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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/837eb8d9098e/ changeset: 837eb8d9098e user: dan date: 2012-10-11 19:47:10 summary: Fix for viewing errors by bug link on a copied dataset. affected #: 1 file diff -r 046634d0500730333eb181399eaa097b1d9f4343 -r 837eb8d9098ed1e9faa3e651dc7552ef014238fe lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -221,7 +221,7 @@ return trans.show_error_message( "Error reporting has been disabled for this galaxy instance" ) # Get the dataset and associated job hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) - job = hda.creating_job_associations[0].job + job = hda.creating_job # Get the name of the server hosting the Galaxy instance from which this report originated host = trans.request.host history_view_link = "%s/history/view?id=%s" % ( str( host ), trans.security.encode_id( hda.history_id ) ) https://bitbucket.org/galaxy/galaxy-central/changeset/b27aa5db944d/ changeset: b27aa5db944d user: dan date: 2012-10-11 19:47:11 summary: When sending bug report email on a copied dataset, fill in Job info. affected #: 1 file diff -r 837eb8d9098ed1e9faa3e651dc7552ef014238fe -r b27aa5db944d3c3a79c9bedf9d91fe2a2e89e01d templates/dataset/errors.mako --- a/templates/dataset/errors.mako +++ b/templates/dataset/errors.mako @@ -19,9 +19,9 @@ <body><h2>Dataset generation errors</h2><p><b>Dataset ${hda.hid}: ${hda.display_name()}</b></p> - - %if hda.creating_job_associations: - <% job = hda.creating_job_associations[0].job %> + <% job = hda.creating_job %> + %if job: + %if job.traceback: The Galaxy framework encountered the following error while attempting to run the tool: <pre>${ util.unicodify( job.traceback ) | h}</pre> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32ea61c97ac8/ changeset: 32ea61c97ac8 user: dan date: 2012-10-11 18:28:21 summary: Add creating_job as a property to DatasetInstance. affected #: 1 file diff -r 05dfdda805908059de813a303e6ed02ea5e97117 -r 32ea61c97ac8472a781c9f4056c2044da0d06356 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1261,6 +1261,18 @@ log.warning( e ) return lst return _source_dataset_chain( self, [] ) + @property + def creating_job( self ): + creating_job_associations = None + if self.creating_job_associations: + creating_job_associations = self.creating_job_associations + else: + inherit_chain = self.source_dataset_chain + if inherit_chain: + creating_job_associations = inherit_chain[-1][0].creating_job_associations + if creating_job_associations: + return creating_job_associations[0].job + return None def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) https://bitbucket.org/galaxy/galaxy-central/changeset/046634d05007/ changeset: 046634d05007 user: dan date: 2012-10-11 18:28:21 summary: Have DatasetInstance controller use .creating_job property for call to _get_job_for_dataset(). affected #: 1 file diff -r 32ea61c97ac8472a781c9f4056c2044da0d06356 -r 046634d0500730333eb181399eaa097b1d9f4343 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -157,14 +157,11 @@ def _get_job_for_dataset( self, trans, dataset_id ): ''' Return the job for the given dataset. This will throw an error if the - dataset is either nonexistent or inaccessible to the user. This looks - up the job by mapping the dataset to an HDA and then mapping the HDA - to its job. This will throw exceptions so that the caller can determine - the appropriate response. + dataset is either nonexistent or inaccessible to the user. ''' hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) assert hda and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) - return hda.creating_job_associations[0].job + return hda.creating_job @web.expose def errors( self, trans, 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.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a21e7bd8a41d/ changeset: a21e7bd8a41d user: dan date: 2012-10-11 18:09:06 summary: Add source_dataset_chain as a property to DatasetInstance. affected #: 1 file diff -r 62b89df24ab159aa12b6a15d63001c4cd01cab2e -r a21e7bd8a41d6d84b9acd63095ea18de80eba76f lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1242,7 +1242,25 @@ return source return ( None, None ) return get_source( self ) - + @property + def source_dataset_chain( self ): + def _source_dataset_chain( dataset, lst ): + try: + cp_from_ldda = dataset.copied_from_library_dataset_dataset_association + if cp_from_ldda: + lst.append( (cp_from_ldda, "(Data Library)") ) + return _source_dataset_chain( cp_from_ldda, lst ) + except Exception, e: + log.warning( e ) + try: + cp_from_hda = dataset.copied_from_history_dataset_association + if cp_from_hda: + lst.append( (cp_from_hda, cp_from_hda.history.name) ) + return _source_dataset_chain( cp_from_hda, lst ) + except Exception, e: + log.warning( e ) + return lst + return _source_dataset_chain( self, [] ) def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) https://bitbucket.org/galaxy/galaxy-central/changeset/05dfdda80590/ changeset: 05dfdda80590 user: dan date: 2012-10-11 18:09:06 summary: Refactor show_params for hda controller. affected #: 1 file diff -r a21e7bd8a41d6d84b9acd63095ea18de80eba76f -r 05dfdda805908059de813a303e6ed02ea5e97117 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -977,21 +977,6 @@ """ Show the parameters used for an HDA """ - - def source_dataset_chain( dataset, lst ): - try: - cp_from_ldda = dataset.copied_from_library_dataset_dataset_association - cp_from_hda = dataset.copied_from_history_dataset_association - if cp_from_ldda: - lst.append( (cp_from_ldda, "(Data Library)") ) - return source_dataset_chain( cp_from_ldda, lst ) - elif cp_from_hda: - lst.append( (cp_from_hda, cp_from_hda.history.name) ) - return source_dataset_chain( cp_from_hda, lst ) - except: - pass - return lst - hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) if not hda: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) @@ -999,15 +984,17 @@ return trans.show_error_message( "You are not allowed to access this dataset" ) # Get the associated job, if any. If this hda was copied from another, - # we need to find the job that created the origial hda + # we need to find the job that created the origial dataset association. params_objects = None + job = None tool = None - job_hda = hda - while job_hda.copied_from_history_dataset_association: - job_hda = job_hda.copied_from_history_dataset_association - if job_hda.creating_job_associations: - job = None - for assoc in job_hda.creating_job_associations: + inherit_chain = hda.source_dataset_chain + if inherit_chain: + job_dataset_association, dataset_association_container_name = inherit_chain[-1] + else: + job_dataset_association = hda + if job_dataset_association.creating_job_associations: + for assoc in job_dataset_association.creating_job_associations: job = assoc.job break if job: @@ -1020,8 +1007,8 @@ params_objects = job.get_param_values( trans.app ) except: pass - - inherit_chain = source_dataset_chain(hda, []) + if job is None: + return trans.show_error_message( "Job information is not available for this dataset." ) return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects ) @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not use backrefs for copied_from_library_dataset/history_dataset_association as it confuses sqlalchemy ('is not available, due to conflicting property').
