- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Fix for a minor bug in e28ebc25b2e7
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c32929b315bd/ changeset: c32929b315bd user: natefoo date: 2011-09-30 21:07:11 summary: Fix for a minor bug in e28ebc25b2e7 affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/dataset.py Fri Sep 30 14:21:51 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Sep 30 15:07:11 2011 -0400 @@ -690,7 +690,7 @@ # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): - trans.response.set_content_type( data.get_mime() ) + trans.response.set_content_type( dataset.get_mime() ) return open( dataset.file_name ) else: # Get rating data. 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: fixes for adding a dataset to a new visualization.
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1478b77001bd/ changeset: 1478b77001bd user: jgoecks date: 2011-09-30 20:21:51 summary: Trackster: fixes for adding a dataset to a new visualization. affected #: 3 files (-1 bytes) --- a/static/scripts/packed/trackster_ui.js Fri Sep 30 14:03:58 2011 -0400 +++ b/static/scripts/packed/trackster_ui.js Fri Sep 30 14:21:51 2011 -0400 @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file --- a/static/scripts/trackster_ui.js Fri Sep 30 14:03:58 2011 -0400 +++ b/static/scripts/trackster_ui.js Fri Sep 30 14:21:51 2011 -0400 @@ -89,15 +89,17 @@ view = new View(parent_elt, title, id, dbkey); view.editor = true; $.when( view.load_chroms_deferred ).then(function() { - // Viewport config. - var - chrom = viewport_config.chrom, - start = viewport_config.start, - end = viewport_config.end, - overview_track_name = viewport_config.overview; + // Viewport config. + if (viewport_config) { + var + chrom = viewport_config.chrom, + start = viewport_config.start, + end = viewport_config.end, + overview_track_name = viewport_config.overview; - if (chrom && (start !== undefined) && end) { - view.change_chrom(chrom, start, end); + if (chrom && (start !== undefined) && end) { + view.change_chrom(chrom, start, end); + } } // Add drawables to view. --- a/templates/tracks/browser.mako Fri Sep 30 14:03:58 2011 -0400 +++ b/templates/tracks/browser.mako Fri Sep 30 14:21:51 2011 -0400 @@ -166,7 +166,7 @@ url: "${h.url_for( action='add_track_async' )}", data: { hda_id: "${add_dataset}" }, dataType: "json", - success: function(track_data) { view.add_drawable( track_from_dict(track_data) ) } + success: function(track_data) { view.add_drawable( track_from_dict(track_data, view) ) } }); %endif 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: greg: Two minor fixes.
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/be9f3aa6c324/ changeset: be9f3aa6c324 user: greg date: 2011-09-30 20:03:58 summary: Two minor fixes. affected #: 2 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Fri Sep 30 10:50:02 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Sep 30 14:03:58 2011 -0400 @@ -1305,7 +1305,7 @@ if webapp == 'galaxy': cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ .filter( trans.model.ToolShedRepository.deleted == False ) \ - .all() + .first() return trans.fill_template( '/webapps/galaxy/admin/index.mako', webapp=webapp, cloned_repositories=cloned_repositories, --- a/templates/webapps/galaxy/admin/index.mako Fri Sep 30 10:50:02 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Fri Sep 30 14:03:58 2011 -0400 @@ -63,7 +63,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> %if cloned_repositories: - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage cloned tool shed repositories</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </div></div> 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: greg: Fix for retrieving the list of cloned tool shed repositories from a local Galaxy instance.
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/418f75a6041a/ changeset: 418f75a6041a user: greg date: 2011-09-30 16:50:02 summary: Fix for retrieving the list of cloned tool shed repositories from a local Galaxy instance. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/base/controller.py Fri Sep 30 09:48:56 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Sep 30 10:50:02 2011 -0400 @@ -1304,7 +1304,8 @@ status = params.get( 'status', 'done' ) if webapp == 'galaxy': cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ - .filter( trans.model.ToolShedRepository.deleted == False ) + .filter( trans.model.ToolShedRepository.deleted == False ) \ + .all() return trans.fill_template( '/webapps/galaxy/admin/index.mako', webapp=webapp, cloned_repositories=cloned_repositories, 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: greg: Add the ability for a Galaxy admin to get updates from the tool shed for cloned tool shed repositories installed on their local Galaxy instance.
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8dce400655d6/ changeset: 8dce400655d6 user: greg date: 2011-09-30 15:48:56 summary: Add the ability for a Galaxy admin to get updates from the tool shed for cloned tool shed repositories installed on their local Galaxy instance. affected #: 10 files (-1 bytes) --- a/lib/galaxy/model/__init__.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/model/__init__.py Fri Sep 30 09:48:56 2011 -0400 @@ -2630,6 +2630,17 @@ class APIKeys( object ): pass +class ToolShedRepository( object ): + def __init__( self, id=None, create_time=None, tool_shed=None, name=None, description=None, owner=None, changeset_revision=None, deleted=False ): + self.id = id + self.create_time = create_time + self.tool_shed = tool_shed + self.name = name + self.description = description + self.owner = owner + self.changeset_revision = changeset_revision + self.deleted = deleted + ## ---- Utility methods ------------------------------------------------------- def directory_hash_id( id ): --- a/lib/galaxy/model/mapping.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/model/mapping.py Fri Sep 30 09:48:56 2011 -0400 @@ -363,6 +363,17 @@ Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), Column( "deleted", Boolean, index=True, default=False ) ) +ToolShedRepository.table = Table( "tool_shed_repository", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "tool_shed", TrimmedString( 255 ), index=True ), + Column( "name", TrimmedString( 255 ), index=True ), + Column( "description" , TEXT ), + Column( "owner", TrimmedString( 255 ), index=True ), + Column( "changeset_revision", TrimmedString( 255 ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + Job.table = Table( "job", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -1583,7 +1594,9 @@ annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" ), ratings=relation( PageRatingAssociation, order_by=PageRatingAssociation.table.c.id, backref="pages" ) ) ) - + +assign_mapper( context, ToolShedRepository, ToolShedRepository.table ) + # Set up proxy so that # Page.users_shared_with # returns a list of users that page is shared with. --- a/lib/galaxy/web/base/controller.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Sep 30 09:48:56 2011 -0400 @@ -1293,6 +1293,7 @@ role_list_grid = None group_list_grid = None quota_list_grid = None + repository_list_grid = None @web.expose @web.require_admin @@ -1302,8 +1303,11 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if webapp == 'galaxy': + cloned_repositories = trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( trans.model.ToolShedRepository.deleted == False ) return trans.fill_template( '/webapps/galaxy/admin/index.mako', webapp=webapp, + cloned_repositories=cloned_repositories, message=message, status=status ) else: @@ -2382,362 +2386,9 @@ msg = msg, status = status, job_lock = trans.app.job_manager.job_queue.job_lock ) - @web.expose - @web.require_admin - def browse_tool_shed( self, trans, **kwd ): - tool_shed_url = kwd[ 'tool_shed_url' ] - galaxy_url = trans.request.host - url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) - return trans.response.send_redirect( url ) - @web.expose - @web.require_admin - def install_tool_shed_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - tool_shed_url = kwd[ 'tool_shed_url' ] - repository_name = kwd[ 'repository_name' ] - changeset_revision = kwd[ 'changeset_revision' ] - repository_clone_url = kwd[ 'repository_clone_url' ] - if kwd.get( 'select_tool_panel_section_button', False ): - shed_tool_conf = kwd[ 'shed_tool_conf' ] - # Get the tool path. - for k, tool_path in trans.app.toolbox.shed_tool_confs.items(): - if k == shed_tool_conf: - break - if 'tool_panel_section' in kwd: - section_key = 'section_%s' % kwd[ 'tool_panel_section' ] - tool_section = trans.app.toolbox.tool_panel[ section_key ] - # Clone the repository to the configured location. - current_working_dir = os.getcwd() - clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) - if os.path.exists( clone_dir ): - # Repository and revision has already been cloned. - # TODO: implement the ability to re-install or revert an existing repository. - message = 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.' % \ - ( changeset_revision, repository_name ) - status = 'error' - else: - os.makedirs( clone_dir ) - log.debug( 'Cloning %s...' % repository_clone_url ) - cmd = 'hg clone %s' % repository_clone_url - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( clone_dir ) - proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode == 0: - repo_files_dir = os.path.join( clone_dir, repository_name ) - log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) - cmd = 'hg update -r %s' % changeset_revision - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( repo_files_dir ) - proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode == 0: - sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) - if repository_tools_tups: - # Handle missing data table entries for tool parameters that are dynamically generated select lists. - repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) - # Handle missing index files for tool parameters that are dynamically generated select lists. - repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) - # Handle tools that use fabric scripts to install dependencies. - self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) - # Generate an in-memory tool conf section that includes the new tools. - new_tool_section = self.__generate_tool_panel_section( repository_name, - repository_clone_url, - changeset_revision, - tool_section, - repository_tools_tups ) - # Create a temporary file to persist the in-memory tool section - # TODO: Figure out how to do this in-memory using xml.etree. - tmp_name = tempfile.NamedTemporaryFile().name - persisted_new_tool_section = open( tmp_name, 'wb' ) - persisted_new_tool_section.write( new_tool_section ) - persisted_new_tool_section.close() - # Parse the persisted tool panel section - tree = ElementTree.parse( tmp_name ) - root = tree.getroot() - ElementInclude.include( root ) - # Load the tools in the section into the tool panel. - trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path ) - # Remove the temporary file - try: - os.unlink( tmp_name ) - except: - pass - # Append the new section to the shed_tool_config file. - self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section ) - message = 'Revision <b>%s</b> of repository <b>%s</b> has been installed in tool panel section <b>%s</b>.' % \ - ( changeset_revision, repository_name, tool_section.name ) - return trans.show_ok_message( message ) - else: - tmp_stderr = open( tmp_name, 'rb' ) - message = tmp_stderr.read() - tmp_stderr.close() - status = 'error' - else: - tmp_stderr = open( tmp_name, 'rb' ) - message = tmp_stderr.read() - tmp_stderr.close() - status = 'error' - else: - message = 'Choose the section in your tool panel to contain the installed tools.' - status = 'error' - if len( trans.app.toolbox.shed_tool_confs.keys() ) > 1: - shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans ) - shed_tool_conf = None - else: - shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' ) - shed_tool_conf_select_field = None - tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) - return trans.fill_template( '/admin/select_tool_panel_section.mako', - tool_shed_url=tool_shed_url, - repository_name=repository_name, - changeset_revision=changeset_revision, - repository_clone_url=repository_clone_url, - shed_tool_conf=shed_tool_conf, - shed_tool_conf_select_field=shed_tool_conf_select_field, - tool_panel_section_select_field=tool_panel_section_select_field, - message=message, - status=status ) - def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): - # Inspect each tool to see if any have input parameters that are dynamically - # generated select lists that require entries in the tool_data_table_conf.xml file. - missing_data_table_entry = False - for index, repository_tools_tup in enumerate( repository_tools_tups ): - tup_path, repository_tool = repository_tools_tup - if repository_tool.params_with_missing_data_table_entry: - missing_data_table_entry = True - break - if missing_data_table_entry: - # The repository must contain a tool_data_table_conf.xml.sample file that includes - # all required entries for all tools in the repository. - for sample_file in sample_files: - head, tail = os.path.split( sample_file ) - if tail == 'tool_data_table_conf.xml.sample': - break - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) - if error: - # TODO: Do more here than logging an exception. - log.debug( exception_msg ) - # Reload the tool into the local list of repository_tools_tups. - repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) - repository_tools_tups[ index ] = ( tup_path, repository_tool ) - return repository_tools_tups - def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ): - # Inspect each tool to see if it has any input parameters that - # are dynamically generated select lists that depend on a .loc file. - missing_files_handled = [] - for index, repository_tools_tup in enumerate( repository_tools_tups ): - tup_path, repository_tool = repository_tools_tup - params_with_missing_index_file = repository_tool.params_with_missing_index_file - for param in params_with_missing_index_file: - options = param.options - missing_head, missing_tail = os.path.split( options.missing_index_file ) - if missing_tail not in missing_files_handled: - # The repository must contain the required xxx.loc.sample file. - for sample_file in sample_files: - sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: - copy_sample_loc_file( trans, sample_file ) - if options.tool_data_table and options.tool_data_table.missing_index_file: - options.tool_data_table.handle_found_index_file( options.missing_index_file ) - missing_files_handled.append( missing_tail ) - break - # Reload the tool into the local list of repository_tools_tups. - repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) - repository_tools_tups[ index ] = ( tup_path, repository_tool ) - return repository_tools_tups - def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ): - # Inspect each tool to see if it includes a "requirement" that refers to a fabric - # script. For those that do, execute the fabric script to install tool dependencies. - for index, repository_tools_tup in enumerate( repository_tools_tups ): - tup_path, repository_tool = repository_tools_tup - for requirement in repository_tool.requirements: - if requirement.type == 'fabfile': - log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) - fabfile = requirement.fabfile - method = requirement.method - # Find the relative path to the fabfile. - relative_fabfile_path = None - for root, dirs, files in os.walk( repo_files_dir ): - for name in files: - if name == fabfile: - relative_fabfile_path = os.path.join( root, name ) - break - if relative_fabfile_path: - # cmd will look something like: fab -f fabfile.py install_bowtie - cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( repo_files_dir ) - proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode != 0: - # TODO: do something more here than logging the problem. - tmp_stderr = open( tmp_name, 'rb' ) - error = tmp_stderr.read() - tmp_stderr.close() - log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) - def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): - # The sample_files list contains all files whose name ends in .sample - sample_files = [] - # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs - repository_tools_tups = [] - for root, dirs, files in os.walk( repo_files_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - # Find all special .sample files first. - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - relative_path = os.path.join( root, name ) - full_path = os.path.abspath( os.path.join( root, name ) ) - try: - repository_tool = trans.app.toolbox.load_tool( full_path ) - if repository_tool: - # At this point, we need to lstrip tool_path from relative_path. - tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) - repository_tools_tups.append( ( tup_path, repository_tool ) ) - except Exception, e: - # We have an invalid .xml file, so not a tool config. - log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) - return sample_files, repository_tools_tups - def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): - # Add an entry in the shed_tool_conf file. An entry looks something like: - # <section name="Filter and Sort" id="filter"> - # <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/> - # </section> - # Make a backup of the hgweb.config file since we're going to be changing it. - if not os.path.exists( shed_tool_conf ): - output = open( shed_tool_conf, 'w' ) - output.write( '<?xml version="1.0"?>\n' ) - output.write( '<toolbox tool_path="%s">\n' % tool_path ) - output.write( '</toolbox>\n' ) - output.close() - self.__make_shed_tool_conf_copy( trans, shed_tool_conf ) - tmp_fd, tmp_fname = tempfile.mkstemp() - new_shed_tool_conf = open( tmp_fname, 'wb' ) - for i, line in enumerate( open( shed_tool_conf ) ): - if line.startswith( '</toolbox>' ): - # We're at the end of the original config file, so add our entry. - new_shed_tool_conf.write( new_tool_section ) - new_shed_tool_conf.write( line ) - else: - new_shed_tool_conf.write( line ) - new_shed_tool_conf.close() - shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) ) - def __make_shed_tool_conf_copy( self, trans, shed_tool_conf ): - # Make a backup of the shed_tool_conf file. - today = date.today() - backup_date = today.strftime( "%Y_%m_%d" ) - shed_tool_conf_copy = '%s/%s_%s_backup' % ( trans.app.config.root, shed_tool_conf, backup_date ) - shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) ) - def __clean_tool_shed_url( self, tool_shed_url ): - if tool_shed_url.find( ':' ) > 0: - # Eliminate the port, if any, since it will result in an invalid directory name. - return tool_shed_url.split( ':' )[ 0 ] - return tool_shed_url.rstrip( '/' ) - def __clean_repository_clone_url( self, repository_clone_url ): - if repository_clone_url.find( '@' ) > 0: - # We have an url that includes an authenticated user, something like: - # http://test@bx.psu.edu:9009/repos/some_username/column - items = repository_clone_url.split( '@' ) - tmp_url = items[ 1 ] - elif repository_clone_url.find( '\/\/' ) > 0: - # We have an url that includes only a protocol, something like: - # http://bx.psu.edu:9009/repos/some_username/column - items = repository_clone_url.split( '\/\/' ) - tmp_url = items[ 1 ] - else: - tmp_url = repository_clone_url - return tmp_url - def __get_repository_owner( self, cleaned_repository_url ): - items = cleaned_repository_url.split( 'repos' ) - repo_path = items[ 1 ] - return repo_path.lstrip( '/' ).split( '/' )[ 0 ] - 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> - http://test@bx.psu.edu:9009/repos/test/filter - """ - tmp_url = self.__clean_repository_clone_url( repository_clone_url ) - # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column - items = tmp_url.split( 'repos' ) - tool_shed_url = items[ 0 ] - repo_path = items[ 1 ] - tool_shed_url = self.__clean_tool_shed_url( tool_shed_url ) - return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision ) - def __generate_tool_guid( self, repository_clone_url, tool ): - """ - Generate a guid for the installed tool. It is critical that this guid matches the guid for - the tool in the Galaxy tool shed from which it is being installed. The form of the guid is - <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version> - """ - tmp_url = self.__clean_repository_clone_url( repository_clone_url ) - return '%s/%s/%s' % ( tmp_url, tool.id, tool.version ) - def __generate_tool_panel_section( self, repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups ): - """ - Write an in-memory tool panel section so we can load it into the tool panel and then - append it to the appropriate shed tool config. - TODO: re-write using ElementTree. - """ - tmp_url = self.__clean_repository_clone_url( repository_clone_url ) - section_str = '' - section_str += ' <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id ) - for repository_tool_tup in repository_tools_tups: - tool_file_path, tool = repository_tool_tup - guid = self.__generate_tool_guid( repository_clone_url, tool ) - section_str += ' <tool file="%s" guid="%s">\n' % ( tool_file_path, guid ) - section_str += ' <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) - section_str += ' <repository_name>%s</repository_name>\n' % repository_name - section_str += ' <repository_owner>%s</repository_owner>\n' % self.__get_repository_owner( tmp_url ) - section_str += ' <changeset_revision>%s</changeset_revision>\n' % changeset_revision - section_str += ' <id>%s</id>\n' % tool.id - section_str += ' <version>%s</version>\n' % tool.version - section_str += ' </tool>\n' - section_str += ' </section>\n' - return section_str ## ---- Utility methods ------------------------------------------------------- -def build_shed_tool_conf_select_field( trans ): - """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs.""" - options = [] - for shed_tool_conf_filename, tool_path in trans.app.toolbox.shed_tool_confs.items(): - options.append( ( shed_tool_conf_filename.lstrip( './' ), shed_tool_conf_filename ) ) - select_field = SelectField( name='shed_tool_conf' ) - for option_tup in options: - select_field.add_option( option_tup[0], option_tup[1] ) - return select_field -def build_tool_panel_section_select_field( trans ): - """Build a SelectField whose options are the sections of the current in-memory toolbox.""" - options = [] - for k, tool_section in trans.app.toolbox.tool_panel.items(): - options.append( ( tool_section.name, tool_section.id ) ) - select_field = SelectField( name='tool_panel_section', display='radio' ) - for option_tup in options: - select_field.add_option( option_tup[0], option_tup[1] ) - return select_field def copy_sample_loc_file( trans, filename ): """Copy xxx.loc.sample to ~/tool-data/xxx.loc.sample and ~/tool-data/xxx.loc""" head, sample_loc_file = os.path.split( filename ) @@ -2757,6 +2408,12 @@ if not user: return trans.show_error_message( "User not found for id (%s)" % str( id ) ) return user +def get_user_by_username( trans, username ): + """Get a user from the database by username""" + # TODO: Add exception handling here. + return trans.sa_session.query( trans.model.User ) \ + .filter( trans.model.User.table.c.username == username ) \ + .one() def get_role( trans, id ): """Get a Role from the database by id.""" # Load user from database --- a/lib/galaxy/web/controllers/admin.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Sep 30 09:48:56 2011 -0400 @@ -384,14 +384,66 @@ preserve_state = False use_paging = True +class RepositoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_shed_repository ): + return tool_shed_repository.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_shed_repository ): + return tool_shed_repository.description + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_shed_repository ): + return tool_shed_repository.owner + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_shed_repository ): + return tool_shed_repository.changeset_revision + class ToolShedColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool_shed_repository ): + return tool_shed_repository.tool_shed + # Grid definition + title = "Tool shed repositories" + model_class = model.ToolShedRepository + template='/admin/tool_shed_repository/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + attach_popup=True ), + DescriptionColumn( "Description" ), + OwnerColumn( "Owner" ), + RevisionColumn( "Revision" ), + ToolShedColumn( "Tool shed" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Get updates", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + standard_filters = [] + default_filter = dict( deleted="False" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( self.model_class ) + class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() quota_list_grid = QuotaListGrid() + repository_list_grid = RepositoryListGrid() - # Galaxy Quota Stuff @web.expose @web.require_admin def quotas( self, trans, **kwargs ): @@ -417,7 +469,6 @@ return self.edit_quota( trans, **kwargs ) # Render the list view return self.quota_list_grid( trans, **kwargs ) - @web.expose @web.require_admin def create_quota( self, trans, **kwd ): @@ -464,7 +515,6 @@ out_groups=params.out_groups, message=params.message, status=params.status ) - @web.expose @web.require_admin def rename_quota( self, trans, **kwd ): @@ -478,7 +528,6 @@ webapp=params.webapp, message=params.message, status=params.status ) - @web.expose @web.require_admin def manage_users_and_groups_for_quota( self, trans, **kwd ): @@ -513,7 +562,6 @@ webapp=params.webapp, message=params.message, status=params.status ) - @web.expose @web.require_admin def edit_quota( self, trans, **kwd ): @@ -527,7 +575,6 @@ webapp=params.webapp, message=params.message, status=params.status ) - @web.expose @web.require_admin def set_quota_default( self, trans, **kwd ): @@ -546,7 +593,6 @@ webapp=params.webapp, message=params.message, status=params.status ) - @web.expose @web.require_admin def unset_quota_default( self, trans, **kwd ): @@ -558,8 +604,6 @@ webapp=params.webapp, message=util.sanitize_text( params.message ), status='error' ) ) - - @web.expose @web.require_admin def mark_quota_deleted( self, trans, **kwd ): @@ -571,7 +615,6 @@ webapp=params.webapp, message=util.sanitize_text( params.message ), status='error' ) ) - @web.expose @web.require_admin def undelete_quota( self, trans, **kwd ): @@ -583,7 +626,6 @@ webapp=params.webapp, message=util.sanitize_text( params.message ), status='error' ) ) - @web.expose @web.require_admin def purge_quota( self, trans, **kwd ): @@ -595,7 +637,6 @@ webapp=params.webapp, message=util.sanitize_text( params.message ), status='error' ) ) - def _quota_op( self, trans, do_op, op_method, kwd, listify=False ): params = self.get_quota_params( kwd ) if listify: @@ -633,3 +674,488 @@ params.message = e.err_msg params.status = e.type return quota, params + @web.expose + @web.require_admin + def browse_repositories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd.pop('operation').lower() + if operation == "get updates": + return self.check_for_updates( trans, **kwd ) + # Render the list view + return self.repository_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tool_shed( self, trans, **kwd ): + tool_shed_url = kwd[ 'tool_shed_url' ] + galaxy_url = trans.request.host + url = '%s/repository/browse_downloadable_repositories?galaxy_url=%s&webapp=community' % ( tool_shed_url, galaxy_url ) + return trans.response.send_redirect( url ) + @web.expose + @web.require_admin + def install_tool_shed_repository( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + tool_shed_url = kwd[ 'tool_shed_url' ] + name = kwd[ 'name' ] + description = kwd[ 'description' ] + changeset_revision = kwd[ 'changeset_revision' ] + repository_clone_url = kwd[ 'repository_clone_url' ] + if kwd.get( 'select_tool_panel_section_button', False ): + shed_tool_conf = kwd[ 'shed_tool_conf' ] + # Get the tool path. + for k, tool_path in trans.app.toolbox.shed_tool_confs.items(): + if k == shed_tool_conf: + break + if 'tool_panel_section' in kwd: + section_key = 'section_%s' % kwd[ 'tool_panel_section' ] + tool_section = trans.app.toolbox.tool_panel[ section_key ] + # Clone the repository to the configured location. + current_working_dir = os.getcwd() + clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) ) + if os.path.exists( clone_dir ): + # Repository and revision has already been cloned. + # TODO: implement the ability to re-install or revert an existing repository. + message = 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.' % \ + ( changeset_revision, name ) + status = 'error' + else: + os.makedirs( clone_dir ) + log.debug( 'Cloning %s...' % repository_clone_url ) + cmd = 'hg clone %s' % repository_clone_url + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( clone_dir ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode == 0: + # Add a new record to the tool_shed_repository table. + tool_shed_repository = self.__create_tool_shed_repository( trans, + name, + description, + changeset_revision, + repository_clone_url ) + # Update the cloned repository to changeset_revision. + repo_files_dir = os.path.join( clone_dir, name ) + log.debug( 'Updating cloned repository to revision "%s"...' % changeset_revision ) + cmd = 'hg update -r %s' % changeset_revision + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode == 0: + sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) + if repository_tools_tups: + # Handle missing data table entries for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) + # Handle missing index files for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) + # Handle tools that use fabric scripts to install dependencies. + self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) + # Generate an in-memory tool conf section that includes the new tools. + new_tool_section = self.__generate_tool_panel_section( name, + repository_clone_url, + changeset_revision, + tool_section, + repository_tools_tups ) + # Create a temporary file to persist the in-memory tool section + # TODO: Figure out how to do this in-memory using xml.etree. + tmp_name = tempfile.NamedTemporaryFile().name + persisted_new_tool_section = open( tmp_name, 'wb' ) + persisted_new_tool_section.write( new_tool_section ) + persisted_new_tool_section.close() + # Parse the persisted tool panel section + tree = ElementTree.parse( tmp_name ) + root = tree.getroot() + ElementInclude.include( root ) + # Load the tools in the section into the tool panel. + trans.app.toolbox.load_section_tag_set( root, trans.app.toolbox.tool_panel, tool_path ) + # Remove the temporary file + try: + os.unlink( tmp_name ) + except: + pass + # Append the new section to the shed_tool_config file. + self.__add_shed_tool_conf_entry( trans, shed_tool_conf, new_tool_section ) + message = 'Revision <b>%s</b> of repository <b>%s</b> has been installed in tool panel section <b>%s</b>.' % \ + ( changeset_revision, name, tool_section.name ) + return trans.show_ok_message( message ) + else: + tmp_stderr = open( tmp_name, 'rb' ) + message = tmp_stderr.read() + tmp_stderr.close() + status = 'error' + else: + tmp_stderr = open( tmp_name, 'rb' ) + message = tmp_stderr.read() + tmp_stderr.close() + status = 'error' + else: + message = 'Choose the section in your tool panel to contain the installed tools.' + status = 'error' + if len( trans.app.toolbox.shed_tool_confs.keys() ) > 1: + shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans ) + shed_tool_conf = None + else: + shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' ) + shed_tool_conf_select_field = None + tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + return trans.fill_template( '/admin/select_tool_panel_section.mako', + tool_shed_url=tool_shed_url, + name=name, + description=description, + changeset_revision=changeset_revision, + repository_clone_url=repository_clone_url, + shed_tool_conf=shed_tool_conf, + shed_tool_conf_select_field=shed_tool_conf_select_field, + tool_panel_section_select_field=tool_panel_section_select_field, + message=message, + status=status ) + @web.expose + @web.require_admin + def check_for_updates( self, trans, **kwd ): + params = util.Params( kwd ) + repository_id = params.get( 'id', None ) + repository = get_repository( trans, repository_id ) + galaxy_url = trans.request.host + # Send a request to the relevant tool shed to see if there are any updates. + # TODO: support https in the following url. + url = 'http://%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=community' % \ + ( repository.tool_shed, galaxy_url, repository.name, repository.owner, repository.changeset_revision ) + return trans.response.send_redirect( url ) + @web.expose + @web.require_admin + def update_to_changeset_revision( self, trans, **kwd ): + """Update a cloned repository to the latest revision possible.""" + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + tool_shed_url = kwd[ 'tool_shed_url' ] + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + latest_changeset_revision = params.get( 'latest_changeset_revision', None ) + if changeset_revision and latest_changeset_revision: + if changeset_revision == latest_changeset_revision: + message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name + else: + repository = get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ) + current_working_dir = os.getcwd() + # Get the directory where the repository is cloned. + cleaned_tool_shed_url = self.__clean_tool_shed_url( tool_shed_url ) + partial_cloned_dir = '%s/repos/%s/%s/%s' % ( cleaned_tool_shed_url, owner, name, changeset_revision ) + # Get the relative tool installation paths from each of the shed tool configs. + shed_tool_confs = trans.app.toolbox.shed_tool_confs + relative_cloned_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(): + relative_cloned_dir = os.path.join( tool_path, partial_cloned_dir ) + if os.path.isdir( relative_cloned_dir ): + break + if relative_cloned_dir: + # Update the cloned repository to changeset_revision. + repo_files_dir = os.path.join( relative_cloned_dir, name ) + log.debug( "Updating cloned repository named '%s' from revision '%s' to revision '%s'..." % \ + ( name, changeset_revision, latest_changeset_revision ) ) + cmd = 'hg pull' + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode == 0: + cmd = 'hg update -r %s' % latest_changeset_revision + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode == 0: + # Update the repository changeset_revision in the database. + repository.changeset_revision = latest_changeset_revision + trans.sa_session.add( repository ) + trans.sa_session.flush() + message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \ + ( name, latest_changeset_revision ) + else: + tmp_stderr = open( tmp_name, 'rb' ) + message = tmp_stderr.read() + tmp_stderr.close() + status = 'error' + else: + tmp_stderr = open( tmp_name, 'rb' ) + message = tmp_stderr.read() + tmp_stderr.close() + status = 'error' + else: + message = "The directory containing the cloned repository named '%s' cannot be found." % name + status = 'error' + else: + message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name + status = 'error' + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_repositories', + message=message, + status=status ) ) + def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if any have input parameters that are dynamically + # generated select lists that require entries in the tool_data_table_conf.xml file. + missing_data_table_entry = False + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + if repository_tool.params_with_missing_data_table_entry: + missing_data_table_entry = True + break + if missing_data_table_entry: + # The repository must contain a tool_data_table_conf.xml.sample file that includes + # all required entries for all tools in the repository. + for sample_file in sample_files: + head, tail = os.path.split( sample_file ) + if tail == 'tool_data_table_conf.xml.sample': + break + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + if error: + # TODO: Do more here than logging an exception. + log.debug( exception_msg ) + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if it has any input parameters that + # are dynamically generated select lists that depend on a .loc file. + missing_files_handled = [] + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + params_with_missing_index_file = repository_tool.params_with_missing_index_file + for param in params_with_missing_index_file: + options = param.options + missing_head, missing_tail = os.path.split( options.missing_index_file ) + if missing_tail not in missing_files_handled: + # The repository must contain the required xxx.loc.sample file. + for sample_file in sample_files: + sample_head, sample_tail = os.path.split( sample_file ) + if sample_tail == '%s.sample' % missing_tail: + copy_sample_loc_file( trans, sample_file ) + if options.tool_data_table and options.tool_data_table.missing_index_file: + options.tool_data_table.handle_found_index_file( options.missing_index_file ) + missing_files_handled.append( missing_tail ) + break + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ): + # Inspect each tool to see if it includes a "requirement" that refers to a fabric + # script. For those that do, execute the fabric script to install tool dependencies. + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + for requirement in repository_tool.requirements: + if requirement.type == 'fabfile': + log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) + fabfile = requirement.fabfile + method = requirement.method + # Find the relative path to the fabfile. + relative_fabfile_path = None + for root, dirs, files in os.walk( repo_files_dir ): + for name in files: + if name == fabfile: + relative_fabfile_path = os.path.join( root, name ) + break + if relative_fabfile_path: + # cmd will look something like: fab -f fabfile.py install_bowtie + cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode != 0: + # TODO: do something more here than logging the problem. + tmp_stderr = open( tmp_name, 'rb' ) + error = tmp_stderr.read() + tmp_stderr.close() + log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): + # The sample_files list contains all files whose name ends in .sample + sample_files = [] + # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs + repository_tools_tups = [] + for root, dirs, files in os.walk( repo_files_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + # Find all special .sample files first. + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + relative_path = os.path.join( root, name ) + full_path = os.path.abspath( os.path.join( root, name ) ) + try: + repository_tool = trans.app.toolbox.load_tool( full_path ) + if repository_tool: + # At this point, we need to lstrip tool_path from relative_path. + tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) + repository_tools_tups.append( ( tup_path, repository_tool ) ) + except Exception, e: + # We have an invalid .xml file, so not a tool config. + log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) + return sample_files, repository_tools_tups + def __create_tool_shed_repository( self, trans, name, description, changeset_revision, repository_clone_url ): + tmp_url = self.__clean_repository_clone_url( repository_clone_url ) + tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) + owner = self.__get_repository_owner( tmp_url ) + tool_shed_repository = trans.model.ToolShedRepository( tool_shed=tool_shed, + name=name, + description=description, + owner=owner, + changeset_revision=changeset_revision ) + trans.sa_session.add( tool_shed_repository ) + trans.sa_session.flush() + def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): + # Add an entry in the shed_tool_conf file. An entry looks something like: + # <section name="Filter and Sort" id="filter"> + # <tool file="filter/filtering.xml" guid="toolshed.g2.bx.psu.edu/repos/test/filter/1.0.2"/> + # </section> + # Make a backup of the hgweb.config file since we're going to be changing it. + if not os.path.exists( shed_tool_conf ): + output = open( shed_tool_conf, 'w' ) + output.write( '<?xml version="1.0"?>\n' ) + output.write( '<toolbox tool_path="%s">\n' % tool_path ) + output.write( '</toolbox>\n' ) + output.close() + self.__make_shed_tool_conf_copy( trans, shed_tool_conf ) + tmp_fd, tmp_fname = tempfile.mkstemp() + new_shed_tool_conf = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( shed_tool_conf ) ): + if line.startswith( '</toolbox>' ): + # We're at the end of the original config file, so add our entry. + new_shed_tool_conf.write( new_tool_section ) + new_shed_tool_conf.write( line ) + else: + new_shed_tool_conf.write( line ) + new_shed_tool_conf.close() + shutil.move( tmp_fname, os.path.abspath( shed_tool_conf ) ) + def __make_shed_tool_conf_copy( self, trans, shed_tool_conf ): + # Make a backup of the shed_tool_conf file. + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + shed_tool_conf_copy = '%s/%s_%s_backup' % ( trans.app.config.root, shed_tool_conf, backup_date ) + shutil.copy( os.path.abspath( shed_tool_conf ), os.path.abspath( shed_tool_conf_copy ) ) + def __clean_tool_shed_url( self, tool_shed_url ): + if tool_shed_url.find( ':' ) > 0: + # Eliminate the port, if any, since it will result in an invalid directory name. + return tool_shed_url.split( ':' )[ 0 ] + return tool_shed_url.rstrip( '/' ) + def __clean_repository_clone_url( self, repository_clone_url ): + if repository_clone_url.find( '@' ) > 0: + # We have an url that includes an authenticated user, something like: + # http://test@bx.psu.edu:9009/repos/some_username/column + items = repository_clone_url.split( '@' ) + tmp_url = items[ 1 ] + elif repository_clone_url.find( '\/\/' ) > 0: + # We have an url that includes only a protocol, something like: + # http://bx.psu.edu:9009/repos/some_username/column + items = repository_clone_url.split( '\/\/' ) + tmp_url = items[ 1 ] + else: + tmp_url = repository_clone_url + return tmp_url + def __get_repository_owner( self, cleaned_repository_url ): + items = cleaned_repository_url.split( 'repos' ) + repo_path = items[ 1 ] + return repo_path.lstrip( '/' ).split( '/' )[ 0 ] + 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> + http://test@bx.psu.edu:9009/repos/test/filter + """ + tmp_url = self.__clean_repository_clone_url( repository_clone_url ) + # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column + items = tmp_url.split( 'repos' ) + tool_shed_url = items[ 0 ] + repo_path = items[ 1 ] + tool_shed_url = self.__clean_tool_shed_url( tool_shed_url ) + return '%s/repos%s/%s' % ( tool_shed_url, repo_path, changeset_revision ) + def __generate_tool_guid( self, repository_clone_url, tool ): + """ + Generate a guid for the installed tool. It is critical that this guid matches the guid for + the tool in the Galaxy tool shed from which it is being installed. The form of the guid is + <tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool version> + """ + tmp_url = self.__clean_repository_clone_url( repository_clone_url ) + return '%s/%s/%s' % ( tmp_url, tool.id, tool.version ) + def __generate_tool_panel_section( self, repository_name, repository_clone_url, changeset_revision, tool_section, repository_tools_tups ): + """ + Write an in-memory tool panel section so we can load it into the tool panel and then + append it to the appropriate shed tool config. + TODO: re-write using ElementTree. + """ + tmp_url = self.__clean_repository_clone_url( repository_clone_url ) + section_str = '' + section_str += ' <section name="%s" id="%s">\n' % ( tool_section.name, tool_section.id ) + for repository_tool_tup in repository_tools_tups: + tool_file_path, tool = repository_tool_tup + guid = self.__generate_tool_guid( repository_clone_url, tool ) + section_str += ' <tool file="%s" guid="%s">\n' % ( tool_file_path, guid ) + section_str += ' <tool_shed>%s</tool_shed>\n' % tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) + section_str += ' <repository_name>%s</repository_name>\n' % repository_name + section_str += ' <repository_owner>%s</repository_owner>\n' % self.__get_repository_owner( tmp_url ) + section_str += ' <changeset_revision>%s</changeset_revision>\n' % changeset_revision + section_str += ' <id>%s</id>\n' % tool.id + section_str += ' <version>%s</version>\n' % tool.version + section_str += ' </tool>\n' + section_str += ' </section>\n' + return section_str + +## ---- Utility methods ------------------------------------------------------- + +def build_shed_tool_conf_select_field( trans ): + """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs.""" + options = [] + for shed_tool_conf_filename, tool_path in trans.app.toolbox.shed_tool_confs.items(): + options.append( ( shed_tool_conf_filename.lstrip( './' ), shed_tool_conf_filename ) ) + select_field = SelectField( name='shed_tool_conf' ) + for option_tup in options: + select_field.add_option( option_tup[0], option_tup[1] ) + return select_field +def build_tool_panel_section_select_field( trans ): + """Build a SelectField whose options are the sections of the current in-memory toolbox.""" + options = [] + for k, tool_section in trans.app.toolbox.tool_panel.items(): + options.append( ( tool_section.name, tool_section.id ) ) + select_field = SelectField( name='tool_panel_section', display='radio' ) + for option_tup in options: + select_field.add_option( option_tup[0], option_tup[1] ) + return select_field +def get_repository( trans, id ): + """Get a tool_shed_repository from the database via id""" + return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) +def get_repository_by_name_owner_changeset_revision( trans, name, owner, changeset_revision ): + """Get a repository from the database via name owner and changeset_revision""" + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( and_( trans.model.ToolShedRepository.table.c.name == name, + trans.model.ToolShedRepository.table.c.owner == owner, + trans.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \ + .first() --- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 30 09:48:56 2011 -0400 @@ -86,6 +86,13 @@ def get_repository( trans, id ): """Get a repository from the database via id""" return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) +def get_repository_by_name_and_owner( trans, name, owner ): + """Get a repository from the database via name and owner""" + user = get_user_by_username( trans, owner ) + return trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.name == name, + trans.model.Repository.table.c.user_id == user.id ) ) \ + .first() def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ @@ -95,6 +102,10 @@ def get_repository_metadata_by_id( trans, id ): """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) +def get_repository_metadata_by_repository_id( trans, id ): + """Get all metadata records for a specified repository.""" + return trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) def get_revision_label( trans, repository, changeset_revision ): """ Return a string consisting of the human read-able @@ -469,7 +480,7 @@ _ui.setconfig( 'ui', 'quiet', True ) return _ui def get_user( trans, id ): - """Get a user from the database""" + """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) def handle_email_alerts( trans, repository ): repo_dir = repository.repo_path --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 30 09:26:22 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Sep 30 09:48:56 2011 -0400 @@ -341,8 +341,100 @@ tool_shed_url = trans.request.host repository_clone_url = generate_clone_url( trans, repository_id ) # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&repository_name=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, tool_shed_url, repository.name, repository_clone_url, changeset_revision ) + url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ + ( galaxy_url, tool_shed_url, repository.name, repository.description, repository_clone_url, changeset_revision ) + return trans.response.send_redirect( url ) + @web.expose + def check_for_updates( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # The sender didn't store galaxy_url in a cookie since + # this method immediately redirects back to the caller. + galaxy_url = kwd[ 'galaxy_url' ] + name = params.get( 'name', None ) + owner = params.get( 'owner', None ) + changeset_revision = params.get( 'changeset_revision', None ) + webapp = params.get( 'webapp', None ) + tool_shed_url = trans.request.host + # Start building up the url to redirect back to the calling Galaxy instance. + # TODO: support https in the following url. + url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, tool_shed_url ) + repository = get_repository_by_name_and_owner( trans, name, owner ) + #if error: + # url += '&message=%s&status=error' % message + #else: + url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ + ( repository.name, repository.user.username, changeset_revision ) + if changeset_revision == repository.tip: + # If changeset_revision is the repository tip, then + # we know there are no additional updates for the tools. + url += repository.tip + else: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + # If changeset_revision is in the repository_metadata table for this + # repository, then we know there are no additional updates for the tools. + url += changeset_revision + else: + # The changeset_revision column in the repository_metadata table has been + # updated with a new changeset_revision value since the repository was cloned. + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + # Load each tool in the repository's changeset_revision to generate a list of + # tool guids, since guids differentiate tools by id and version. + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + if ctx is not None: + tool_guids = [] + for filename in ctx: + # Find all tool configs in this repository changeset_revision. + if filename.endswith( '.xml' ): + fctx = ctx[ filename ] + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + if tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + except: + # File must not be a valid tool config even though it has a .xml extension. + pass + try: + os.unlink( tmp_filename ) + except: + pass + tool_guids.sort() + if tool_guids: + # Compare our list of tool guids against those in each repository_metadata record + # for the repository to find the repository_metadata record with the changeset_revision + # value we want to pass back to the caller. + found = False + for repository_metadata in get_repository_metadata_by_repository_id( trans, trans.security.encode_id( repository.id ) ): + metadata = repository_metadata.metadata + metadata_tool_guids = [] + for tool_dict in metadata[ 'tools' ]: + metadata_tool_guids.append( tool_dict[ 'guid' ] ) + metadata_tool_guids.sort() + if tool_guids == metadata_tool_guids: + # We've found the repository_metadata record whose changeset_revision + # value has been updated. + url += repository_metadata.changeset_revision + found = True + break + if not found: + # There must be a problem in the data, so we'll just send back the received changeset_revision. + log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) + url += changeset_revision + else: + # There are not tools in the changeset_revision, so no tool updates are possible. + url += changeset_revision return trans.response.send_redirect( url ) @web.expose def browse_repositories( self, trans, **kwd ): --- a/templates/admin/select_tool_panel_section.mako Fri Sep 30 09:26:22 2011 -0400 +++ b/templates/admin/select_tool_panel_section.mako Fri Sep 30 09:48:56 2011 -0400 @@ -23,9 +23,9 @@ <br/><div class="toolForm"> - <div class="toolFormTitle">Install tools from repository '${repository_name}'</div> + <div class="toolFormTitle">Install tools from repository '${name}'</div><div class="toolFormBody"> - <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repository_name=repository_name, changeset_revision=changeset_revision, repository_clone_url=repository_clone_url )}" method="post" > + <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, name=name, description=description, changeset_revision=changeset_revision, repository_clone_url=repository_clone_url )}" method="post" > %if shed_tool_conf_select_field: <div class="form-row"><label>Shed tool configuration file:</label> --- a/templates/webapps/galaxy/admin/index.mako Fri Sep 30 09:26:22 2011 -0400 +++ b/templates/webapps/galaxy/admin/index.mako Fri Sep 30 09:48:56 2011 -0400 @@ -62,6 +62,9 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='reload_tool' )}" target="galaxy_main">Reload a tool's configuration</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='memdump' )}" target="galaxy_main">Profile memory usage</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='jobs' )}" target="galaxy_main">Manage jobs</a></div> + %if cloned_repositories: + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_repositories' )}" target="galaxy_main">Manage cloned tool shed repositories</a></div> + %endif </div></div> %if trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds: 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 improvements: (a) groups now have menus and can be renamed and deleted; (b) mode is again saved and restored; (c) tracks can be added directly to groups rather than only the view; running a tool inside trackster creates its own group and places new tracks in group.
by Bitbucket 30 Sep '11

