data""" - self.object_store.delete(self.id) + self.object_store.delete(self) @property def user_can_purge( self ): return self.purged == False \ @@ -730,9 +724,9 @@ def full_delete( self ): """Remove the file and extra files, marks deleted and purged""" # os.unlink( self.file_name ) - self.object_store.delete(self.id) - if self.object_store.exists(self.id, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): - self.object_store.delete(self.id, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True) + self.object_store.delete(self) + if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): + self.object_store.delete(self, entire_dir=True, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True) # if os.path.exists( self.extra_files_path ): # shutil.rmtree( self.extra_files_path ) # TODO: purge metadata files @@ -1798,8 +1792,11 @@ assert self.id is not None, "ID must be set before filename used (commit the object)" # Ensure the directory structure and the metadata file object exist try: - self.history_dataset.dataset.object_store.create( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) - path = self.history_dataset.dataset.object_store.get_filename( self.id, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) + da = self.history_dataset or self.library_dataset + if self.object_store_id is None and da is not None: + self.object_store_id = da.dataset.object_store_id + da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) + path = da.dataset.object_store.get_filename( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) return path except AttributeError: # In case we're not working with the history_dataset diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -130,6 +130,7 @@ Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ), Column( "purgable", Boolean, default=True ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "external_filename" , TEXT ), Column( "_extra_files_path", TEXT ), Column( 'file_size', Numeric( 15, 0 ) ), @@ -410,6 +411,7 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ), Column( "job_runner_name", String( 255 ) ), Column( "job_runner_external_id", String( 255 ) ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "imported", Boolean, default=False, index=True ) ) JobParameter.table = Table( "job_parameter", metadata, @@ -641,6 +643,7 @@ Column( "lda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True, nullable=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, index=True, default=now, onupdate=now ), + Column( "object_store_id", TrimmedString( 255 ), index=True ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py @@ -0,0 +1,38 @@ +""" +Migration script to add 'object_store_id' column to various tables +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import logging +log = logging.getLogger( __name__ ) +from galaxy.model.custom_types import TrimmedString + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + for t_name in ( 'dataset', 'job', 'metadata_file' ): + t = Table( t_name, metadata, autoload=True ) + c = Column( "object_store_id", TrimmedString( 255 ), index=True ) + try: + c.create( t ) + assert c is t.c.object_store_id + except Exception, e: + print "Adding object_store_id column to %s table failed: %s" % ( t_name, str( e ) ) + log.debug( "Adding object_store_id column to %s table failed: %s" % ( t_name, str( e ) ) ) + +def downgrade(): + metadata.reflect() + for t_name in ( 'dataset', 'job', 'metadata_file' ): + t = Table( t_name, metadata, autoload=True ) + try: + t.c.object_store_id.drop() + except Exception, e: + print "Dropping object_store_id column from %s table failed: %s" % ( t_name, str( e ) ) + log.debug( "Dropping object_store_id column from %s table failed: %s" % ( t_name, str( e ) ) ) diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -18,7 +18,9 @@ from galaxy.jobs import Sleeper from galaxy.model import directory_hash_id from galaxy.objectstore.s3_multipart_upload import multipart_upload -from galaxy.exceptions import ObjectNotFound +from galaxy.exceptions import ObjectNotFound, ObjectInvalid + +from sqlalchemy.orm import object_session from boto.s3.key import Key from boto.s3.connection import S3Connection @@ -40,14 +42,15 @@ self.running = False self.extra_dirs = {} - def exists(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Returns True if the object identified by `dataset_id` exists in this - file store, False otherwise. + Returns True if the object identified by `obj` exists in this file + store, False otherwise. FIELD DESCRIPTIONS (these apply to all the methods in this class): - :type dataset_id: int - :param dataset_id: Galaxy-assigned database ID of the dataset to be checked. + :type obj: object + :param obj: A Galaxy object with an assigned database ID accessible via + the .id attribute. :type base_dir: string :param base_dir: A key in self.extra_dirs corresponding to the base @@ -56,21 +59,21 @@ :type dir_only: bool :param dir_only: If True, check only the path where the file - identified by `dataset_id` should be located, not the - dataset itself. This option applies to `extra_dir` - argument as well. + identified by `obj` should be located, not the dataset + itself. This option applies to `extra_dir` argument as + well. :type extra_dir: string :param extra_dir: Append `extra_dir` to the directory structure where - the dataset identified by `dataset_id` should be located. - (e.g., 000/extra_dir/dataset_id) + the dataset identified by `obj` should be located. + (e.g., 000/extra_dir/obj.id) :type extra_dir_at_root: bool :param extra_dir_at_root: Applicable only if `extra_dir` is set. If True, the `extra_dir` argument is placed at root of the created directory structure rather - than at the end (e.g., extra_dir/000/dataset_id - vs. 000/extra_dir/dataset_id) + than at the end (e.g., extra_dir/000/obj.id + vs. 000/extra_dir/obj.id) :type alt_name: string :param alt_name: Use this name as the alternative name for the created @@ -78,53 +81,39 @@ """ raise NotImplementedError() - def store_name(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): - """ - Returns the name of the store in which the object identified by - `dataset_id` exists, or None if it does not exist or the store is the - default store. - """ - return None - - def file_ready(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return True if so, False otherwise.""" return True - def create(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, store_name=None): + def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Mark the object identified by `dataset_id` as existing in the store, but - with no content. This method will create a proper directory structure for + Mark the object identified by `obj` as existing in the store, but with + no content. This method will create a proper directory structure for the file if the directory does not already exist. See `exists` method for the description of other fields. - - :type store_name: string - :param store_name: Backend store in which to create the dataset, if - this store contains more than one backend. If the - named backend does not exist, a backend will be - chosen by the store. """ raise NotImplementedError() - - def empty(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + + def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Test if the object identified by `dataset_id` has content. + Test if the object identified by `obj` has content. If the object does not exist raises `ObjectNotFound`. See `exists` method for the description of the fields. """ raise NotImplementedError() - def size(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Return size of the object identified by `dataset_id`. + Return size of the object identified by `obj`. If the object does not exist, return 0. See `exists` method for the description of the fields. """ raise NotImplementedError() - def delete(self, dataset_id, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ - Deletes the object identified by `dataset_id`. + Deletes the object identified by `obj`. See `exists` method for the description of other fields. :type entire_dir: bool :param entire_dir: If True, delete the entire directory pointed to by @@ -133,10 +122,10 @@ """ raise NotImplementedError() - def get_data(self, dataset_id, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Fetch `count` bytes of data starting at offset `start` from the - object identified uniquely by `dataset_id`. + object identified uniquely by `obj`. If the object does not exist raises `ObjectNotFound`. See `exists` method for the description of other fields. @@ -148,15 +137,15 @@ """ raise NotImplementedError() - def get_filename(self, dataset_id, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Get the expected filename (including the absolute path) which can be used - to access the contents of the object uniquely identified by `dataset_id`. + to access the contents of the object uniquely identified by `obj`. See `exists` method for the description of the fields. """ raise NotImplementedError() - def update_from_file(self, dataset_id, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False): + def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, file_name=None, create=False): """ Inform the store that the file associated with the object has been updated. If `file_name` is provided, update from that file instead @@ -166,14 +155,14 @@ :type file_name: string :param file_name: Use file pointed to by `file_name` as the source for - updating the dataset identified by `dataset_id` + updating the dataset identified by `obj` :type create: bool :param create: If True and the default dataset does not exist, create it first. """ raise NotImplementedError() - def get_object_url(self, dataset_id, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ If the store supports direct URL access, return a URL. Otherwise return None. @@ -210,22 +199,24 @@ super(DiskObjectStore, self).__init__() self.file_path = file_path or config.file_path self.config = config + self.extra_dirs['job_work'] = config.job_working_directory + self.extra_dirs['temp'] = config.new_file_path if extra_dirs is not None: - self.extra_dirs = extra_dirs + self.extra_dirs.update( extra_dirs ) - def _get_filename(self, dataset_id, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """Class method that returns the absolute path for the file corresponding - to the `dataset_id` regardless of whether the file exists. + to the `obj`.id regardless of whether the file exists. """ - path = self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, old_style=True) + path = self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name, old_style=True) # For backward compatibility, check the old style root path first; otherwise, # construct hashed path if not os.path.exists(path): - return self._construct_path(dataset_id, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) + return self._construct_path(obj, base_dir=base_dir, dir_only=dir_only, extra_dir=extra_dir, extra_dir_at_root=extra_dir_at_root, alt_name=alt_name) - def _construct_path(self, dataset_id, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): + def _construct_path(self, obj, old_style=False, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None): """ Construct the expected absolute path for accessing the object - identified by `dataset_id`. + identified by `obj`.id. :type base_dir: string :param base_dir: A key in self.extra_dirs corresponding to the base @@ -234,13 +225,13 @@ :type dir_only: bool :param dir_only: If True, check only the path where the file - identified by `dataset_id` should be located, not the + identified by `obj` should be located, not the dataset itself. This option applies to `extra_dir` argument as well. :type extra_dir: string :param extra_dir: Append the value of this parameter to the expected path - used to access the object identified by `dataset_id` + used to access the object identified by `obj` (e.g., /files/000/<extra_dir>/dataset_10.dat). :type alt_name: string @@ -252,16 +243,16 @@ the composed directory structure does not include a hash id (e.g., /files/dataset_10.dat (old) vs. /files/000/dataset_10.dat (new)) """ - base = self.file_path - if base_dir in self.extra_dirs: - base = self.extra_dirs.get(base_dir) + base = self.extra_dirs.get(base_dir, self.file_path) if old_style: if extra_dir is not None: path = os.path.join(base, extra_dir) else: path = base else: - rel_path = os.path.join(*directory_hash_id(dataset_id)) + # Construct hashed path + rel_path = os.path.join(*directory_hash_id(obj.id)) + # Optionally append extra_dir if extra_dir is not None: if extra_dir_at_root: rel_path = os.path.join(extra_dir, rel_path) @@ -269,103 +260,86 @@ rel_path = os.path.join(rel_path, extra_dir) path = os.path.join(base, rel_path) if not dir_only: - path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return os.path.abspath(path) - def exists(self, dataset_id, **kwargs): - path = self._construct_path(dataset_id, old_style=True, **kwargs) + def exists(self, obj, **kwargs): + path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility, check root path first; otherwise, construct # and check hashed path - if not os.path.exists(path): - path = self._construct_path(dataset_id, **kwargs) - return os.path.exists(path) + if os.path.exists(path): + return True + else: + path = self._construct_path(obj, **kwargs) + return os.path.exists(path) - def create(self, dataset_id, **kwargs): - kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): - # Pull out locally used fields - extra_dir = kwargs.get('extra_dir', None) - extra_dir_at_root = kwargs.get('extra_dir_at_root', False) + def create(self, obj, **kwargs): + if not self.exists(obj, **kwargs): + path = self._construct_path(obj, **kwargs) dir_only = kwargs.get('dir_only', False) - alt_name = kwargs.get('alt_name', None) - base_dir_key = kwargs.get('base_dir', None) - # Construct hashed path - path = os.path.join(*directory_hash_id(dataset_id)) - # Optionally append extra_dir - if extra_dir is not None: - if extra_dir_at_root: - path = os.path.join(extra_dir, path) - else: - path = os.path.join(path, extra_dir) - # Combine the constructted path with the root dir for all files - base_dir = self.extra_dirs.get(base_dir_key, self.file_path) - path = os.path.join(base_dir, path) # Create directory if it does not exist - if not os.path.exists(path): - os.makedirs(path) + dir = path if dir_only else os.path.dirname(path) + if not os.path.exists(dir): + os.makedirs(dir) + # Create the file if it does not exist if not dir_only: - path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) open(path, 'w').close() - util.umask_fix_perms( path, self.config.umask, 0666 ) + util.umask_fix_perms(path, self.config.umask, 0666) - def empty(self, dataset_id, **kwargs): - return os.path.getsize(self.get_filename(dataset_id, **kwargs)) > 0 + def empty(self, obj, **kwargs): + return os.path.getsize(self.get_filename(obj, **kwargs)) > 0 - def size(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): + def size(self, obj, **kwargs): + if self.exists(obj, **kwargs): try: - return os.path.getsize(self.get_filename(dataset_id, **kwargs)) + return os.path.getsize(self.get_filename(obj, **kwargs)) except OSError: return 0 else: return 0 - def delete(self, dataset_id, entire_dir=False, **kwargs): - path = self.get_filename(dataset_id, **kwargs) + def delete(self, obj, entire_dir=False, **kwargs): + path = self.get_filename(obj, **kwargs) extra_dir = kwargs.get('extra_dir', None) try: if entire_dir and extra_dir: shutil.rmtree(path) return True - if self.exists(dataset_id, **kwargs): + if self.exists(obj, **kwargs): os.remove(path) return True except OSError, ex: - log.critical('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex)) + log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex)) return False - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - data_file = open(self.get_filename(dataset_id, **kwargs), 'r') + def get_data(self, obj, start=0, count=-1, **kwargs): + data_file = open(self.get_filename(obj, **kwargs), 'r') data_file.seek(start) content = data_file.read(count) data_file.close() return content - def get_filename(self, dataset_id, **kwargs): - path = self._construct_path(dataset_id, old_style=True, **kwargs) + def get_filename(self, obj, **kwargs): + path = self._construct_path(obj, old_style=True, **kwargs) # For backward compatibility, check root path first; otherwise, construct - # and check hashed path + # and return hashed path if os.path.exists(path): return path else: - path = self._construct_path(dataset_id, **kwargs) - if os.path.exists(path): - return path - else: - raise ObjectNotFound() + return self._construct_path(obj, **kwargs) - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): + def update_from_file(self, obj, file_name=None, create=False, **kwargs): """ `create` parameter is not used in this implementation """ if create: - self.create(dataset_id, **kwargs) - if file_name and self.exists(dataset_id, **kwargs): + self.create(obj, **kwargs) + if file_name and self.exists(obj, **kwargs): try: - shutil.copy(file_name, self.get_filename(dataset_id, **kwargs)) + shutil.copy(file_name, self.get_filename(obj, **kwargs)) except IOError, ex: log.critical('Error copying %s to %s: %s' % (file_name, - self._get_filename(dataset_id, **kwargs), ex)) + self._get_filename(obj, **kwargs), ex)) - def get_object_url(self, dataset_id, **kwargs): + def get_object_url(self, obj, **kwargs): return None @@ -494,8 +468,8 @@ continue util.umask_fix_perms( path, self.config.umask, 0666, self.config.gid ) - def _construct_path(self, dataset_id, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): - rel_path = os.path.join(*directory_hash_id(dataset_id)) + def _construct_path(self, obj, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None): + rel_path = os.path.join(*directory_hash_id(obj.id)) if extra_dir is not None: if extra_dir_at_root: rel_path = os.path.join(extra_dir, rel_path) @@ -504,7 +478,7 @@ # S3 folders are marked by having trailing '/' so add it now rel_path = '%s/' % rel_path if not dir_only: - rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) return rel_path def _get_cache_path(self, rel_path): @@ -665,18 +639,18 @@ log.error("Trouble pushing S3 key '%s' from file '%s': %s" % (rel_path, source_file, ex)) return False - def file_ready(self, dataset_id, **kwargs): + def file_ready(self, obj, **kwargs): """ A helper method that checks if a file corresponding to a dataset is ready and available to be used. Return True if so, False otherwise.""" - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) # Make sure the size in cache is available in its entirety if self._in_cache(rel_path) and os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_s3(rel_path): return True return False - def exists(self, dataset_id, **kwargs): + def exists(self, obj, **kwargs): in_cache = in_s3 = False - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) # Check cache if self._in_cache(rel_path): in_cache = True @@ -699,9 +673,8 @@ else: return False - def create(self, dataset_id, **kwargs): - kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): + def create(self, obj, **kwargs): + if not self.exists(obj, **kwargs): #print "S3 OS creating a dataset with ID %s" % dataset_id # Pull out locally used fields extra_dir = kwargs.get('extra_dir', None) @@ -710,7 +683,7 @@ alt_name = kwargs.get('alt_name', None) # print "---- Processing: %s; %s" % (alt_name, locals()) # Construct hashed path - rel_path = os.path.join(*directory_hash_id(dataset_id)) + rel_path = os.path.join(*directory_hash_id(obj)) # Optionally append extra_dir if extra_dir is not None: if extra_dir_at_root: @@ -728,30 +701,30 @@ # self._push_to_s3(s3_dir, from_string='') # If instructed, create the dataset in cache & in S3 if not dir_only: - rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % dataset_id) + rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id) open(os.path.join(self.staging_path, rel_path), 'w').close() self._push_to_s3(rel_path, from_string='') - def empty(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): - return bool(self.size(dataset_id, **kwargs) > 0) + def empty(self, obj, **kwargs): + if self.exists(obj, **kwargs): + return bool(self.size(obj, **kwargs) > 0) else: raise ObjectNotFound() - def size(self, dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def size(self, obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) if self._in_cache(rel_path): try: return os.path.getsize(self._get_cache_path(rel_path)) except OSError, ex: log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s" % (rel_path, ex)) - elif self.exists(dataset_id, **kwargs): + elif self.exists(obj, **kwargs): return self._get_size_in_s3(rel_path) log.warning("Did not find dataset '%s', returning 0 for size" % rel_path) return 0 - def delete(self, dataset_id, entire_dir=False, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def delete(self, obj, entire_dir=False, **kwargs): + rel_path = self._construct_path(obj, **kwargs) extra_dir = kwargs.get('extra_dir', None) try: # For the case of extra_files, because we don't have a reference to @@ -777,11 +750,11 @@ except S3ResponseError, ex: log.error("Could not delete key '%s' from S3: %s" % (rel_path, ex)) except OSError, ex: - log.error('%s delete error %s' % (self._get_filename(dataset_id, **kwargs), ex)) + log.error('%s delete error %s' % (self._get_filename(obj, **kwargs), ex)) return False - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def get_data(self, obj, start=0, count=-1, **kwargs): + rel_path = self._construct_path(obj, **kwargs) # Check cache first and get file if not there if not self._in_cache(rel_path): self._pull_into_cache(rel_path) @@ -794,10 +767,10 @@ data_file.close() return content - def get_filename(self, dataset_id, **kwargs): + def get_filename(self, obj, **kwargs): #print "S3 get_filename for dataset: %s" % dataset_id dir_only = kwargs.get('dir_only', False) - rel_path = self._construct_path(dataset_id, **kwargs) + rel_path = self._construct_path(obj, **kwargs) cache_path = self._get_cache_path(rel_path) # S3 does not recognize directories as files so cannot check if those exist. # So, if checking dir only, ensure given dir exists in cache and return @@ -811,7 +784,7 @@ if self._in_cache(rel_path): return cache_path # Check if the file exists in persistent storage and, if it does, pull it into cache - elif self.exists(dataset_id, **kwargs): + elif self.exists(obj, **kwargs): if dir_only: # Directories do not get pulled into cache return cache_path else: @@ -824,11 +797,11 @@ raise ObjectNotFound() # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): + def update_from_file(self, obj, file_name=None, create=False, **kwargs): if create: - self.create(dataset_id, **kwargs) - if self.exists(dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + self.create(obj, **kwargs) + if self.exists(obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) # Chose whether to use the dataset file itself or an alternate file if file_name: source_file = os.path.abspath(file_name) @@ -848,9 +821,9 @@ else: raise ObjectNotFound() - def get_object_url(self, dataset_id, **kwargs): - if self.exists(dataset_id, **kwargs): - rel_path = self._construct_path(dataset_id, **kwargs) + def get_object_url(self, obj, **kwargs): + if self.exists(obj, **kwargs): + rel_path = self._construct_path(obj, **kwargs) try: key = Key(self.bucket, rel_path) return key.generate_url(expires_in = 86400) # 24hrs @@ -873,7 +846,7 @@ "requires a config file, please set one in " \ "'distributed_object_store_config_file')" self.backends = {} - self.weighted_backend_names = [] + self.weighted_backend_ids = [] random.seed() @@ -884,7 +857,7 @@ root = tree.getroot() log.debug('Loading backends for distributed object store from %s' % self.distributed_config) for elem in [ e for e in root if e.tag == 'backend' ]: - name = elem.get('name') + id = elem.get('id') weight = int(elem.get('weight', 1)) if elem.get('type', 'disk'): path = None @@ -895,94 +868,90 @@ elif sub.tag == 'extra_dir': type = sub.get('type') extra_dirs[type] = sub.get('path') - self.backends[name] = DiskObjectStore(config, file_path=path, extra_dirs=extra_dirs) - log.debug("Loaded disk backend '%s' with weight %s and file_path: %s" % (name, weight, path)) + self.backends[id] = DiskObjectStore(config, file_path=path, extra_dirs=extra_dirs) + log.debug("Loaded disk backend '%s' with weight %s and file_path: %s" % (id, weight, path)) if extra_dirs: log.debug(" Extra directories:") for type, dir in extra_dirs.items(): log.debug(" %s: %s" % (type, dir)) for i in range(0, weight): - # The simplest way to do weighting: add backend names to a + # The simplest way to do weighting: add backend ids to a # sequence the number of times equalling weight, then randomly # choose a backend from that sequence at creation - self.weighted_backend_names.append(name) + self.weighted_backend_ids.append(id) - def exists(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - return store is not None + def exists(self, obj, **kwargs): + return self.