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/62b89df24ab1/ changeset: 62b89df24ab1 user: dan date: 2012-10-11 17:49:47 summary: Do not use backrefs for copied_from_library_dataset/history_dataset_association as it confuses sqlalchemy ('is not available, due to conflicting property'). affected #: 1 file diff -r 1b031693bd3470172c90533726e4ad6dd7d54e5f -r 62b89df24ab159aa12b6a15d63001c4cd01cab2e lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1222,14 +1222,21 @@ Dataset, primaryjoin=( Dataset.table.c.id == HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), # .history defined in History mapper + copied_from_history_dataset_association=relation( + HistoryDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + remote_side=[HistoryDatasetAssociation.table.c.id], + uselist=False ), copied_to_history_dataset_associations=relation( HistoryDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), - backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), remote_side=[HistoryDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ) ), + copied_from_library_dataset_dataset_association=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + uselist=False ), copied_to_library_dataset_dataset_associations=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_history_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == HistoryDatasetAssociation.table.c.id ) ), @@ -1484,14 +1491,21 @@ library_dataset = relation( LibraryDataset, primaryjoin=( LibraryDatasetDatasetAssociation.table.c.library_dataset_id == LibraryDataset.table.c.id ) ), user=relation( User.mapper ), + copied_from_library_dataset_dataset_association=relation( + LibraryDatasetDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), + remote_side=[LibraryDatasetDatasetAssociation.table.c.id], + uselist=False ), copied_to_library_dataset_dataset_associations=relation( LibraryDatasetDatasetAssociation, - primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id] ) ), + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), + copied_from_history_dataset_association=relation( + HistoryDatasetAssociation, + primaryjoin=( LibraryDatasetDatasetAssociation.table.c.copied_from_history_dataset_association_id == HistoryDatasetAssociation.table.c.id ), + uselist=False ), copied_to_history_dataset_associations=relation( HistoryDatasetAssociation, - primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), - backref=backref( "copied_from_library_dataset_dataset_association", primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ), remote_side=[LibraryDatasetDatasetAssociation.table.c.id], uselist=False ) ), + primaryjoin=( HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == LibraryDatasetDatasetAssociation.table.c.id ) ), implicitly_converted_datasets=relation( ImplicitlyConvertedDatasetAssociation, primaryjoin=( ImplicitlyConvertedDatasetAssociation.table.c.ldda_parent_id == LibraryDatasetDatasetAssociation.table.c.id ) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster: support data indexing and loading for datasets not previously indexed. Also add visual indicator when drawing/loading tracks.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1b031693bd34/ changeset: 1b031693bd34 user: jgoecks date: 2012-10-11 16:31:13 summary: Circster: support data indexing and loading for datasets not previously indexed. Also add visual indicator when drawing/loading tracks. affected #: 5 files diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -184,9 +184,15 @@ chrom = chrom_info[ 'chrom' ] chrom_len = chrom_info[ 'len' ] chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs ) - if chrom_data: - chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) - genome_data.append( chrom_data ) + # FIXME: data providers probably should never return None. + # Some data providers return None when there's no data, so + # create a dummy dict if necessary. + if not chrom_data: + chrom_data = { + 'data': None + } + chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) + genome_data.append( chrom_data ) return { 'data': genome_data, diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -52,7 +52,7 @@ elif data_type == 'track_config': rval = self.get_new_track_config( trans, dataset ) elif data_type == 'genome_data': - rval = self._get_genome_data( self, trans, dataset, kwd.get('dbkey', None) ) + rval = self._get_genome_data( trans, dataset, kwd.get('dbkey', None) ) else: # Default: return dataset as API value. rval = dataset.get_api_value() @@ -89,12 +89,13 @@ if msg: return msg - # Check for data in the genome window. - data_provider_registry = trans.app.data_provider_registry - data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset= dataset, source='index' ) - if not data_provider.has_data( chrom ): - return messages.NO_DATA - + # If there is a chrom, check for data on the chrom. + if chrom: + data_provider_registry = trans.app.data_provider_registry + data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset= dataset, source='index' ) + if not data_provider.has_data( chrom ): + return messages.NO_DATA + # Have data if we get here return { "status": messages.DATA, "valid_chroms": None } diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -143,9 +143,12 @@ initialize: function(options) { this.options = options; this.options.bg_stroke = 'ccc'; + // Fill color when loading data. + this.options.loading_bg_fill = '000'; + // Fill color when data has been loaded. this.options.bg_fill = 'ccc'; this.options.chroms_layout = this._chroms_layout(); - this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + this.options.data_bounds = []; this.options.scale = 1; this.options.parent_elt = null; }, @@ -154,34 +157,49 @@ * Render track's data by adding SVG elements to parent. */ render: function(parent) { - // Create track group element. + // -- Create track group element. -- this.options.parent_elt = parent.append("g").attr("id", "parent-" + this.options.track_index); var track_parent_elt = this.options.parent_elt; - // Render background arcs. + // -- Render background arcs. -- var genome_arcs = this.options.chroms_layout, arc_gen = d3.svg.arc() .innerRadius(this.options.radius_bounds[0]) .outerRadius(this.options.radius_bounds[1]), + // Attach data to group element. chroms_elts = track_parent_elt.selectAll('g') - .data(genome_arcs).enter().append('svg:g'); + .data(genome_arcs).enter().append('svg:g'), - // Draw arcs. - chroms_elts.append("path") - .attr("d", arc_gen) - .style("stroke", this.options.bg_stroke) - .style("fill", this.options.bg_fill) - .append("title").text(function(d) { return d.data.chrom; }); + // Draw chrom arcs/paths. + chroms_paths = chroms_elts.append("path") + .attr("d", arc_gen) + .style("stroke", this.options.bg_stroke) + .style("fill", this.options.loading_bg_fill); + + // Append titles to paths. + chroms_paths.append("title").text(function(d) { return d.data.chrom; }); - // Render track data. - this._render_data(track_parent_elt); + // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. -- - // Apply prefs. - var prefs = this.options.track.get('prefs'), - block_color = prefs.block_color; - if (!block_color) { block_color = prefs.color; } - track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + var self = this, + data_manager = self.options.track.get('data_manager'), + // If track has a data manager, get deferred that resolves when data is ready. + data_ready_deferred = (data_manager ? data_manager.data_is_ready() : true ); + + // When data is ready, render track. + $.when(data_ready_deferred).then(function() { + $.when(self._render_data(track_parent_elt)).then(function() { + // Apply prefs to all track data. + // TODO: move to _render_data? + var prefs = self.options.track.get('prefs'), + block_color = prefs.block_color; + if (!block_color) { block_color = prefs.color; } + track_parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + + chroms_paths.style("fill", self.options.bg_fill); + }); + }); }, /** @@ -243,7 +261,7 @@ * Update data bounds. */ _update_data_bounds: function() { - this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); + //this.options.data_bounds = this.get_data_bounds(this.options.track.get_genome_wide_data(this.options.genome)); // TODO: transition all paths to use the new data bounds. }, @@ -255,8 +273,13 @@ var self = this, chrom_arcs = this.options.chroms_layout, track = this.options.track, - genome_wide_data = track.get_genome_wide_data(this.options.genome), - + rendered_deferred = $.Deferred(); + + // When genome-wide data is available, render data. + $.when(track.get('data_manager').get_genome_wide_data(this.options.genome)).then(function(genome_wide_data) { + // Set bounds. + self.options.data_bounds = self.get_data_bounds(genome_wide_data); + // Merge chroms layout with data. layout_and_data = _.zip(chrom_arcs, genome_wide_data), @@ -267,7 +290,10 @@ return self._render_chrom_data(svg, chrom_arc, data); }); - return svg; + rendered_deferred.resolve(svg); + }); + + return rendered_deferred; }, /** @@ -348,7 +374,7 @@ */ _render_chrom_data: function(svg, chrom_arc, chrom_data) { // If no chrom data, return null. - if (!chrom_data || typeof chrom_data === "string" || chrom_data.data.length === 0) { + if (typeof chrom_data === "string" || !chrom_data.data || chrom_data.data.length === 0) { return null; } @@ -407,7 +433,7 @@ get_data_bounds: function(data) { // Get max across data. var max_data = _.map(data, function(d) { - if (!d || typeof d === 'string') { return 0; } + if (typeof d === 'string' || !d.max) { return 0; } return d.max; }); return [ 0, (max_data && typeof max_data !