30 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3541bcdb236c/ changeset: 3541bcdb236c user: jgoecks date: 2011-09-30 15:26:22 summary: Trackster improvements: (a) groups now have menus and can be renamed and deleted; (b) mode is again saved and restored; (c) tracks can be added directly to groups rather than only the view; running a tool inside trackster creates its own group and places new tracks in group. affected #: 7 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Thu Sep 29 16:45:19 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Sep 30 09:26:22 2011 -0400 @@ -337,6 +337,7 @@ "hda_ldda": track_dict.get("hda_ldda", "hda"), "dataset_id": trans.security.encode_id( dataset.id ), "prefs": prefs, + "mode": track_dict.get( 'mode', 'Auto' ), "filters": track_data_provider.get_filters(), "tool": get_tool_def( trans, dataset ) } --- a/lib/galaxy/web/controllers/tracks.py Thu Sep 29 16:45:19 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Sep 30 09:26:22 2011 -0400 @@ -623,7 +623,8 @@ "hda_ldda": track_json.get('hda_ldda', "hda"), "name": track_json['name'], "track_type": track_json['track_type'], - "prefs": track_json['prefs'] + "prefs": track_json['prefs'], + "mode": track_json['mode'] } def unpack_collection( collection_json ): --- a/static/scripts/packed/trackster.js Thu Sep 29 16:45:19 2011 -0400 +++ b/static/scripts/packed/trackster.js Fri Sep 30 09:26:22 2011 -0400 @@ -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 trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,aj,am,al,ah){this.name=ak;this.view=ai;this.parent_element=am;this.drag_handle_class=al;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;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.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,aj,an,am,ah){r.call(this,ak,ai,aj,an,am,ah);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,aj,am,ah){A.call(this,"DrawableGroup",ak,ai,aj,am,"group-handle",ah);if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.parent_element);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.content_div);m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.content_div.click(function(al){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,this.top_labeltrack));this.add_label_track(new ad(this,this.nav_labeltrack));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.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(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){var ay=this.track.parent_element;ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={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,ai=ah.tool_id+aj.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ak;if(aj instanceof e){ak=new X(ai,view,aj.hda_ldda,undefined,{},{},aj);ak.change_mode(aj.mode)}this.track.view.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ah,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};if(ah.saved_values){this.restore_values(ah.saved_values)}this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(aj,ah,ai,am,ak,al){r.call(this,aj,ah,{},am,"draghandle",ah);this.data_url=(ak?ak:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am,ap){var ai=this,aq=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=(ao!==undefined?new ac(this,ao):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(ar){return function(){ai.change_mode(ar)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw()},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ah,ai){this.hidden=true;j.call(this,"label",ah,{},ai);this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,null,ah,{},ah.top_labeltrack);O.call(this);ah.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:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(al,aj,am,ah,ak){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,al,aj,ak,aj.viewport_container);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:"black"},{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:ak,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,am,al,ap,ao,aj,ak,an){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,am,ao,am.viewport_container);O.call(this,aj,ak,an);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new R(aI,aE,aj,aw.data,aw.message)}});var W=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:aj,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=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,an,ah,ak,am,ai){e.call(this,al,aj,an,ah,ak,am,{},ai);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,ah,aj,al){this.name=ak;this.view=ai;this.container=ah;this.drag_handle_class=al;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;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.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,ah,aj,am){r.call(this,ak,ai,ah,aj,am);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,ah,aj){A.call(this,"DrawableGroup",ak,ai,ah,aj,"group-handle");if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.browser_content_div.click(function(al){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.browser_content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,{content_div:this.top_labeltrack}));this.add_label_track(new ad(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.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(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai={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},al=this.track,aj=ai.tool_id+al.tool_region_and_parameters_str(ai.chrom,ai.low,ai.high),ah,am;if(al.container===view){var ak=new S(this.name,this.track.view,this.track.container);al.container.add_drawable(ak);al.container.remove_drawable(al);ak.add_drawable(al);al.container_div.appendTo(ak.content_div);ah=ak}else{ah=al.container}if(al instanceof e){am=new X(aj,view,ah,"hda");am.change_mode(al.mode);ah.add_drawable(am)}am.content_div.text("Starting job.");this.run(ai,am,function(an){am.dataset_id=an.dataset_id;am.content_div.text("Running job.");am.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};this.restore_values((ah.saved_values?ah.saved_values:{}));this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(ak,ai,ah,aj,al,am){r.call(this,ak,ai,ah,{},"draghandle");this.data_url=(al?al:default_data_url);this.data_url_extra_params={};this.data_query_wait=(am?am:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(aq){return function(){ai.change_mode(aq)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json: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,}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw();return ah},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.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:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(am,ak,aj,an,ah,al){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,am,ak,aj,al);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=an;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:am},{key:"color",label:"Color",type:"color",default_value:"black"},{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:al,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,an,ai,am,ap,ao,ak,al){var aj=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,an,ai,ao);O.call(this,ak,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){aj.set_name(aj.prefs.name);aj.tile_cache.clear();aj.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=am;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new R(aI,aE,aj,aw.data,aw.message)}});var W=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:ak,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=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,ai,an,ah,ak,am){e.call(this,al,aj,ai,an,ah,ak,am,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 --- a/static/scripts/packed/trackster_ui.js Thu Sep 29 16:45:19 2011 -0400 +++ b/static/scripts/packed/trackster_ui.js Fri Sep 30 09:26:22 2011 -0400 @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(a){return new addable_objects[a.track_type](a.name,view,a.hda_ldda,a.dataset_id,a.prefs,a.filters,a.tool)};var drawable_collection_from_dict=function(e){var d=new addable_objects[e.obj_type](e.name,view,e.prefs,view.viewport_container,view);for(var c=0;c<e.drawables.length;c++){var a=e.drawables[c],b;if(a.track_type){b=track_from_dict(a)}else{b=drawable_collection_from_dict(a)}d.add_drawable(b);d.content_div.append(b.container_div)}return d};var drawable_from_dict=function(a){return(a.track_type?track_from_dict(a):drawable_collection_from_dict(a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d<f.drawables.length;d++){var b=f.drawables[d],c;if(b.track_type){c=track_from_dict(b,e)}else{c=drawable_collection_from_dict(b)}e.add_drawable(c);e.content_div.append(c.container_div)}return e};var drawable_from_dict=function(b,a){return(b.track_type?track_from_dict(b,a):drawable_collection_from_dict(b,a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o,view))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file --- a/static/scripts/trackster.js Thu Sep 29 16:45:19 2011 -0400 +++ b/static/scripts/trackster.js Fri Sep 30 09:26:22 2011 -0400 @@ -573,14 +573,14 @@ */ /** - * Base interface for all drawable objects. + * Base interface for all drawable objects. Drawable objects have a name and are + * associated with a view and container. They optionally have a drag handle class. */ -var Drawable = function(name, view, prefs, parent_element, drag_handle_class, container) { +var Drawable = function(name, view, container, prefs, drag_handle_class) { this.name = name; this.view = view; - this.parent_element = parent_element; + this.container = container; this.drag_handle_class = drag_handle_class; - this.container = container; this.config = new DrawableConfig({ track: this, params: [ @@ -633,8 +633,8 @@ /** * A collection of drawable objects. */ -var DrawableCollection = function(obj_type, name, view, prefs, parent_element, drag_handle_class, container) { - Drawable.call(this, name, view, prefs, parent_element, drag_handle_class, container); +var DrawableCollection = function(obj_type, name, view, container, prefs, drag_handle_class) { + Drawable.call(this, name, view, container, prefs, drag_handle_class); // Attribute init. this.obj_type = obj_type; @@ -722,20 +722,21 @@ /** * A group of drawables that are moveable, visible. */ -var DrawableGroup = function(name, view, prefs, parent_element, container) { - DrawableCollection.call(this, "DrawableGroup", name, view, prefs, parent_element, "group-handle", container); +var DrawableGroup = function(name, view, container, prefs) { + DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); // HTML elements. if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; } var group_id = DrawableGroup.id_counter++ - this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.parent_element); + this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.container.content_div); this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); this.header_div.append($("<div/>").addClass(this.drag_handle_class)); this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div); - // Set up containers/moving for group: register both container and content div as container - // because both are used as containers. Group can be moved. + // Set up containers/moving for group: register both container_div and content div as container + // because both are used as containers (container div to recognize container, content_div to + // store elements). Group can be moved. is_container(this.container_div, this); is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); @@ -820,14 +821,16 @@ view = this; // Top container for things that are fixed at the top this.top_container = $("<div/>").addClass("top-container").appendTo(parent_element); - // Content container, primary tracks are contained in here - this.content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); + // Browser content, primary tracks are contained in here + this.browser_content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element); // Bottom container for things that are fixed at the bottom this.bottom_container = $("<div/>").addClass("bottom-container").appendTo(parent_element); // Label track fixed at top this.top_labeltrack = $("<div/>").addClass("top-labeltrack").appendTo(this.top_container); // Viewport for dragging tracks in center - this.viewport_container = $("<div/>").addClass("viewport-container").attr("id", "viewport-container").appendTo(this.content_div); + this.viewport_container = $("<div/>").addClass("viewport-container").attr("id", "viewport-container").appendTo(this.browser_content_div); + // Alias viewport_container as content_div so that it matches function of DrawableCollection/Group content_div. + this.content_div = this.viewport_container; is_container(this.viewport_container, view); // Introduction div shown when there are no tracks. this.intro_div = $("<div/>").addClass("intro"); @@ -884,7 +887,7 @@ }); /* - this.content_div.bind("mousewheel", function( e, delta ) { + this.browser_content_div.bind("mousewheel", function( e, delta ) { if (Math.abs(delta) < 0.5) { return; } @@ -898,12 +901,12 @@ */ // Blur tool/filter inputs when user clicks on content div. - this.content_div.click(function( e ) { + this.browser_content_div.click(function( e ) { $(this).find("input").trigger("blur"); }); // Double clicking zooms in - this.content_div.bind("dblclick", function( e ) { + this.browser_content_div.bind("dblclick", function( e ) { view.zoom_in(e.pageX, this.viewport_container); }); @@ -954,7 +957,7 @@ // to zoom in this.top_labeltrack.bind( "dragstart", function( e, d ) { return $("<div />").css( { - "height": view.content_div.height() + view.top_labeltrack.height() + "height": view.browser_content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height() + 1, "top": "0px", "position": "absolute", @@ -982,8 +985,8 @@ view.request_redraw(); }); - this.add_label_track( new LabelTrack( this, this.top_labeltrack ) ); - this.add_label_track( new LabelTrack( this, this.nav_labeltrack ) ); + this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); + this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); $(window).bind("resize", function() { view.resize_window(); }); $(document).bind("redraw", function() { view.redraw(); }); @@ -1414,13 +1417,6 @@ var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); var tool = this; run_on_region_button.click( function() { - // Create group for track + new tracks and put track in group. - var - parent_elt = this.track.parent_element; - //new_group = new DrawableCollection("New Group", parent_elt); - //this.track.view.add_drawable(new_group); - - // Run tool to create new track. tool.run_on_region(); }); @@ -1497,15 +1493,29 @@ // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), + container, new_track; - // Create and add track. - // TODO: add support for other kinds of tool data tracks. + // If track not in a group, create a group for it and add new track to group. If track + // already in group, add track to group. + if (current_track.container === view) { + var group = new DrawableGroup(this.name, this.track.view, this.track.container); + current_track.container.add_drawable(group); + // TODO: this is ugly way to move track from one container to another -- make this easier via + // a Drawable or DrawableCollection function. + current_track.container.remove_drawable(current_track); + group.add_drawable(current_track); + current_track.container_div.appendTo(group.content_div); + container = group; + } + else { + container = current_track.container; + } if (current_track instanceof FeatureTrack) { - new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); + new_track = new ToolDataFeatureTrack(track_name, view, container, "hda"); new_track.change_mode(current_track.mode); + container.add_drawable(new_track); } - this.track.view.add_drawable(new_track); new_track.content_div.text("Starting job."); // Run tool. @@ -1985,9 +1995,7 @@ this.track = options.track; this.params = options.params; this.values = {} - if ( options.saved_values ) { - this.restore_values( options.saved_values ); - } + this.restore_values( (options.saved_values ? options.saved_values : {}) ); this.onchange = options.onchange }; @@ -2111,9 +2119,9 @@ * -------> ToolDataFeatureTrack * -------> VcfTrack */ -var Track = function(name, view, prefs, parent_element, data_url, data_query_wait) { +var Track = function(name, view, container, prefs, data_url, data_query_wait) { // For now, track's container is always view. - Drawable.call(this, name, view, {}, parent_element, "draghandle", view); + Drawable.call(this, name, view, container, {}, "draghandle"); // // Attribute init. @@ -2140,7 +2148,7 @@ // Create content div, which is where track is displayed. // this.content_div = $("<div class='track-content'>").appendTo(this.container_div); - this.parent_element.append(this.container_div); + this.container.content_div.append(this.container_div); }; extend(Track.prototype, Drawable.prototype, { /** Returns track type. */ @@ -2230,7 +2238,7 @@ // predraw_init may be asynchronous, wait for it and then draw $.when(track.predraw_init()).done(function() { track.container_div.removeClass("nodata error pending"); - track.request_draw() + track.request_draw(); }); } } @@ -2242,7 +2250,7 @@ predraw_init: function() {}, }); -var TiledTrack = function(filters_list, tool_dict, parent_track) { +var TiledTrack = function(filters_list, tool_dict) { var track = this, view = track.view; @@ -2250,7 +2258,7 @@ moveable(track.container_div, track.drag_handle_class, ".group", track); // Attribute init. - this.filters_manager = (filters_list !== undefined ? new FiltersManager(this, filters_list) : undefined); + this.filters_manager = new FiltersManager( this, (filters_list !== undefined ? filters_list : {}) ); // filters_available is determined by data, filters_visible is set by user. this.filters_available = false; this.filters_visible = false; @@ -2311,7 +2319,8 @@ "name": this.name, "hda_ldda": this.hda_ldda, "dataset_id": this.dataset_id, - "prefs": this.prefs + "prefs": this.prefs, + "mode": this.mode, }; }, /** @@ -2325,6 +2334,7 @@ track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); + return track; }, /** * Make popup menu for track name. @@ -2712,9 +2722,9 @@ } }); -var LabelTrack = function (view, parent_element) { +var LabelTrack = function (view, container) { this.hidden = true; - Track.call(this, "label", view, {}, parent_element ); + Track.call(this, "label", view, container, {} ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -2741,7 +2751,7 @@ var ReferenceTrack = function (view) { this.hidden = true; - Track.call(this, null, view, {}, view.top_labeltrack); + Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); TiledTrack.call(this); view.reference_track = this; @@ -2786,11 +2796,11 @@ } }); -var LineTrack = function (name, view, hda_ldda, dataset_id, prefs) { +var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) { var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - Track.call( this, name, view, prefs, view.viewport_container ); + Track.call( this, name, view, container, prefs ); TiledTrack.call( this ); this.min_height_px = 16; @@ -2927,7 +2937,7 @@ } }); -var FeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) { +var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) { // // Preinitialization: do things that need to be done before calling Track and TiledTrack // initialization code. @@ -2938,8 +2948,10 @@ // // Initialization. // - Track.call(this, name, view, prefs, view.viewport_container); - TiledTrack.call(this, filters, tool, parent_track); + + // FIXME: cleaner init needed; should just be able to call TiledTrack() + Track.call(this, name, view, container, prefs); + TiledTrack.call(this, filters, tool); // Define and restore track configuration. this.config = new DrawableConfig( { @@ -3315,16 +3327,16 @@ } }); -var VcfTrack = function(name, view, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); +var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); this.painter = painters.VariantPainter; }; extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); -var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); +var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); this.config = new DrawableConfig( { track: this, @@ -3354,8 +3366,8 @@ /** * Feature track that displays data generated from tool. */ -var ToolDataFeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, parent_track) { - FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters, {}, parent_track); +var ToolDataFeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, {}); // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- // is ready. --- a/static/scripts/trackster_ui.js Thu Sep 29 16:45:19 2011 -0400 +++ b/static/scripts/trackster_ui.js Fri Sep 30 09:26:22 2011 -0400 @@ -36,23 +36,27 @@ /** * Decode a track from a dictionary. */ -var track_from_dict = function(track_dict) { - return new addable_objects[track_dict.track_type]( - track_dict.name, view, track_dict.hda_ldda, track_dict.dataset_id, +var track_from_dict = function(track_dict, container) { + var track = new addable_objects[track_dict.track_type]( + track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id, track_dict.prefs, track_dict.filters, track_dict.tool); + if (track_dict.mode) { + track.change_mode(track_dict.mode); + } + return track; }; /** * Decode a drawable collection from a dictionary. */ -var drawable_collection_from_dict = function(collection_dict) { - var collection = new addable_objects[collection_dict.obj_type](collection_dict.name, view, collection_dict.prefs, view.viewport_container, view); +var drawable_collection_from_dict = function(collection_dict, container) { + var collection = new addable_objects[collection_dict.obj_type](collection_dict.name, view, container, collection_dict.prefs, view.viewport_container, view); for (var i = 0; i < collection_dict.drawables.length; i++) { var drawable_dict = collection_dict.drawables[i], drawable; if (drawable_dict['track_type']) { - drawable = track_from_dict(drawable_dict); + drawable = track_from_dict(drawable_dict, collection); } else { drawable = drawable_collection_from_dict(drawable_dict); @@ -70,10 +74,10 @@ /** * Decode a drawable from a dict. */ -var drawable_from_dict = function(drawable_dict) { +var drawable_from_dict = function(drawable_dict, container) { return (drawable_dict['track_type'] ? - track_from_dict(drawable_dict) : - drawable_collection_from_dict(drawable_dict)); + track_from_dict(drawable_dict, container) : + drawable_collection_from_dict(drawable_dict, container)); }; /** @@ -101,7 +105,7 @@ var track_config; for (var i = 0; i < tracks_config.length; i++) { track_config = tracks_config[i]; - view.add_drawable( drawable_from_dict(track_config) ); + view.add_drawable( drawable_from_dict(track_config, view) ); } } --- a/templates/tracks/browser.mako Thu Sep 29 16:45:19 2011 -0400 +++ b/templates/tracks/browser.mako Fri Sep 30 09:26:22 2011 -0400 @@ -101,7 +101,7 @@ [ arguments[0] ] ); for (var i= 0; i < track_defs.length; i++) { - view.add_drawable( track_from_dict(track_defs[i]) ); + view.add_drawable( track_from_dict(track_defs[i], view) ); } }); hide_modal(); @@ -178,7 +178,7 @@ make_popupmenu( $("#viz-actions-button"), { "Add Tracks": add_tracks, "Add Group": function() { - var group = new DrawableGroup("New Group", view, {}, view.viewport_container, view); + var group = new DrawableGroup("New Group", view, view); view.add_drawable(group); }, "Save": function() { 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: Don't include purged histories in usage calculation.
by Bitbucket 29 Sep '11