__call_method('exists', obj, False, False, **kwargs) - def store_name(self, dataset_id, **kwargs): - for name, store in self.backends.items(): - if store.exists(dataset_id, **kwargs): - return name - return None + #def store_id(self, obj, **kwargs): + # return self.__get_store_id_for(obj, **kwargs)[0] - def file_ready(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.file_ready(dataset_id, **kwargs) - return False + def file_ready(self, obj, **kwargs): + return self.__call_method('file_ready', obj, False, False, **kwargs) - def create(self, dataset_id, **kwargs): - store_name = kwargs.pop('store_name', None) - if not self.exists(dataset_id, **kwargs): - if store_name is None or store_name not in self.backends: - store_name = random.choice(self.weighted_backend_names) - log.debug("Selected backend '%s' for creation of dataset %s" % (store_name, dataset_id)) + def create(self, obj, **kwargs): + """ + create() is the only method in which obj.object_store_id may be None + """ + if obj.object_store_id is None or not self.exists(obj, **kwargs): + if obj.object_store_id is None or obj.object_store_id not in self.backends: + obj.object_store_id = random.choice(self.weighted_backend_ids) + object_session( obj ).add( obj ) + object_session( obj ).flush() + log.debug("Selected backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) else: - log.debug("Using preferred backend '%s' for creation of dataset %s" % (store_name, dataset_id)) - return self.backends[store_name].create(dataset_id, **kwargs) + log.debug("Using preferred backend '%s' for creation of %s %s" % (obj.object_store_id, obj.__class__.__name__, obj.id)) + self.backends[obj.object_store_id].create(obj, **kwargs) - def empty(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.empty(dataset_id, **kwargs) - return True + def empty(self, obj, **kwargs): + return self.__call_method('empty', obj, True, False, **kwargs) - def size(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.size(dataset_id, **kwargs) - return 0 + def size(self, obj, **kwargs): + return self.__call_method('size', obj, 0, False, **kwargs) - def delete(self, dataset_id, entire_dir=False, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.delete(dataset_id, entire_dir=entire_dir, **kwargs) - return False + def delete(self, obj, entire_dir=False, **kwargs): + return self.__call_method('delete', obj, False, False, **kwargs) - def get_data(self, dataset_id, start=0, count=-1, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_data(dataset_id, start=0, count=-1, **kwargs) - raise ObjectNotFound() + def get_data(self, obj, start=0, count=-1, **kwargs): + return self.__call_method('get_data', obj, ObjectNotFound, True, **kwargs) - def get_filename(self, dataset_id, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_filename(dataset_id, **kwargs) - raise ObjectNotFound() + def get_filename(self, obj, **kwargs): + return self.__call_method('get_filename', obj, ObjectNotFound, True, **kwargs) - def update_from_file(self, dataset_id, file_name=None, create=False, **kwargs): - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.update_from_file(dataset_id, file_name=file_name, create=create, **kwargs) - if create: - store_name = random.choice(self.weighted_backend_names) - return self.backends[store_name].update_from_file(dataset_id, file_name=file_name, create=create, **kwargs) - raise ObjectNotFound() + def update_from_file(self, obj, file_name=None, create=False, **kwargs): + # can raise ObjectLocationMismatch + # TODO: handling create=True here? probably not since create() is called from w/in, so a store will be selected there + #if create and not self.exists(obj, **kwargs): + # store_id = random.choice(self.weighted_backend_names) + return self.__call_method('update_from_file', obj, ObjectNotFound, True, **kwargs) - def get_object_url(self, dataset_id, **kwargs): - # FIXME: dir_only - store = self.__get_store_for(dataset_id, **kwargs) - if store is not None: - return store.get_object_url(dataset_id, **kwargs) - return None + def get_object_url(self, obj, **kwargs): + return self.__call_method('get_object_url', obj, None, False, **kwargs) - def __get_store_for(self, dataset_id, **kwargs): - for store in self.backends.values(): - if store.exists(dataset_id, **kwargs): - return store + def __call_method(self, method, obj, default, default_is_exception, **kwargs): + object_store_id = self.__get_store_id_for(obj, **kwargs) + if object_store_id is not None: + return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs) + if default_is_exception: + raise default() + else: + return default + + def __get_store_id_for(self, obj, **kwargs): + if obj.object_store_id is not None and obj.object_store_id in self.backends: + return obj.object_store_id + else: + # if this instance has been switched from a non-distributed to a + # distributed object store, or if the object's store id is invalid, + # try to locate the object + log.warning('The backend object store ID (%s) for %s object with ID %s is invalid' % (obj.object_store_id, obj.__class__.__name__, obj.id)) + for id, store in self.backends.items(): + if store.exists(obj, **kwargs): + log.warning('%s object with ID %s found in backend object store with ID %s' % (obj.__class__.__name__, obj.id, id)) + obj.object_store_id = id + object_session( obj ).add( obj ) + object_session( obj ).flush() + return id return None class HierarchicalObjectStore(ObjectStore): diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1859,7 +1859,7 @@ a_files = os.listdir( temp_file_path ) if len( a_files ) > 0: for f in a_files: - self.app.object_store.update_from_file(hda.dataset.id, + self.app.object_store.update_from_file(hda.dataset, extra_dir="dataset_%d_files" % hda.dataset.id, alt_name = f, file_name = os.path.join(temp_file_path, f), @@ -1899,7 +1899,7 @@ sa_session=self.sa_session ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset ) # Move data from temp location to dataset location - self.app.object_store.update_from_file(child_dataset.dataset.id, filename, create=True) + self.app.object_store.update_from_file(child_dataset.dataset, filename, create=True) self.sa_session.add( child_dataset ) self.sa_session.flush() child_dataset.set_size() @@ -1967,7 +1967,7 @@ self.sa_session.add( primary_data ) self.sa_session.flush() # Move data from temp location to dataset location - self.app.object_store.update_from_file(primary_data.dataset.id, filename, create=True) + self.app.object_store.update_from_file(primary_data.dataset, filename, create=True) primary_data.set_size() primary_data.name = "%s (%s)" % ( outdata.name, designation ) primary_data.info = outdata.info diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -228,8 +228,7 @@ # datasets first, then create the associations parent_to_child_pairs = [] child_dataset_names = set() - store_name = None - store_name_set = False # this is needed since None is a valid value for store_name + object_store_id = None for name, output in tool.outputs.items(): for filter in output.filters: try: @@ -292,12 +291,12 @@ trans.sa_session.add( data ) trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) - # Create an empty file immediately - trans.app.object_store.create( data.id, store_name=store_name ) - if not store_name_set: - # Ensure all other datasets in this job are created in the same store - store_name = trans.app.object_store.store_name( data.id ) - store_name_set = True + # Create an empty file immediately. The first dataset will be + # created in the "default" store, all others will be created in + # the same store as the first. + data.dataset.object_store_id = object_store_id + trans.app.object_store.create( data.dataset ) + object_store_id = data.dataset.object_store_id # these will be the same thing after the first output # This may not be neccesary with the new parent/child associations data.designation = name # Copy metadata from one of the inputs if requested. @@ -382,6 +381,7 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) + job.object_store_id = object_store_id trans.sa_session.add( job ) trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -319,8 +319,7 @@ for name, value in tool.params_to_strings( params, trans.app ).iteritems(): job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) - store_name = None - store_name_set = False # this is needed since None is a valid value for store_name + object_store_id = None for i, dataset in enumerate( data_list ): if folder: job.add_output_library_dataset( 'output%i' % i, dataset ) @@ -328,11 +327,12 @@ job.add_output_dataset( 'output%i' % i, dataset ) # Create an empty file immediately if not dataset.dataset.external_filename: - trans.app.object_store.create( dataset.dataset.id, store_name=store_name ) + dataset.dataset.object_store_id = object_store_id + trans.app.object_store.create( dataset.dataset ) + object_store_id = dataset.dataset.object_store_id + trans.sa_session.add( dataset ) # open( dataset.file_name, "w" ).close() - if not store_name_set: - store_name = trans.app.object_store.store_name( dataset.dataset.id ) - store_name_set = True + job.object_store_id = object_store_id job.state = job.states.NEW trans.sa_session.add( job ) trans.sa_session.flush() diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -360,16 +360,16 @@ data = self._check_dataset(trans, dataset_id) if isinstance( data, basestring ): return data - log.debug( "dataset.py -> transfer_status: Checking transfer status for dataset %s..." % data.id ) + log.debug( "Checking transfer status for dataset %s..." % data.dataset.id ) # Pulling files in extra_files_path into cache is not handled via this # method but that's primarily because those files are typically linked to # through tool's output page anyhow so tying a JavaScript event that will # call this method does not seem doable? - if trans.app.object_store.file_ready(data.id): + if data.dataset.external_filename: return True else: - return False + return trans.app.object_store.file_ready(data.dataset) @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): @@ -382,7 +382,7 @@ if filename and filename != "index": # For files in extra_files_path - file_path = trans.app.object_store.get_filename(data.dataset.id, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) + file_path = trans.app.object_store.get_filename(data.dataset, extra_dir='dataset_%s_files' % data.dataset.id, alt_name=filename) if os.path.exists( file_path ): if os.path.isdir( file_path ): return trans.show_error_message( "Directory listing is not allowed." ) #TODO: Reconsider allowing listing of directories? diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -663,7 +663,7 @@ trans.response.set_content_type( 'application/x-gzip' ) else: trans.response.set_content_type( 'application/x-tar' ) - return trans.app.object_store.get_data(jeha.dataset.id) + return trans.app.object_store.get_data(jeha.dataset) elif jeha.job.state in [ model.Job.states.RUNNING, model.Job.states.QUEUED, model.Job.states.WAITING ]: return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \ % ( { 'n' : history.name, 's' : url_for( action="export_archive", id=id, qualified=True ) } ) ) diff -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f -r ff576e7f989c186dcec3c6af76ffa37aad4994bf lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -1647,6 +1647,7 @@ for ldda_id in ldda_ids: try: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + assert not ldda.dataset.purged lddas.append( ldda ) except: ldda = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: fix bug with multiple color pickers in track config.