== 'string' ? _.max(max_data) : 0) ]; diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -928,7 +928,7 @@ }, output.first().get('track_config')), track_obj = tracks.object_from_template(track_config, self, null); - // Track uses only raw data. + // Track uses raw data. track_obj.data_manager.set('data_type', 'raw_data'); // Set track block colors. diff -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 -r 1b031693bd3470172c90533726e4ad6dd7d54e5f static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -136,6 +136,7 @@ var GenomeDataManager = Cache.extend({ defaults: _.extend({}, Cache.prototype.defaults, { dataset: null, + init_data: null, filters_manager: null, data_type: "data", data_mode_compatible: function(entry, mode) { return true; }, @@ -143,18 +144,52 @@ }), /** + * Initialization. + */ + initialize: function(options) { + Cache.prototype.initialize.call(this); + + // Set initial entries in data manager. + var initial_entries = this.get('init_data'); + if (initial_entries) { + this.add_data(initial_entries); + } + }, + + /** + * Add data entries to manager; each entry should be a dict with attributes region (key), data, and data_type. + * If necessary, manager size is increased to hold all data. + */ + add_data: function(entries) { + // Increase size to accomodate all entries. + if (this.get('num_elements') < entries.length) { + this.set('num_elements', entries.length); + } + + // Put data into manager. + var self = this; + _.each(entries, function(entry) { + self.set_data(entry.region, entry); + }); + }, + + /** * Returns deferred that resolves to true when dataset is ready (or false if dataset * cannot be used). */ data_is_ready: function() { var dataset = this.get('dataset'), ready_deferred = $.Deferred(), + // If requesting raw data, query dataset state; if requesting (converted) data, + // need to query converted datasets state. + query_type = (this.get('data_type') == 'raw_data' ? 'state' : + this.get('data_type') == 'data' ? 'converted_datasets_state' : "error" ), ss_deferred = new util_mod.ServerStateDeferred({ ajax_settings: { url: this.get('dataset').url(), data: { hda_ldda: dataset.get('hda_ldda'), - data_type: 'state' + data_type: query_type }, dataType: "json" }, @@ -312,8 +347,7 @@ // Get additional data, append to current data, and set new data. Use a custom deferred object // to signal when new data is available. // - var - data_manager = this, + var data_manager = this, new_data_request = this.load_data(query_region, mode, resolution, extra_params), new_data_available = $.Deferred(); // load_data sets cache to new_data_request, but use custom deferred object so that signal and data @@ -372,6 +406,49 @@ entry.stale = true; return entry; }, + + /** + * Returns an array of data with each entry representing one chromosome/contig + * of data or, if data is not available, returns a Deferred that resolves to the + * data when it becomes available. + */ + get_genome_wide_data: function(genome) { + // -- Get all data. -- + + var self = this, + all_data_available = true, + + // Map chromosome info into genome data. + gw_data = _.map(genome.get('chroms_info').chrom_info, function(chrom_info) { + var chrom_data = self.get_elt( + new GenomeRegion({ + chrom: chrom_info.chrom, + start: 0, + end: chrom_info.len + }) + ); + + // Set flag if data is not available. + if (!chrom_data) { all_data_available = false; } + + return chrom_data; + }); + + // -- If all data is available, return it. -- + if (all_data_available) { + return gw_data; + } + + // -- All data is not available, so load from server. -- + + var deferred = $.Deferred(); + $.getJSON(this.get('dataset').url(), { data_type: 'genome_data' }, function(genome_wide_data) { + self.add_data(genome_wide_data.data); + deferred.resolve(genome_wide_data.data); + }); + + return deferred; + }, /** * Get data from the cache. @@ -397,7 +474,6 @@ }, load_data: function(region, mode, resolution, extra_params) { - console.log(region, mode, resolution); if (resolution > 1) { // Now that data is pre-fetched before draw, we don't load reference tracks // unless it's at the bottom level. @@ -598,41 +674,17 @@ this.set('id', options.dataset_id); // Set up data manager. - var data_manager = new GenomeDataManager({ - dataset: this - }); - this.set('data_manager', data_manager); - - // If there's preloaded data, add it to data manager. var preloaded_data = this.get('preloaded_data'); if (preloaded_data) { - // Increase size to accomodate all preloaded data. - data_manager.set('num_elements', preloaded_data.data.length); - - // Put data into manager. - _.each(preloaded_data.data, function(entry) { - data_manager.set_data(entry.region, entry); - }); + preloaded_data = preloaded_data.data } - }, - - /** - * Returns an array of data with each entry representing one chromosome/contig - * of data. - */ - get_genome_wide_data: function(genome) { - var data_manager = this.get('data_manager'); - - // Map chromosome data into track data. - return _.map(genome.get('chroms_info').chrom_info, function(chrom_info) { - return data_manager.get_elt( - new GenomeRegion({ - chrom: chrom_info.chrom, - start: 0, - end: chrom_info.len - }) - ); - }); + else { + preloaded_data = []; + } + this.set('data_manager', new GenomeDataManager({ + dataset: this, + init_data: preloaded_data + })); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: scatterplot.js: minor changes; data_providers/basic.py: ensure numeric stats only on numeric columns;
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/60757a1ab164/ changeset: 60757a1ab164 user: carlfeberhard date: 2012-10-11 16:24:43 summary: scatterplot.js: minor changes; data_providers/basic.py: ensure numeric stats only on numeric columns; affected #: 5 files diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -163,16 +163,19 @@ f.close() for index, meta in enumerate( response[ 'meta' ] ): - count = meta[ 'count' ] - meta[ 'mean' ] = float( meta[ 'sum' ] ) / count + column_type = column_types[ index ] - sorted_data = sorted( response[ 'data' ][ index ] ) - # even data count - - middle_index = count / 2 - 1 - if count % 2 == 0: - meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + if( column_type == 'float' or column_type == 'int' ): + count = meta[ 'count' ] + meta[ 'mean' ] = float( meta[ 'sum' ] ) / count - else: - meta[ 'median' ] = sorted_data[ middle_index ] + sorted_data = sorted( response[ 'data' ][ index ] ) + # even data count - + middle_index = count / 2 - 1 + if count % 2 == 0: + meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + + else: + meta[ 'median' ] = sorted_data[ middle_index ] return response diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/templates/compiled/template-visualization-chartSettings.js --- a/static/scripts/templates/compiled/template-visualization-chartSettings.js +++ b/static/scripts/templates/compiled/template-visualization-chartSettings.js @@ -13,7 +13,7 @@ foundHelper = helpers.maxDataPoints; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.maxDataPoints; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; + buffer += escapeExpression(stack1) + "</div>\n <div style=\"clear: both;\"></div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; foundHelper = helpers.datapointSize; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -97,6 +97,7 @@ <div id="maxDataPoints" class="form-input numeric-slider-input"><label for="maxDataPoints">Maximum data points allowed on graph: </label><div class="slider-output">{{maxDataPoints}}</div> + <div style="clear: both;"></div><div class="slider"></div><p class="form-help help-text-small"> Change the maximum number of data points displayable on this graph (higher values will @@ -152,4 +153,4 @@ </div><input id="render-button" type="button" value="Draw" /> -</script> \ No newline at end of file +</script> diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,6 +1,4 @@ define([ - //"../libs/jquery/jquery", - "../libs/underscore", "../mvc/base-mvc", "../templates/compiled/template-visualization-scatterplotControlForm", @@ -13,8 +11,6 @@ "../libs/jquery/jquery-ui-1.8.23.custom.min" ], function(){ - - /* ============================================================================= todo: outside this: @@ -54,6 +50,9 @@ how to know what sort of Tabular the data is? smarter about headers validate columns selection (here or server) + + set stats column names by selected columns + move chart into tabbed area... Scatterplot.mako: multiple plots on one page (small multiples) @@ -103,8 +102,8 @@ yNumTicks : 10, xAxisLabelBumpY : 40, yAxisLabelBumpX : -35, - width : 500, - height : 500, + width : 320, + height : 320, //TODO: anyway to make this a sub-obj? marginTop : 50, marginRight : 50, @@ -456,16 +455,10 @@ */ var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ //logger : console, - tagName : 'form', className : 'scatterplot-settings-form', loadingIndicatorImage : 'loading_large_white_bg.gif', - events : { - 'click #render-button' : 'renderPlot', - 'click #include-id-checkbox' : 'toggleThirdColumnSelector' - }, - initialize : function( attributes ){ if( !attributes || !attributes.dataset ){ @@ -571,6 +564,11 @@ return $chartSettingsPanel; }, + events : { + 'click #render-button' : 'renderPlot', + 'click #include-id-checkbox' : 'toggleThirdColumnSelector' + }, + toggleThirdColumnSelector : function(){ this.$el.find( 'select[name="ID"]' ).parent().toggle(); }, @@ -709,4 +707,4 @@ return { TwoVarScatterplot : TwoVarScatterplot, ScatterplotControlForm : ScatterplotControlForm -};}); \ No newline at end of file +};}); diff -r 3b9db9c4206602859dee02164aa32a925138866e -r 60757a1ab16476d3fc19b21bc1fb9bd42f567cf3 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -20,11 +20,11 @@ .left-column { float: left; - width: 30%; + width: 40%; } .right-column { - margin-left: 32%; + margin-left: 41%; } div.tab-pane { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Galaxy admin menu option for resetting metadata on selected tool shed repositories.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b9db9c42066/ changeset: 3b9db9c42066 user: greg date: 2012-10-11 16:22:04 summary: Galaxy admin menu option for resetting metadata on selected tool shed repositories. affected #: 1 file diff -r b037978114caede484df1b25bd4004e0591820f5 -r 3b9db9c4206602859dee02164aa32a925138866e templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -75,6 +75,7 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=installing_repository_ids )}" target="galaxy_main">Monitor installing tool shed repositories</a></div> %endif %if installed_repositories: + <div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" target="galaxy_main">Reset metadata for tool shed repositories</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin_toolshed', action='browse_repositories' )}" target="galaxy_main">Manage installed tool shed repositories</a></div> %endif </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.

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commit/galaxy-central: greg: Add the abiltiy for a Galaxy admin to reset metadata on selected installed tool shed repositories.