29 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/338ead4737ba/ changeset: 338ead4737ba user: natefoo date: 2011-09-29 22:45:19 summary: Don't include purged histories in usage calculation. affected #: 1 file (-1 bytes) --- a/lib/galaxy/model/__init__.py Wed Sep 28 15:41:21 2011 -0400 +++ b/lib/galaxy/model/__init__.py Thu Sep 29 16:45:19 2011 -0400 @@ -90,7 +90,7 @@ total = 0 # this can be a huge number and can run out of memory, so we avoid the mappers db_session = object_session( self ) - for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id ).yield_per( 1000 ): + for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id, purged=False ).yield_per( 1000 ): for hda in db_session.query( HistoryDatasetAssociation ).enable_eagerloads( False ).filter_by( history_id=history.id, purged=False ).yield_per( 1000 ): if not hda.dataset.id in dataset_ids and not hda.dataset.purged and not hda.dataset.library_associations: dataset_ids.append( hda.dataset.id ) 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: Fix openid_associate upon logging in with an unassociated account, drop Flickr from OpenID since it no longer works (you have to use your photostream URL now).
by Bitbucket 28 Sep '11

28 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ec5c9d242d9f/ changeset: ec5c9d242d9f user: natefoo date: 2011-09-28 21:41:21 summary: Fix openid_associate upon logging in with an unassociated account, drop Flickr from OpenID since it no longer works (you have to use your photostream URL now). affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/user.py Wed Sep 28 10:56:30 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Wed Sep 28 15:41:21 2011 -0400 @@ -28,7 +28,6 @@ OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', 'Yahoo!' : 'http://yahoo.com', 'AOL/AIM' : 'http://openid.aol.com', - 'Flickr' : 'http://flickr.com', 'Launchpad' : 'http://login.launchpad.net', } @@ -195,7 +194,7 @@ message=message, status=status ) ) @web.expose - def openid_associate( self, trans, cntrller, webapp='galaxy', **kwd ): + def openid_associate( self, trans, cntrller='user', webapp='galaxy', **kwd ): if not trans.app.config.enable_openid: return trans.show_error_message( 'OpenID authentication is not enabled in this instance of Galaxy' ) use_panels = util.string_as_bool( kwd.get( 'use_panels', False ) ) @@ -266,7 +265,7 @@ if user_type_fd_id == 'none' and user_type_form_definition is not None: user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) user_type_fd_id_select_field = self.__build_user_type_fd_id_select_field( trans, selected_value=user_type_fd_id ) - widgets = self.__get_widgets( self, trans, user_type_form_definition, user=user, **kwd ) + widgets = self.__get_widgets( trans, user_type_form_definition, user=user, **kwd ) else: user_type_fd_id_select_field = None user_type_form_definition = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Fix for the mime type when a dataset instance's extension is None.
by Bitbucket 28 Sep '11

28 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e28ebc25b2e7/ changeset: e28ebc25b2e7 user: natefoo date: 2011-09-28 16:56:30 summary: Fix for the mime type when a dataset instance's extension is None. affected #: 4 files (-1 bytes) --- a/lib/galaxy/model/__init__.py Wed Sep 28 10:47:54 2011 -0400 +++ b/lib/galaxy/model/__init__.py Wed Sep 28 10:56:30 2011 -0400 @@ -862,7 +862,11 @@ self.datatype.set_raw_data(self, data) def get_mime( self ): """Returns the mime type of the data""" - return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) + try: + return datatypes_registry.get_mimetype_by_extension( self.extension.lower() ) + except AttributeError: + # extension is None + return 'data' def is_multi_byte( self ): """Data consists of multi-byte characters""" return self.dataset.is_multi_byte() --- a/lib/galaxy/web/controllers/dataset.py Wed Sep 28 10:47:54 2011 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Wed Sep 28 10:56:30 2011 -0400 @@ -358,8 +358,7 @@ else: return trans.show_error_message( "Could not find '%s' on the extra files path %s." % ( filename, file_path ) ) - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) + trans.response.set_content_type(data.get_mime()) trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) if to_ext or isinstance(data.datatype, datatypes.binary.Binary): # Saving the file, or binary file @@ -691,8 +690,7 @@ # If data is binary or an image, stream without template; otherwise, use display template. # TODO: figure out a way to display images in display template. if isinstance(dataset.datatype, datatypes.binary.Binary) or isinstance(dataset.datatype, datatypes.images.Image) or isinstance(dataset.datatype, datatypes.images.Html): - mime = trans.app.datatypes_registry.get_mimetype_by_extension( dataset.extension.lower() ) - trans.response.set_content_type( mime ) + trans.response.set_content_type( data.get_mime() ) return open( dataset.file_name ) else: # Get rating data. --- a/lib/galaxy/web/controllers/library_common.py Wed Sep 28 10:47:54 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Wed Sep 28 10:56:30 2011 -0400 @@ -1404,8 +1404,7 @@ kwd['do_action'] = 'zip' return self.act_on_multiple_datasets( trans, cntrller, library_id, ldda_ids=[id,], **kwd ) else: - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) + trans.response.set_content_type( ldda.get_mime() ) fStat = os.stat( ldda.file_name ) trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' --- a/lib/galaxy/web/controllers/root.py Wed Sep 28 10:47:54 2011 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Sep 28 10:56:30 2011 -0400 @@ -241,8 +241,7 @@ if data: current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.can_access_dataset( current_user_roles, data.dataset ): - mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) - trans.response.set_content_type(mime) + trans.response.set_content_type(data.get_mime()) if tofile: fStat = os.stat(data.file_name) trans.response.headers['Content-Length'] = int(fStat.st_size) 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: (a) enable renaming and removing of groups and (b) more refactoring to enable groups to have preferences. Pack scripts.
by Bitbucket 28 Sep '11