by Bitbucket 09 Jan '12

09 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/94d54ff122b0/ changeset: 94d54ff122b0 user: jgoecks date: 2012-01-07 18:02:30 summary: Trackster: fix bug with multiple color pickers in track config. affected #: 1 file diff -r d48aa90428593ec9a1ede108aaf97a03b69a086f -r 94d54ff122b0dead007901d1a0fcaebf5c329d0f static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2411,25 +2411,33 @@ var input = $('<input />').attr("id", id ).attr("name", id ).val( value ); // Color picker in tool tip style float var tip = $( "<div class='tipsy tipsy-west' style='position: absolute;' />" ).hide(); - // Inner div for padding purposes - var tip_inner = $("<div style='background-color: black; padding: 10px;'></div>").appendTo(tip); - var farb_container = $("<div/>") - .appendTo(tip_inner) - .farbtastic( { width: 100, height: 100, callback: input, color: value }); - // Outer div container input and tip for hover to work - $("<div />").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) { - tip.css( { - // left: $(this).position().left + ( $(input).width() / 2 ) - 60, - // top: $(this).position().top + $(this.height) - left: $(this).position().left + $(input).width() + 5, - top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(input).height() / 2 ) - } ).show(); - $(document).bind( "click.color-picker", function() { - tip.hide(); - $(document).unbind( "click.color-picker" ); - }); - e.stopPropagation(); - }); + + // Use function to fix values of input and tip. + (function(fixed_input, fixed_tip) { + // Inner div for padding purposes + var tip_inner = $("<div style='background-color: black; padding: 10px;'></div>").appendTo(fixed_tip); + var farb_container = $("<div/>") + .appendTo(tip_inner) + .farbtastic( { width: 100, height: 100, callback: fixed_input, color: value }); + // Outer div container input and tip for hover to work + $("<div />").append( fixed_input ).append( fixed_tip ).appendTo( row ).bind( "click", function ( e ) { + // Hide other pickers. + $(".tipsy").hide(); + + // Show current picker. + fixed_tip.css( { + // left: $(this).position().left + ( $(input).width() / 2 ) - 60, + // top: $(this).position().top + $(this.height) + left: $(this).position().left + $(fixed_input).width() + 5, + top: $(this).position().top - ( $(fixed_tip).height() / 2 ) + ( $(fixed_input).height() / 2 ) + } ).show(); + $(document).bind( "click.color-picker", function() { + fixed_tip.hide(); + $(document).unbind( "click.color-picker" ); + }); + e.stopPropagation(); + }); + })(input, tip); } else { row.append( $('<input />').attr("id", id ).attr("name", id ).val( value ) ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing.
by Bitbucket 06 Jan '12

06 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d48aa9042859/ changeset: d48aa9042859 user: greg date: 2012-01-06 21:43:35 summary: Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing. affected #: 13 files diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -35,12 +35,6 @@ <datatype extension="bigwig" type="galaxy.datatypes.binary:BigWig" mimetype="application/octet-stream" display_in_upload="true"><display file="ucsc/bigwig.xml" /></datatype> - <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> - <indexer file="coverage.xml" /> - </datatype> - <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> - <indexer file="coverage.xml" /> - </datatype><datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> @@ -95,7 +89,6 @@ <converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/><converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/><converter file="interval_to_bed12_converter.xml" target_datatype="bed12"/> - <indexer file="interval_awk.xml" /><display file="genetrack.xml" inherit="True"/><display file="ensembl/ensembl_interval_as_bed.xml" inherit="True"/> diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -74,15 +74,12 @@ self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load history import/export tools load_history_imp_exp_tools( self.toolbox ) - #load external metadata tool + # Load external metadata tool self.datatypes_registry.load_external_metadata_tool( self.toolbox ) - # Load datatype indexers defined in local datatypes_conf.xml - self.datatypes_registry.load_datatype_indexers( self.toolbox ) - # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool - # shed repositories. This will also load all proprietary datatype converters, indexers - # and display_applications. + # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed + # repositories. This will also load all proprietary datatype converters and display_applications. self.installed_repository_manager.load_proprietary_datatypes() - #Load security policy + # Load security policy self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) # Load quota management diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/coverage.py --- a/lib/galaxy/datatypes/indexers/coverage.py +++ /dev/null @@ -1,81 +0,0 @@ -#!/usr/bin/env python - -""" -Read a chromosome of coverage data, and write it as a npy array, as -well as averages over regions of progressively larger size in powers of 10 -""" - -from __future__ import division - -import sys -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -import bx.wiggle -from bx.cookbook import doc_optparse -from bx import misc -max2 = max -pkg_resources.require("numpy>=1.2.1") -from numpy import * -import tempfile -import os - -def write_chrom(max, out_base, instream): - - scores = zeros( max, float32 ) * nan - # Fill array from wiggle - max_value = 0 - min_value = 0 - for line in instream: - line = line.rstrip("\n\r") - (chrom, pos, val) = line.split("\t") - pos, val = int(pos), float(val) - scores[pos] = val - - # Write ra - fname = "%s_%d" % ( out_base, 1 ) - save( fname, scores ) - os.rename( fname+".npy", fname ) - - # Write average - for window in 10, 100, 1000, 10000, 100000: - input = scores.copy() - size = len( input ) - input.resize( ( ( size / window ), window ) ) - masked = ma.masked_array( input, isnan( input ) ) - averaged = mean( masked, 1 ) - averaged.set_fill_value( nan ) - fname = "%s_%d" % ( out_base, window ) - save( fname, averaged.filled() ) - del masked, averaged - os.rename( fname+".npy", fname ) - -def main(): - max = int( 512*1024*1024 ) - # get chroms and lengths - chroms = {} - LEN = {} - for line in open(sys.argv[1],"r"): - line = line.rstrip("\r\n") - fields = line.split("\t") - (chrom, pos, forward) = fields[0:3] - reverse = 0 - if len(fields) == 4: reverse = int(fields[3]) - forward = int(forward)+reverse - pos = int(pos) - chrom_file = chroms.get(chrom, None) - if not chrom_file: - chrom_file = chroms[chrom] = tempfile.NamedTemporaryFile() - chrom_file.write("%s\t%s\t%s\n" % (chrom,pos,forward)) - LEN[chrom] = max2( LEN.get(chrom,0), pos+1 ) - for chrom, stream in chroms.items(): - stream.seek(0) - prefix = os.path.join(sys.argv[2], chrom) - write_chrom( LEN[chrom], prefix, stream ) - - manifest_file = open( os.path.join( sys.argv[2], "manifest.tab" ),"w" ) - for key, value in LEN.items(): - print >> manifest_file, "%s\t%s" % (key, value) - manifest_file.close() - - -if __name__ == "__main__": main() diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/coverage.xml --- a/lib/galaxy/datatypes/indexers/coverage.xml +++ /dev/null @@ -1,12 +0,0 @@ -<tool id="INDEXER_Coverage_0" name="Index Coverage for Track Viewer"> -  - <command interpreter="python">coverage.py $input_dataset $store_path 2>&1 - </command> - <inputs> - <page> - <param format="coverage" name="input_dataset" type="data" label="Choose coverage"/> - </page> - </inputs> - <help> - </help> -</tool> diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/interval.awk --- a/lib/galaxy/datatypes/indexers/interval.awk +++ /dev/null @@ -1,43 +0,0 @@ -BEGIN { - # from galaxy.utils - mapped_chars[">"] = "__gt__" - mapped_chars["<"] = "__lt__" - mapped_chars["'"] = "__sq__" - mapped_chars["\""] = "__dq__" - mapped_chars["\\["] = "__ob__" - mapped_chars["\\]"] = "__cb__" - mapped_chars["\\{"] = "__oc__" - mapped_chars["\\}"] = "__cc__" - mapped_chars["@"] = "__at__" - # additional, not in galaxy.utils - mapped_chars["/"] = "__fs__" - mapped_chars["^manifest\.tab$"] = "__manifest.tab__" -} -function escape_filename( name ) -{ - for( char in mapped_chars ) { - gsub( char, mapped_chars[char], name ) - } - return name -} -!_[$chrom]++ { - # close files only when we switch to a new one. - fn && close(fn) - fn = storepath "/" escape_filename($1) } -{ - print $0 >> fn; - # the || part is needed to catch 0 length chromosomes, which - # should never happen but... - if ($end > chroms[$chrom] || !chroms[$chrom]) - chroms[$chrom] = $end } -END { - fn = storepath "/manifest.tab" - for( x in chroms ) { - # add line to manifest - print x "\t" chroms[x] >> fn - chromfile = storepath "/" escape_filename(x) - # sort in-place - system( "sort -f -n -k " chrom " -k " start " -k " end " -o " chromfile " " chromfile ) - close(chromfile) - } -} \ No newline at end of file diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/interval.py --- a/lib/galaxy/datatypes/indexers/interval.py +++ /dev/null @@ -1,66 +0,0 @@ -#!