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b037978114ca/ changeset: b037978114ca user: greg date: 2012-10-11 16:20:57 summary: Add the abiltiy for a Galaxy admin to reset metadata on selected installed tool shed repositories. affected #: 2 files diff -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b -r b037978114caede484df1b25bd4004e0591820f5 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1447,7 +1447,59 @@ status=status ) @web.expose @web.require_admin - def reset_repository_metadata( self, trans, id ): + def reset_metadata_on_selected_repositories( self, trans, **kwd ): + # TODO: merge this with the similar method in the repository controller. + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_ids = util.listify( kwd.get( 'repository_names_by_owner', None ) ) + if 'reset_metadata_on_selected_repositories_button' in kwd: + if repository_ids: + successful_count = 0 + unsuccessful_count = 0 + for repository_id in repository_ids: + repository = get_repository( trans, repository_id ) + try: + invalid_file_tups, metadata_dict = self.reset_repository_metadata( trans, + trans.security.encode_id( repository.id ), + resetting_all_repositories=True ) + if invalid_file_tups: + unsuccessful_count += 1 + else: + successful_count += 1 + except Exception, e: + log.debug( "Error attempting to reset metadata on repository '%s': %s" % ( repository.name, str( e ) ) ) + unsuccessful_count += 1 + message = "Successfully reset metadata on %d %s. " % ( successful_count, + inflector.cond_plural( successful_count, "repository" ) ) + if unsuccessful_count: + message += "Error setting metadata on %d %s - see the paster log for details. " % ( unsuccessful_count, + inflector.cond_plural( unsuccessful_count, + "repository" ) ) + trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=util.sanitize_text( message ), + status=status ) ) + else: + 'Select at least one repository to on which to reset all metadata.' + status = 'error' + repositories_select_field = SelectField( name='repository_names_by_owner', + multiple=True, + display='checkboxes' ) + for repository in trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( trans.model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( trans.model.ToolShedRepository.table.c.name, + trans.model.ToolShedRepository.table.c.owner ): + option_label = '%s (%s)' % ( repository.name, repository.owner ) + option_value = trans.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', + repositories_select_field=repositories_select_field, + message=message, + status=status ) + @web.expose + @web.require_admin + def reset_repository_metadata( self, trans, id, resetting_all_repositories=False ): """Reset all metadata on the installed tool shed repository.""" repository = get_repository( trans, id ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) @@ -1465,23 +1517,33 @@ updating_installed_repository=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: - update_in_shed_tool_config( trans.app, repository )#def update_in_shed_tool_config( trans, shed_tool_conf_dict, elem_list ): + update_in_shed_tool_config( trans.app, repository ) trans.sa_session.add( repository ) trans.sa_session.flush() - message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name - status = 'done' + if resetting_all_repositories: + log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + else: + message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name - status = 'done' + if resetting_all_repositories: + log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + else: + message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name + status = 'done' else: - message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name - status = 'error' - new_kwd = dict( id=id, - message=message, - status=status ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repository', - **new_kwd ) ) + if resetting_all_repositories: + log.debug( 'Error locating installation directory for repository %s.' % repository.name ) + else: + message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name + status = 'error' + if resetting_all_repositories: + return invalid_file_tups, metadata_dict + else: + new_kwd = dict( id=id, message=message, status=status ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repository', + **new_kwd ) ) @web.expose @web.require_admin def reset_to_install( self, trans, **kwd ): diff -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b -r b037978114caede484df1b25bd4004e0591820f5 templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -0,0 +1,71 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="local_javascripts()"> + <script type="text/javascript"> + function checkAllFields() + { + var chkAll = document.getElementById('checkAll'); + var checks = document.getElementsByTagName('input'); + var boxLength = checks.length; + var allChecked = false; + var totalChecked = 0; + if ( chkAll.checked == true ) + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = true; + } + } + } + else + { + for ( i=0; i < boxLength; i++ ) + { + if ( checks[i].name.indexOf( 'repository_names_by_owner' ) != -1) + { + checks[i].checked = false + } + } + } + } + </script> +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${local_javascripts()} +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="warningmessage"> + Resetting metadata may take a while, so wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as + doing anything else will not be helpful. +</div> + +<div class="toolForm"> + <div class="toolFormTitle">Reset all metadata on each selected tool shed repository</div> + <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin_toolshed', action='reset_metadata_on_selected_repositories' )}" method="post" > + <div class="form-row"> + Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="checkbox" id="checkAll" name=select_all_repositories_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_repositories_checkbox value="true"/><b>Select/unselect all repositories</b> + </div> + <div style="clear: both"></div> + <div class="form-row"> + ${repositories_select_field.get_html()} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> + </div> + </form> + </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.

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commit/galaxy-central: carlfeberhard: scatterplot: added stats panel, added chart config panel; dataproviders/basic.py: compute, pass gen. stats in response.meta; base-mvc: fixed bug in chrome LoggableMixin; pack scripts
by Bitbucket 10 Oct '12

10 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0684f69e527d/ changeset: 0684f69e527d user: carlfeberhard date: 2012-10-10 23:55:34 summary: scatterplot: added stats panel, added chart config panel; dataproviders/basic.py: compute, pass gen. stats in response.meta; base-mvc: fixed bug in chrome LoggableMixin; pack scripts affected #: 17 files diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b lib/galaxy/visualization/data_providers/basic.py --- a/lib/galaxy/visualization/data_providers/basic.py +++ b/lib/galaxy/visualization/data_providers/basic.py @@ -105,7 +105,12 @@ # set up the response, column lists response = {} response[ 'data' ] = data = [ [] for column in columns ] - response[ 'meta' ] = meta = [ { 'min': None, 'max': None } for column in columns ] + response[ 'meta' ] = meta = [{ + 'min' : None, + 'max' : None, + 'count' : 0, + 'sum' : 0 + } for column in columns ] column_types = [ self.original_dataset.metadata.column_types[ column ] for column in columns ] @@ -135,18 +140,39 @@ #NOTE: this will return None/null for abberrant column values (including bad indeces) for index, column in enumerate( columns ): column_val = None + column_type = column_types[ index ] if column < fields_len: - column_val = cast_val( fields[ column ], column_types[ index ] ) + column_val = cast_val( fields[ column ], column_type ) if column_val != None: - if( meta[ index ][ 'min' ] == None - or column_val < meta[ index ][ 'min' ] ): - meta[ index ][ 'min' ] = column_val - if( meta[ index ][ 'max' ] == None - or column_val > meta[ index ][ 'max' ] ): - meta[ index ][ 'max' ] = column_val + + # if numeric, maintain min, max, sum + if( column_type == 'float' or column_type == 'int' ): + if( ( meta[ index ][ 'min' ] == None ) or ( column_val < meta[ index ][ 'min' ] ) ): + meta[ index ][ 'min' ] = column_val + + if( ( meta[ index ][ 'max' ] == None ) or ( column_val > meta[ index ][ 'max' ] ) ): + meta[ index ][ 'max' ] = column_val + + meta[ index ][ 'sum' ] += column_val + + # maintain a count - for other stats + meta[ index ][ 'count' ] += 1 data[ index ].append( column_val ) response[ 'endpoint' ] = dict( last_line=( count - 1 ), file_ptr=f.tell() ) f.close() + for index, meta in enumerate( response[ 'meta' ] ): + count = meta[ 'count' ] + meta[ 'mean' ] = float( meta[ 'sum' ] ) / count + + sorted_data = sorted( response[ 'data' ][ index ] ) + # even data count - + middle_index = count / 2 - 1 + if count % 2 == 0: + meta[ 'median' ] = sum( sorted_data[ middle_index : ( middle_index + 1 ) ] ) / 2.0 + + else: + meta[ 'median' ] = sorted_data[ middle_index ] + return response diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js --- a/static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js +++ b/static/scripts/libs/jquery/jquery-ui-1.8.23.custom.min.js @@ -22,4 +22,4 @@ * https://github.com/jquery/jquery-ui * Includes: jquery.ui.slider.js * Copyright (c) 2012 AUTHORS.txt; Licensed MIT, GPL */ -(function(a,b){var c=5;a.widget("ui.slider",a.ui.mouse,{widgetEventPrefix:"slide",options:{animate:!1,distance:0,max:100,min:0,orientation:"horizontal",range:!1,step:1,value:0,values:null},_create:function(){var b=this,d=this.options,e=this.element.find(".ui-slider-handle").addClass("ui-state-default ui-corner-all"),f="<a class='ui-slider-handle ui-state-default ui-corner-all' href='#'></a>",g=d.values&&d.values.length||1,h=[];this._keySliding=!1,this._mouseSliding=!1,this._animateOff=!0,this._handleIndex=null,this._detectOrientation(),this._mouseInit(),this.element.addClass("ui-slider ui-slider-"+this.orientation+" ui-widget"+" ui-widget-content"+" ui-corner-all"+(d.disabled?" ui-slider-disabled ui-disabled":"")),this.range=a([]),d.range&&(d.range===!0&&(d.values||(d.values=[this._valueMin(),this._valueMin()]),d.values.length&&d.values.length!