28 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bde5e3086b7c/ changeset: bde5e3086b7c user: jgoecks date: 2011-09-28 16:47:54 summary: Trackster: (a) enable renaming and removing of groups and (b) more refactoring to enable groups to have preferences. Pack scripts. affected #: 7 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Wed Sep 28 09:26:30 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Wed Sep 28 10:47:54 2011 -0400 @@ -349,8 +349,10 @@ else: drawables.append( pack_collection( drawable_dict ) ) return { + 'name': collection_dict.get( 'name', 'dummy' ), 'obj_type': collection_dict[ 'obj_type' ], - 'drawables': drawables + 'drawables': drawables, + 'prefs': collection_dict.get( 'prefs', [] ) } # Set tracks. --- a/lib/galaxy/web/controllers/tracks.py Wed Sep 28 09:26:30 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed Sep 28 10:47:54 2011 -0400 @@ -637,8 +637,10 @@ drawable = unpack_collection( drawable_json ) unpacked_drawables.append( drawable ) return { + "name": collection_json.get( 'name', '' ), "obj_type": collection_json[ 'obj_type' ], - "drawables": unpacked_drawables + "drawables": unpacked_drawables, + "prefs": collection_json.get( 'prefs' , [] ) } # TODO: unpack and validate bookmarks: --- a/static/scripts/packed/trackster.js Wed Sep 28 09:26:30 2011 -0400 +++ b/static/scripts/packed/trackster.js Wed Sep 28 10:47:54 2011 -0400 @@ -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 trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(aj,ai,al,ak,ah){this.name=aj;this.view=ai;this.parent_element=al;this.drag_handle_class=ak;this.container=ah;this.config=new H({track:this})};r.prototype.init=function(){};r.prototype.request_draw=function(){};r.prototype._draw=function(){};r.prototype.to_json=function(){};var A=function(ak,aj,ai,al,ah){r.call(this,aj,ai,al,ah);this.obj_type=ak;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(aj,ai,al,ah){A.call(this,"DrawableGroup",aj,ai,al,"group-handle",ah);if(!S.id_counter){S.id_counter=0}var ak=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+ak).appendTo(this.parent_element);this.container_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+ak+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this)};q(S.prototype,r.prototype,A.prototype);var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.content_div);m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.content_div.click(function(al){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,this.top_labeltrack));this.add_label_track(new ad(this,this.nav_labeltrack));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.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(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){var ay=this.track.parent_element;ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={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,ai=ah.tool_id+aj.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ak;if(aj instanceof e){ak=new X(ai,view,aj.hda_ldda,undefined,{},{},aj);ak.change_mode(aj.mode)}this.track.view.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ah,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};if(ah.saved_values){this.restore_values(ah.saved_values)}this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(ai,ah,al,aj,ak){r.call(this,ai,ah,al,"draghandle",ah);this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};q(j.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var O=function(ao,am,ap){var ai=this,aq=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=(ao!==undefined?new ac(this,ao):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(ar){return function(){ai.change_mode(ar)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw()},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){view.remove_drawable(ai,true);if(view.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ah,ai){this.hidden=true;j.call(this,null,ah,ai);this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,null,ah,ah.top_labeltrack);O.call(this);ah.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:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(al,aj,am,ah,ak){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,al,aj,aj.viewport_container);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:"black"},{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:ak,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_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()};q(k.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,am,al,ap,ao,aj,ak,an){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;j.call(this,ah,am,am.viewport_container);O.call(this,aj,ak,an);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new R(aI,aE,aj,aw.data,aw.message)}});var W=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.painter=N.VariantPainter};q(W.prototype,O.prototype,e.prototype);var Z=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:aj,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=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,O.prototype,e.prototype);var X=function(al,aj,an,ah,ak,am,ai){e.call(this,al,aj,an,ah,ak,am,{},ai);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(ak,ai,aj,am,al,ah){this.name=ak;this.view=ai;this.parent_element=am;this.drag_handle_class=al;this.container=ah;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak}],saved_values:aj,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values};q(r.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},make_name_popup_menu:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;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.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var A=function(al,ak,ai,aj,an,am,ah){r.call(this,ak,ai,aj,an,am,ah);this.obj_type=al;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(ak,ai,aj,am,ah){A.call(this,"DrawableGroup",ak,ai,aj,am,"group-handle",ah);if(!S.id_counter){S.id_counter=0}var al=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+al).appendTo(this.parent_element);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+al+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.make_name_popup_menu()};q(S.prototype,r.prototype,A.prototype,{make_name_popup_menu:function(){var ai=this;var ah={};ah["Edit configuration"]=function(){var al=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(am){if((am.keyCode||am.which)===27){al()}else{if((am.keyCode||am.which)===13){aj()}}};$(window).bind("keypress.check_enter_esc",ak);show_modal("Configure Group",ai.config.build_form(),{Cancel:al,OK:aj})};ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)}});var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.content_div);m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.content_div.click(function(al){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,this.top_labeltrack));this.add_label_track(new ad(this,this.nav_labeltrack));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.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(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){var ay=this.track.parent_element;ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={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,ai=ah.tool_id+aj.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ak;if(aj instanceof e){ak=new X(ai,view,aj.hda_ldda,undefined,{},{},aj);ak.change_mode(aj.mode)}this.track.view.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ah,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};if(ah.saved_values){this.restore_values(ah.saved_values)}this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(aj,ah,ai,am,ak,al){r.call(this,aj,ah,{},am,"draghandle",ah);this.data_url=(ak?ak:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am,ap){var ai=this,aq=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=(ao!==undefined?new ac(this,ao):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(ar){return function(){ai.change_mode(ar)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,r.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw()},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ah,ai){this.hidden=true;j.call(this,"label",ah,{},ai);this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,null,ah,{},ah.top_labeltrack);O.call(this);ah.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:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(al,aj,am,ah,ak){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,al,aj,ak,aj.viewport_container);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:"black"},{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:ak,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};q(k.prototype,r.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,am,al,ap,ao,aj,ak,an){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];j.call(this,ah,am,ao,am.viewport_container);O.call(this,aj,ak,an);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,r.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new R(aI,aE,aj,aw.data,aw.message)}});var W=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.painter=N.VariantPainter};q(W.prototype,r.prototype,O.prototype,e.prototype);var Z=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:aj,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=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,r.prototype,O.prototype,e.prototype);var X=function(al,aj,an,ah,ak,am,ai){e.call(this,al,aj,an,ah,ak,am,{},ai);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,r.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 --- a/static/scripts/packed/trackster_ui.js Wed Sep 28 09:26:30 2011 -0400 +++ b/static/scripts/packed/trackster_ui.js Wed Sep 28 10:47:54 2011 -0400 @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(a){return new addable_objects[a.track_type](a.name,view,a.hda_ldda,a.dataset_id,a.prefs,a.filters,a.tool)};var drawable_collection_from_dict=function(e){var d=new addable_objects[e.obj_type]("New Group",view,view.viewport_container,view);for(var c=0;c<e.drawables.length;c++){var a=e.drawables[c],b;if(a.track_type){b=track_from_dict(a)}else{b=drawable_collection_from_dict(a)}d.add_drawable(b);d.content_div.append(b.container_div)}return d};var drawable_from_dict=function(a){return(a.track_type?track_from_dict(a):drawable_collection_from_dict(a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&p&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(a){return new addable_objects[a.track_type](a.name,view,a.hda_ldda,a.dataset_id,a.prefs,a.filters,a.tool)};var drawable_collection_from_dict=function(e){var d=new addable_objects[e.obj_type](e.name,view,e.prefs,view.viewport_container,view);for(var c=0;c<e.drawables.length;c++){var a=e.drawables[c],b;if(a.track_type){b=track_from_dict(a)}else{b=drawable_collection_from_dict(a)}d.add_drawable(b);d.content_div.append(b.container_div)}return d};var drawable_from_dict=function(a){return(a.track_type?track_from_dict(a):drawable_collection_from_dict(a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&(p!==undefined)&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file --- a/static/scripts/trackster.js Wed Sep 28 09:26:30 2011 -0400 +++ b/static/scripts/trackster.js Wed Sep 28 10:47:54 2011 -0400 @@ -575,27 +575,66 @@ /** * Base interface for all drawable objects. */ -var Drawable = function(name, view, parent_element, drag_handle_class, container) { +var Drawable = function(name, view, prefs, parent_element, drag_handle_class, container) { this.name = name; this.view = view; this.parent_element = parent_element; this.drag_handle_class = drag_handle_class; this.container = container; this.config = new DrawableConfig({ - track: this - }); + track: this, + params: [ + { key: 'name', label: 'Name', type: 'text', default_value: name } + ], + saved_values: prefs, + onchange: function() { + this.track.set_name(this.track.config.values.name); + } + }); + this.prefs = this.config.values; }; -Drawable.prototype.init = function() {}; -Drawable.prototype.request_draw = function() {}; -Drawable.prototype._draw = function() {}; -Drawable.prototype.to_json = function() {}; +extend(Drawable.prototype, { + init: function() {}, + request_draw: function() {}, + _draw: function() {}, + to_json: function() {}, + make_name_popup_menu: function() {}, + /** + * Set drawable name. + */ + set_name: function(new_name) { + this.old_name = this.name; + this.name = new_name; + this.name_div.text(this.name); + }, + /** + * Revert track name; currently name can be reverted only once. + */ + revert_name: function() { + this.name = this.old_name; + this.name_div.text(this.name); + }, + /** + * Remove drawable (a) from its container and (b) from the HTML. + */ + remove: function() { + this.container.remove_drawable(this); + + this.container_div.fadeOut('slow', function() { + $(this).remove(); + // HACK: is there a better way to update the view? + view.update_intro_div(); + view.has_changes = true; + }); + } +}); /** * A collection of drawable objects. */ -var DrawableCollection = function(obj_type, name, view, parent_element, container) { - Drawable.call(this, name, view, parent_element, container); +var DrawableCollection = function(obj_type, name, view, prefs, parent_element, drag_handle_class, container) { + Drawable.call(this, name, view, prefs, parent_element, drag_handle_class, container); // Attribute init. this.obj_type = obj_type; @@ -626,7 +665,9 @@ for (var i = 0; i < this.drawables.length; i++) { jsonified_drawables.push(this.drawables[i].to_json()); } - return { + return { + name: this.name, + prefs: this.prefs, obj_type: this.obj_type, drawables: jsonified_drawables }; @@ -650,15 +691,15 @@ return false; }, /** - * Tries to remove drawable from the collection. Returns true if drawable removed from - * collection, false otherwise. + * Remove drawable from this collection. */ remove_drawable: function(drawable) { var index = this.drawables.indexOf(drawable); if (index != -1) { + // Found drawable to remove. this.drawables.splice(index, 1); drawable.container = null; - return true; + return true; } return false; }, @@ -681,15 +722,16 @@ /** * A group of drawables that are moveable, visible. */ -var DrawableGroup = function(name, view, parent_element, container) { - DrawableCollection.call(this, "DrawableGroup", name, view, parent_element, "group-handle", container); - +var DrawableGroup = function(name, view, prefs, parent_element, container) { + DrawableCollection.call(this, "DrawableGroup", name, view, prefs, parent_element, "group-handle", container); + // HTML elements. if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; } var group_id = DrawableGroup.id_counter++ this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.parent_element); - this.container_div.append($("<div/>").addClass(this.drag_handle_class)); - this.name_div = $("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div); + this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); + this.header_div.append($("<div/>").addClass(this.drag_handle_class)); + this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div); // Set up containers/moving for group: register both container and content div as container @@ -697,9 +739,54 @@ is_container(this.container_div, this); is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); + + this.make_name_popup_menu(); }; -extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype); +extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { + /** + * Make popup menu for group. + */ + make_name_popup_menu: function() { + var group = this; + + var group_dropdown = {}; + + // + // Edit config option. + // + group_dropdown["Edit configuration"] = function() { + var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + group.config.update_from_form( $(".dialog-box") ); + hide_modal(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + show_modal("Configure Group", group.config.build_form(), { + "Cancel": cancel_fn, + "OK": ok_fn + }); + }; + + // + // Remove option. + // + group_dropdown.Remove = function() { + group.remove(); + }; + + make_popupmenu(group.name_div, group_dropdown); + } +}); /** * View object manages complete viz view, including tracks and user interactions. @@ -2024,9 +2111,9 @@ * -------> ToolDataFeatureTrack * -------> VcfTrack */ -var Track = function(name, view, parent_element, data_url, data_query_wait) { +var Track = function(name, view, prefs, parent_element, data_url, data_query_wait) { // For now, track's container is always view. - Drawable.call(this, name, view, parent_element, "draghandle", view); + Drawable.call(this, name, view, {}, parent_element, "draghandle", view); // // Attribute init. @@ -2055,7 +2142,7 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); this.parent_element.append(this.container_div); }; -extend(Track.prototype, { +extend(Track.prototype, Drawable.prototype, { /** Returns track type. */ get_type: function() { // Order is important: start with most-specific classes and go up the track hierarchy. @@ -2153,21 +2240,6 @@ * Additional initialization required before drawing track for the first time. */ predraw_init: function() {}, - /** - * Set track name. - */ - set_name: function(new_name) { - this.old_name = this.name; - this.name = new_name; - this.name_div.text(this.name); - }, - /** - * Revert track name; currently name can be reverted only once. - */ - revert_name: function() { - this.name = this.old_name; - this.name_div.text(this.name); - } }); var TiledTrack = function(filters_list, tool_dict, parent_track) { @@ -2229,7 +2301,7 @@ this.make_name_popup_menu(); }; -extend(TiledTrack.prototype, Track.prototype, { +extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** * Convert track to JSON object. */ @@ -2351,10 +2423,7 @@ // Remove option. // track_dropdown.Remove = function() { - view.remove_drawable(track, true); - if (view.num_tracks === 0) { - $("#no-tracks").show(); - } + track.remove(); }; make_popupmenu(track.name_div, track_dropdown); @@ -2645,7 +2714,7 @@ var LabelTrack = function (view, parent_element) { this.hidden = true; - Track.call( this, null, view, parent_element ); + Track.call(this, "label", view, {}, parent_element ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -2672,7 +2741,7 @@ var ReferenceTrack = function (view) { this.hidden = true; - Track.call(this, null, view, view.top_labeltrack); + Track.call(this, null, view, {}, view.top_labeltrack); TiledTrack.call(this); view.reference_track = this; @@ -2687,7 +2756,7 @@ this.data_manager = new ReferenceTrackDataManager(CACHED_DATA, this, false); this.tile_cache = new Cache(CACHED_TILES_LINE); }; -extend(ReferenceTrack.prototype, TiledTrack.prototype, { +extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** * Draw ReferenceTrack tile. */ @@ -2721,7 +2790,7 @@ var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - Track.call( this, name, view, view.viewport_container ); + Track.call( this, name, view, prefs, view.viewport_container ); TiledTrack.call( this ); this.min_height_px = 16; @@ -2763,7 +2832,7 @@ this.add_resize_handle(); }; -extend(LineTrack.prototype, TiledTrack.prototype, { +extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { add_resize_handle: function () { // Add control for resizing // Trickery here to deal with the hovering drag handle, can probably be @@ -2865,6 +2934,13 @@ // var track = this; this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"]; + + // + // Initialization. + // + Track.call(this, name, view, prefs, view.viewport_container); + TiledTrack.call(this, filters, tool, parent_track); + // Define and restore track configuration. this.config = new DrawableConfig( { track: this, @@ -2884,12 +2960,6 @@ }); this.prefs = this.config.values; - // - // Initialization. - // - Track.call(this, name, view, view.viewport_container); - TiledTrack.call(this, filters, tool, parent_track); - this.height_px = 0; this.container_div.addClass( "feature-track" ); this.hda_ldda = hda_ldda; @@ -2906,7 +2976,7 @@ this.painter = painters.LinkedFeaturePainter; }; -extend(FeatureTrack.prototype, TiledTrack.prototype, { +extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. @@ -3250,7 +3320,7 @@ this.painter = painters.VariantPainter; }; -extend(VcfTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype); +extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { @@ -3279,7 +3349,7 @@ this.painter = painters.ReadPainter; this.make_name_popup_menu(); }; -extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype); +extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); /** * Feature track that displays data generated from tool. @@ -3294,7 +3364,7 @@ this.dataset_check_url = dataset_state_url; }; -extend(ToolDataFeatureTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { +extend(ToolDataFeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, { /** * For this track type, the predraw init sets up postdraw init. */ --- a/static/scripts/trackster_ui.js Wed Sep 28 09:26:30 2011 -0400 +++ b/static/scripts/trackster_ui.js Wed Sep 28 10:47:54 2011 -0400 @@ -46,7 +46,7 @@ * Decode a drawable collection from a dictionary. */ var drawable_collection_from_dict = function(collection_dict) { - var collection = new addable_objects[collection_dict.obj_type]("New Group", view, view.viewport_container, view); + var collection = new addable_objects[collection_dict.obj_type](collection_dict.name, view, collection_dict.prefs, view.viewport_container, view); for (var i = 0; i < collection_dict.drawables.length; i++) { var drawable_dict = collection_dict.drawables[i], @@ -92,7 +92,7 @@ end = viewport_config.end, overview_track_name = viewport_config.overview; - if (chrom && start && end) { + if (chrom && (start !== undefined) && end) { view.change_chrom(chrom, start, end); } --- a/templates/tracks/browser.mako Wed Sep 28 09:26:30 2011 -0400 +++ b/templates/tracks/browser.mako Wed Sep 28 10:47:54 2011 -0400 @@ -178,7 +178,7 @@ make_popupmenu( $("#viz-actions-button"), { "Add Tracks": add_tracks, "Add Group": function() { - var group = new DrawableGroup("New Group", view, view.viewport_container, view); + var group = new DrawableGroup("New Group", view, {}, view.viewport_container, view); view.add_drawable(group); }, "Save": function() { 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: Quota refactor bugfixes.
by Bitbucket 28 Sep '11

28 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0073d0897a18/ changeset: 0073d0897a18 user: natefoo date: 2011-09-28 15:26:30 summary: Quota refactor bugfixes. affected #: 2 files (-1 bytes) --- a/lib/galaxy/actions/admin.py Tue Sep 27 14:16:52 2011 -0400 +++ b/lib/galaxy/actions/admin.py Wed Sep 28 09:26:30 2011 -0400 @@ -41,7 +41,7 @@ self.sa_session.add( quota ) # If this is a default quota, create the DefaultQuotaAssociation if params.default != 'no': - self.app.quota_agent.set_default_quota( params.default, params.quota ) + self.app.quota_agent.set_default_quota( params.default, quota ) else: # Create the UserQuotaAssociations for user in [ self.sa_session.query( self.app.model.User ).get( x ) for x in params.in_users ]: --- a/lib/galaxy/web/controllers/admin.py Tue Sep 27 14:16:52 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Wed Sep 28 09:26:30 2011 -0400 @@ -424,7 +424,7 @@ params = self.get_quota_params( kwd ) if params.get( 'create_quota_button', False ): try: - quota, message = self._create_quota( trans, params ) + quota, message = self._create_quota( params ) return trans.response.send_redirect( web.url_for( controller='admin', action='quotas', webapp=params.webapp, 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 bugs in cloning a visualization.
by Bitbucket 27 Sep '11

27 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f8a94b3bbc3a/ changeset: f8a94b3bbc3a user: jgoecks date: 2011-09-27 20:16:52 summary: Fix bugs in cloning a visualization. affected #: 1 file (-1 bytes) --- a/lib/galaxy/web/controllers/visualization.py Tue Sep 27 13:06:34 2011 -0400 +++ b/lib/galaxy/web/controllers/visualization.py Tue Sep 27 14:16:52 2011 -0400 @@ -92,13 +92,14 @@ @web.expose @web.require_login() def clone(self, trans, id, *args, **kwargs): - visualization = self.get_visualization( trans, id, check_ownership=False ) + visualization = self.get_visualization( trans, id, check_ownership=False ) user = trans.get_user() - if trans.sa_session.query( model.VisualizationUserShareAssociation ) \ - .filter_by( user=user, visualization=visualization ).count() == 0: - error( "Visualization is not owned by or shared with current user" ) + owner = ( visualization.user == user ) + new_title = "Copy of '%s'" % visualization.title + if not owner: + new_title += " shared by %s" % visualization.user.email - cloned_visualization = visualization.copy( user=trans.user, title="Copy of '%s'" % visualization.title ) + cloned_visualization = visualization.copy( user=trans.user, title=new_title ) # Persist session = trans.sa_session 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: use jQuery Deferred objects rather than callbacks for cleaner initialization of saved visualizations. This prevents intermittent 'no data for this chrom/contig' message from appearing incorrectly.
by Bitbucket 27 Sep '11

