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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 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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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