==2&&(d.values=[d.values[0],d.values[0]])),this.range=a("<div></div>").appendTo(this.element).addClass("ui-slider-range ui-widget-header"+(d.range==="min"||d.range==="max"?" ui-slider-range-"+d.range:"")));for(var i=e.length;i<g;i+=1)h.push(f);this.handles=e.add(a(h.join("")).appendTo(b.element)),this.handle=this.handles.eq(0),this.handles.add(this.range).filter("a").click(function(a){a.preventDefault()}).hover(function(){d.disabled||a(this).addClass("ui-state-hover")},function(){a(this).removeClass("ui-state-hover")}).focus(function(){d.disabled?a(this).blur():(a(".ui-slider .ui-state-focus").removeClass("ui-state-focus"),a(this).addClass("ui-state-focus"))}).blur(function(){a(this).removeClass("ui-state-focus")}),this.handles.each(function(b){a(this).data("index.ui-slider-handle",b)}),this.handles.keydown(function(d){var e=a(this).data("index.ui-slider-handle"),f,g,h,i;if(b.options.disabled)return;switch(d.keyCode){case a.ui.keyCode.HOME:case a.ui.keyCode.END:case a.ui.keyCode.PAGE_UP:case a.ui.keyCode.PAGE_DOWN:case a.ui.keyCode.UP:case a.ui.keyCode.RIGHT:case a.ui.keyCode.DOWN:case a.ui.keyCode.LEFT:d.preventDefault();if(!b._keySliding){b._keySliding=!0,a(this).addClass("ui-state-active"),f=b._start(d,e);if(f===!1)return}}i=b.options.step,b.options.values&&b.options.values.length?g=h=b.values(e):g=h=b.value();switch(d.keyCode){case a.ui.keyCode.HOME:h=b._valueMin();break;case a.ui.keyCode.END:h=b._valueMax();break;case a.ui.keyCode.PAGE_UP:h=b._trimAlignValue(g+(b._valueMax()-b._valueMin())/c);break;case a.ui.keyCode.PAGE_DOWN:h=b._trimAlignValue(g-(b._valueMax()-b._valueMin())/c);break;case a.ui.keyCode.UP:case a.ui.keyCode.RIGHT:if(g===b._valueMax())return;h=b._trimAlignValue(g+i);break;case a.ui.keyCode.DOWN:case a.ui.keyCode.LEFT:if(g===b._valueMin())return;h=b._trimAlignValue(g-i)}b._slide(d,e,h)}).keyup(function(c){var d=a(this).data("index.ui-slider-handle");b._keySliding&&(b._keySliding=!1,b._stop(c,d),b._change(c,d),a(this).removeClass("ui-state-active"))}),this._refreshValue(),this._animateOff=!1},destroy:function(){return this.handles.remove(),this.range.remove(),this.element.removeClass("ui-slider ui-slider-horizontal ui-slider-vertical ui-slider-disabled ui-widget ui-widget-content ui-corner-all").removeData("slider").unbind(".slider"),this._mouseDestroy(),this},_mouseCapture:function(b){var c=this.options,d,e,f,g,h,i,j,k,l;return c.disabled?!1:(this.elementSize={width:this.element.outerWidth(),height:this.element.outerHeight()},this.elementOffset=this.element.offset(),d={x:b.pageX,y:b.pageY},e=this._normValueFromMouse(d),f=this._valueMax()-this._valueMin()+1,h=this,this.handles.each(function(b){var c=Math.abs(e-h.values(b));f>c&&(f=c,g=a(this),i=b)}),c.range===!0&&this.values(1)===c.min&&(i+=1,g=a(this.handles[i])),j=this._start(b,i),j===!1?!1:(this._mouseSliding=!0,h._handleIndex=i,g.addClass("ui-state-active").focus(),k=g.offset(),l=!a(b.target).parents().andSelf().is(".ui-slider-handle"),this._clickOffset=l?{left:0,top:0}:{left:b.pageX-k.left-g.width()/2,top:b.pageY-k.top-g.height()/2-(parseInt(g.css("borderTopWidth"),10)||0)-(parseInt(g.css("borderBottomWidth"),10)||0)+(parseInt(g.css("marginTop"),10)||0)},this.handles.hasClass("ui-state-hover")||this._slide(b,i,e),this._animateOff=!0,!0))},_mouseStart:function(a){return!0},_mouseDrag:function(a){var b={x:a.pageX,y:a.pageY},c=this._normValueFromMouse(b);return this._slide(a,this._handleIndex,c),!1},_mouseStop:function(a){return this.handles.removeClass("ui-state-active"),this._mouseSliding=!1,this._stop(a,this._handleIndex),this._change(a,this._handleIndex),this._handleIndex=null,this._clickOffset=null,this._animateOff=!1,!1},_detectOrientation:function(){this.orientation=this.options.orientation==="vertical"?"vertical":"horizontal"},_normValueFromMouse:function(a){var b,c,d,e,f;return this.orientation==="horizontal"?(b=this.elementSize.width,c=a.x-this.elementOffset.left-(this._clickOffset?this._clickOffset.left:0)):(b=this.elementSize.height,c=a.y-this.elementOffset.top-(this._clickOffset?this._clickOffset.top:0)),d=c/b,d>1&&(d=1),d<0&&(d=0),this.orientation==="vertical"&&(d=1-d),e=this._valueMax()-this._valueMin(),f=this._valueMin()+d*e,this._trimAlignValue(f)},_start:function(a,b){var c={handle:this.handles[b],value:this.value()};return this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("start",a,c)},_slide:function(a,b,c){var d,e,f;this.options.values&&this.options.values.length?(d=this.values(b?0:1),this.options.values.length===2&&this.options.range===!0&&(b===0&&c>d||b===1&&c<d)&&(c=d),c!==this.values(b)&&(e=this.values(),e[b]=c,f=this._trigger("slide",a,{handle:this.handles[b],value:c,values:e}),d=this.values(b?0:1),f!==!1&&this.values(b,c,!0))):c!==this.value()&&(f=this._trigger("slide",a,{handle:this.handles[b],value:c}),f!==!1&&this.value(c))},_stop:function(a,b){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("stop",a,c)},_change:function(a,b){if(!this._keySliding&&!this._mouseSliding){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("change",a,c)}},value:function(a){if(arguments.length){this.options.value=this._trimAlignValue(a),this._refreshValue(),this._change(null,0);return}return this._value()},values:function(b,c){var d,e,f;if(arguments.length>1){this.options.values[b]=this._trimAlignValue(c),this._refreshValue(),this._change(null,b);return}if(!arguments.length)return this._values();if(!a.isArray(arguments[0]))return this.options.values&&this.options.values.length?this._values(b):this.value();d=this.options.values,e=arguments[0];for(f=0;f<d.length;f+=1)d[f]=this._trimAlignValue(e[f]),this._change(null,f);this._refreshValue()},_setOption:function(b,c){var d,e=0;a.isArray(this.options.values)&&(e=this.options.values.length),a.Widget.prototype._setOption.apply(this,arguments);switch(b){case"disabled":c?(this.handles.filter(".ui-state-focus").blur(),this.handles.removeClass("ui-state-hover"),this.handles.propAttr("disabled",!0),this.element.addClass("ui-disabled")):(this.handles.propAttr("disabled",!1),this.element.removeClass("ui-disabled"));break;case"orientation":this._detectOrientation(),this.element.removeClass("ui-slider-horizontal ui-slider-vertical").addClass("ui-slider-"+this.orientation),this._refreshValue();break;case"value":this._animateOff=!0,this._refreshValue(),this._change(null,0),this._animateOff=!1;break;case"values":this._animateOff=!0,this._refreshValue();for(d=0;d<e;d+=1)this._change(null,d);this._animateOff=!1}},_value:function(){var a=this.options.value;return a=this._trimAlignValue(a),a},_values:function(a){var b,c,d;if(arguments.length)return b=this.options.values[a],b=this._trimAlignValue(b),b;c=this.options.values.slice();for(d=0;d<c.length;d+=1)c[d]=this._trimAlignValue(c[d]);return c},_trimAlignValue:function(a){if(a<=this._valueMin())return this._valueMin();if(a>=this._valueMax())return this._valueMax();var b=this.options.step>0?this.options.step:1,c=(a-this._valueMin())%b,d=a-c;return Math.abs(c)*2>=b&&(d+=c>0?b:-b),parseFloat(d.toFixed(5))},_valueMin:function(){return this.options.min},_valueMax:function(){return this.options.max},_refreshValue:function(){var b=this.options.range,c=this.options,d=this,e=this._animateOff?!1:c.animate,f,g={},h,i,j,k;this.options.values&&this.options.values.length?this.handles.each(function(b,i){f=(d.values(b)-d._valueMin())/(d._valueMax()-d._valueMin())*100,g[d.orientation==="horizontal"?"left":"bottom"]=f+"%",a(this).stop(1,1)[e?"animate":"css"](g,c.animate),d.options.range===!0&&(d.orientation==="horizontal"?(b===0&&d.range.stop(1,1)[e?"animate":"css"]({left:f+"%"},c.animate),b===1&&d.range[e?"animate":"css"]({width:f-h+"%"},{queue:!1,duration:c.animate})):(b===0&&d.range.stop(1,1)[e?"animate":"css"]({bottom:f+"%"},c.animate),b===1&&d.range[e?"animate":"css"]({height:f-h+"%"},{queue:!1,duration:c.animate}))),h=f}):(i=this.value(),j=this._valueMin(),k=this._valueMax(),f=k!==j?(i-j)/(k-j)*100:0,g[d.orientation==="horizontal"?"left":"bottom"]=f+"%",this.handle.stop(1,1)[e?"animate":"css"](g,c.animate),b==="min"&&this.orientation==="horizontal"&&this.range.stop(1,1)[e?"animate":"css"]({width:f+"%"},c.animate),b==="max"&&this.orientation==="horizontal"&&this.range[e?"animate":"css"]({width:100-f+"%"},{queue:!1,duration:c.animate}),b==="min"&&this.orientation==="vertical"&&this.range.stop(1,1)[e?"animate":"css"]({height:f+"%"},c.animate),b==="max"&&this.orientation==="vertical"&&this.range[e?"animate":"css"]({height:100-f+"%"},{queue:!1,duration:c.animate}))}}),a.extend(a.ui.slider,{version:"1.8.23"})})(jQuery);; \ No newline at end of file +(function(a,b){var c=5;a.widget("ui.slider",a.ui.mouse,{widgetEventPrefix:"slide",options:{animate:!1,distance:0,max:100,min:0,orientation:"horizontal",range:!1,step:1,value:0,values:null},_create:function(){var b=this,d=this.options,e=this.element.find(".ui-slider-handle").addClass("ui-state-default ui-corner-all"),f="<a class='ui-slider-handle ui-state-default ui-corner-all' href='#'></a>",g=d.values&&d.values.length||1,h=[];this._keySliding=!1,this._mouseSliding=!1,this._animateOff=!0,this._handleIndex=null,this._detectOrientation(),this._mouseInit(),this.element.addClass("ui-slider ui-slider-"+this.orientation+" ui-widget"+" ui-widget-content"+" ui-corner-all"+(d.disabled?" ui-slider-disabled ui-disabled":"")),this.range=a([]),d.range&&(d.range===!0&&(d.values||(d.values=[this._valueMin(),this._valueMin()]),d.values.length&&d.values.length!