/usr/bin/env python -""" -Generate indices for track browsing of an interval file. - -usage: %prog bed_file out_directory - -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file -""" -import sys -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.intervals import io -from bx.cookbook import doc_optparse -import psyco_full -import commands -import os -from os import environ -import tempfile -from bisect import bisect - -def divide( intervals, out_path ): - manifest = {} - current_file = None - lastchrom = "" - for line in intervals: - try: - chrom = line.chrom - except AttributeError, e: - continue - manifest[chrom] = max(manifest.get(chrom,0),line.end) - if not lastchrom == chrom: - if current_file: - current_file.close() - current_file = open( os.path.join( out_path, "%s" % chrom), "a" ) - print >> current_file, "\t".join(line) - lastchrom = chrom - if current_file: - current_file.close() - return manifest - -if __name__ == "__main__": - options, args = doc_optparse.parse( __doc__ ) - try: - chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x)-1 for x in options.cols1.split(',')] - in_fname, out_path = args - except: - doc_optparse.exception() - - # Sort through a tempfile first - temp_file = tempfile.NamedTemporaryFile(mode="r") - environ['LC_ALL'] = 'POSIX' - commandline = "sort -f -n -k %d -k %d -k %d -o %s %s" % (chr_col_1+1,start_col_1+1,end_col_1+1, temp_file.name, in_fname) - errorcode, stdout = commands.getstatusoutput(commandline) - - temp_file.seek(0) - interval = io.NiceReaderWrapper( temp_file, - chrom_col=chr_col_1, - start_col=start_col_1, - end_col=end_col_1, - strand_col=strand_col_1, - fix_strand=True ) - manifest = divide( interval, out_path ) - manifest_file = open( os.path.join( out_path, "manifest.tab" ),"w" ) - for key, value in manifest.items(): - print >> manifest_file, "%s\t%s" % (key, value) - manifest_file.close() - temp_file.close() diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/interval.xml --- a/lib/galaxy/datatypes/indexers/interval.xml +++ /dev/null @@ -1,14 +0,0 @@ -<tool id="INDEXER_Interval_0" name="Index Interval for Track Viewer"> -  - <command interpreter="python">interval.py $input_dataset - -1 ${input_dataset.metadata.chromCol},${input_dataset.metadata.startCol},${input_dataset.metadata.endCol},${input_dataset.metadata.strandCol} - $store_path 2>&1 - </command> - <inputs> - <page> - <param format="interval" name="input_dataset" type="data" label="Choose intervals"/> - </page> - </inputs> - <help> - </help> -</tool> diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/interval_awk.xml --- a/lib/galaxy/datatypes/indexers/interval_awk.xml +++ /dev/null @@ -1,16 +0,0 @@ -<tool id="INDEXER_Interval_0" name="Index Interval for Track Viewer"> -  - <command interpreter="awk -f">interval.awk - chrom=${input_dataset.metadata.chromCol} start=${input_dataset.metadata.startCol} - end=${input_dataset.metadata.endCol} strand=${input_dataset.metadata.strandCol} - storepath=${store_path} - $input_dataset 2>&1 - </command> - <inputs> - <page> - <param format="interval" name="input_dataset" type="data" label="Choose intervals"/> - </page> - </inputs> - <help> - </help> -</tool> diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/wiggle.py --- a/lib/galaxy/datatypes/indexers/wiggle.py +++ /dev/null @@ -1,74 +0,0 @@ -#!/usr/bin/env python - -""" -Read a chromosome of wiggle data, and write it as a npy array, as -well as averages over regions of progressively larger size in powers of 10 -""" - -from __future__ import division - -import sys -from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -import bx.wiggle -from bx.cookbook import doc_optparse -from bx import misc -max2 = max -pkg_resources.require("numpy>=1.2.1") -from numpy import * -import tempfile -import os -from galaxy.tracks.store import sanitize_name - - -def write_chrom(max, out_base, instream): - - scores = zeros( max, float32 ) * nan - # Fill array from wiggle - for line in instream: - line = line.rstrip("\n\r") - (chrom, pos, val) = line.split("\t") - pos, val = int(pos), float(val) - scores[pos] = val - - # Write ra - fname = "%s_%d" % ( out_base, 1 ) - save( fname, scores ) - os.rename( fname+".npy", fname ) - - # Write average - for window in 10, 100, 1000, 10000, 100000: - input = scores.copy() - size = len( input ) - input.resize( ( ( size / window ), window ) ) - masked = ma.masked_array( input, isnan( input ) ) - averaged = mean( masked, 1 ) - averaged.set_fill_value( nan ) - fname = "%s_%d" % ( out_base, window ) - save( fname, averaged.filled() ) - del masked, averaged - os.rename( fname+".npy", fname ) - -def main(): - max = int( 512*1024*1024 ) - # get chroms and lengths - chroms = {} - LEN = {} - for (chrom, pos, val) in bx.wiggle.Reader( open(sys.argv[1],"r") ): - chrom_file = chroms.get(chrom, None) - if not chrom_file: - chrom_file = chroms[chrom] = tempfile.NamedTemporaryFile() - chrom_file.write("%s\t%s\t%s\n" % (chrom,pos,val)) - LEN[chrom] = max2( LEN.get(chrom,0), pos+1 ) - for chrom, stream in chroms.items(): - stream.seek(0) - prefix = os.path.join(sys.argv[2], sanitize_name(chrom)) - write_chrom( LEN[chrom], prefix, stream ) - - manifest_file = open( os.path.join( sys.argv[2], "manifest.tab" ),"w" ) - for key, value in LEN.items(): - print >> manifest_file, "%s\t%s" % (key, value) - manifest_file.close() - - -if __name__ == "__main__": main() diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/indexers/wiggle.xml --- a/lib/galaxy/datatypes/indexers/wiggle.xml +++ /dev/null @@ -1,12 +0,0 @@ -<tool id="INDEXER_Wiggle_0" name="Index Wiggle for Track Viewer"> -  - <command interpreter="python">wiggle.py $input_dataset $store_path 2>&1 - </command> - <inputs> - <page> - <param format="wiggle" name="input_dataset" type="data" label="Choose wiggle"/> - </page> - </inputs> - <help> - </help> -</tool> diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -18,7 +18,6 @@ self.datatypes_by_extension = {} self.mimetypes_by_extension = {} self.datatype_converters = odict() - self.datatype_indexers = odict() # Converters defined in local datatypes_conf.xml self.converters = [] # Converters defined in datatypes_conf.xml included @@ -27,11 +26,6 @@ self.converter_deps = {} self.available_tracks = [] self.set_external_metadata_tool = None - # Indexers defined in local datatypes_conf.xml - self.indexers = [] - # Indexers defined in datatypes_conf.xml included - # in installed tool shed repositories. - self.proprietary_indexers = [] self.sniff_order = [] self.upload_file_formats = [] # Map a display application id to a display application @@ -39,10 +33,6 @@ self.converters_path_attr = None # The 'default' converters_path defined in local datatypes_conf.xml self.datatype_converters_path = None - self.indexers_path_attr = None - # The 'default' indexers_path defined in local datatypes_conf.xml - self.datatype_indexers_path = None - self.display_path_attr = None # The 'default' display_path defined in local datatypes_conf.xml self.display_applications_path = None self.datatype_elems = [] @@ -63,11 +53,6 @@ self.datatype_converters_path = os.path.join( root_dir, self.converters_path_attr ) if not os.path.isdir( self.datatype_converters_path ): raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path ) - if not self.datatype_indexers_path: - self.indexers_path_attr = registration.get( 'indexers_path', 'lib/galaxy/datatypes/indexers' ) - self.datatype_indexers_path = os.path.join( root_dir, self.indexers_path_attr ) - if not os.path.isdir( self.datatype_indexers_path ): - raise ConfigurationError( "Directory does not exist: %s" % self.datatype_indexers_path ) if not self.display_applications_path: self.display_path_attr = registration.get( 'display_path', 'display_applications' ) self.display_applications_path = os.path.join( root_dir, self.display_path_attr ) @@ -134,11 +119,6 @@ self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) else: self.converters.append( ( converter_config, extension, target_datatype ) ) - for indexer in elem.findall( 'indexer' ): - # Build the list of datatype indexers for track building - indexer_config = indexer.get( 'file', None ) - if indexer_config: - self.indexers.append( (indexer_config, extension) ) for composite_file in elem.findall( 'composite_file' ): # add composite files name = composite_file.get( 'name', None ) @@ -393,26 +373,6 @@ toolbox.tools_by_id[ set_meta_tool.id ] = set_meta_tool self.set_external_metadata_tool = set_meta_tool self.log.debug( "Loaded external metadata tool: %s", self.set_external_metadata_tool.id ) - def load_datatype_indexers( self, toolbox, indexer_path=None ): - """Adds indexers from self.indexers to the toolbox from app""" - if indexer_path: - # Load indexers defined by datatypes_conf.xml - # included in installed tool shed repository. - indexers = self.proprietary_indexers - else: - # Load indexers defined by local datatypes_conf.xml. - indexers = self.indexers - for elem in indexers: - tool_config = elem[0] - datatype = elem[1] - if indexer_path: - config_path = os.path.join( indexer_path, tool_config ) - else: - config_path = os.path.join( self.datatype_indexers_path, tool_config ) - indexer = toolbox.load_tool( config_path ) - toolbox.tools_by_id[ indexer.id ] = indexer - self.datatype_indexers[ datatype ] = indexer - self.log.debug( "Loaded indexer: %s", indexer.id ) def get_converters_by_datatype(self, ext): """Returns available converters by source type""" converters = odict() @@ -425,18 +385,6 @@ if ext in self.datatype_converters.keys(): converters.update(self.datatype_converters[ext]) return converters - def get_indexers_by_datatype( self, ext ): - """Returns indexers based on datatype""" - class_chain = list() - source_datatype = type(self.get_datatype_by_extension(ext)) - for ext_spec in self.datatype_indexers.keys(): - datatype = type(self.get_datatype_by_extension(ext_spec)) - if issubclass( source_datatype, datatype ): - class_chain.append( ext_spec ) - # Prioritize based on class chain - ext2type = lambda x: self.get_datatype_by_extension(x) - class_chain = sorted(class_chain, lambda x,y: issubclass(ext2type(x),ext2type(y)) and -1 or 1) - return [self.datatype_indexers[x] for x in class_chain] def get_converter_by_target_type(self, source_ext, target_ext): """Returns a converter based on source and target datatypes""" converters = self.get_converters_by_datatype(source_ext) @@ -494,17 +442,13 @@ converters_path_str = ' converters_path="%s"' % self.converters_path_attr else: converters_path_str = '' - if self.indexers_path_attr: - indexers_path_str = ' indexers_path="%s"' % self.indexers_path_attr - else: - indexers_path_str = '' if self.display_path_attr: display_path_str = ' display_path="%s"' % self.display_path_attr else: display_path_str = '' os.write( fd, '<?xml version="1.0"?