27 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5ea451365b7c/ changeset: 5ea451365b7c user: jgoecks date: 2011-09-27 19:06:34 summary: Trackster: use jQuery Deferred objects rather than callbacks for cleaner initialization of saved visualizations. This prevents intermittent 'no data for this chrom/contig' message from appearing incorrectly. affected #: 5 files (-1 bytes) --- a/static/scripts/packed/trackster.js Tue Sep 27 09:55:52 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Sep 27 13:06:34 2011 -0400 @@ -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 trackster_module=function(f,Z){var q=f("class").extend,t=f("slotting"),M=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}ar.container.remove_drawable(ar);o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};Z.moveable=n;var af=16,H=9,F=20,U=H+2,B=100,J=12000,S=200,E=5,w=10,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",aa="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var T=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(T.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var I=function(ai,ah,aj){T.call(this,ai,ah,aj)};q(I.prototype,T.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return T.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(aj,ai,ak,ah){this.name=aj;this.view=ai;this.parent_element=ak;this.container=ah};r.prototype.request_draw=function(){};r.prototype.draw=function(){};var A=function(aj,ai,ak,ah){r.call(this,aj,ai,ak,ah);this.drawables=[]};q(A.prototype,r.prototype,{to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var R=function(aj,ai,ak,ah){A.call(this,aj,ai,ak,ah);this.drag_handle_class="group-handle";this.container_div=$("<div/>").addClass("group").appendTo(this.parent_element);this.container_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div);this.content_div=$("<div/>").addClass("content-div").appendTo(this.container_div);m(this.container_div,this)};q(R.prototype,A.prototype,r.prototype);var ae=function(ah,ak,aj,ai,al){A.call(this);this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(al);this.canvas_manager=new ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(al){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.content_div);m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(am){if(am.type==="focusout"||(am.keyCode||am.which)===13||(am.keyCode||am.which)===27){if((am.keyCode||am.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},al);this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.content_div.click(function(am){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(am){ah.zoom_in(am.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(am,an){this.current_x=an.offsetX}).bind("drag",function(am,ao){var ap=ao.offsetX-this.current_x;this.current_x=ao.offsetX;var an=Math.round(ap/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-an)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(am,an){if(am.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(am,an){an.original_low=ah.low;an.current_height=am.clientY;an.current_x=an.offsetX}).bind("drag",function(ao,aq){var am=$(this);var ar=aq.offsetX-aq.current_x;var an=am.scrollTop()-(ao.clientY-aq.current_height);am.scrollTop(an);aq.current_height=ao.clientY;aq.current_x=aq.offsetX;var ap=Math.round(ar/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ap)}).bind("mousewheel",function(ao,aq,an,am){if(an){var ap=Math.round(-an/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ap)}});this.top_labeltrack.bind("dragstart",function(am,an){return $("<div />").css({height:ah.content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(aq,ar){$(ar.proxy).css({left:Math.min(aq.pageX,ar.startX),width:Math.abs(aq.pageX-ar.startX)});var an=Math.min(aq.pageX,ar.startX)-ah.container.offset().left,am=Math.max(aq.pageX,ar.startX)-ah.container.offset().left,ap=(ah.high-ah.low),ao=ah.viewport_container.width();ah.update_location(Math.round(an/ao*ap)+ah.low,Math.round(am/ao*ap)+ah.low)}).bind("dragend",function(ar,at){var an=Math.min(ar.pageX,at.startX),am=Math.max(ar.pageX,at.startX),ap=(ah.high-ah.low),ao=ah.viewport_container.width(),aq=ah.low;ah.low=Math.round(an/ao*ap)+aq;ah.high=Math.round(am/ao*ap)+aq;$(at.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,this.top_labeltrack));this.add_label_track(new ad(this,this.nav_labeltrack));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},to_json:function(){var ah=this,ai=[];this.viewport_container.children(".track,.group").each(function(){var aj=$(this).attr("id");aj=parseInt(aj.slice(aj.lastIndexOf("_")+1));ai.push(ah.tracks[aj].to_json())});return ai},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(ai,aj){ai.num=x;$.extend(ai,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this;$.ajax({url:chrom_url,data:ai,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+ai.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);if(aj){aj()}ah.chrom_start_index=al.start_index},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}})},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_track:function(ah){ah.view=this;ah.track_id=this.track_id_counter;this.tracks.push(ah);if(ah.init){ah.init()}ah.container_div.attr("id","track_"+ah.track_id);n(ah.container_div,ah.drag_handle_class,".group",ah);this.track_id_counter+=1;this.num_tracks+=1;this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_track:function(ai){this.has_changes=true;this.tracks.splice(this.tracks.indexOf(ai),1);this.num_tracks-=1;var ah=this;ai.container_div.fadeOut("slow",function(){$(this).remove();ah.update_intro_div()})},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/S)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj&&aj.enabled){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new O(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){var ay=this.track.parent_element,az=new A("New Group",ay);ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={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,ai=ah.tool_id+aj.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ak;if(aj instanceof e){ak=new W(ai,view,aj.hda_ldda,undefined,{},{},aj);ak.change_mode(aj.mode)}this.track.view.add_track(ak);ak.content_div.text("Starting job.");this.run(ah,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(K)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var O=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){O.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var X=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(X.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new X(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var P=function(ai,ah){M.AlphaGenerator.call(this,ah);this.filter=ai};P.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var ab=function(ah){this.track=ah.track;this.params=ah.params;this.values={};if(ah.saved_values){this.restore_values(ah.saved_values)}this.onchange=ah.onchange};q(ab.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*S*ai;this.high=(aj+1)*S*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var Q=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(ai,ah,al,aj,ak){r.call(this,ai,ah,al,ah);this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:L);this.dataset_check_url=converted_datasets_state_url;this.drag_handle_class="draghandle";this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};q(j.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Y){return"ReadTrack"}else{if(this instanceof W){return"ToolDataFeatureTrack"}else{if(this instanceof V){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(aa);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var N=function(ao,am,ap){var ai=this,aq=ai.view;this.filters_manager=(ao!==undefined?new ac(this,ao):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.track_config&&ai.track_config.values.mode?ai.track_config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(ar){return function(){ai.change_mode(ar)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(N.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.track_config.values.mode=ai;ah.tile_cache.clear();ah.request_draw()},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.track_config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}if(ai.valid_chroms){ah["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ai.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}ah.Remove=function(){view.remove_track(ai);if(parent_obj.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/S)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?U:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/S);var ap=true;var at=[];var ah=0;while((ai*S*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*S*an,ax=ap+S*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*S*ai,al=S*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ah,ai){this.hidden=true;j.call(this,null,ah,ai);this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,null,ah,ah.top_labeltrack);N.call(this);ah.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:ah.dbkey};this.data_manager=new I(D,this,false);this.tile_cache=new c(v)};q(C.prototype,N.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=S*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(al,aj,am,ah,ak){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,al,aj,aj.viewport_container);N.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new T(D,this);this.tile_cache=new c(v);this.left_offset=0;this.track_config=new ab({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:"black"},{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:ak,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};q(k.prototype,N.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.track_config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new M.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,am,al,ap,ao,aj,ak,an){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new ab({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.track_config.values;j.call(this,ah,am,am.viewport_container);N.call(this,aj,ak,an);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new T(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};q(e.prototype,N.prototype,{postdraw_actions:function(ax,ah,ay,aw){N.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>J){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+U;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new M.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,U);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new P(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new Q(aI,aE,aj,aw.data,aw.message)}});var V=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.painter=M.VariantPainter};q(V.prototype,N.prototype,e.prototype);var Y=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.track_config=new ab({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.track_config.values;this.painter=M.ReadPainter;this.make_name_popup_menu()};q(Y.prototype,N.prototype,e.prototype);var W=function(al,aj,an,ah,ak,am,ai){e.call(this,al,aj,an,ah,ak,am,{},ai);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(W.prototype,N.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=L;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});Z.View=ae;Z.DrawableGroup=R;Z.LineTrack=k;Z.FeatureTrack=e;Z.ReadTrack=Y};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 trackster_module=function(f,aa){var q=f("class").extend,t=f("slotting"),N=f("painters");var ag=function(ah,ai){this.document=ah;this.default_font=ai!==undefined?ai:"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")};q(ag.prototype,{load_pattern:function(ah,al){var ai=this.patterns,aj=this.dummy_context,ak=new Image();ak.src=image_path+al;ak.onload=function(){ai[ah]=aj.createPattern(ak,"repeat")}},get_pattern:function(ah){return this.patterns[ah]},new_canvas:function(){var ah=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ah)}ah.manager=this;return ah}});var o={};var m=function(ah,ai){o[ah.attr("id")]=ai};var n=function(ah,aj,al,ak){al=".group";var ai={};o[ah.attr("id")]=ak;ah.bind("drag",{handle:"."+aj,relative:true},function(au,av){var at=$(this);var ay=$(this).parent(),ap=ay.children(),ar=o[$(this).attr("id")],ao,an,aw,am,aq;an=$(this).parents(al);if(an.length!==0){aw=an.position().top;am=aw+an.outerHeight();if(av.offsetY<aw){$(this).insertBefore(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable_before(ar,ax);return}else{if(av.offsetY>am){$(this).insertAfter(an);var ax=o[an.attr("id")];ax.remove_drawable(ar);ax.container.add_drawable(ar);return}}}an=null;for(aq=0;aq<ap.length;aq++){ao=$(ap.get(aq));aw=ao.position().top;am=aw+ao.outerHeight();if(ao.is(al)&&this!==ao.get(0)&&av.offsetY>=aw&&av.offsetY<=am){if(av.offsetY-aw<am-av.offsetY){ao.find(".content-div").prepend(this)}else{ao.find(".content-div").append(this)}if(ar.container){ar.container.remove_drawable(ar)}o[ao.attr("id")].add_drawable(ar);return}}for(aq=0;aq<ap.length;aq++){if(av.offsetY<$(ap.get(aq)).position().top){break}}if(aq===ap.length){if(this!==ap.get(aq-1)){ay.append(this);o[ay.attr("id")].move_drawable(ar,aq)}}else{if(this!==ap.get(aq)){$(this).insertBefore(ap.get(aq));o[ay.attr("id")].move_drawable(ar,(av.deltaY>0?aq-1:aq))}}}).bind("dragstart",function(){ai["border-top"]=ah.css("border-top");ai["border-bottom"]=ah.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ai)})};aa.moveable=n;var af=16,I=9,F=20,V=I+2,B=100,K=12000,T=200,E=5,w=10,M=5000,x=100,p="There was an error in indexing this dataset. ",L="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",u="Currently indexing... please wait",z="Tool cannot be rerun: ",a="Loading data...",ab="Ready for display",d=10,v=5,D=5;function y(ah){return Math.round(ah*1000)/1000}var c=function(ah){this.num_elements=ah;this.clear()};q(c.prototype,{get:function(ai){var ah=this.key_ary.indexOf(ai);if(ah!==-1){if(this.obj_cache[ai].stale){this.key_ary.splice(ah,1);delete this.obj_cache[ai]}else{this.move_key_to_end(ai,ah)}}return this.obj_cache[ai]},set:function(ai,aj){if(!this.obj_cache[ai]){if(this.key_ary.length>=this.num_elements){var ah=this.key_ary.shift();delete this.obj_cache[ah]}this.key_ary.push(ai)}this.obj_cache[ai]=aj;return aj},move_key_to_end:function(ai,ah){this.key_ary.splice(ah,1);this.key_ary.push(ai)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var U=function(ai,ah,aj){c.call(this,ai);this.track=ah;this.subset=(aj!==undefined?aj:true)};q(U.prototype,c.prototype,{load_data:function(aq,al,ao,ai,an){var ap=this.track.view.chrom,ak={chrom:ap,low:aq,high:al,mode:ao,resolution:ai,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ak,an);if(this.track.filters_manager){var ar=[];var ah=this.track.filters_manager.filters;for(var am=0;am<ah.length;am++){ar[ar.length]=ah[am].name}ak.filter_cols=JSON.stringify(ar)}var aj=this;return $.getJSON(this.track.data_url,ak,function(at){aj.set_data(aq,al,ao,at)})},get_data:function(ah,al,am,ai,ak){var aj=this.get_data_from_cache(ah,al,am);if(aj){return aj}aj=this.load_data(ah,al,am,ai,ak);this.set_data(ah,al,am,aj);return aj},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ap,ak,ao,aj,an,al){var aq=this.get_data_from_cache(ap,ak,ao);if(!aq){console.log("ERROR: no current data for: ",this.track,ap,ak,ao,aj,an);return}aq.stale=true;var ai=ap;if(al===this.DEEP_DATA_REQ){$.extend(an,{start_val:aq.data.length+1})}else{if(al===this.BROAD_DATA_REQ){ai=(aq.max_high?aq.max_high:aq.data[aq.data.length-1][2])+1}}var ah=this,am=this.load_data(ai,ak,ao,aj,an);new_data_available=$.Deferred();this.set_data(ap,ak,ao,new_data_available);$.when(am).then(function(ar){if(ar.data){ar.data=aq.data.concat(ar.data);if(ar.max_low){ar.max_low=aq.max_low}if(ar.message){ar.message=ar.message.replace(/[0-9]+/,ar.data.length)}}ah.set_data(ap,ak,ao,ar);new_data_available.resolve(ar)});return new_data_available},get_data_from_cache:function(ah,ai,aj){return this.get(this.gen_key(ah,ai,aj))},set_data:function(ai,aj,ak,ah){return this.set(this.gen_key(ai,aj,ak),ah)},gen_key:function(ah,aj,ak){var ai=ah+"_"+aj+"_"+ak;return ai},split_key:function(ah){return ah.split("_")}});var J=function(ai,ah,aj){U.call(this,ai,ah,aj)};q(J.prototype,U.prototype,c.prototype,{load_data:function(aj,ah,al,am,ai,ak){if(ai>1){return}return U.prototype.load_data.call(this,aj,ah,al,am,ai,ak)}});var r=function(aj,ai,al,ak,ah){this.name=aj;this.view=ai;this.parent_element=al;this.drag_handle_class=ak;this.container=ah;this.config=new H({track:this})};r.prototype.init=function(){};r.prototype.request_draw=function(){};r.prototype._draw=function(){};r.prototype.to_json=function(){};var A=function(ak,aj,ai,al,ah){r.call(this,aj,ai,al,ah);this.obj_type=ak;this.drawables=[]};q(A.prototype,r.prototype,{init:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah].init()}},_draw:function(){for(var ah=0;ah<this.drawables.length;ah++){this.drawables[ah]._draw()}},to_json:function(){var ai=[];for(var ah=0;ah<this.drawables.length;ah++){ai.push(this.drawables[ah].to_json())}return{obj_type:this.obj_type,drawables:ai}},add_drawable:function(ah){this.drawables.push(ah);ah.container=this},add_drawable_before:function(aj,ah){var ai=this.drawables.indexOf(ah);if(ai!=-1){this.drawables.splice(ai,0,aj);return true}return false},remove_drawable:function(ai){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);ai.container=null;return true}return false},move_drawable:function(ai,aj){var ah=this.drawables.indexOf(ai);if(ah!=-1){this.drawables.splice(ah,1);this.drawables.splice(aj,0,ai);return true}return false}});var S=function(aj,ai,al,ah){A.call(this,"DrawableGroup",aj,ai,al,"group-handle",ah);if(!S.id_counter){S.id_counter=0}var ak=S.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+ak).appendTo(this.parent_element);this.container_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+ak+"_content_div").appendTo(this.container_div);m(this.container_div,this);m(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this)};q(S.prototype,r.prototype,A.prototype);var ae=function(ah,ak,aj,ai){A.call(this,"View");this.container=ah;this.chrom=null;this.vis_id=aj;this.dbkey=ai;this.title=ak;this.tracks=this.drawables;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 ag(ah.get(0).ownerDocument);this.reset()};q(ae.prototype,A.prototype,{init:function(){var aj=this.container,ah=this;this.top_container=$("<div/>").addClass("top-container").appendTo(aj);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(aj);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(aj);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.content_div);m(this.viewport_container,ah);this.intro_div=$("<div/>").addClass("intro");var ak=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<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 ai=function(al){if(al.type==="focusout"||(al.keyCode||al.which)===13||(al.keyCode||al.which)===27){if((al.keyCode||al.which)!==27){ah.go_to($(this).val())}$(this).hide();$(this).val("");ah.location_span.show();ah.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ai).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ah.location_span.hide();ah.chrom_select.hide();ah.nav_input.val(ah.chrom+":"+ah.low+"-"+ah.high);ah.nav_input.css("display","inline-block");ah.nav_input.select();ah.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ah.zoom_out();ah.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ah.zoom_in();ah.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ah.change_chrom(ah.chrom_select.val())});this.content_div.click(function(al){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(al){ah.zoom_in(al.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(al,am){this.current_x=am.offsetX}).bind("drag",function(al,an){var ao=an.offsetX-this.current_x;this.current_x=an.offsetX;var am=Math.round(ao/ah.viewport_container.width()*(ah.max_high-ah.max_low));ah.move_delta(-am)});this.overview_close.click(function(){ah.reset_overview()});this.viewport_container.bind("draginit",function(al,am){if(al.clientX>ah.viewport_container.width()-16){return false}}).bind("dragstart",function(al,am){am.original_low=ah.low;am.current_height=al.clientY;am.current_x=am.offsetX}).bind("drag",function(an,ap){var al=$(this);var aq=ap.offsetX-ap.current_x;var am=al.scrollTop()-(an.clientY-ap.current_height);al.scrollTop(am);ap.current_height=an.clientY;ap.current_x=ap.offsetX;var ao=Math.round(aq/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}).bind("mousewheel",function(an,ap,am,al){if(am){var ao=Math.round(-am/ah.viewport_container.width()*(ah.high-ah.low));ah.move_delta(ao)}});this.top_labeltrack.bind("dragstart",function(al,am){return $("<div />").css({height:ah.content_div.height()+ah.top_labeltrack.height()+ah.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ap,aq){$(aq.proxy).css({left:Math.min(ap.pageX,aq.startX),width:Math.abs(ap.pageX-aq.startX)});var am=Math.min(ap.pageX,aq.startX)-ah.container.offset().left,al=Math.max(ap.pageX,aq.startX)-ah.container.offset().left,ao=(ah.high-ah.low),an=ah.viewport_container.width();ah.update_location(Math.round(am/an*ao)+ah.low,Math.round(al/an*ao)+ah.low)}).bind("dragend",function(aq,ar){var am=Math.min(aq.pageX,ar.startX),al=Math.max(aq.pageX,ar.startX),ao=(ah.high-ah.low),an=ah.viewport_container.width(),ap=ah.low;ah.low=Math.round(am/an*ao)+ap;ah.high=Math.round(al/an*ao)+ap;$(ar.proxy).remove();ah.request_redraw()});this.add_label_track(new ad(this,this.top_labeltrack));this.add_label_track(new ad(this,this.nav_labeltrack));$(window).bind("resize",function(){ah.resize_window()});$(document).bind("redraw",function(){ah.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ah,ai){this.location_span.text(commatize(ah)+" - "+commatize(ai));this.nav_input.val(this.chrom+":"+commatize(ah)+"-"+commatize(ai))},load_chroms:function(aj){aj.num=x;$.extend(aj,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ah=this,ai=$.Deferred();$.ajax({url:chrom_url,data:aj,dataType:"json",success:function(al){if(al.chrom_info.length===0){alert("Invalid chromosome: "+aj.chrom);return}if(al.reference){ah.add_label_track(new C(ah))}ah.chrom_data=al.chrom_info;var ao='<option value="">Select Chrom/Contig</option>';for(var an=0,ak=ah.chrom_data.length;an<ak;an++){var am=ah.chrom_data[an].chrom;ao+='<option value="'+am+'">'+am+"</option>"}if(al.prev_chroms){ao+='<option value="previous">Previous '+x+"</option>"}if(al.next_chroms){ao+='<option value="next">Next '+x+"</option>"}ah.chrom_select.html(ao);ah.chrom_start_index=al.start_index;ai.resolve(al)},error:function(){alert("Could not load chroms for this dbkey:",ah.dbkey)}});return ai},change_chrom:function(al,ai,an){if(!al||al==="None"){return}var ak=this;if(al==="previous"){ak.load_chroms({low:this.chrom_start_index-x});return}if(al==="next"){ak.load_chroms({low:this.chrom_start_index+x});return}var am=$.grep(ak.chrom_data,function(ap,aq){return ap.chrom===al})[0];if(am===undefined){ak.load_chroms({chrom:al},function(){ak.change_chrom(al,ai,an)});return}else{if(al!==ak.chrom){ak.chrom=al;ak.chrom_select.val(ak.chrom);ak.max_high=am.len-1;ak.reset();ak.request_redraw(true);for(var ao=0,ah=ak.tracks.length;ao<ah;ao++){var aj=ak.tracks[ao];if(aj.init){aj.init()}}}if(ai!==undefined&&an!==undefined){ak.low=Math.max(ai,0);ak.high=Math.min(an,ak.max_high)}ak.reset_overview();ak.request_redraw()}},go_to:function(al){var ap=this,ah,ak,ai=al.split(":"),an=ai[0],ao=ai[1];if(ao!==undefined){try{var am=ao.split("-");ah=parseInt(am[0].replace(/,/g,""),10);ak=parseInt(am[1].replace(/,/g,""),10)}catch(aj){return false}}ap.change_chrom(an,ah,ak)},move_fraction:function(aj){var ah=this;var ai=ah.high-ah.low;this.move_delta(aj*ai)},move_delta:function(aj){var ah=this;var ai=ah.high-ah.low;if(ah.low-aj<ah.max_low){ah.low=ah.max_low;ah.high=ah.max_low+ai}else{if(ah.high-aj>ah.max_high){ah.high=ah.max_high;ah.low=ah.max_high-ai}else{ah.high-=aj;ah.low-=aj}}ah.request_redraw()},add_drawable:function(ah){A.prototype.add_drawable.call(this,ah);if(ah.init){ah.init()}this.has_changes=true;this.update_intro_div()},add_label_track:function(ah){ah.view=this;this.label_tracks.push(ah)},remove_drawable:function(aj,ai){A.prototype.remove_drawable.call(this,aj);if(ai){var ah=this;aj.container_div.fadeOut("slow",function(){$(this).remove();ah.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(ap,ah,ao,ai){var an=this,al=(ai?[ai]:an.tracks),aj;var ai;for(var am=0;am<al.length;am++){ai=al[am];aj=-1;for(var ak=0;ak<an.tracks_to_be_redrawn.length;ak++){if(an.tracks_to_be_redrawn[ak][0]===ai){aj=ak;break}}if(aj<0){an.tracks_to_be_redrawn.push([ai,ah,ao])}else{an.tracks_to_be_redrawn[am][1]=ah;an.tracks_to_be_redrawn[am][2]=ao}}requestAnimationFrame(function(){an._redraw(ap)})},_redraw:function(ar){var ao=this.low,ak=this.high;if(ao<this.max_low){ao=this.max_low}if(ak>this.max_high){ak=this.max_high}var aq=this.high-this.low;if(this.high!==0&&aq<this.min_separation){ak=ao+this.min_separation}this.low=Math.floor(ao);this.high=Math.ceil(ak);this.resolution=Math.pow(E,Math.ceil(Math.log((this.high-this.low)/T)/Math.log(E)));this.zoom_res=Math.pow(w,Math.max(0,Math.ceil(Math.log(this.resolution,w)/Math.log(w))));var ah=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var at=13;this.overview_box.css({left:ah,width:Math.max(at,an)}).show();if(an<at){this.overview_box.css("left",ah-(at-an)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ah,width:an})}this.update_location(this.low,this.high);if(!ar){var aj,ai,ap;for(var al=0,am=this.tracks_to_be_redrawn.length;al<am;al++){aj=this.tracks_to_be_redrawn[al][0];ai=this.tracks_to_be_redrawn[al][1];ap=this.tracks_to_be_redrawn[al][2];if(aj){aj._draw(ai,ap)}}this.tracks_to_be_redrawn=[];for(al=0,am=this.label_tracks.length;al<am;al++){this.label_tracks[al]._draw()}}},zoom_in:function(ai,aj){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ak=this.high-this.low,al=ak/2+this.low,ah=(ak/this.zoom_factor)/2;if(ai){al=ai/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(al-ah);this.high=Math.round(al+ah);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ai=this.high-this.low,aj=ai/2+this.low,ah=(ai*this.zoom_factor)/2;this.low=Math.round(aj-ah);this.high=Math.round(aj+ah);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){$.when(ah.get_overview_tile()).then(function(ai){view.overview_viewport.find(".track-tile").remove();view.overview_close.show();view.overview_viewport.append(ai.canvas);view.overview_highlight.show().height(ai.canvas.height());view.overview_viewport.height(ai.canvas.height()+view.overview_box.outerHeight());view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=ah;ah.set_is_overview(true)});view.has_changes=true},reset_overview:function(){this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();if(view.overview_track){view.overview_track.set_is_overview(false)}view.overview_track=null}});var s=function(aj,an){this.track=aj;this.name=an.name;this.params=[];var av=an.params;for(var ak=0;ak<av.length;ak++){var ap=av[ak],ai=ap.name,au=ap.label,al=unescape(ap.html),aw=ap.value,ar=ap.type;if(ar==="number"){this.params[this.params.length]=new g(ai,au,al,aw,ap.min,ap.max)}else{if(ar=="select"){this.params[this.params.length]=new P(ai,au,al,aw)}else{console.log("WARNING: unrecognized tool parameter type:",ai,ar)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ay){ay.stopPropagation()}).click(function(ay){ay.stopPropagation()}).bind("dblclick",function(ay){ay.stopPropagation()});var at=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var aq=this.params;var ao=this;$.each(this.params,function(az,aC){var aB=$("<div>").addClass("param-row").appendTo(ao.parent_div);var ay=$("<div>").addClass("param-label").text(aC.label).appendTo(aB);var aA=$("<div/>").addClass("slider").html(aC.html).appendTo(aB);aA.find(":input").val(aC.value);$("<div style='clear: both;'/>").appendTo(aB)});this.parent_div.find("input").click(function(){$(this).select()});var ax=$("<div>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ax);var ah=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ax);var ao=this;ah.click(function(){var ay=this.track.parent_element;ao.run_on_region()});am.click(function(){ao.run_on_dataset()})};q(s.prototype,{get_param_values_dict:function(){var ah={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();ah[ai]=JSON.stringify(aj)});return ah},get_param_values:function(){var ai=[];var ah={};this.parent_div.find(":input").each(function(){var aj=$(this).attr("name"),ak=$(this).val();if(aj){ai[ai.length]=ak}});return ai},run_on_dataset:function(){var ah=this;ah.run({dataset_id:this.track.original_dataset_id,tool_id:ah.name},null,function(ai){show_modal(ah.name+" is Running",ah.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={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,ai=ah.tool_id+aj.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ak;if(aj instanceof e){ak=new X(ai,view,aj.hda_ldda,undefined,{},{},aj);ak.change_mode(aj.mode)}this.track.view.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ah,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ai,aj,ak){$.extend(ai,this.get_param_values_dict());var ah=function(){$.getJSON(rerun_tool_url,ai,function(al){if(al==="no converter"){aj.container_div.addClass("error");aj.content_div.text(L)}else{if(al.error){aj.container_div.addClass("error");aj.content_div.text(z+al.message)}else{if(al==="pending"){aj.container_div.addClass("pending");aj.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ah,2000)}else{ak(al)}}}})};ah()}});var P=function(ai,ah,aj,ak){this.name=ai;this.label=ah;this.html=aj;this.value=ak};var g=function(aj,ai,al,am,ak,ah){P.call(this,aj,ai,al,am);this.min=ak;this.max=ah};var h=function(ai,ah,aj,ak){this.name=ai;this.index=ah;this.tool_id=aj;this.tool_exp_name=ak};var Y=function(ai,ah,aj,ak){h.call(this,ai,ah,aj,ak);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};q(Y.prototype,{applies_to:function(ah){if(ah.length>this.index){return true}return false},keep:function(ah){if(!this.applies_to(ah)){return true}var ai=parseFloat(ah[this.index]);return(isNaN(ai)||(ai>=this.low&&ai<=this.high))},update_attrs:function(ai){var ah=false;if(!this.applies_to(ai)){return ah}if(ai[this.index]<this.min){this.min=Math.floor(ai[this.index]);ah=true}if(ai[this.index]>this.max){this.max=Math.ceil(ai[this.index]);ah=true}return ah},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var aj=function(am,ak){var al=ak-am;return(al<=2?0.01:1)};var ai=this.slider.slider("option","min"),ah=this.slider.slider("option","max");if(this.min<ai||this.max>ah){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",aj(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ac=function(ar,ay){this.track=ar;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,ah=au.type,ak=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(ah==="int"||ah==="float"){this.filters[at]=new Y(az,ak,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,ah)}}var al=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ap=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];ap.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;al(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var am=$("<div/>").addClass("param-row").appendTo(av);var ao=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(am);var aj=this;ao.click(function(){aj.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),an=$("<span/>").addClass("elt-label").text("Transparency:").appendTo(aq),ai=$("<select/>").attr("name","alpha_dropdown").appendTo(aq);this.alpha_filter=null;$("<option/>").attr("value",-1).text("== None ==").appendTo(ai);for(var at=0;at<this.filters.length;at++){$("<option/>").attr("value",at).text(this.filters[at].name).appendTo(ai)}ai.change(function(){$(this).children("option:selected").each(function(){var aA=parseInt($(this).val());ap.alpha_filter=(aA>=0?ap.filters[aA]:null);ap.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(this.parent_div)};q(ac.prototype,{reset_filters:function(){for(var ah=0;ah<this.filters.length;ah++){filter=this.filters[ah];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null},run_on_dataset:function(){var ap=function(au,ar,at){if(!(ar in au)){au[ar]=at}return au[ar]};var aj={},ah,ai,ak;for(var al=0;al<this.filters.length;al++){ah=this.filters[al];if(ah.tool_id){if(ah.min!=ah.low){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" >= "+ah.low}if(ah.max!=ah.high){ai=ap(aj,ah.tool_id,[]);ai[ai.length]=ah.tool_exp_name+" <= "+ah.high}}}var an=[];for(var aq in aj){an[an.length]=[aq,aj[aq]]}var ao=an.length;(function am(ay,av){var at=av[0],au=at[0],ax=at[1],aw="("+ax.join(") and (")+")",ar={cond:aw,input:ay,target_dataset_id:ay,tool_id:au},av=av.slice(1);$.getJSON(run_tool_url,ar,function(az){if(az.error){show_modal("Filter Dataset","Error running tool "+au,{Close:hide_modal})}else{if(av.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{am(az.dataset_id,av)}}})})(this.track.dataset_id,an)}});var Q=function(ai,ah){N.AlphaGenerator.call(this,ah);this.filter=ai};Q.prototype.gen_alpha=function(ah){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_alpha}return((parseFloat(ah[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var H=function(ah){this.track=ah.track;this.params=ah.params;this.values={};if(ah.saved_values){this.restore_values(ah.saved_values)}this.onchange=ah.onchange};q(H.prototype,{restore_values:function(ah){var ai=this;$.each(this.params,function(aj,ak){if(ah[ak.key]!==undefined){ai.values[ak.key]=ah[ak.key]}else{ai.values[ak.key]=ak.default_value}})},build_form:function(){var ai=this;var ah=$("<div />");$.each(this.params,function(am,ak){if(!ak.hidden){var aj="param_"+am;var ao=ai.values[ak.key];var ar=$("<div class='form-row' />").appendTo(ah);ar.append($("<label />").attr("for",aj).text(ak.label+":"));if(ak.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",ao))}else{if(ak.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(ao).click(function(){$(this).select()}))}else{if(ak.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(ao);var ap=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var al=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ap);var aq=$("<div/>").appendTo(al).farbtastic({width:100,height:100,callback:an,color:ao});$("<div />").append(an).append(ap).appendTo(ar).bind("click",function(at){ap.css({left:$(this).position().left+($(an).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ap.hide();$(document).unbind("click.color-picker")});at.stopPropagation()})}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(ao))}}}}});return ah},update_from_form:function(ah){var aj=this;var ai=false;$.each(this.params,function(ak,am){if(!am.hidden){var an="param_"+ak;var al=ah.find("#"+an).val();if(am.type==="float"){al=parseFloat(al)}else{if(am.type==="int"){al=parseInt(al)}else{if(am.type==="bool"){al=ah.find("#"+an).is(":checked")}}}if(al!==aj.values[am.key]){aj.values[am.key]=al;ai=true}}});if(ai){this.onchange()}}});var b=function(aj,ai,ah,ak){this.index=aj;this.low=aj*T*ai;this.high=(aj+1)*T*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};var l=function(aj,ai,ah,ak,al){b.call(this,aj,ai,ah,ak);this.max_val=al};var R=function(aj,ai,ah,al,ak){b.call(this,aj,ai,ah,al);this.message=ak};var j=function(ai,ah,al,aj,ak){r.call(this,ai,ah,al,"draghandle",ah);this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:M);this.dataset_check_url=converted_datasets_state_url;if(!j.id_counter){j.id_counter=0}this.container_div=$("<div />").addClass("track").attr("id","track_"+j.id_counter++).css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};q(j.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},set_name:function(ah){this.old_name=this.name;this.name=ah;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var O=function(ao,am,ap){var ai=this,aq=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=(ao!==undefined?new ac(this,ao):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak<an;ak++){var al=ai.display_modes[ak];ah[al]=function(ar){return function(){ai.change_mode(ar)}}(al)}make_popupmenu(ai.mode_div,ah)}else{ai.mode_div.hide()}}this.make_name_popup_menu()};q(O.prototype,j.prototype,{to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs}},change_mode:function(ai){var ah=this;ah.mode_div.text(ai);ah.mode=ai;ah.config.values.mode=ai;ah.tile_cache.clear();ah.request_draw()},make_name_popup_menu:function(){var ai=this;var ah={};ah[(this.is_overview?"Hide overview":"Set as overview")]=function(){if(ai.is_overview){ai.view.reset_overview()}else{ai.view.set_overview(ai)}};ah["Edit configuration"]=function(){var am=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ak=function(){ai.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},al=function(an){if((an.keyCode||an.which)===27){am()}else{if((an.keyCode||an.which)===13){ak()}}};$(window).bind("keypress.check_enter_esc",al);show_modal("Configure Track",ai.config.build_form(),{Cancel:am,OK:ak})};if(ai.filters_available>0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){view.remove_drawable(ai,true);if(view.num_tracks===0){$("#no-tracks").show()}};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("<div style='position: relative;'></div>");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)<an){tile=this.draw_helper(aj,ak,ai,am,au,av);if(tile){at.push(tile)}else{ap=false}ai+=1;ah++}var al=this;if(ap){al.postdraw_actions(at,ak,av,ar)}},postdraw_actions:function(al,am,an,ah){var aj=this;var ak=false;for(var ai=0;ai<al.length;ai++){if(al[ai].message){ak=true;break}}if(ak){for(var ai=0;ai<al.length;ai++){tile=al[ai];if(!tile.message){tile.canvas.css("padding-top",F)}}}},draw_helper:function(ai,aj,ak,an,au,ay,av,ao){var al=this,at=this._gen_tile_cache_key(aj,ay,ak),ap=ak*T*an,ax=ap+T*an;var aq=(ai?undefined:al.tile_cache.get(at));if(aq){al.show_tile(aq,au,ay);return aq}var ar=function(az){return("isResolved" in az)};var am=true;var ah=al.data_manager.get_data(ap,ax,al.mode,an,al.data_url_extra_params);if(ar(ah)){am=false}var aw;if(view.reference_track&&ay>view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$("<div/>"),ap=$("<div/>").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(ap),ah=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ah,ai){this.hidden=true;j.call(this,null,ah,ai);this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("<div style='position: relative; height: 1.3em;'></div>");while(ah<aj.high){var am=(ah-aj.low)/ak*al;ai.append($("<div class='label'>"+commatize(ah)+"</div>").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,null,ah,ah.top_labeltrack);O.call(this);ah.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:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao<ap;ao++){var ah=Math.round(ao*at);aq.fillText(ar[ao],ah+al.left_offset,10)}return new b(ai,am,ak,ar)}this.content_div.css("height","0px")}});var k=function(al,aj,am,ah,ak){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,al,aj,aj.viewport_container);O.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ah;this.original_dataset_id=ah;this.data_manager=new U(D,this);this.tile_cache=new c(v);this.left_offset=0;this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:"black"},{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:ak,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.track_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.track_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()};q(k.prototype,O.prototype,{add_resize_handle:function(){var ah=this;var ak=false;var aj=false;var ai=$("<div class='track-resize'>");$(ah.container_div).hover(function(){ak=true;ai.show()},function(){ak=false;if(!aj){ai.hide()}});ai.hide().bind("dragstart",function(al,am){aj=true;am.original_height=$(ah.content_div).height()}).bind("drag",function(am,an){var al=Math.min(Math.max(an.original_height+an.deltaY,ah.min_height_px),ah.max_height_px);$(ah.content_div).css("height",al);ah.height_px=al;ah.request_draw(true)}).bind("dragend",function(al,am){ah.tile_cache.clear();aj=false;if(!ak){ai.hide()}ah.config.values.height=ah.height_px}).appendTo(ah.container_div)},predraw_init:function(){var ah=this,ai=ah.view.tracks.indexOf(ah);ah.vertical_range=undefined;return $.getJSON(ah.data_url,{stats:true,chrom:ah.view.chrom,low:null,high:null,hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id},function(aj){ah.container_div.addClass("line-track");var al=aj.data;if(isNaN(parseFloat(ah.prefs.min_value))||isNaN(parseFloat(ah.prefs.max_value))){ah.prefs.min_value=al.min;ah.prefs.max_value=al.max;$("#track_"+ai+"_minval").val(ah.prefs.min_value);$("#track_"+ai+"_maxval").val(ah.prefs.max_value)}ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;ah.total_frequency=al.total_frequency;ah.container_div.find(".yaxislabel").remove();var am=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_minval").text(y(ah.prefs.min_value));var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ai+"_maxval").text(y(ah.prefs.max_value));ak.css({position:"absolute",top:"24px",left:"10px"});ak.prependTo(ah.container_div);am.css({position:"absolute",bottom:"2px",left:"10px"});am.prependTo(ah.container_div)})},draw_tile:function(au,am,al,aj,at){if(this.vertical_range===undefined){return}var ah=this._get_tile_bounds(aj,al),an=ah[0],ar=ah[1],ai=Math.ceil((ar-an)*at),ap=this.height_px;var ak=this.view.canvas_manager.new_canvas();ak.width=ai,ak.height=ap;var aq=ak.getContext("2d");var ao=new N.LinePainter(au.data,an,ar,this.prefs,am);ao.draw(aq,ai,ap);return new b(aj,al,ak,au.data)}});var e=function(ah,am,al,ap,ao,aj,ak,an){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ao,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;j.call(this,ah,am,am.viewport_container);O.call(this,aj,ak,an);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ap;this.original_dataset_id=ap;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new U(20,this);this.left_offset=200;this.painter=N.LinkedFeaturePainter};q(e.prototype,O.prototype,{postdraw_actions:function(ax,ah,ay,aw){O.prototype.postdraw_actions.call(this,ax,aw);var ak=this;if(aw){var am=ak.content_div.children();var an=false;for(var al=am.length-1,ar=0;al>=ar;al--){var aj=$(am[al]);if(an){aj.remove()}else{if(aj.children().length!==0){an=true}}}}if(ak.mode=="Histogram"){var aq=-1;for(var al=0;al<ax.length;al++){var av=ax[al].max_val;if(av>aq){aq=av}}for(var al=0;al<ax.length;al++){var au=ax[al];if(au.max_val!==aq){au.canvas.remove();ak.draw_helper(true,ah,au.index,au.resolution,au.canvas.parent(),ay,[],{max:aq})}}}if(ak.filters_manager){var ai=ak.filters_manager.filters;for(var ap=0;ap<ai.length;ap++){ai[ap].update_ui_elt()}var ao=false,at;for(var al=0;al<ax.length;al++){if(ax[al].data.length){at=ax[al].data[0];for(var ap=0;ap<ai.length;ap++){if(ai[ap].applies_to(at)){ao=true;break}}}}if(ak.filters_available!==ao){ak.filters_available=ao;if(!ak.filters_available){ak.filters_div.hide()}ak.make_name_popup_menu()}}},update_auto_mode:function(ah){if(this.mode=="Auto"){if(ah=="no_detail"){ah="feature spans"}else{if(ah=="summary_tree"){ah="coverage histogram"}}this.mode_div.text("Auto ("+ah+")")}},incremental_slots:function(al,ai,ak){var aj=this.view.canvas_manager.dummy_context,ah=this.inc_slots[al];if(!ah||(ah.mode!==ak)){ah=new (t.FeatureSlotter)(al,ak==="Pack",B,function(am){return aj.measureText(am)});ah.mode=ak;this.inc_slots[al]=ah}return ah.slot_features(ai)},get_summary_tree_data:function(al,ao,aj,ax){if(ax>aj-ao){ax=aj-ao}var at=Math.floor((aj-ao)/ax),aw=[],ak=0;var am=0,an=0,ar,av=0,ap=[],au,aq;var ai=function(aA,az,aB,ay){aA[0]=az+aB*ay;aA[1]=az+(aB+1)*ay};while(av<ax&&am!==al.length){var ah=false;for(;av<ax&&!ah;av++){ai(ap,ao,av,at);for(an=am;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){ah=true;break}}if(ah){break}}data_start_index=an;aw[aw.length]=au=[ap[0],0];for(;an<al.length;an++){ar=al[an].slice(1,3);if(is_overlap(ar,ap)){au[1]++}else{break}}if(au[1]>ak){ak=au[1]}av++}return{max:ak,delta:at,data:aw}},draw_tile:function(aw,az,aE,aI,ar,ak){var aB=this,am=aB._get_tile_bounds(aI,aE),aK=am[0],ai=am[1],ay=ai-aK,aC=Math.ceil(ay*ar),aO=25,al=this.left_offset,ax,an;if(az==="Auto"){if(aw.dataset_type==="summary_tree"){az=aw.dataset_type}else{if(aw.extra_info==="no_detail"){az="no_detail"}else{var aN=aw.data;if(this.view.high-this.view.low>K){az="Squish"}else{az="Pack"}}}this.update_auto_mode(az)}if(az==="summary_tree"||az==="Histogram"){an=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ah=$("<div />").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aF<aH;aF++){var ao=aw.data[aF];var aG=false;var av;for(var aJ=0,aM=au.length;aJ<aM;aJ++){av=au[aJ];av.update_attrs(ao);if(!av.keep(ao)){aG=true;break}}if(!aG){aq.push(ao)}}}var aA=(this.filters_manager.alpha_filter?new Q(this.filters_manager.alpha_filter):null);var aL=new (this.painter)(aq,aK,ai,this.prefs,az,aA,ak);var an=Math.max(af,aL.get_required_height(ap));var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an;var aD=aj.getContext("2d");aD.fillStyle=this.prefs.block_color;aD.font=aD.canvas.manager.default_font;aD.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aw.data){aD.translate(al,0);aL.draw(aD,aC,an,ax)}return new R(aI,aE,aj,aw.data,aw.message)}});var W=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.painter=N.VariantPainter};q(W.prototype,O.prototype,e.prototype);var Z=function(ak,ai,am,ah,aj,al){e.call(this,ak,ai,am,ah,aj,al);this.config=new H({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{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:aj,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=N.ReadPainter;this.make_name_popup_menu()};q(Z.prototype,O.prototype,e.prototype);var X=function(al,aj,an,ah,ak,am,ai){e.call(this,al,aj,an,ah,ak,am,{},ai);this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};q(X.prototype,O.prototype,e.prototype,{predraw_init:function(){var ai=this;var ah=function(){if(ai.data_manager.size()===0){setTimeout(ah,300)}else{ai.data_url=default_data_url;ai.data_query_wait=M;ai.dataset_state_url=converted_datasets_state_url;$.getJSON(ai.dataset_state_url,{dataset_id:ai.dataset_id,hda_ldda:ai.hda_ldda},function(aj){})}};ah()}});aa.View=ae;aa.DrawableGroup=S;aa.LineTrack=k;aa.FeatureTrack=e;aa.ReadTrack=Z};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;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(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}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(k,x){var u=k("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 g=function(y){this.default_alpha=(y?y:1)};g.prototype.gen_alpha=function(y){return this.default_alpha};var n=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};n.prototype.default_prefs={};var v=function(A,C,y,z,B){n.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 c=function(y,C,E,F,A){n.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}};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(N,M,K){var F=false,H=this.prefs.min_value,D=this.prefs.max_value,J=D-H,z=K,A=this.view_start,L=this.view_end-this.view_start,B=M/L,I=this.mode,T=this.data;N.save();var U=Math.round(K+H/J*K);if(I!=="Intensity"){N.fillStyle="#aaa";N.fillRect(0,U,M,1)}N.beginPath();var R,E,C;if(T.length>1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;O<P;O++){N.fillStyle=this.prefs.color;R=Math.round((T[O][0]-A)*B);E=T[O][1];var Q=false,G=false;if(E===null){if(F&&I==="Filled"){N.lineTo(R,z)}F=false;continue}if(E<H){G=true;E=H}else{if(E>D){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;D<F;D++){var M=E[D],C=M[0],y=M[1],z=M[2],I=(G&&G[C]!==undefined?G[C]:null);if((y<L&&z>H)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;ad<A;ad++){var E=C[ad],z=Math.floor(Math.max(0,(E[0]-M)*ag)),T=Math.ceil(Math.min(y,Math.max((E[1]-M)*ag)));if(z>T){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||T<O)){var ab=Math.max(z,O),G=Math.min(T,ai);K.fillRect(ab,V+1,G-ab,Q);if(C.length==1&&D=="Pack"){if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}if(ab+14<G){ab+=2;G-=2}K.fillRect(ab,V+1,G-ab,Q)}}}}if(D==="Pack"&&ae>M){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M<X;M++){var J=I[M],B="MIDNSHP=X"[J[0]],N=J[1];if(B==="H"||B==="S"){O-=N}var G=T+O,ad=Math.floor(Math.max(0,(G-Z)*L)),H=Math.floor(Math.max(0,(G+N-Z)*L));if(ad===H){H+=1}switch(B){case"H":break;case"S":case"M":case"=":if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(R>0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab<y;ab++){if(this.prefs.show_differences&&ref_seq){var K=ref_seq[G-Z+ab];if(!K||K.toLowerCase()===Q[ab].toLowerCase()){continue}}if(G+ab>=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:s))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){q(U,af[0],af[1],af[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,V=this.prefs.block_color,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)}R.fillStyle=V;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,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){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+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(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 --- a/static/scripts/packed/trackster_ui.js Tue Sep 27 09:55:52 2011 -0400 +++ b/static/scripts/packed/trackster_ui.js Tue Sep 27 13:06:34 2011 -0400 @@ -1,1 +1,1 @@ -var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_track_types={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack};var track_from_dict=function(a){return new addable_track_types[a.track_type](a.name,view,a.hda_ldda,a.dataset_id,a.prefs,a.filters,a.tool)};var create_visualization=function(d,j,a,g,l,k,n){view=new View(d,j,a,g,l);view.editor=true;if(k){var m,b,h,e;for(var c=0;c<k.length;c++){m=k[c];b=track_from_dict(m);e=view;if(m.is_child){e=h}else{h=b}e.add_track(b)}}if(n){var f;for(var c=0;c<n.length;c++){f=n[c];add_bookmark(f.position,f.annotation)}}view.has_changes=false;return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file +var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("<div/>").addClass("bookmark").appendTo(g),c=$("<div/>").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("<a href=''/>").addClass("icon-button delete").appendTo(c),f=$("<div/>").addClass("position").appendTo(d),h=$("<a href=''/>").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(a){return new addable_objects[a.track_type](a.name,view,a.hda_ldda,a.dataset_id,a.prefs,a.filters,a.tool)};var drawable_collection_from_dict=function(e){var d=new addable_objects[e.obj_type]("New Group",view,view.viewport_container,view);for(var c=0;c<e.drawables.length;c++){var a=e.drawables[c],b;if(a.track_type){b=track_from_dict(a)}else{b=drawable_collection_from_dict(a)}d.add_drawable(b);d.content_div.append(b.container_div)}return d};var drawable_from_dict=function(a){return(a.track_type?track_from_dict(a):drawable_collection_from_dict(a))};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){var k=a.chrom,p=a.start,h=a.end,m=a.overview;if(k&&p&&h){view.change_chrom(k,p,h)}if(d){var o;for(var j=0;j<d.length;j++){o=d[j];view.add_drawable(drawable_from_dict(o))}}var n;for(var j=0;j<view.tracks.length;j++){if(view.tracks[j].name==m){view.set_overview(view.tracks[j]);break}}if(f){var l;for(var j=0;j<f.length;j++){l=f[j];add_bookmark(l.position,l.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("-="+c+"px");break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTo("+="+c+"px");break}})}; \ No newline at end of file --- a/static/scripts/trackster.js Tue Sep 27 09:55:52 2011 -0400 +++ b/static/scripts/trackster.js Tue Sep 27 13:06:34 2011 -0400 @@ -704,7 +704,7 @@ /** * View object manages complete viz view, including tracks and user interactions. */ -var View = function(container, title, vis_id, dbkey, callback) { +var View = function(container, title, vis_id, dbkey) { DrawableCollection.call(this, "View"); this.container = container; this.chrom = null; @@ -720,12 +720,14 @@ this.zoom_factor = 3; this.min_separation = 30; this.has_changes = false; - this.init(callback); + // Deferred object that indicates when view's chrom data has been loaded. + this.load_chroms_deferred = null; + this.init(); this.canvas_manager = new CanvasManager( container.get(0).ownerDocument ); this.reset(); }; extend( View.prototype, DrawableCollection.prototype, { - init: function( callback ) { + init: function() { // Create DOM elements var parent_element = this.container, view = this; @@ -789,7 +791,7 @@ this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls); // Get initial set of chroms. - this.load_chroms({low: 0}, callback); + this.load_chroms_deferred = this.load_chroms({low: 0}); this.chrom_select.bind("change", function() { view.change_chrom(view.chrom_select.val()); }); @@ -916,10 +918,15 @@ this.location_span.text( commatize(low) + ' - ' + commatize(high) ); this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) ); }, - load_chroms: function(url_parms, callback) { + /** + * Load chrom data for the view. Returns a jQuery Deferred. + */ + load_chroms: function(url_parms) { url_parms['num'] = MAX_CHROMS_SELECTABLE; $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) ); - var view = this; + var + view = this, + chrom_data = $.Deferred(); $.ajax({ url: chrom_url, data: url_parms, @@ -948,16 +955,16 @@ chrom_options += '<option value="next">Next ' + MAX_CHROMS_SELECTABLE + '</option>'; } view.chrom_select.html(chrom_options); - if ( callback ) { - callback(); - } view.chrom_start_index = result.start_index; + + chrom_data.resolve(result); }, error: function() { alert("Could not load chroms for this dbkey:", view.dbkey); } }); + return chrom_data; }, change_chrom: function(chrom, low, high) { // Don't do anything if chrom is "None" (hackish but some browsers already have this set), or null/blank --- a/static/scripts/trackster_ui.js Tue Sep 27 09:55:52 2011 -0400 +++ b/static/scripts/trackster_ui.js Tue Sep 27 13:06:34 2011 -0400 @@ -79,32 +79,53 @@ /** * Create a complete Trackster visualization. Returns view. */ -var create_visualization = function(parent_elt, title, id, dbkey, callback, tracks_config, bookmarks_config) { +var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, tracks_config, bookmarks_config) { // Create view. - view = new View(parent_elt, title, id, dbkey, callback); + view = new View(parent_elt, title, id, dbkey); view.editor = true; - - // Add drawables to view. - if (tracks_config) { - var track_config; - for (var i = 0; i < tracks_config.length; i++) { - track_config = tracks_config[i]; - view.add_drawable( drawable_from_dict(track_config) ); + $.when( view.load_chroms_deferred ).then(function() { + // Viewport config. + var + chrom = viewport_config.chrom, + start = viewport_config.start, + end = viewport_config.end, + overview_track_name = viewport_config.overview; + + if (chrom && start && end) { + view.change_chrom(chrom, start, end); } - } - - // Load bookmarks. - if (bookmarks_config) { - var bookmark; - for (var i = 0; i < bookmarks_config.length; i++) { - bookmark = bookmarks_config[i]; - add_bookmark(bookmark['position'], bookmark['annotation']); + + // Add drawables to view. + if (tracks_config) { + var track_config; + for (var i = 0; i < tracks_config.length; i++) { + track_config = tracks_config[i]; + view.add_drawable( drawable_from_dict(track_config) ); + } } - } - - // View has no changes as of yet. - view.has_changes = false; + + // Set overview. + var overview_track; + for (var i = 0; i < view.tracks.length; i++) { + if (view.tracks[i].name == overview_track_name) { + view.set_overview(view.tracks[i]); + break; + } + } + + // Load bookmarks. + if (bookmarks_config) { + var bookmark; + for (var i = 0; i < bookmarks_config.length; i++) { + bookmark = bookmarks_config[i]; + add_bookmark(bookmark['position'], bookmark['annotation']); + } + } + + // View has no changes as of yet. + view.has_changes = false; + }); return view; }; --- a/templates/tracks/browser.mako Tue Sep 27 09:55:52 2011 -0400 +++ b/templates/tracks/browser.mako Tue Sep 27 13:06:34 2011 -0400 @@ -120,31 +120,11 @@ $("#right-border").click(function() { view.resize_window(); }); %if config: - var callback; - %if 'viewport' in config: - // TODO: find better way to handle this code. - var callback = function() { - view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); - // Set overview. - %if 'viewport' in config and 'overview' in config['viewport'] and config['viewport']['overview']: - - var - overview_track_name = "${config['viewport']['overview']}", - overview_track; - for (var i = 0; i < view.tracks.length; i++) { - if (view.tracks[i].name == overview_track_name) { - view.set_overview(view.tracks[i]); - break; - } - } - %endif - view.has_changes = false; - }; - %endif view = create_visualization( $("#browser-container"), "${config.get('title') | h}", - "${config.get('vis_id')}", "${config.get('dbkey')}", callback, - JSON.parse('${ h.to_json_string( config.get('tracks') ) }'), - JSON.parse('${ h.to_json_string( config.get('bookmarks') ) }') + "${config.get('vis_id')}", "${config.get('dbkey')}", + JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), + JSON.parse('${ h.to_json_string( config['tracks'] ) }'), + JSON.parse('${ h.to_json_string( config['bookmarks'] ) }') ); init_editor(); %else: 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: greg: Fix for finding versions of tools within repository changesets in the tool shed.
by Bitbucket 27 Sep '11