==2&&(d.values=[d.values[0],d.values[0]])),this.range=a("<div></div>").appendTo(this.element).addClass("ui-slider-range ui-widget-header"+(d.range==="min"||d.range==="max"?" ui-slider-range-"+d.range:"")));for(var i=e.length;i<g;i+=1)h.push(f);this.handles=e.add(a(h.join("")).appendTo(b.element)),this.handle=this.handles.eq(0),this.handles.add(this.range).filter("a").click(function(a){a.preventDefault()}).hover(function(){d.disabled||a(this).addClass("ui-state-hover")},function(){a(this).removeClass("ui-state-hover")}).focus(function(){d.disabled?a(this).blur():(a(".ui-slider .ui-state-focus").removeClass("ui-state-focus"),a(this).addClass("ui-state-focus"))}).blur(function(){a(this).removeClass("ui-state-focus")}),this.handles.each(function(b){a(this).data("index.ui-slider-handle",b)}),this.handles.keydown(function(d){var e=a(this).data("index.ui-slider-handle"),f,g,h,i;if(b.options.disabled)return;switch(d.keyCode){case a.ui.keyCode.HOME:case a.ui.keyCode.END:case a.ui.keyCode.PAGE_UP:case a.ui.keyCode.PAGE_DOWN:case a.ui.keyCode.UP:case a.ui.keyCode.RIGHT:case a.ui.keyCode.DOWN:case a.ui.keyCode.LEFT:d.preventDefault();if(!b._keySliding){b._keySliding=!0,a(this).addClass("ui-state-active"),f=b._start(d,e);if(f===!1)return}}i=b.options.step,b.options.values&&b.options.values.length?g=h=b.values(e):g=h=b.value();switch(d.keyCode){case a.ui.keyCode.HOME:h=b._valueMin();break;case a.ui.keyCode.END:h=b._valueMax();break;case a.ui.keyCode.PAGE_UP:h=b._trimAlignValue(g+(b._valueMax()-b._valueMin())/c);break;case a.ui.keyCode.PAGE_DOWN:h=b._trimAlignValue(g-(b._valueMax()-b._valueMin())/c);break;case a.ui.keyCode.UP:case a.ui.keyCode.RIGHT:if(g===b._valueMax())return;h=b._trimAlignValue(g+i);break;case a.ui.keyCode.DOWN:case a.ui.keyCode.LEFT:if(g===b._valueMin())return;h=b._trimAlignValue(g-i)}b._slide(d,e,h)}).keyup(function(c){var d=a(this).data("index.ui-slider-handle");b._keySliding&&(b._keySliding=!1,b._stop(c,d),b._change(c,d),a(this).removeClass("ui-state-active"))}),this._refreshValue(),this._animateOff=!1},destroy:function(){return this.handles.remove(),this.range.remove(),this.element.removeClass("ui-slider ui-slider-horizontal ui-slider-vertical ui-slider-disabled ui-widget ui-widget-content ui-corner-all").removeData("slider").unbind(".slider"),this._mouseDestroy(),this},_mouseCapture:function(b){var c=this.options,d,e,f,g,h,i,j,k,l;return c.disabled?!1:(this.elementSize={width:this.element.outerWidth(),height:this.element.outerHeight()},this.elementOffset=this.element.offset(),d={x:b.pageX,y:b.pageY},e=this._normValueFromMouse(d),f=this._valueMax()-this._valueMin()+1,h=this,this.handles.each(function(b){var c=Math.abs(e-h.values(b));f>c&&(f=c,g=a(this),i=b)}),c.range===!0&&this.values(1)===c.min&&(i+=1,g=a(this.handles[i])),j=this._start(b,i),j===!1?!1:(this._mouseSliding=!0,h._handleIndex=i,g.addClass("ui-state-active").focus(),k=g.offset(),l=!a(b.target).parents().andSelf().is(".ui-slider-handle"),this._clickOffset=l?{left:0,top:0}:{left:b.pageX-k.left-g.width()/2,top:b.pageY-k.top-g.height()/2-(parseInt(g.css("borderTopWidth"),10)||0)-(parseInt(g.css("borderBottomWidth"),10)||0)+(parseInt(g.css("marginTop"),10)||0)},this.handles.hasClass("ui-state-hover")||this._slide(b,i,e),this._animateOff=!0,!0))},_mouseStart:function(a){return!0},_mouseDrag:function(a){var b={x:a.pageX,y:a.pageY},c=this._normValueFromMouse(b);return this._slide(a,this._handleIndex,c),!1},_mouseStop:function(a){return this.handles.removeClass("ui-state-active"),this._mouseSliding=!1,this._stop(a,this._handleIndex),this._change(a,this._handleIndex),this._handleIndex=null,this._clickOffset=null,this._animateOff=!1,!1},_detectOrientation:function(){this.orientation=this.options.orientation==="vertical"?"vertical":"horizontal"},_normValueFromMouse:function(a){var b,c,d,e,f;return this.orientation==="horizontal"?(b=this.elementSize.width,c=a.x-this.elementOffset.left-(this._clickOffset?this._clickOffset.left:0)):(b=this.elementSize.height,c=a.y-this.elementOffset.top-(this._clickOffset?this._clickOffset.top:0)),d=c/b,d>1&&(d=1),d<0&&(d=0),this.orientation==="vertical"&&(d=1-d),e=this._valueMax()-this._valueMin(),f=this._valueMin()+d*e,this._trimAlignValue(f)},_start:function(a,b){var c={handle:this.handles[b],value:this.value()};return this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("start",a,c)},_slide:function(a,b,c){var d,e,f;this.options.values&&this.options.values.length?(d=this.values(b?0:1),this.options.values.length===2&&this.options.range===!0&&(b===0&&c>d||b===1&&c<d)&&(c=d),c!==this.values(b)&&(e=this.values(),e[b]=c,f=this._trigger("slide",a,{handle:this.handles[b],value:c,values:e}),d=this.values(b?0:1),f!==!1&&this.values(b,c,!0))):c!==this.value()&&(f=this._trigger("slide",a,{handle:this.handles[b],value:c}),f!==!1&&this.value(c))},_stop:function(a,b){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("stop",a,c)},_change:function(a,b){if(!this._keySliding&&!this._mouseSliding){var c={handle:this.handles[b],value:this.value()};this.options.values&&this.options.values.length&&(c.value=this.values(b),c.values=this.values()),this._trigger("change",a,c)}},value:function(a){if(arguments.length){this.options.value=this._trimAlignValue(a),this._refreshValue(),this._change(null,0);return}return this._value()},values:function(b,c){var d,e,f;if(arguments.length>1){this.options.values[b]=this._trimAlignValue(c),this._refreshValue(),this._change(null,b);return}if(!arguments.length)return this._values();if(!a.isArray(arguments[0]))return this.options.values&&this.options.values.length?this._values(b):this.value();d=this.options.values,e=arguments[0];for(f=0;f<d.length;f+=1)d[f]=this._trimAlignValue(e[f]),this._change(null,f);this._refreshValue()},_setOption:function(b,c){var d,e=0;a.isArray(this.options.values)&&(e=this.options.values.length),a.Widget.prototype._setOption.apply(this,arguments);switch(b){case"disabled":c?(this.handles.filter(".ui-state-focus").blur(),this.handles.removeClass("ui-state-hover"),this.handles.propAttr("disabled",!0),this.element.addClass("ui-disabled")):(this.handles.propAttr("disabled",!1),this.element.removeClass("ui-disabled"));break;case"orientation":this._detectOrientation(),this.element.removeClass("ui-slider-horizontal ui-slider-vertical").addClass("ui-slider-"+this.orientation),this._refreshValue();break;case"value":this._animateOff=!0,this._refreshValue(),this._change(null,0),this._animateOff=!1;break;case"values":this._animateOff=!0,this._refreshValue();for(d=0;d<e;d+=1)this._change(null,d);this._animateOff=!1}},_value:function(){var a=this.options.value;return a=this._trimAlignValue(a),a},_values:function(a){var b,c,d;if(arguments.length)return b=this.options.values[a],b=this._trimAlignValue(b),b;c=this.options.values.slice();for(d=0;d<c.length;d+=1)c[d]=this._trimAlignValue(c[d]);return c},_trimAlignValue:function(a){if(a<=this._valueMin())return this._valueMin();if(a>=this._valueMax())return this._valueMax();var b=this.options.step>0?this.options.step:1,c=(a-this._valueMin())%b,d=a-c;return Math.abs(c)*2>=b&&(d+=c>0?b:-b),parseFloat(d.toFixed(5))},_valueMin:function(){return this.options.min},_valueMax:function(){return this.options.max},_refreshValue:function(){var 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diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -65,8 +65,10 @@ logger : null, log : function(){ - return ( this.logger )?( this.logger.log.apply( this, arguments ) ) - :( undefined ); + if( this.logger ){ + return this.logger.log.apply( this.logger, arguments ); + } + return undefined; } }; diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){return(this.logger)?(this.logger.log.apply(this,arguments)):(undefined)}};var GalaxyLocalization=jQuery.extend({},{aliasName:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){var a=b;if(_.has(this.localizedStrings,b)){a=this.localizedStrings[b]}return a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.aliasName]=function(a){return GalaxyLocalization.localize(a)};var TemplateLoader=_.extend({},LoggableMixin,{getTemplateLoadFn:function(){throw ("There is no templateLoadFn. Make sure you're using a subclass of TemplateLoader")},getTemplates:function(d,e){e=e||false;this.log(this,"getTemplates:",d,", forceReload:",e);var c={},a=this,b=this.getTemplateLoadFn();if(!d){return c}jQuery.each(d,function(f,g){jQuery.each(g,function(h,i){a.log(a+", templateFile:",f,"templateName:",h,", templateID:",i);c[h]=b.call(a,f,h,i)})});return c}});var CompiledTemplateLoader=_.extend({},TemplateLoader,{getTemplateLoadFn:function(){return this.loadCompiledHandlebarsTemplate},loadCompiledHandlebarsTemplate:function(b,a,c){this.log("getInDomTemplates, templateFile:",b,"templateName:",a,", templateID:",c);if(!Handlebars.templates||!Handlebars.templates[c]){throw ("Template not found: Handlebars."