>\n' ) os.write( fd, '<datatypes>\n' ) - os.write( fd, '<registration%s%s%s>\n' % ( converters_path_str, indexers_path_str, display_path_str ) ) + os.write( fd, '<registration%s%s>\n' % ( converters_path_str, display_path_str ) ) for elem in self.datatype_elems: os.write( fd, '%s' % galaxy.util.xml_to_string( elem ) ) os.write( fd, '</registration>\n' ) diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -23,12 +23,9 @@ path_items = datatypes_config.split( 'repos' ) relative_install_dir = '%srepos/%s/%s/%s' % \ ( path_items[0], tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) - converter_path, indexer_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) + converter_path = load_datatypes( self.app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, converter_path=converter_path ) - if indexer_path: - # Load proprietary datatype indexers - self.app.datatypes_registry.load_datatype_indexers( self.app.toolbox, indexer_path=indexer_path ) # TODO: handle display_applications \ No newline at end of file diff -r 4fdceec512f5c38e1a8bdb03cba6afe77a6e8fef -r d48aa90428593ec9a1ede108aaf97a03b69a086f lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -109,7 +109,6 @@ Update the received metadata_dict with changes that have been applied to the received datatypes_config. This method is used by the InstallManager, which does not have access to trans. - TODO: Handle converters, indexers, sniffers, etc... """ # Parse datatypes_config. tree = ElementTree.parse( datatypes_config ) @@ -451,7 +450,6 @@ tree = util.parse_xml( datatypes_config ) datatypes_config_root = tree.getroot() converter_path = None - indexer_path = None relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) datatype_class_modules = [] @@ -502,7 +500,7 @@ log.debug( "Exception importing datatypes code file %s: %s" % ( str( relative_path_to_datatype_file_name ), str( e ) ) ) finally: lock.release() - # Handle data type converters and indexers. + # Handle data type converters. for elem in registration.findall( 'datatype' ): if not converter_path: # If any of the <datatype> tag sets contain <converter> tags, set the converter_path @@ -520,23 +518,7 @@ break if converter_path: break - if not indexer_path: - # If any of the <datatype> tag sets contain <indexer> tags, set the indexer_path - # if it is not already set. This requires repsitories to place all indexers in the - # same subdirectory within the repository hierarchy. - for indexer in elem.findall( 'indexer' ): - indexer_path = None - indexer_config = indexer.get( 'file', None ) - if indexer_config: - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == indexer_config: - indexer_path = root - break - if indexer_path: - break - if converter_path and indexer_path: + else: break # TODO: handle display_applications else: @@ -546,7 +528,7 @@ imported_modules = [] # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules ) - return converter_path, indexer_path + return converter_path def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): # This method is used by the InstallManager, which does not have access to trans. @@ -562,13 +544,10 @@ if 'datatypes_config' in metadata_dict: datatypes_config = os.path.abspath( metadata_dict[ 'datatypes_config' ] ) # Load data types required by tools. - converter_path, indexer_path = load_datatypes( app, datatypes_config, relative_install_dir ) + converter_path = load_datatypes( app, datatypes_config, relative_install_dir ) if converter_path: # Load proprietary datatype converters app.datatypes_registry.load_datatype_converters( app.toolbox, converter_path=converter_path ) - if indexer_path: - # Load proprietary datatype indexers - app.datatypes_registry.load_datatype_indexers( app.toolbox, indexer_path=indexer_path ) # TODO: handle display_applications if 'tools' in metadata_dict: repository_tools_tups = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 06 Jan '12

06 Jan '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ea42944229df/ changeset: ea42944229df user: jgoecks date: 2012-01-06 17:30:04 summary: Trackster: ensure all visible composite track tiles have the same height so that line tracks are rendered correctly. affected #: 1 file diff -r 85075ee87e1630104ee66f45e77ab2af2d28941c -r ea42944229df83e5db5227af945232ca564db6d5 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3144,11 +3144,14 @@ * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a * jQuery.Deferred object that is fulfilled when tile can be drawn again. */ - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) { + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), tile_low = tile_index * DENSITY * resolution, tile_high = tile_low + DENSITY * resolution; + + // Init kwargs if necessary to avoid having to check if kwargs defined. + if (!kwargs) { kwargs = {}; } // Check tile cache, if found show existing tile in correct position var tile = (force ? undefined : track.tile_cache.get(key)); @@ -3178,7 +3181,7 @@ // If we can draw now, do so. if ( can_draw_now ) { // Set up and draw tile. - extend(tile_data, more_tile_data); + extend(tile_data, kwargs[ 'more_tile_data' ] ); // HACK: this is FeatureTrack-specific. // If track mode is Auto, determine mode and update. @@ -3459,12 +3462,15 @@ this.action_icons.tools_icon.hide(); }, can_draw: Drawable.prototype.can_draw, - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) { + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), tile_low = tile_index * DENSITY * resolution, tile_high = tile_low + DENSITY * resolution; + + // Init kwargs if necessary to avoid having to check if kwargs defined. + if (!kwargs) { kwargs = {}; } // Check tile cache, if found show existing tile in correct position var tile = (force ? undefined : track.tile_cache.get(key)); @@ -3503,7 +3509,7 @@ // If we can draw now, do so. if ( can_draw_now ) { // Set up and draw tile. - extend(tile_data, more_tile_data); + extend(tile_data, kwargs[ 'more_tile_data' ] ); this.tile_predraw_init(); @@ -3517,7 +3523,7 @@ height = 0, track_modes = []; - // Set height to be the max height for all tracks. Also, record track modes. + // Get max height for all tracks and record track modes. var track_canvas_height = 0; for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { track = this.drawables[i]; @@ -3536,9 +3542,12 @@ if (track_canvas_height > height) { height = track_canvas_height; } } + // // Draw all tracks on a single tile. + // canvas.width = width; - canvas.height = height; + // Height is specified in kwargs or is the height found above. + canvas.height = (kwargs['height'] ? kwargs['height'] : height); all_data_index = 0; var ctx = canvas.getContext('2d'); ctx.translate(this.left_offset, 0); @@ -3605,7 +3614,22 @@ postdraw_actions: function(tiles, width, w_scale, clear_after) { TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after); - // TODO: all tiles must be the same size in order to draw LineTracks. + // All tiles must be the same height in order to draw LineTracks, so redraw tiles as needed. + var max_height = -1; + for (var i = 0; i < tiles.length; i++) { + var height = tiles[i].html_elt.find("canvas").height(); + if (height > max_height) { + max_height = height; + } + } + + for (var i = 0; i < tiles.length; i++) { + var tile = tiles[i]; + if (tile.html_elt.find("canvas").height() !== max_height) { + this.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { height: max_height } ); + tile.html_elt.remove(); + } + } } }); @@ -3905,7 +3929,7 @@ var tile = tiles[i]; if (tile.max_val !== global_max) { tile.html_elt.remove(); - track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { max: global_max }); + track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } ); } } } https://bitbucket.org/galaxy/galaxy-central/changeset/24b1918b7a8a/ changeset: 24b1918b7a8a user: jgoecks date: 2012-01-06 17:41:15 summary: Trackster: update criteria for allowing composite tracks; any number of line tracks and a feature track can now be composited. affected #: 1 file diff -r ea42944229df83e5db5227af945232ca564db6d5 -r 24b1918b7a8a50482d210d84b76ef7e2071efba1 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1061,33 +1061,26 @@ // Determine if a composite track can be created. Current criteria: // (a) all tracks are the same; // OR - // (b) there is a LineTrack and a FeatureTrack. + // (b) there is a single FeatureTrack. // /// All tracks the same? - var can_composite = true, - a_type = this.drawables[0].get_type(); + var drawable, + same_type = true, + a_type = this.drawables[0].get_type(), + num_feature_tracks = 0; for (var i = 0; i < this.drawables.length; i++) { - if ( this.drawables[i].get_type() !== a_type ) { + drawable = this.drawables[i] + if (drawable.get_type() !== a_type) { can_composite = false; break; } + if (drawable instanceof FeatureTrack) { + num_feature_tracks++; + } } - if (!can_composite) { - if ( this.drawables.length == 2 && - ( - (this.drawables[0] instanceof FeatureTrack && - this.drawables[1] instanceof LineTrack) - || - (this.drawables[0] instanceof LineTrack && - this.drawables[1] instanceof FeatureTrack) - ) - ) - can_composite = true; - } - - if (can_composite) { + if (same_type || num_feature_tracks === 1) { this.action_icons.composite_icon.show(); } else { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: enable composite tracks composed of a FeatureTrack and LineTrack. Refactor to always handle left_offset only in draw_helper.