27 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/802ae59b9f7b/ changeset: 802ae59b9f7b user: greg date: 2011-09-27 15:55:52 summary: Fix for finding versions of tools within repository changesets in the tool shed. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 27 14:37:17 2011 +1000 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Sep 27 09:55:52 2011 -0400 @@ -1132,7 +1132,8 @@ ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) fctx = None for filename in ctx: - if filename == old_tool_config_file_name: + filename_head, filename_tail = os.path.split( filename ) + if filename_tail == old_tool_config_file_name: fctx = ctx[ filename ] break if fctx: 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: fubar: Fixes to picard HSmetrics and GCbias tools for warning message appearing in paster.log from a test parameter (maxmem) which
by Bitbucket 27 Sep '11

27 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8271faa173f6/ changeset: 8271faa173f6 user: fubar date: 2011-09-27 06:37:17 summary: Fixes to picard HSmetrics and GCbias tools for warning message appearing in paster.log from a test parameter (maxmem) which is available in the xml wrapper for sites wanting it but is commented out as distributed. Simple solution now requires the test params to be uncommented too where sites want to expose the option affected #: 2 files (-1 bytes) --- a/tools/picard/rgPicardGCBiasMetrics.xml Mon Sep 26 16:40:16 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue Sep 27 14:37:17 2011 +1000 @@ -1,4 +1,4 @@ -<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.01"> +<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" @@ -64,7 +64,9 @@ </outputs><tests><test> + <param name="out_prefix" value="CollectGCBias" /><param name="windowsize" value="100" /><param name="mingenomefrac" value="0.00001" /> --- a/tools/picard/rgPicardHsMetrics.xml Mon Sep 26 16:40:16 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue Sep 27 14:37:17 2011 +1000 @@ -1,4 +1,4 @@ -<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.01"> +<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02"><description>for targeted resequencing data</description><command interpreter="python"> @@ -33,11 +33,13 @@ </outputs><tests><test> + <param name="out_prefix" value="HSMetrics" /><param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" /><param name="bait_bed" value="picard_input_bait.bed" /><param name="target_bed" value="picard_input_bait.bed" /> - <param name="maxheap" value="8G" /><output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/></test></tests> 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 new method in the quota agent and refactored quota UI.
by Bitbucket 26 Sep '11

26 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b5742d5409b7/ changeset: b5742d5409b7 user: natefoo date: 2011-09-26 22:40:16 summary: Bugfix for new method in the quota agent and refactored quota UI. affected #: 2 files (-1 bytes) --- a/lib/galaxy/quota/__init__.py Mon Sep 26 15:59:52 2011 -0400 +++ b/lib/galaxy/quota/__init__.py Mon Sep 26 16:40:16 2011 -0400 @@ -166,6 +166,7 @@ rval.append( dqa.quota ) for uqa in user.quotas: rval.append( uqa.quota ) - for gqa in [ uga.group for uga in user.groups ]: - rval.append( gqa.quota ) + for group in [ uga.group for uga in user.groups ]: + for gqa in group.quotas: + rval.append( gqa.quota ) return rval --- a/lib/galaxy/web/controllers/admin.py Mon Sep 26 15:59:52 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Sep 26 16:40:16 2011 -0400 @@ -384,7 +384,7 @@ preserve_state = False use_paging = True -class AdminGalaxy( BaseUIController, Admin, AdminActions, QuotaParamParser ): +class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamParser ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() 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: richard_burhans: changed output type for aaChanges (from tabular to interval)
by Bitbucket 26 Sep '11

26 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5d561e2b9d8a/ changeset: 5d561e2b9d8a user: richard_burhans date: 2011-09-26 21:59:52 summary: changed output type for aaChanges (from tabular to interval) affected #: 1 file (-1 bytes) --- a/tools/evolution/codingSnps.xml Mon Sep 26 15:56:01 2011 -0400 +++ b/tools/evolution/codingSnps.xml Mon Sep 26 15:59:52 2011 -0400 @@ -20,7 +20,7 @@ </inputs><outputs> - <data format="tabular" name="out_file1" /> + <data format="interval" name="out_file1" /></outputs><code file="codingSnps_filter.py"></code> 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: richard_burhans: Fixed outstanding bugs in CTD tool (Human Genome Variation)
by Bitbucket 26 Sep '11

26 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2e6b536c797f/ changeset: 2e6b536c797f user: richard_burhans date: 2011-09-26 21:56:01 summary: Fixed outstanding bugs in CTD tool (Human Genome Variation) H: Enter commit message. Lines beginning with 'HG:' are removed. affected #: 2 files (-1 bytes) --- a/tools/human_genome_variation/ctd.pl Mon Sep 26 15:29:19 2011 -0400 +++ b/tools/human_genome_variation/ctd.pl Mon Sep 26 15:56:01 2011 -0400 @@ -1,8 +1,5 @@ -#!/usr/bin/env perl - +#!/usr/bin/perl -w use strict; -use warnings; - use LWP::UserAgent; require HTTP::Cookies; @@ -54,6 +51,9 @@ if ($resType eq 'cgixns') { #only add if this type push(@form, 'actionTypes', $actType); } +if ($resType eq 'go' or $resType eq 'go_enriched') { + push(@form, 'ontology', 'go_bp', 'ontology', 'go_mf', 'ontology', 'go_cc'); +} my $ua = LWP::UserAgent->new; $ua->cookie_jar(HTTP::Cookies->new( () )); $ua->agent('Mozilla/5.0'); --- a/tools/human_genome_variation/ctd.xml Mon Sep 26 15:29:19 2011 -0400 +++ b/tools/human_genome_variation/ctd.xml Mon Sep 26 15:56:01 2011 -0400 @@ -1,7 +1,7 @@ <tool id="ctdBatch_1" name="CTD" version="1.0.0"><description>analysis of chemicals, diseases, or genes</description><command interpreter="perl">#if $inType.inputType=="disease" #ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1 -#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report $inType.reportType.actType $out_file1 +#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report "$inType.reportType.actType" $out_file1 #else #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1 #end if</command><inputs> @@ -18,14 +18,13 @@ <param name="report" label="Data to extract" type="select"><option value="cgixns">Curated chemical-gene interactions</option><option value="genes">Curated gene associations</option> - <option value="pathways">Pathway associations</option> + <option value="pathways_inferred">Inferred pathway associations</option> + <option value="pathways_enriched">Enriched pathway associations</option><option value="diseases" selected="true">All disease relationships</option><option value="diseases_curated"> Curated disease relationships only</option><option value="diseases_inferred"> Inferred disease relationships only</option><option value="go">All GO associations</option> - <option value="go_p"> GO biological Processes only</option> - <option value="go_f"> GO molecular Functions only</option> - <option value="go_c"> GO cellular Components only</option> + <option value="go_enriched">Enriched GO associations only</option></param><when value="genes"> @@ -33,6 +32,12 @@ <when value="pathways"></when> + <when value="pathways_curated"> +  + </when> + <when value="pathways_inferred"> +  + </when><when value="diseases"></when> @@ -45,13 +50,7 @@ <when value="go"></when> - <when value="go_p"> -  - </when> - <when value="go_f"> -  - </when> - <when value="go_c"> + <when value="go_enriched"></when><when value="cgixns"> @@ -117,30 +116,29 @@ <when value="disease"><param name="report" label="Data to extract" type="select"><option value="chems">Chemical associations</option> - <option value="chems_direct">Chemical associations direct relationships only</option> - <option value="chems_inferred">Chemical associations inferred relationships only</option> - <option value="genes">Curated gene associations</option> - <option value="pathways">Pathway associations</option> + <option value="chems_curated">Curated chemical associations only</option> + <option value="chems_inferred">Inferred chemical associations only</option> + <option value="genes">Gene associations</option> + <option value="genes_curated">Curated gene associations</option> + <option value="genes_inferred">Inferred gene associations</option> + <option value="pathways_inferred">Inferred pathway associations</option></param></when><when value="gene"><conditional name='reportType'><param name="report" label="Data to extract" type="select"><option value="cgixns">Curated chemical-gene interactions</option> - <option value="chems">Curated chemical associations</option> - <option value="pathways">Pathway associations</option> + <option value="chems_curated">Curated chemical associations</option> + <option value="pathways_curated">Curated pathway associations</option><option value="diseases" selected="true">All disease relationships</option><option value="diseases_curated"> Curated disease relationships only</option><option value="diseases_inferred"> Inferred disease relationships only</option><option value="go">All GO associations</option> - <option value="go_p"> GO biological Processes only</option> - <option value="go_f"> GO molecular Functions only</option> - <option value="go_c"> GO cellular Components only</option></param> - <when value="chems"> + <when value="chems_curated"></when> - <when value="pathways"> + <when value="pathways_curated"></when><when value="diseases"> @@ -155,15 +153,6 @@ <when value="go"></when> - <when value="go_p"> -  - </when> - <when value="go_f"> -  - </when> - <when value="go_c"> -  - </when><when value="cgixns"><param name="actType" label="Interaction type" type="select"><option value="ANY">ANY</option> 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: greg: Fixes for installing tool shed repositories into a local Galaxy instance where the repository includes tools that have parameters that are dynamically generated select lists with various conbinations of tool_data_table entries and index files dependencies.
by Bitbucket 26 Sep '11