+c+". Check your h.templates() call in the mako file that rendered this page")}this.log("found template function:",c);return Handlebars.templates[c]}});var InDomTemplateLoader=_.extend({},TemplateLoader,{compileTemplate:function(a){if(!Handlebars||!Handlebars.compile){throw ("No Handlebars.compile found. You may only have Handlebars.runtime loaded.Include handlebars.full for this to work")}this.log("compiling template:",a);return Handlebars.compile(a)},findTemplateInDom:function(b,a,c){return $("script#"+c).last()},getTemplateLoadFn:function(){return this.loadInDomTemplate},loadInDomTemplate:function(b,a,c){this.log("getInDomTemplate, templateFile:",b,"templateName:",a,", templateID:",c);var d=this.findTemplateInDom(b,a,c);if(!d||!d.length){throw ("Template not found within the DOM: "+c+". Check that this template has been included in the page")}this.log("found template in dom:",d.html());return this.compileTemplate(d.html())}});var RemoteTemplateLoader=_.extend({},InDomTemplateLoader,{templateBaseURL:"static/scripts/templates/",getTemplateLoadFn:function(){return this.loadViaHttpGet},loadViaHttpGet:function(d,c,f){var b="static/scripts/templates/";this.log("loadViaHttpGet, templateFile:",d,"templateName:",c,", templateID:",f,"templateBaseURL:",this.templateBaseURL);var h=null;try{h=this.loadInDomTemplate(d,c,f)}catch(g){this.log("getInDomTemplate exception:"+g);if(!Handlebars.compile){throw (g)}this.log("Couldn't locate template in DOM: "+f);var a=this;var e=b+d;jQuery.ajax(e,{method:"GET",async:false,success:function(i){a.log(d+" loaded via GET. Attempting compile...");$("body").append(i);h=a.loadInDomTemplate(d,c,f)},error:function(j,i,k){throw ("Failed to fetch "+e+":"+i)}})}if(!h){throw ("Couldn't load or fetch template: "+f)}return h}}); \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(b){var a=b;if(_.has(this.localizedStrings,b)){a=this.localizedStrings[b]}return a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;var e=function(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this.save();return this},deleteKey:function(j){delete i[j];this.save();return this},save:function(){return h.save()},toString:function(){return("StorageRecursionHelper("+i+")")}}};var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);f.save=function(h){c(g,f.get())};f.destroy=function(){a(g)};f.toString=function(){return"PersistantStorage("+data+")"};return f}; \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/mvc/history.js --- a/static/scripts/packed/mvc/history.js +++ b/static/scripts/packed/mvc/history.js @@ -1,1 +1,1 @@ -var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(){this.log(this+".initialize:",this,this.model)},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(){this.log(this+".toggleBodyVisibility");this.$el.find(".historyItemBody").toggle()},toString:function(){var a=(this.model)?(this.model+""):("");return"HistoryItemView("+a+")"}});HistoryItemView.templates=CompiledTemplateLoader.getTemplates({"common-templates.html":{warningMsg:"template-warningmessagesmall"},"history-templates.html":{messages:"template-history-warning-messages",titleLink:"template-history-titleLink",hdaSummary:"template-history-hdaSummary",downloadLinks:"template-history-downloadLinks",failedMetadata:"template-history-failedMetaData",tagArea:"template-history-tagArea",annotationArea:"template-history-annotationArea",displayApps:"template-history-displayApps"}});var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.itemViews=[];var a=this;this.model.items.each(function(c){var b=new HistoryItemView({model:c});a.itemViews.push(b)})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(c){a.log(a+".render_items:",c);b.prepend(c.render())});return b},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates=CompiledTemplateLoader.getTemplates({"history-templates.html":{historyPanel:"template-history-historyPanel"}}); \ No newline at end of file +var HistoryItem=BaseModel.extend(LoggableMixin).extend({defaults:{id:null,name:"",data_type:null,file_size:0,genome_build:null,metadata_data_lines:0,metadata_dbkey:null,metadata_sequences:0,misc_blurb:"",misc_info:"",model_class:"",state:"",deleted:false,purged:false,visible:true,for_editing:true,bodyIsShown:false},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryItem.STATES.NOT_VIEWABLE)}},isEditable:function(){return(!(this.get("deleted")||this.get("purged")))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryItem("+a+")"}});HistoryItem.STATES={NOT_VIEWABLE:"not_viewable",NEW:"new",UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",OK:"ok",EMPTY:"empty",ERROR:"error",DISCARDED:"discarded",SETTING_METADATA:"setting_metadata",FAILED_METADATA:"failed_metadata"};var HistoryItemView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",this,this.model);this.visible=a.visible},render:function(){var c=this.model.get("id"),b=this.model.get("state");this.clearReferences();this.$el.attr("id","historyItemContainer-"+c);var a=$("<div/>").attr("id","historyItem-"+c).addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+b);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);a.find(".tooltip").tooltip({placement:"bottom"});make_popup_menus(a);this.$el.children().remove();return this.$el.append(a)},clearReferences:function(){this.displayButton=null;this.editButton=null;this.deleteButton=null;this.errButton=null},_render_warnings:function(){return $(jQuery.trim(HistoryItemView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_displayButton:function(){if(this.model.get("state")===HistoryItem.STATES.UPLOAD){return null}displayBtnData=(this.model.get("purged"))?({title:"Cannot display datasets removed from disk",enabled:false,icon_class:"display"}):({title:"Display data in browser",href:this.model.get("display_url"),target:(this.model.get("for_editing"))?("galaxy_main"):(null),icon_class:"display"});this.displayButton=new IconButtonView({model:new IconButton(displayBtnData)});return this.displayButton.render().$el},_render_editButton:function(){if((this.model.get("state")===HistoryItem.STATES.UPLOAD)||(!this.model.get("for_editing"))){return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:"Edit attributes",href:this.model.get("edit_url"),target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false}if(a){b.title="Undelete dataset to edit attributes"}else{if(c){b.title="Cannot edit attributes of datasets removed from disk"}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if(!this.model.get("for_editing")){return null}var a={title:"Delete",href:this.model.get("delete_url"),id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if((this.model.get("deleted")||this.model.get("purged"))&&(!this.model.get("delete_url"))){a={title:"Dataset is already deleted",icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HistoryItemView.templates.titleLink(this.model.toJSON())))},_render_hdaSummary:function(){var a=this.model.toJSON();if(this.model.get("metadata_dbkey")==="?"&&this.model.isEditable()){_.extend(a,{dbkey_unknown_and_editable:true})}return HistoryItemView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var b=$("<div/>").attr("id","primary-actions-"+this.model.get("id")),a=this;_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")){return null}var a=HistoryItemView.templates.downloadLinks(this.model.toJSON());return $(a)},_render_errButton:function(){if((this.model.get("state")!==HistoryItem.STATES.ERROR)||(!this.model.get("for_editing"))){return null}this.errButton=new IconButtonView({model:new IconButton({title:"View or report this error",href:this.model.get("report_error_url"),target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:"View details",href:this.model.get("show_params_url"),target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_rerunButton:function(){if(!this.model.get("for_editing")){return null}this.rerunButton=new IconButtonView({model:new IconButton({title:"Run this job again",href:this.model.get("rerun_url"),target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_tracksterButton:function(){var a=this.model.get("trackster_urls");if(!(this.model.hasData())||!(this.model.get("for_editing"))||!(a)){return null}this.tracksterButton=new IconButtonView({model:new IconButton({title:"View in Trackster",icon_class:"chart_curve"})});this.errButton.render();this.errButton.$el.addClass("trackster-add").attr({"data-url":a["data-url"],"action-url":a["action-url"],"new-url":a["new-url"]});return this.errButton.$el},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("retag_url"))){return null}this.tagButton=new IconButtonView({model:new IconButton({title:"Edit dataset tags",target:"galaxy_main",href:this.model.get("retag_url"),icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||!(this.model.get("for_editing"))||(!this.model.get("annotate_url"))){return null}this.annotateButton=new IconButtonView({model:new IconButton({title:"Edit dataset annotation",target:"galaxy_main",href:this.model.get("annotate_url"),icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.model.get("retag_url")){return null}return $(HistoryItemView.templates.tagArea(this.model.toJSON()))},_render_annotationArea:function(){if(!this.model.get("annotate_url")){return null}return $(HistoryItemView.templates.annotationArea(this.model.toJSON()))},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_types}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HistoryItemView.templates.displayApps({displayApps:this.model.toJSON().display_apps}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body_not_viewable:function(a){a.append($("<div>You do not have permission to view dataset.