by Bitbucket 05 Jan '12

05 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/85075ee87e16/ changeset: 85075ee87e16 user: jgoecks date: 2012-01-06 01:46:49 summary: Trackster: enable composite tracks composed of a FeatureTrack and LineTrack. Refactor to always handle left_offset only in draw_helper. affected #: 1 file diff -r 999dc276912c8beda98b0a978d2ad945bd13c726 -r 85075ee87e1630104ee66f45e77ab2af2d28941c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1057,7 +1057,14 @@ this.request_draw(); }, update_icons: function() { - // Only show composite icon if all tracks are the same type. + // + // Determine if a composite track can be created. Current criteria: + // (a) all tracks are the same; + // OR + // (b) there is a LineTrack and a FeatureTrack. + // + + /// All tracks the same? var can_composite = true, a_type = this.drawables[0].get_type(); for (var i = 0; i < this.drawables.length; i++) { @@ -1067,13 +1074,26 @@ } } + if (!can_composite) { + if ( this.drawables.length == 2 && + ( + (this.drawables[0] instanceof FeatureTrack && + this.drawables[1] instanceof LineTrack) + || + (this.drawables[0] instanceof LineTrack && + this.drawables[1] instanceof FeatureTrack) + ) + ) + can_composite = true; + } + if (can_composite) { this.action_icons.composite_icon.show(); } else { this.action_icons.composite_icon.hide(); $(".tipsy").remove(); - } + } }, /** * Add composite track to group that includes all of group's tracks. @@ -2930,7 +2950,8 @@ // Create copy. var new_track = new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, this.filters, this.tool, this.data_manager); - // Misc. init and return. + // Misc. init and return. + new_track.change_mode(this.mode); new_track.enabled = this.enabled; return new_track; }, @@ -3178,7 +3199,9 @@ canvas.width = width; canvas.height = height; - var tile = track.draw_tile(tile_data, canvas, mode, resolution, tile_index, w_scale, seq_data); + var ctx = canvas.getContext('2d'); + ctx.translate(this.left_offset, 0); + var tile = track.draw_tile(tile_data, ctx, mode, resolution, tile_index, w_scale, seq_data); // Don't cache, show if no tile. if (tile !== undefined) { @@ -3208,14 +3231,14 @@ /** * Draw a track tile. * @param result result from server - * @param canvas canvas to draw on + * @param ctx canvas context to draw on * @param mode mode to draw in * @param resolution view resolution * @param tile_index index of tile to be drawn * @param w_scale pixels per base * @param ref_seq reference sequence data */ - draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) { + draw_tile: function(result, ctx, mode, resolution, tile_index, w_scale, ref_seq) { console.log("Warning: TiledTrack.draw_tile() not implemented."); }, /** @@ -3356,12 +3379,13 @@ var CompositeTrack = function(name, view, container, drawables) { // HACK: modes should be static class vars for most tracks and should update as // needed for CompositeTracks - this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; + this.display_modes = drawables[0].display_modes; TiledTrack.call(this, name, view, container); // Init drawables; each drawable is a copy so that config/preferences - // are independent of each other. + // are independent of each other. Also init left offset. this.drawables = []; + this.left_offset = 0; if (drawables) { var ids = [], @@ -3370,6 +3394,11 @@ drawable = drawables[i]; ids.push(drawable.dataset_id); this.drawables[i] = drawable.copy(); + + // Track's left offset is the max of all tracks. + if (drawable.left_offset > this.left_offset) { + this.left_offset = drawable.left_offset; + } } this.enabled = true; } @@ -3483,24 +3512,46 @@ tile_bounds = track._get_tile_bounds(tile_index, resolution), tile_low = tile_bounds[0], tile_high = tile_bounds[1], - width = Math.ceil( (tile_high - tile_low) * w_scale ), - // FIXME: need to set height to be max for all tracks. - height = track.get_canvas_height(tile_data, track.mode, w_scale, width); + all_data_index = 0, + width = Math.ceil( (tile_high - tile_low) * w_scale ) + this.left_offset, + height = 0, + track_modes = []; + + // Set height to be the max height for all tracks. Also, record track modes. + var track_canvas_height = 0; + for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { + track = this.drawables[i]; + tile_data = all_data[ all_data_index ]; + + // HACK: this is FeatureTrack-specific. + // If track mode is Auto, determine mode and update. + var mode = track.mode; + if (mode === "Auto") { + mode = track.get_mode(tile_data); + track.update_auto_mode(mode); + } + track_modes.push(mode) + + track_canvas_height = track.get_canvas_height(tile_data, mode, w_scale, width); + if (track_canvas_height > height) { height = track_canvas_height; } + } // Draw all tracks on a single tile. canvas.width = width; canvas.height = height; - var all_data_index = 0 + all_data_index = 0; + var ctx = canvas.getContext('2d'); + ctx.translate(this.left_offset, 0); for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { track = this.drawables[i]; tile_data = all_data[ all_data_index ]; seq_data = all_data[ all_data_index + 1 ]; - tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data); + tile = track.draw_tile(tile_data, ctx, track_modes[i], resolution, tile_index, w_scale, seq_data); } // Don't cache, show if no tile. - track.tile_cache.set(key, tile); - track.show_tile(tile, parent_element, w_scale); + this.tile_cache.set(key, tile); + this.show_tile(tile, parent_element, w_scale); return tile; } @@ -3546,6 +3597,15 @@ track.prefs.min_value = min; track.prefs.max_value = max; } + }, + /** + * Actions to be taken after draw has been completed. Draw is completed when all tiles have been + * drawn/fetched and shown. + */ + postdraw_actions: function(tiles, width, w_scale, clear_after) { + TiledTrack.prototype.postdraw_actions.call(this, tiles, width, w_scale, clear_after); + + // TODO: all tiles must be the same size in order to draw LineTracks. } }); @@ -3573,7 +3633,7 @@ /** * Draw ReferenceTrack tile. */ - draw_tile: function(seq, canvas, mode, resolution, tile_index, w_scale) { + draw_tile: function(seq, ctx, mode, resolution, tile_index, w_scale) { var track = this; if (w_scale > this.view.canvas_manager.char_width_px) { @@ -3581,7 +3641,7 @@ track.content_div.css("height", "0px"); return; } - var ctx = canvas.getContext("2d"); + var canvas = ctx.canvas; ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "center"; seq = seq.data; @@ -3720,7 +3780,7 @@ /** * Draw LineTrack tile. */ - draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale) { + draw_tile: function(result, ctx, mode, resolution, tile_index, w_scale) { // FIXME: is this needed? if (this.vertical_range === undefined) { return; @@ -3728,7 +3788,7 @@ // Paint onto canvas. var - ctx = canvas.getContext("2d"), + canvas = ctx.canvas, tile_bounds = this._get_tile_bounds(tile_index, resolution), tile_low = tile_bounds[0], tile_high = tile_bounds[1], @@ -4057,15 +4117,16 @@ /** * Draw FeatureTrack tile. * @param result result from server - * @param canvas canvas to draw on + * @param cxt canvas context to draw on * @param mode mode to draw in * @param resolution view resolution * @param tile_index index of tile to be drawn * @param w_scale pixels per base * @param ref_seq reference sequence data */ - draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) { + draw_tile: function(result, ctx, mode, resolution, tile_index, w_scale, ref_seq) { var track = this, + canvas = ctx.canvas, tile_bounds = this._get_tile_bounds(tile_index, resolution), tile_low = tile_bounds[0], tile_high = tile_bounds[1], @@ -4092,9 +4153,9 @@ } // Paint summary tree into canvas var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); - var ctx = canvas.getContext("2d"); - // Deal with left_offset by translating. - ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); + // FIXME: it shouldn't be necessary to build in padding. + ctx.translate(0, SUMMARY_TREE_TOP_PADDING); + ctx.globalCompositeOperation = "darker"; painter.draw(ctx, canvas.width, canvas.height, w_scale); return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); } @@ -4131,7 +4192,7 @@ var feature_mapper = null; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - var ctx = canvas.getContext("2d"); + ctx.globalCompositeOperation = "darker"; ctx.fillStyle = this.prefs.block_color; ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "right"; @@ -4140,7 +4201,6 @@ if (result.data) { // Draw features. slots = this.inc_slots[w_scale].slots; - ctx.translate(left_offset, 0); feature_mapper = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots); feature_mapper.translation = -left_offset; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fixes and enhancements for supporting tool shed repositories that include data types that use class modules included in the repository. More than 1 class modules can now be included in the repository.