26 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6c488ed46f93/ changeset: 6c488ed46f93 user: greg date: 2011-09-26 21:29:19 summary: Fixes for installing tool shed repositories into a local Galaxy instance where the repository includes tools that have parameters that are dynamically generated select lists with various conbinations of tool_data_table entries and index files dependencies. affected #: 6 files (-1 bytes) --- a/lib/galaxy/tools/__init__.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Sep 26 15:29:19 2011 -0400 @@ -1320,7 +1320,32 @@ errors[ input.name ] = error state[ input.name ] = value return errors - + @property + def params_with_missing_data_table_entry( self ): + """ + Return all parameters that are dynamically generated select lists whose + options require an entry not currently in the tool_data_table_conf.xml file. + """ + params = [] + for input_param in self.input_params: + if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + options = input_param.options + if options and options.missing_tool_data_table_name and input_param not in params: + params.append( input_param ) + return params + @property + def params_with_missing_index_file( self ): + """ + Return all parameters that are dynamically generated + select lists whose options refer to a missing .loc file. + """ + params = [] + for input_param in self.input_params: + if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + options = input_param.options + if options and options.missing_index_file and input_param not in params: + params.append( input_param ) + return params def get_static_param_values( self, trans ): """ Returns a map of parameter names and values if the tool does not --- a/lib/galaxy/tools/data/__init__.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/data/__init__.py Mon Sep 26 15:29:19 2011 -0400 @@ -106,6 +106,9 @@ self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) self.data = all_rows + def handle_found_index_file( self, filename ): + self.missing_index_file = None + self.data.extend( self.parse_file_fields( open( filename ) ) ) def get_fields( self ): return self.data def parse_column_spec( self, config_element ): --- a/lib/galaxy/tools/parameters/dynamic_options.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Mon Sep 26 15:29:19 2011 -0400 @@ -399,6 +399,7 @@ self.separator = elem.get( 'separator', '\t' ) self.line_startswith = elem.get( 'startswith', None ) data_file = elem.get( 'from_file', None ) + self.index_file = None self.missing_index_file = None dataset_file = elem.get( 'from_dataset', None ) from_parameter = elem.get( 'from_parameter', None ) @@ -414,15 +415,16 @@ # which the tool_data_table refers does not exist. if self.tool_data_table.missing_index_file: self.missing_index_file = self.tool_data_table.missing_index_file - # Column definitions are optional, but if provided override those from the table - if elem.find( "column" ) is not None: - self.parse_column_definitions( elem ) else: - self.columns = self.tool_data_table.columns + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns else: self.missing_tool_data_table_name = tool_data_table_name log.warn( "Data table named '%s' is required by tool but not configured" % tool_data_table_name ) - # Options are defined by parsing tabular text data from an data file + # Options are defined by parsing tabular text data from a data file # on disk, a dataset, or the value of another parameter elif data_file is not None or dataset_file is not None or from_parameter is not None: self.parse_column_definitions( elem ) @@ -431,6 +433,7 @@ if not os.path.isabs( data_file ): full_path = os.path.join( self.tool_param.tool.app.config.tool_data_path, data_file ) if os.path.exists( full_path ): + self.index_file = data_file self.file_fields = self.parse_file_fields( open( full_path ) ) else: self.missing_index_file = data_file --- a/lib/galaxy/web/base/controller.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Mon Sep 26 15:29:19 2011 -0400 @@ -2437,96 +2437,14 @@ os.chdir( current_working_dir ) tmp_stderr.close() if returncode == 0: - # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs - repository_tools_tups = [] - # The sample_files list contains all files whose name ends in .sample - sample_files = [] - for root, dirs, files in os.walk( repo_files_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - # Find all special .sample files first. - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - relative_path = os.path.join( root, name ) - full_path = os.path.abspath( os.path.join( root, name ) ) - try: - repository_tool = trans.app.toolbox.load_tool( full_path ) - if repository_tool: - # Check all of the tool's input parameters, looking for any that are dynamically - # generated using external data files to make sure the files exist. - for input_param in repository_tool.input_params: - if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the - # tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.missing_tool_data_table_name: - # The repository must contain a tool_data_table_conf.xml.sample file. - for sample_file in sample_files: - head, tail = os.path.split( sample_file ) - if tail == 'tool_data_table_conf.xml.sample': - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) - if error: - log.debug( exception_msg ) - break - if options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # The repository must contain the required xxx.loc.sample file. - for sample_file in sample_files: - sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: - copy_sample_loc_file( trans, sample_file ) - break - # At this point, we need to lstrip tool_path from relative_path. - tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) - repository_tools_tups.append( ( tup_path, repository_tool ) ) - except Exception, e: - # We have an inavlid .xml file, so not a tool config. - log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) + sample_files, repository_tools_tups = self.__get_repository_tools_and_sample_files( trans, tool_path, repo_files_dir ) if repository_tools_tups: - # Look at each tool to see if it includes a "requirement" that refers to - # a fabric script. For those that do, execute the fabric script to install - # tool dependencies. - for repository_tools_tup in repository_tools_tups: - tup_path, repository_tool = repository_tools_tup - for requirement in repository_tool.requirements: - if requirement.type == 'fabfile': - log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) - fabfile = requirement.fabfile - method = requirement.method - # Find the relative path to the fabfile. - relative_fabfile_path = None - for root, dirs, files in os.walk( repo_files_dir ): - for name in files: - if name == fabfile: - relative_fabfile_path = os.path.join( root, name ) - break - if relative_fabfile_path: - # cmd will look something like: fab -f fabfile.py install_bowtie - cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) - tmp_name = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_name, 'wb' ) - os.chdir( repo_files_dir ) - proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) - returncode = proc.wait() - os.chdir( current_working_dir ) - tmp_stderr.close() - if returncode != 0: - # TODO: do something more here than logging the problem. - tmp_stderr = open( tmp_name, 'rb' ) - error = tmp_stderr.read() - tmp_stderr.close() - log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + # Handle missing data table entries for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_data_table_entry( trans, tool_path, sample_files, repository_tools_tups ) + # Handle missing index files for tool parameters that are dynamically generated select lists. + repository_tools_tups = self.__handle_missing_index_file( trans, tool_path, sample_files, repository_tools_tups ) + # Handle tools that use fabric scripts to install dependencies. + self.__handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ) # Generate an in-memory tool conf section that includes the new tools. new_tool_section = self.__generate_tool_panel_section( repository_name, repository_clone_url, @@ -2585,6 +2503,120 @@ tool_panel_section_select_field=tool_panel_section_select_field, message=message, status=status ) + def __handle_missing_data_table_entry( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if any have input parameters that are dynamically + # generated select lists that require entries in the tool_data_table_conf.xml file. + missing_data_table_entry = False + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + if repository_tool.params_with_missing_data_table_entry: + missing_data_table_entry = True + break + if missing_data_table_entry: + # The repository must contain a tool_data_table_conf.xml.sample file that includes + # all required entries for all tools in the repository. + for sample_file in sample_files: + head, tail = os.path.split( sample_file ) + if tail == 'tool_data_table_conf.xml.sample': + break + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + if error: + # TODO: Do more here than logging an exception. + log.debug( exception_msg ) + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_missing_index_file( self, trans, tool_path, sample_files, repository_tools_tups ): + # Inspect each tool to see if it has any input parameters that + # are dynamically generated select lists that depend on a .loc file. + missing_files_handled = [] + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + params_with_missing_index_file = repository_tool.params_with_missing_index_file + for param in params_with_missing_index_file: + options = param.options + missing_head, missing_tail = os.path.split( options.missing_index_file ) + if missing_tail not in missing_files_handled: + # The repository must contain the required xxx.loc.sample file. + for sample_file in sample_files: + sample_head, sample_tail = os.path.split( sample_file ) + if sample_tail == '%s.sample' % missing_tail: + copy_sample_loc_file( trans, sample_file ) + if options.tool_data_table and options.tool_data_table.missing_index_file: + options.tool_data_table.handle_found_index_file( options.missing_index_file ) + missing_files_handled.append( missing_tail ) + break + # Reload the tool into the local list of repository_tools_tups. + repository_tool = trans.app.toolbox.load_tool( os.path.join( tool_path, tup_path ) ) + repository_tools_tups[ index ] = ( tup_path, repository_tool ) + return repository_tools_tups + def __handle_tool_dependencies( self, current_working_dir, repo_files_dir, repository_tools_tups ): + # Inspect each tool to see if it includes a "requirement" that refers to a fabric + # script. For those that do, execute the fabric script to install tool dependencies. + for index, repository_tools_tup in enumerate( repository_tools_tups ): + tup_path, repository_tool = repository_tools_tup + for requirement in repository_tool.requirements: + if requirement.type == 'fabfile': + log.debug( 'Executing fabric script to install dependencies for tool "%s"...' % repository_tool.name ) + fabfile = requirement.fabfile + method = requirement.method + # Find the relative path to the fabfile. + relative_fabfile_path = None + for root, dirs, files in os.walk( repo_files_dir ): + for name in files: + if name == fabfile: + relative_fabfile_path = os.path.join( root, name ) + break + if relative_fabfile_path: + # cmd will look something like: fab -f fabfile.py install_bowtie + cmd = 'fab -f %s %s' % ( relative_fabfile_path, method ) + tmp_name = tempfile.NamedTemporaryFile().name + tmp_stderr = open( tmp_name, 'wb' ) + os.chdir( repo_files_dir ) + proc = subprocess.Popen( cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + os.chdir( current_working_dir ) + tmp_stderr.close() + if returncode != 0: + # TODO: do something more here than logging the problem. + tmp_stderr = open( tmp_name, 'rb' ) + error = tmp_stderr.read() + tmp_stderr.close() + log.debug( 'Problem installing dependencies for tool "%s"\n%s' % ( repository_tool.name, error ) ) + def __get_repository_tools_and_sample_files( self, trans, tool_path, repo_files_dir ): + # The sample_files list contains all files whose name ends in .sample + sample_files = [] + # The repository_tools_tups list contains tuples of ( relative_path_to_tool_config, tool ) pairs + repository_tools_tups = [] + for root, dirs, files in os.walk( repo_files_dir ): + if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: + if '.hg' in dirs: + # Don't visit .hg directories - should be impossible since we don't + # allow uploaded archives that contain .hg dirs, but just in case... + dirs.remove( '.hg' ) + if 'hgrc' in files: + # Don't include hgrc files in commit. + files.remove( 'hgrc' ) + # Find all special .sample files first. + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + for name in files: + # Find all tool configs. + if name.endswith( '.xml' ): + relative_path = os.path.join( root, name ) + full_path = os.path.abspath( os.path.join( root, name ) ) + try: + repository_tool = trans.app.toolbox.load_tool( full_path ) + if repository_tool: + # At this point, we need to lstrip tool_path from relative_path. + tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) + repository_tools_tups.append( ( tup_path, repository_tool ) ) + except Exception, e: + # We have an invalid .xml file, so not a tool config. + log.debug( "Ignoring invalid tool config (%s). Error: %s" % ( str( relative_path ), str( e ) ) ) + return sample_files, repository_tools_tups def __add_shed_tool_conf_entry( self, trans, shed_tool_conf, new_tool_section ): # Add an entry in the shed_tool_conf file. An entry looks something like: # <section name="Filter and Sort" id="filter"> @@ -2704,12 +2736,15 @@ select_field.add_option( option_tup[0], option_tup[1] ) return select_field def copy_sample_loc_file( trans, filename ): - """Copy xxx.loc.sample to ~/tool-data/xxx.loc""" + """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.rstrip( '.sample' ) + loc_file = sample_loc_file.replace( '.sample', '' ) tool_data_path = os.path.abspath( trans.app.config.tool_data_path ) - if not ( os.path.exists( os.path.join( tool_data_path, loc_file ) ) or os.path.exists( os.path.join( tool_data_path, sample_loc_file ) ) ): - shutil.copy( os.path.abspath( filename ), os.path.join( tool_data_path, sample_loc_file ) ) + # 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, id ): """Get a User from the database by id.""" @@ -2774,7 +2809,7 @@ if line.find( '</tables>' ) >= 0: for new_table_elem in new_table_elems: new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) - new_tdt_config.write( '</tables>' ) + new_tdt_config.write( '</tables>\n' ) else: new_tdt_config.write( line ) new_tdt_config.close() --- a/lib/galaxy/webapps/community/controllers/common.py Mon Sep 26 10:23:15 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Sep 26 15:29:19 2011 -0400 @@ -176,8 +176,8 @@ # tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options: - if options.missing_tool_data_table_name: - # See if the repository contains a tool_data_table_conf.xml.sample file. + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. sample_found = False for sample_file in sample_files: head, tail = os.path.split( sample_file ) @@ -187,6 +187,8 @@ if error: can_set_metadata = False invalid_files.append( ( tail, correction_msg ) ) + else: + options.missing_tool_data_table_name = None break if not sample_found: can_set_metadata = False @@ -194,20 +196,24 @@ correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " correction_msg += "that includes the required entry to resolve this issue.<br/>" invalid_files.append( ( name, correction_msg ) ) - elif options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # See if the repository contains the required xxx.loc.sample file. + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_head, index_tail = os.path.split( index_file ) sample_found = False for sample_file in sample_files: sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: + if sample_tail == '%s.sample' % index_tail: copy_sample_loc_file( trans, sample_file ) + options.index_file = index_tail + options.missing_index_file = None + options.tool_data_table.missing_index_file = None sample_found = True break if not sample_found: can_set_metadata = False - correction_msg = "This file refers to a missing file <b>%s</b>. " % str( options.missing_index_file ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( missing_tail ) + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_tail ) invalid_files.append( ( name, correction_msg ) ) return can_set_metadata, invalid_files def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): --- a/templates/tool_form.mako Mon Sep 26 10:23:15 2011 -0400 +++ b/templates/tool_form.mako Mon Sep 26 15:29:19 2011 -0400 @@ -250,20 +250,15 @@ <% # Render an error message if a dynamically generated select list is missing a required # index file or entry in the tool_data_table_conf.xml file. - from galaxy.tools.parameters.basic import SelectToolParameter message = "" - for input_param in tool.input_params: - if isinstance( input_param, SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the - # tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.missing_tool_data_table_name: - message = "Data table named '%s' is required by tool but not configured" % options.missing_tool_data_table_name - break - if options.missing_index_file: - message = "Index file named '%s' is required by tool but not availble" % options.missing_index_file - break + params_with_missing_data_table_entry = tool.params_with_missing_data_table_entry + params_with_missing_index_file = tool.params_with_missing_index_file + if params_with_missing_data_table_entry: + param = params_with_missing_data_table_entry[0] + message += "Data table named '%s' is required by tool but not configured. " % param.options.missing_tool_data_table_name + if tool.params_with_missing_index_file: + param = params_with_missing_index_file[0] + message += "Index file named '%s' is required by tool but not available. " % param.options.missing_index_file # Handle calculating the redirect url for the special case where we have nginx proxy # upload and need to do url_for on the redirect portion of the tool action. 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: rename TrackConfig to DrawableConfig and provide every Drawable object with a config.
by Bitbucket 26 Sep '11

26 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f4d8554b0715/ changeset: f4d8554b0715 user: jgoecks date: 2011-09-26 16:23:15 summary: Trackster: rename TrackConfig to DrawableConfig and provide every Drawable object with a config. affected #: 1 file (-1 bytes) --- a/static/scripts/trackster.js Sun Sep 25 13:27:14 2011 -0400 +++ b/static/scripts/trackster.js Mon Sep 26 10:23:15 2011 -0400 @@ -581,6 +581,9 @@ this.parent_element = parent_element; this.drag_handle_class = drag_handle_class; this.container = container; + this.config = new DrawableConfig({ + track: this + }); }; Drawable.prototype.init = function() {}; @@ -1882,9 +1885,9 @@ }; /** - * Container for track configuration data. + * Container for Drawable configuration data. */ -var TrackConfig = function( options ) { +var DrawableConfig = function( options ) { this.track = options.track; this.params = options.params; this.values = {} @@ -1894,7 +1897,7 @@ this.onchange = options.onchange }; -extend(TrackConfig.prototype, { +extend(DrawableConfig.prototype, { restore_values: function( values ) { var track_config = this; $.each( this.params, function( index, param ) { @@ -2199,8 +2202,8 @@ if (track.display_modes !== undefined) { if (track.mode_div === undefined) { track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div); - var init_mode = (track.track_config && track.track_config.values['mode'] ? - track.track_config.values['mode'] : track.display_modes[0]); + var init_mode = (track.config && track.config.values['mode'] ? + track.config.values['mode'] : track.display_modes[0]); track.mode = init_mode; track.mode_div.text(init_mode); @@ -2240,7 +2243,7 @@ track.mode_div.text(name); // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = name; - track.track_config.values['mode'] = name; + track.config.values['mode'] = name; track.tile_cache.clear(); track.request_draw(); }, @@ -2270,7 +2273,7 @@ track_dropdown["Edit configuration"] = function() { var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { - track.track_config.update_from_form( $(".dialog-box") ); + track.config.update_from_form( $(".dialog-box") ); hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, @@ -2283,7 +2286,7 @@ }; $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Track", track.track_config.build_form(), { + show_modal("Configure Track", track.config.build_form(), { "Cancel": cancel_fn, "OK": ok_fn }); @@ -2329,11 +2332,13 @@ // // List chrom/contigs with data option. // + /* if (track.valid_chroms) { track_dropdown["List chrom/contigs with data"] = function() { show_modal("Chrom/contigs with data", "<p>" + track.valid_chroms.join("<br/>") + "</p>", { "Close": function() { hide_modal(); } }); }; } + */ // // Remove option. @@ -2723,7 +2728,7 @@ this.left_offset = 0; // Define track configuration - this.track_config = new TrackConfig( { + this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, @@ -2745,9 +2750,9 @@ } }); - this.prefs = this.track_config.values; - this.height_px = this.track_config.values.height; - this.vertical_range = this.track_config.values.max_value - this.track_config.values.min_value; + 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(); }; @@ -2782,7 +2787,7 @@ track.tile_cache.clear(); in_drag = false; if (!in_handle) { drag_control.hide(); } - track.track_config.values.height = track.height_px; + track.config.values.height = track.height_px; }).appendTo(track.container_div); }, predraw_init: function() { @@ -2854,7 +2859,7 @@ var track = this; this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"]; // Define and restore track configuration. - this.track_config = new TrackConfig( { + this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, @@ -2870,7 +2875,7 @@ track.request_draw(); } }); - this.prefs = this.track_config.values; + this.prefs = this.config.values; // // Initialization. @@ -3244,7 +3249,7 @@ var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); - this.track_config = new TrackConfig( { + this.config = new DrawableConfig( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, @@ -3262,7 +3267,7 @@ this.track.request_draw(); } }); - this.prefs = this.track_config.values; + this.prefs = this.config.values; this.painter = painters.ReadPainter; this.make_name_popup_menu(); 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: dan: Some random lines tool tweaks.
by Bitbucket 25 Sep '11

25 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2469c53051ea/ changeset: 2469c53051ea user: dan date: 2011-09-25 19:27:14 summary: Some random lines tool tweaks. affected #: 3 files (-1 bytes) --- a/test-data/1_bed_random_lines_1_seed_asdf_out.bed Sat Sep 24 10:45:34 2011 -0400 +++ b/test-data/1_bed_random_lines_1_seed_asdf_out.bed Sun Sep 25 13:27:14 2011 -0400 @@ -1,1 +1,1 @@ -chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + --- a/tools/filters/random_lines_two_pass.py Sat Sep 24 10:45:34 2011 -0400 +++ b/tools/filters/random_lines_two_pass.py Sun Sep 25 13:27:14 2011 -0400 @@ -2,9 +2,25 @@ #Dan Blankenberg #Selects N random lines from a file and outputs to another file, maintaining original line order #allows specifying a seed -#does two passes to determine line counts and offsets, and then to output contents +#does two passes to determine line offsets/count, and then to output contents -import optparse, random +import optparse, random + +def get_random_by_subtraction( line_offsets, num_lines ): + while len( line_offsets ) > num_lines: + del line_offsets[ random.randint( 0, len( line_offsets ) - 1 ) ] + return line_offsets + +def get_random_by_sample( line_offsets, num_lines ): + line_offsets = random.sample( line_offsets, num_lines ) + line_offsets.sort() + return line_offsets + +def get_random( line_offsets, num_lines ): + if num_lines > ( len( line_offsets ) / 2 ): + return get_random_by_subtraction( line_offsets, num_lines ) + else: + return get_random_by_sample( line_offsets, num_lines ) def __main__(): #Parse Command Line @@ -14,7 +30,7 @@ assert len( args ) == 3, "Invalid command line specified." - input = open( args[0] ) + input = open( args[0], 'rb' ) output = open( args[1], 'wb' ) num_lines = int( args[2] ) assert num_lines > 0, "You must select at least one line." @@ -24,10 +40,13 @@ #get line offsets line_offsets = [] + teller = input.tell + readliner = input.readline + appender = line_offsets.append while True: - offset = input.tell() - if input.readline(): - line_offsets.append( offset ) + offset = teller() + if readliner(): + appender( offset ) else: break @@ -35,13 +54,14 @@ assert num_lines <= total_lines, "Error: asked to select more lines (%i) than there were in the file (%i)." % ( num_lines, total_lines ) #get random line offsets - while len( line_offsets ) > num_lines: - line_offsets.pop( random.randint( 0, len( line_offsets ) - 1 ) ) + line_offsets = get_random( line_offsets, num_lines ) #write out random lines + seeker = input.seek + writer = output.write for line_offset in line_offsets: - input.seek( line_offset ) - output.write( input.readline() ) + seeker( line_offset ) + writer( readliner() ) input.close() output.close() print "Kept %i of %i total lines." % ( num_lines, total_lines ) --- a/tools/filters/randomlines.xml Sat Sep 24 10:45:34 2011 -0400 +++ b/tools/filters/randomlines.xml Sun Sep 25 13:27:14 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="random_lines1" name="Select random lines" version="2.0.0"> +<tool id="random_lines1" name="Select random lines" version="2.0.1"><description>from a file</description><command interpreter="python">random_lines_two_pass.py "${input}" "${out_file1}" "${num_lines}" #if str( $seed_source.seed_source_selector ) == "set_seed": 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: (1) save and restore track groups; (2) support nested groups; (3) make View a DrawableCollection.
by Bitbucket 24 Sep '11