by Bitbucket 05 Jan '12

05 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4d131422777f/ changeset: 4d131422777f user: greg date: 2012-01-05 18:24:45 summary: Fixes and enhancements for supporting tool shed repositories that include data types that use class modules included in the repository. More than 1 class modules can now be included in the repository. affected #: 4 files diff -r 82af6b933a0af1c4af0958aa378af846e7efc449 -r 4d131422777f436f3b3eebfc7a9f61cec61810b1 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -71,7 +71,7 @@ # Manage installed tool shed repositories self.installed_repository_manager = galaxy.tool_shed.InstalledRepositoryManager( self ) # Add additional datatypes from installed tool shed repositories to the datatypes registry. - self.installed_repository_manager.load_datatypes() + self.installed_repository_manager.load_proprietary_datatypes() # Load datatype converters self.datatypes_registry.load_datatype_converters( self.toolbox ) # Load history import/export tools diff -r 82af6b933a0af1c4af0958aa378af846e7efc449 -r 4d131422777f436f3b3eebfc7a9f61cec61810b1 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -36,7 +36,7 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None - def load_datatypes( self, root_dir=None, config=None, imported_module=None ): + def load_datatypes( self, root_dir=None, config=None, imported_modules=None ): if root_dir and config: inherit_display_application_by_class = [] # Parse datatypes_conf.xml @@ -81,8 +81,11 @@ fields = dtype.split( ':' ) datatype_module = fields[0] datatype_class_name = fields[1] - if imported_module: - datatype_class = getattr( imported_module, datatype_class_name ) + if imported_modules: + for imported_module in imported_modules: + if hasattr( imported_module, datatype_class_name ): + datatype_class = getattr( imported_module, datatype_class_name ) + break else: fields = datatype_module.split( '.' ) module = __import__( fields.pop(0) ) diff -r 82af6b933a0af1c4af0958aa378af846e7efc449 -r 4d131422777f436f3b3eebfc7a9f61cec61810b1 lib/galaxy/tool_shed/__init__.py --- a/lib/galaxy/tool_shed/__init__.py +++ b/lib/galaxy/tool_shed/__init__.py @@ -2,6 +2,7 @@ Classes encapsulating the management of repositories installed from Galaxy tool sheds. """ import os, logging +from galaxy.util.shed_util import load_datatypes from galaxy.model.orm import * log = logging.getLogger(__name__) @@ -11,13 +12,16 @@ self.app = app self.model = self.app.model self.sa_session = self.model.context.current - def load_datatypes( self ): + def load_proprietary_datatypes( self ): for tool_shed_repository in self.sa_session.query( self.model.ToolShedRepository ) \ .filter( and_( self.model.ToolShedRepository.table.c.includes_datatypes==True, self.model.ToolShedRepository.table.c.deleted==False ) ) \ .order_by( self.model.ToolShedRepository.table.c.id ): metadata = tool_shed_repository.metadata datatypes_config = metadata[ 'datatypes_config' ] - full_path = os.path.abspath( datatypes_config ) - self.app.datatypes_registry.load_datatypes( self.app.config.root, full_path ) + # We need the repository installation directory, which we can get from the path to the datatypes config. + path_items = datatypes_config.split( 'repos' ) + relative_install_dir = '%srepos/%s/%s/%s' % \ + ( path_items[0], tool_shed_repository.owner, tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) + load_datatypes( self.app, datatypes_config, relative_install_dir ) \ No newline at end of file diff -r 82af6b933a0af1c4af0958aa378af846e7efc449 -r 4d131422777f436f3b3eebfc7a9f61cec61810b1 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,4 +1,4 @@ -import os, tempfile, shutil, subprocess, logging +import os, sys, tempfile, shutil, subprocess, threading, logging from datetime import date, datetime, timedelta from time import strftime from galaxy import util @@ -439,14 +439,20 @@ error = tmp_stderr.read() tmp_stderr.close() log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) -def load_datatypes( app, datatypes_config, relative_intall_dir ): +def load_datatypes( app, datatypes_config, relative_install_dir ): # This method is used by the InstallManager, which does not have access to trans. - imported_module = None + def __import_module( relative_path, datatype_module ): + sys.path.insert( 0, relative_path ) + imported_module = __import__( datatype_module ) + sys.path.pop( 0 ) + return imported_module + imported_modules = [] # Parse datatypes_config. tree = util.parse_xml( datatypes_config ) datatypes_config_root = tree.getroot() relative_path_to_datatype_file_name = None datatype_files = datatypes_config_root.find( 'datatype_files' ) + datatype_class_modules = [] if datatype_files: # Currently only a single datatype_file is supported. For example: # <datatype_files> @@ -456,40 +462,47 @@ datatype_file_name = elem.get( 'name', None ) if datatype_file_name: # Find the file in the installed repository. - for root, dirs, files in os.walk( relative_intall_dir ): + for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0: for name in files: if name == datatype_file_name: - relative_path_to_datatype_file_name = os.path.join( root, name ) + datatype_class_modules.append( os.path.join( root, name ) ) break break - if relative_path_to_datatype_file_name: - relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name ) - registration = datatypes_config_root.find( 'registration' ) - # Get the module by parsing the <datatype> tag. - for elem in registration.findall( 'datatype' ): - # A 'type' attribute is currently required. The attribute - # should be something like: type="gmap:GmapDB". - dtype = elem.get( 'type', None ) - if dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] - # Since we currently support only a single datatype_file, - # we have what we need. - break - try: - sys.path.insert( 0, relative_head ) - imported_module = __import__( datatype_module ) - sys.path.pop( 0 ) - except Exception, e: - log.debug( "Exception importing datatypes code file included in installed repository: %s" % str( e ) ) + if datatype_class_modules: + for relative_path_to_datatype_file_name in datatype_class_modules: + relative_head, relative_tail = os.path.split( relative_path_to_datatype_file_name ) + registration = datatypes_config_root.find( 'registration' ) + # Get the module by parsing the <datatype> tag. + for elem in registration.findall( 'datatype' ): + # A 'type' attribute is currently required. The attribute + # should be something like one of the following: + # type="gmap:GmapDB" + # type="galaxy.datatypes.gmap:GmapDB" + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + datatype_module = fields[ 0 ] + if datatype_module.find( '.' ) >= 0: + # Handle the case where datatype_module is "galaxy.datatypes.gmap" + datatype_module = datatype_module.split( '.' )[ -1 ] + datatype_class_name = fields[ 1 ] + # We need to change the value of sys.path, so do it in a way that is thread-safe. + lock = threading.Lock() + lock.acquire( True ) + try: + imported_module = __import_module( relative_head, datatype_module ) + imported_modules.append( imported_module ) + except Exception, e: + log.debug( "Exception importing datatypes code file %s: %s" % ( str( relative_path_to_datatype_file_name ), str( e ) ) ) + finally: + lock.release() else: - # The repository includes a datayptes_conf.xml file, but no code file that + # The repository includes a dataypes_conf.xml file, but no code file that # contains data type classes. This implies that the data types in datayptes_conf.xml # are all subclasses of data types that are in the distribution. - imported_module = None - app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_module=imported_module ) + imported_modules = [] + app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=datatypes_config, imported_modules=imported_modules ) def load_repository_contents( app, name, description, owner, changeset_revision, tool_path, repository_clone_url, relative_install_dir, current_working_dir, tmp_name, tool_section=None, shed_tool_conf=None, new_install=True ): # This method is used by the InstallManager, which does not have access to trans. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Handle NaN values to produce correct JSON in data providers.
by Bitbucket 04 Jan '12

04 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/82af6b933a0a/ changeset: 82af6b933a0a user: jgoecks date: 2012-01-05 00:01:04 summary: Handle NaN values to produce correct JSON in data providers. affected #: 1 file diff -r f46d856dc0db590109a59fbdddf892ddc8785679 -r 82af6b933a0af1c4af0958aa378af846e7efc449 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -3,7 +3,7 @@ """ import sys, time -from math import ceil, log, sqrt +from math import ceil, log, sqrt, isnan import pkg_resources pkg_resources.require( "bx-python" ) if sys.version_info[:2] == (2, 4): @@ -1041,13 +1041,21 @@ # Add filter data to payload. for col in filter_cols: if col == "Score": - try: - payload.append( float( feature.score ) ) + try: + f = float( feature.score ) + if not math.isnan( f ): + payload.append( f ) + else: + payload.append( feature.score ) except: payload.append( feature.score ) elif col in feature.attributes: try: - payload.append( float( feature.attributes[col] ) ) + f = float( feature.attributes[col] ) + if not math.isnan( f ): + payload.append( f ) + else: + payload.append( feature.attributes[col] ) except: # Feature is not a float. payload.append( feature.attributes[col] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: clear track content during initialization.
by Bitbucket 04 Jan '12

04 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f46d856dc0db/ changeset: f46d856dc0db user: jgoecks date: 2012-01-04 20:27:28 summary: Trackster: clear track content during initialization. affected #: 1 file diff -r 705eef780e7255775fe9fed93ff0e1339e59b6ad -r f46d856dc0db590109a59fbdddf892ddc8785679 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2825,6 +2825,8 @@ track.content_div.text(DATA_LOADING); } */ + // Remove old track content (e.g. tiles, messages). + track.content_div.children().remove(); track.container_div.removeClass("nodata error pending"); // Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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