24 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/61b82db00101/ changeset: 61b82db00101 user: jgoecks date: 2011-09-24 16:45:34 summary: Trackster: (1) save and restore track groups; (2) support nested groups; (3) make View a DrawableCollection. affected #: 5 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Fri Sep 23 14:27:29 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Sat Sep 24 10:45:34 2011 -0400 @@ -310,40 +310,62 @@ config = None if visualization.type == 'trackster': - # Trackster config; taken from tracks/browser + # Unpack Trackster config. latest_revision = visualization.latest_revision bookmarks = latest_revision.config.get( 'bookmarks', [] ) - tracks = [] + + def pack_track( track_dict ): + dataset_id = track_dict['dataset_id'] + hda_ldda = track_dict.get('hda_ldda', 'hda') + if hda_ldda == "hda": + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + else: + dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) ) + + try: + prefs = track_dict['prefs'] + except KeyError: + prefs = {} + + track_type, _ = dataset.datatype.get_track_type() + track_data_provider_class = get_data_provider( original_dataset=dataset ) + track_data_provider = track_data_provider_class( original_dataset=dataset ) + + return { + "track_type": track_type, + "name": track_dict['name'], + "hda_ldda": track_dict.get("hda_ldda", "hda"), + "dataset_id": trans.security.encode_id( dataset.id ), + "prefs": prefs, + "filters": track_data_provider.get_filters(), + "tool": get_tool_def( trans, dataset ) + } + + def pack_collection( collection_dict ): + drawables = [] + for drawable_dict in collection_dict[ 'drawables' ]: + if 'track_type' in drawable_dict: + drawables.append( pack_track( drawable_dict ) ) + else: + drawables.append( pack_collection( drawable_dict ) ) + return { + 'obj_type': collection_dict[ 'obj_type' ], + 'drawables': drawables + } # Set tracks. + tracks = [] if 'tracks' in latest_revision.config: - for t in visualization.latest_revision.config['tracks']: - dataset_id = t['dataset_id'] - hda_ldda = t.get('hda_ldda', 'hda') - if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + # Legacy code. + for track_dict in visualization.latest_revision.config[ 'tracks' ]: + tracks.append( pack_track( track_dict ) ) + elif 'view' in latest_revision.config: + for drawable_dict in visualization.latest_revision.config[ 'view' ][ 'drawables' ]: + if 'track_type' in drawable_dict: + tracks.append( pack_track( drawable_dict ) ) else: - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) ) - - try: - prefs = t['prefs'] - except KeyError: - prefs = {} - - track_type, _ = dataset.datatype.get_track_type() - track_data_provider_class = get_data_provider( original_dataset=dataset ) - track_data_provider = track_data_provider_class( original_dataset=dataset ) - - tracks.append( { - "track_type": track_type, - "name": t['name'], - "hda_ldda": t.get("hda_ldda", "hda"), - "dataset_id": trans.security.encode_id( dataset.id ), - "prefs": prefs, - "filters": track_data_provider.get_filters(), - "tool": get_tool_def( trans, dataset ) - } ) - + tracks.append( pack_collection( drawable_dict ) ) + config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), "tracks": tracks, "bookmarks": bookmarks, "chrom": "", "dbkey": visualization.dbkey } --- a/lib/galaxy/web/controllers/tracks.py Fri Sep 23 14:27:29 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Sat Sep 24 10:45:34 2011 -0400 @@ -615,19 +615,40 @@ vis_rev.visualization = vis vis_rev.title = vis.title vis_rev.dbkey = dbkey - # Tracks from payload - tracks = [] - # TODO: why go through the trouble of unpacking config only to repack and - # put in database? How about sticking JSON directly into database? - for track in decoded_payload['tracks']: - tracks.append( { "dataset_id": track['dataset_id'], - "hda_ldda": track.get('hda_ldda', "hda"), - "name": track['name'], - "track_type": track['track_type'], - "prefs": track['prefs'] - } ) - bookmarks = decoded_payload[ 'bookmarks' ] - vis_rev.config = { "tracks": tracks, "bookmarks": bookmarks } + + def unpack_track( track_json ): + """ Unpack a track from its json. """ + return { + "dataset_id": track_json['dataset_id'], + "hda_ldda": track_json.get('hda_ldda', "hda"), + "name": track_json['name'], + "track_type": track_json['track_type'], + "prefs": track_json['prefs'] + } + + def unpack_collection( collection_json ): + """ Unpack a collection from its json. """ + unpacked_drawables = [] + drawables = collection_json[ 'drawables' ] + for drawable_json in drawables: + if 'track_type' in drawable_json: + drawable = unpack_track( drawable_json ) + else: + drawable = unpack_collection( drawable_json ) + unpacked_drawables.append( drawable ) + return { + "obj_type": collection_json[ 'obj_type' ], + "drawables": unpacked_drawables + } + + # TODO: unpack and validate bookmarks: + def unpack_bookmarks( bookmarks_json ): + return + + # Unpack and validate view content. + view_content = unpack_collection( decoded_payload[ 'view' ] ) + bookmarks = unpack_bookmarks( decoded_payload[ 'bookmarks' ] ) + vis_rev.config = { "view": view_content, "bookmarks": bookmarks } # Viewport from payload if 'viewport' in decoded_payload: chrom = decoded_payload['viewport']['chrom'] --- a/static/scripts/trackster.js Fri Sep 23 14:27:29 2011 -0400 +++ b/static/scripts/trackster.js Sat Sep 24 10:45:34 2011 -0400 @@ -213,7 +213,7 @@ } } - // Handle dragging into container. + // Handle dragging into container. Child is appended to container's content_div. container = null; for ( i = 0; i < children.length; i++ ) { child = $(children.get(i)); @@ -229,8 +229,10 @@ else { child.find(".content-div").append(this); } - // Update containers. - this_obj.container.remove_drawable(this_obj); + // Update containers. Object may not have container if it is being moved quickly. + if (this_obj.container) { + this_obj.container.remove_drawable(this_obj); + } html_elt_js_obj_dict[child.attr("id")].add_drawable(this_obj); return; } @@ -250,7 +252,6 @@ if ( i === children.length ) { if ( this !== children.get(i - 1) ) { parent.append(this); - // Update container. html_elt_js_obj_dict[parent.attr("id")].move_drawable(this_obj, i); } } @@ -574,32 +575,58 @@ /** * Base interface for all drawable objects. */ -var Drawable = function(name, view, parent_element, container) { +var Drawable = function(name, view, parent_element, drag_handle_class, container) { this.name = name; this.view = view; this.parent_element = parent_element; + this.drag_handle_class = drag_handle_class; this.container = container; }; +Drawable.prototype.init = function() {}; Drawable.prototype.request_draw = function() {}; -Drawable.prototype.draw = function() {}; +Drawable.prototype._draw = function() {}; +Drawable.prototype.to_json = function() {}; /** * A collection of drawable objects. */ -var DrawableCollection = function(name, view, parent_element, container) { +var DrawableCollection = function(obj_type, name, view, parent_element, container) { Drawable.call(this, name, view, parent_element, container); // Attribute init. + this.obj_type = obj_type; this.drawables = []; }; extend(DrawableCollection.prototype, Drawable.prototype, { + /** + * Init each drawable in the collection. + */ + init: function() { + for (var i = 0; i < this.drawables.length; i++) { + this.drawables[i].init(); + } + }, + /** + * Draw each drawable in the collection. + */ + _draw: function() { + for (var i = 0; i < this.drawables.length; i++) { + this.drawables[i]._draw(); + } + }, + /** + * Returns jsonified representation of collection. + */ to_json: function() { - // For now, just return list of drawables in collection. - var json_obj = []; + var jsonified_drawables = []; for (var i = 0; i < this.drawables.length; i++) { - + jsonified_drawables.push(this.drawables[i].to_json()); } + return { + obj_type: this.obj_type, + drawables: jsonified_drawables + }; }, /** * Add a drawable to the end of the collection. @@ -652,25 +679,30 @@ * A group of drawables that are moveable, visible. */ var DrawableGroup = function(name, view, parent_element, container) { - DrawableCollection.call(this, name, view, parent_element, container); - - this.drag_handle_class = "group-handle"; + DrawableCollection.call(this, "DrawableGroup", name, view, parent_element, "group-handle", container); // HTML elements. - this.container_div = $("<div/>").addClass("group").appendTo(this.parent_element); + if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; } + var group_id = DrawableGroup.id_counter++ + this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.parent_element); this.container_div.append($("<div/>").addClass(this.drag_handle_class)); this.name_div = $("<div/>").addClass("group-name").text(this.name).appendTo(this.container_div); - this.content_div = $("<div/>").addClass("content-div").appendTo(this.container_div); + this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div); + + // Set up containers/moving for group: register both container and content div as container + // because both are used as containers. Group can be moved. is_container(this.container_div, this); + is_container(this.content_div, this); + moveable(this.container_div, this.drag_handle_class, ".group", this); }; -extend(DrawableGroup.prototype, DrawableCollection.prototype, Drawable.prototype); +extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype); /** * View object manages complete viz view, including tracks and user interactions. */ var View = function(container, title, vis_id, dbkey, callback) { - DrawableCollection.call(this); + DrawableCollection.call(this, "View"); this.container = container; this.chrom = null; this.vis_id = vis_id; @@ -682,8 +714,6 @@ this.tracks_to_be_redrawn = []; this.max_low = 0; this.max_high = 0; - this.num_tracks = 0; - this.track_id_counter = 0; this.zoom_factor = 3; this.min_separation = 30; this.has_changes = false; @@ -870,22 +900,6 @@ $(window).trigger("resize"); this.update_intro_div(); }, - /** JSONify view. */ - to_json: function() { - var - view = this, - jsonified_drawables = []; - this.viewport_container.children(".track,.group").each(function() { - // Get object ID. - var id = $(this).attr("id"); - id = parseInt( id.slice(id.lastIndexOf("_") + 1) ); - - // JSONify drawable. - jsonified_drawables.push(view.tracks[id].to_json()); - }); - - return jsonified_drawables; - }, /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.num_tracks === 0) { @@ -1039,17 +1053,11 @@ view.request_redraw(); }, /** - * Add a track to the view. + * Add a drawable to the view. */ - add_track: function(track) { - track.view = this; - track.track_id = this.track_id_counter; - this.tracks.push(track); - if (track.init) { track.init(); } - track.container_div.attr('id', 'track_' + track.track_id); - moveable(track.container_div, track.drag_handle_class, ".group", track); - this.track_id_counter += 1; - this.num_tracks += 1; + add_drawable: function(drawable) { + DrawableCollection.prototype.add_drawable.call(this, drawable); + if (drawable.init) { drawable.init(); } this.has_changes = true; this.update_intro_div(); }, @@ -1058,17 +1066,18 @@ this.label_tracks.push(label_track); }, /** - * Remove a track from the view. + * Remove drawable from the view. */ - remove_track: function(track) { - this.has_changes = true; - this.tracks.splice(this.tracks.indexOf(track), 1); - this.num_tracks -= 1; - var view = this; - track.container_div.fadeOut('slow', function() { - $(this).remove(); - view.update_intro_div(); - }); + remove_drawable: function(drawable, hide) { + DrawableCollection.prototype.remove_drawable.call(this, drawable); + if (hide) { + var view = this; + drawable.container_div.fadeOut('slow', function() { + $(this).remove(); + view.update_intro_div(); + }); + this.has_changes = true; + } }, reset: function() { this.low = this.max_low; @@ -1161,7 +1170,7 @@ track = this.tracks_to_be_redrawn[i][0]; force = this.tracks_to_be_redrawn[i][1]; clear_after = this.tracks_to_be_redrawn[i][2]; - if (track && track.enabled) { + if (track) { track._draw(force, clear_after); } } @@ -1310,9 +1319,9 @@ run_on_region_button.click( function() { // Create group for track + new tracks and put track in group. var - parent_elt = this.track.parent_element, - new_group = new DrawableCollection("New Group", parent_elt); - //this.track.view.add_track(new_group); + parent_elt = this.track.parent_element; + //new_group = new DrawableCollection("New Group", parent_elt); + //this.track.view.add_drawable(new_group); // Run tool to create new track. @@ -1399,7 +1408,7 @@ new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); new_track.change_mode(current_track.mode); } - this.track.view.add_track(new_track); + this.track.view.add_drawable(new_track); new_track.content_div.text("Starting job."); // Run tool. @@ -2007,7 +2016,7 @@ */ var Track = function(name, view, parent_element, data_url, data_query_wait) { // For now, track's container is always view. - Drawable.call(this, name, view, parent_element, view); + Drawable.call(this, name, view, parent_element, "draghandle", view); // // Attribute init. @@ -2016,12 +2025,12 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - this.drag_handle_class = "draghandle"; // // Create HTML element structure for track. // - this.container_div = $("<div />").addClass('track').css("position", "relative"); + if (!Track.id_counter) { Track.id_counter = 0; } + this.container_div = $("<div />").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative"); if (!this.hidden) { this.header_div = $("<div class='track-header' />").appendTo(this.container_div); if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } @@ -2154,6 +2163,9 @@ var TiledTrack = function(filters_list, tool_dict, parent_track) { var track = this, view = track.view; + + // Make track moveable. + moveable(track.container_div, track.drag_handle_class, ".group", track); // Attribute init. this.filters_manager = (filters_list !== undefined ? new FiltersManager(this, filters_list) : undefined); @@ -2327,8 +2339,8 @@ // Remove option. // track_dropdown.Remove = function() { - view.remove_track(track); - if (parent_obj.num_tracks === 0) { + view.remove_drawable(track, true); + if (view.num_tracks === 0) { $("#no-tracks").show(); } }; @@ -2401,6 +2413,8 @@ * can manage drawing. */ _draw: function(force, clear_after) { + if (!this.enabled) { return; } + // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot. if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; } --- a/static/scripts/trackster_ui.js Fri Sep 23 14:27:29 2011 -0400 +++ b/static/scripts/trackster_ui.js Sat Sep 24 10:45:34 2011 -0400 @@ -29,20 +29,54 @@ }; /** - * Types of tracks that can be added to a view. + * Objects that can be added to a view. */ -var addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }; +var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup }; /** * Decode a track from a dictionary. */ var track_from_dict = function(track_dict) { - return new addable_track_types[track_dict.track_type]( + return new addable_objects[track_dict.track_type]( track_dict.name, view, track_dict.hda_ldda, track_dict.dataset_id, track_dict.prefs, track_dict.filters, track_dict.tool); }; /** + * Decode a drawable collection from a dictionary. + */ +var drawable_collection_from_dict = function(collection_dict) { + var collection = new addable_objects[collection_dict.obj_type]("New Group", view, view.viewport_container, view); + for (var i = 0; i < collection_dict.drawables.length; i++) { + var + drawable_dict = collection_dict.drawables[i], + drawable; + if (drawable_dict['track_type']) { + drawable = track_from_dict(drawable_dict); + } + else { + drawable = drawable_collection_from_dict(drawable_dict); + } + collection.add_drawable(drawable); + // HACK: move track from view to collection's content_div. + // FIX: Tracks should be able to be be added to arbitrary containers; + // every moveable should have a container_div, and every container should have + // a content_div (though perhaps name changes are needed). + collection.content_div.append(drawable.container_div); + } + return collection; +}; + +/** + * Decode a drawable from a dict. + */ +var drawable_from_dict = function(drawable_dict) { + return (drawable_dict['track_type'] ? + track_from_dict(drawable_dict) : + drawable_collection_from_dict(drawable_dict)); +}; + +/** * Create a complete Trackster visualization. Returns view. */ var create_visualization = function(parent_elt, title, id, dbkey, callback, tracks_config, bookmarks_config) { @@ -51,21 +85,12 @@ view = new View(parent_elt, title, id, dbkey, callback); view.editor = true; - // Add tracks to view. + // Add drawables to view. if (tracks_config) { - var track_config, track, parent_track, parent_obj; + var track_config; for (var i = 0; i < tracks_config.length; i++) { track_config = tracks_config[i]; - track = track_from_dict(track_config); - parent_obj = view; - if (track_config.is_child) { - parent_obj = parent_track; - } - else { - // New parent track is this track. - parent_track = track; - } - parent_obj.add_track(track); + view.add_drawable( drawable_from_dict(track_config) ); } } --- a/templates/tracks/browser.mako Fri Sep 23 14:27:29 2011 -0400 +++ b/templates/tracks/browser.mako Sat Sep 24 10:45:34 2011 -0400 @@ -101,7 +101,7 @@ [ arguments[0] ] ); for (var i= 0; i < track_defs.length; i++) { - view.add_track( track_from_dict(track_defs[i]) ); + view.add_drawable( track_from_dict(track_defs[i]) ); } }); hide_modal(); @@ -186,7 +186,7 @@ url: "${h.url_for( action='add_track_async' )}", data: { hda_id: "${add_dataset}" }, dataType: "json", - success: function(track_data) { view.add_track( track_from_dict(track_data) ) } + success: function(track_data) { view.add_drawable( track_from_dict(track_data) ) } }); %endif @@ -199,15 +199,12 @@ "Add Tracks": add_tracks, "Add Group": function() { var group = new DrawableGroup("New Group", view, view.viewport_container, view); - view.add_track(group); + view.add_drawable(group); }, "Save": function() { // Show saving dialog box show_modal("Saving...", "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>"); - - // Save tracks. - var saved_tracks = view.to_json(); - + // Save bookmarks. var bookmarks = []; $(".bookmark").each(function() { @@ -219,7 +216,7 @@ var overview_track_name = (view.overview_track ? view.overview_track.name : null); var payload = { - 'tracks': saved_tracks, + 'view': view.to_json(), 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, 'bookmarks': bookmarks }; 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: greg: Correct the message displayed when index files are missing under certain circumstances in the tool shed.
by Bitbucket 23 Sep '11

23 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a88d39b19b01/ changeset: a88d39b19b01 user: greg date: 2011-09-23 20:27:29 summary: Correct the message displayed when index files are missing under certain circumstances in the tool shed. affected #: 1 file (-1 bytes) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 23 13:51:55 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 23 14:27:29 2011 -0400 @@ -426,8 +426,12 @@ exception_items = exception_msg.split() missing_file_items = exception_items[7].split( '/' ) missing_file = missing_file_items[-1].rstrip( '\'' ) + if missing_file.endswith( '.loc' ): + sample_ext = '%s.sample' % missing_file + else: + sample_ext = missing_file correction_msg = "This file refers to a missing file <b>%s</b>. " % str( missing_file ) - correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % missing_file + correction_msg += "Upload a file named <b>%s</b> to the repository to correct this error." % sample_ext else: correction_msg = exception_msg message += "<b>%s</b> - %s<br/>" % ( tool_file, correction_msg ) 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: greg: Make sure dymanically generated select list options exist before checking for missing dependencies.
by Bitbucket 23 Sep '11

23 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc4a8297d0ab/ changeset: dc4a8297d0ab user: greg date: 2011-09-23 19:51:55 summary: Make sure dymanically generated select list options exist before checking for missing dependencies. affected #: 3 files (-1 bytes) --- a/lib/galaxy/web/base/controller.py Fri Sep 23 13:49:33 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Sep 23 13:51:55 2011 -0400 @@ -2447,23 +2447,24 @@ # If the tool refers to .loc files or requires an entry in the # tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options - if options.missing_tool_data_table_name: - # The repository must contain a tool_data_table_conf.xml.sample file. - for sample_file in sample_files: - head, tail = os.path.split( sample_file ) - if tail == 'tool_data_table_conf.xml.sample': - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) - if error: - log.debug( exception_msg ) - break - if options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # The repository must contain the required xxx.loc.sample file. - for sample_file in sample_files: - sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: - copy_sample_loc_file( trans, sample_file ) - break + if options: + if options.missing_tool_data_table_name: + # The repository must contain a tool_data_table_conf.xml.sample file. + for sample_file in sample_files: + head, tail = os.path.split( sample_file ) + if tail == 'tool_data_table_conf.xml.sample': + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + if error: + log.debug( exception_msg ) + break + if options.missing_index_file: + missing_head, missing_tail = os.path.split( options.missing_index_file ) + # The repository must contain the required xxx.loc.sample file. + for sample_file in sample_files: + sample_head, sample_tail = os.path.split( sample_file ) + if sample_tail == '%s.sample' % missing_tail: + copy_sample_loc_file( trans, sample_file ) + break # At this point, we need to lstrip tool_path from relative_path. tup_path = relative_path.replace( tool_path, '' ).lstrip( '/' ) repository_tools_tups.append( ( tup_path, repository_tool ) ) --- a/lib/galaxy/webapps/community/controllers/common.py Fri Sep 23 13:49:33 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Sep 23 13:51:55 2011 -0400 @@ -175,39 +175,40 @@ # If the tool refers to .loc files or requires an entry in the # tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options - if options.missing_tool_data_table_name: - # See if the repository contains a tool_data_table_conf.xml.sample file. - sample_found = False - for sample_file in sample_files: - head, tail = os.path.split( sample_file ) - if tail == 'tool_data_table_conf.xml.sample': - sample_found = True - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) - if error: - can_set_metadata = False - invalid_files.append( ( tail, correction_msg ) ) - break - if not sample_found: - can_set_metadata = False - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " - correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to resolve this issue.<br/>" - invalid_files.append( ( name, correction_msg ) ) - elif options.missing_index_file: - missing_head, missing_tail = os.path.split( options.missing_index_file ) - # See if the repository contains the required xxx.loc.sample file. - sample_found = False - for sample_file in sample_files: - sample_head, sample_tail = os.path.split( sample_file ) - if sample_tail == '%s.sample' % missing_tail: - copy_sample_loc_file( trans, sample_file ) - sample_found = True - break - if not sample_found: - can_set_metadata = False - correction_msg = "This file refers to a missing file <b>%s</b>. " % str( options.missing_index_file ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( missing_tail ) - invalid_files.append( ( name, correction_msg ) ) + if options: + if options.missing_tool_data_table_name: + # See if the repository contains a tool_data_table_conf.xml.sample file. + sample_found = False + for sample_file in sample_files: + head, tail = os.path.split( sample_file ) + if tail == 'tool_data_table_conf.xml.sample': + sample_found = True + error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + if error: + can_set_metadata = False + invalid_files.append( ( tail, correction_msg ) ) + break + if not sample_found: + can_set_metadata = False + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " + correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " + correction_msg += "that includes the required entry to resolve this issue.<br/>" + invalid_files.append( ( name, correction_msg ) ) + elif options.missing_index_file: + missing_head, missing_tail = os.path.split( options.missing_index_file ) + # See if the repository contains the required xxx.loc.sample file. + sample_found = False + for sample_file in sample_files: + sample_head, sample_tail = os.path.split( sample_file ) + if sample_tail == '%s.sample' % missing_tail: + copy_sample_loc_file( trans, sample_file ) + sample_found = True + break + if not sample_found: + can_set_metadata = False + correction_msg = "This file refers to a missing file <b>%s</b>. " % str( options.missing_index_file ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( missing_tail ) + invalid_files.append( ( name, correction_msg ) ) return can_set_metadata, invalid_files def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): """ --- a/templates/tool_form.mako Fri Sep 23 13:49:33 2011 -0400 +++ b/templates/tool_form.mako Fri Sep 23 13:51:55 2011 -0400 @@ -257,12 +257,13 @@ # If the tool refers to .loc files or requires an entry in the # tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options - if options.missing_tool_data_table_name: - message = "Data table named '%s' is required by tool but not configured" % options.missing_tool_data_table_name - break - if options.missing_index_file: - message = "Index file named '%s' is required by tool but not availble" % options.missing_index_file - break + if options: + if options.missing_tool_data_table_name: + message = "Data table named '%s' is required by tool but not configured" % options.missing_tool_data_table_name + break + if options.missing_index_file: + message = "Index file named '%s' is required by tool but not availble" % options.missing_index_file + break # Handle calculating the redirect url for the special case where we have nginx proxy # upload and need to do url_for on the redirect portion of the tool action. 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: dan: Rewrite random lines tool. Does two passes through input file: first pass determines line offsets/count, offsets are randomly removed, second pass writes out lines by seeking to remaining offsets. The random seed can now be optionally specified.
by Bitbucket 23 Sep '11

23 Sep '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/72ed536a988d/ changeset: 72ed536a988d user: dan date: 2011-09-23 19:49:33 summary: Rewrite random lines tool. Does two passes through input file: first pass determines line offsets/count, offsets are randomly removed, second pass writes out lines by seeking to remaining offsets. The random seed can now be optionally specified. affected #: 3 files (-1 bytes) --- a/tools/filters/randomlines.xml Fri Sep 23 13:26:34 2011 -0400 +++ b/tools/filters/randomlines.xml Fri Sep 23 13:49:33 2011 -0400 @@ -1,9 +1,25 @@ -<tool id="random_lines1" name="Select random lines"> +<tool id="random_lines1" name="Select random lines" version="2.0.0"><description>from a file</description> - <command interpreter="python">randomlines.py $input $num_lines $out_file1</command> + <command interpreter="python">random_lines_two_pass.py "${input}" "${out_file1}" "${num_lines}" + #if str( $seed_source.seed_source_selector ) == "set_seed": + --seed "${seed_source.seed}" + #end if + </command><inputs><param name="num_lines" size="5" type="integer" value="1" label="Randomly select" help="lines"/><param format="txt" name="input" type="data" label="from"/> + <conditional name="seed_source"> + <param name="seed_source_selector" type="select" label="Set a random seed"> + <option value="no_seed" selected="True">Don't set seed</option> + <option value="set_seed">Set seed</option> + </param> + <when value="no_seed"> +  + </when> + <when value="set_seed"> + <param name="seed" type="text" label="Random seed" /> + </when> + </conditional></inputs><outputs><data format="input" name="out_file1" metadata_source="input"/> @@ -12,8 +28,16 @@ <test><param name="num_lines" value="65"/><param name="input" value="1.bed"/> + <param name="seed_source_selector" value="no_seed"/><output name="out_file1" file="1.bed"/></test> + <test> + <param name="num_lines" value="1"/> + <param name="input" value="1.bed"/> + <param name="seed_source_selector" value="set_seed"/> + <param name="seed" value="asdf"/> + <output name="out_file1" file="1_bed_random_lines_1_seed_asdf_out.bed"/> + </test></tests><help> 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