</div>"))},_render_body_uploading:function(a){a.append($("<div>Dataset is uploading</div>"))},_render_body_queued:function(a){a.append($("<div>Job is waiting to run.</div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_running:function(a){a.append("<div>Job is currently running.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append(("An error occurred running this job: <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]))},_render_body_discarded:function(a){a.append("<div>The job creating this dataset was cancelled before completion.</div>");a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_setting_metadata:function(a){a.append($("<div>Metadata is being auto-detected.</div>"))},_render_body_empty:function(a){a.append($("<div>No data: <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons([this._render_showParamsButton,this._render_rerunButton]))},_render_body_failed_metadata:function(a){a.append($(HistoryItemView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_errButton,this._render_showParamsButton,this._render_rerunButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},_render_body:function(){var b=this.model.get("state");var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(b){case HistoryItem.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryItem.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryItem.STATES.QUEUED:this._render_body_queued(a);break;case HistoryItem.STATES.RUNNING:this._render_body_running(a);break;case HistoryItem.STATES.ERROR:this._render_body_error(a);break;case HistoryItem.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryItem.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryItem.STATES.EMPTY:this._render_body_empty(a);break;case HistoryItem.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryItem.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+b+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.model.get("bodyIsShown")===false){a.hide()}if(this.visible){a.show()}else{a.hide()}return a},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.model.get("ajax_get_tag_url"),error:function(){alert("Tagging failed")},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.model.get("ajax_set_annotation_url");if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.model.get("ajax_get_annotation_url"),error:function(){alert("Annotations failed")},success:function(e){if(e===""){e="<em>Describe or add notes to dataset</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toggleBodyVisibility:function(b){var a=this.$el.find(".historyItemBody");if(b===undefined){a.toggle()}else{if(b){a.show()}else{a.hide()}}this.trigger("toggleBodyVisibility",this.model.get("id"),a.is(":visible"))},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HistoryItemView("+a+")"}});HistoryItemView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-history-warning-messages"],titleLink:Handlebars.templates["template-history-titleLink"],hdaSummary:Handlebars.templates["template-history-hdaSummary"],downloadLinks:Handlebars.templates["template-history-downloadLinks"],failedMetadata:Handlebars.templates["template-history-failedMetaData"],tagArea:Handlebars.templates["template-history-tagArea"],annotationArea:Handlebars.templates["template-history-annotationArea"],displayApps:Handlebars.templates["template-history-displayApps"]};var HistoryCollection=Backbone.Collection.extend({model:HistoryItem,toString:function(){return("HistoryCollection()")}});var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",state_details:{discarded:0,empty:0,error:0,failed_metadata:0,ok:0,queued:0,running:0,setting_metadata:0,upload:0},userIsAdmin:false,userRoles:[],itemsLength:0,showDeleted:false,showHidden:false,diskSize:0,deleted:false,tags:[],annotation:null,message:null,quotaMsg:false,baseURL:null,hideDeletedURL:null,hideHiddenURL:null,tagURL:null,annotateURL:null},initialize:function(b,a){this.items=new HistoryCollection()},toJSON:function(){var a=Backbone.Model.prototype.toJSON.call(this);a.itemsLength=this.items.length;return a},loadDatasetsAsHistoryItems:function(c){var a=this,b=this.get("id"),d=this.get("state_details");_.each(c,function(f,e){var h=new HistoryItem(_.extend(f,{history_id:b}));a.items.add(h);var g=f.state;d[g]+=1});this.set("state_details",d);this._stateFromStateDetails();return this},_stateFromStateDetails:function(){this.set("state","");var a=this.get("state_details");if((a.error>0)||(a.failed_metadata>0)){this.set("state",HistoryItem.STATES.ERROR)}else{if((a.running>0)||(a.setting_metadata>0)){this.set("state",HistoryItem.STATES.RUNNING)}else{if(a.queued>0){this.set("state",HistoryItem.STATES.QUEUED)}else{if(a.ok===this.items.length){this.set("state",HistoryItem.STATES.OK)}else{throw ("_stateFromStateDetails: unable to determine history state from state details: "+this.state_details)}}}}return this},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryView=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",initialize:function(){this.log(this+".initialize:",this);this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{visibleItems:{}});this.initializeItems()},initializeItems:function(){this.itemViews={};var a=this;this.model.items.each(function(c){var e=c.get("id"),d=a.storage.get("visibleItems").get(e),b=new HistoryItemView({model:c,visible:d});a.setUpItemListeners(b);a.itemViews[e]=b})},setUpItemListeners:function(b){var a=this;b.bind("toggleBodyVisibility",function(d,c){if(c){a.storage.get("visibleItems").set(d,true)}else{a.storage.get("visibleItems").deleteKey(d)}})},render:function(){this.$el.append(HistoryView.templates.historyPanel(this.model.toJSON()));this.log(this+" rendered from template:",this.$el);this.itemsDiv=this.$el.find("#"+this.model.get("id")+"-datasets");async_save_text("history-name-container","history-name",this.model.get("renameURL"),"new_name",18);this.$el.find(".tooltip").tooltip();var b=this.$el.find("#history-annotation-area");$("#history-annotate").click(function(){if(b.is(":hidden")){b.slideDown("fast")}else{b.slideUp("fast")}return false});async_save_text("history-annotation-container","history-annotation",this.model.get("annotateURL"),"new_annotation",18,true,4);if(this.model.items.length){var a=this._render_items();this.itemsDiv.append(a.children());a.remove()}},_render_items:function(){var b=$("<div/>"),a=this;_.each(this.itemViews,function(d,c){a.log(a+".render_items:",c,d);b.prepend(d.render())});return b},events:{"click #history-collapse-all":"hideAllItemBodies","click #history-tag":"loadAndDisplayTags"},hideAllItemBodies:function(){_.each(this.itemViews,function(a){a.toggleBodyVisibility(false)})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:this.model.get("tagURL"),error:function(){alert("Tagging failed")},success:function(e){a.log(a+" tag elt html (ajax)",e);b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryView("+a+")"}});HistoryView.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(k,C,A,s,J){A=A||k.helpers;var B="",o,n,y=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(L,K){return"refresh"}function t(L,K){return"collapse all"}function r(O,N){var L="",M,K;L+='\n <div style="width: 40px; float: right; white-space: nowrap;">\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(6,q,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="';K=A.tagURL;if(K){M=K.call(O,{hash:{}})}else{M=O.tagURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(8,m,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="';K=A.annotateURL;if(K){M=K.call(O,{hash:{}})}else{M=O.annotateURL;M=typeof M===f?M():M}L+=e(M)+'"></a>\n </div>\n ';return L}function q(L,K){return"Edit history tags"}function m(L,K){return"Edit history annotation"}function I(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideDeletedURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideDeletedURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(11,H,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function H(L,K){return"hide deleted"}function G(O,N){var L="",M,K;L+='\n<div class="historyLinks">\n <a href="';K=A.hideHiddenURL;if(K){M=K.call(O,{hash:{}})}else{M=O.hideHiddenURL;M=typeof M===f?M():M}L+=e(M)+'">';K=A.local;if(K){M=K.call(O,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:y.noop,fn:y.program(14,F,N)})}if(M||M===0){L+=M}L+="</a>\n</div>\n";return L}function F(L,K){return"hide hidden"}function E(O,N){var L="",M,K;L+="\n ";L+='\n <div id="history-size" style="position: absolute; top: 3px; right: 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\ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-visualization-chartSettings.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-chartSettings.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-chartSettings"]=b(function(f,m,e,l,k){e=e||f.helpers;var i="",c,h,g="function",j=this.escapeExpression,n=this;function d(p,o){return"checked"}i+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n </p>\n \n <div id="maxDataPoints" class="form-input numeric-slider-input">\n <label for="maxDataPoints">Maximum data points allowed on graph: </label>\n <div class="slider-output">';h=e.maxDataPoints;if(h){c=h.call(m,{hash:{}})}else{c=m.maxDataPoints;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">';h=e.datapointSize;if(h){c=h.call(m,{hash:{}})}else{c=m.datapointSize;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id="entryAnimDuration" class="form-input checkbox-input">\n <label for="animated">Animate graph transitions?: </label>\n <input type="checkbox" id="animated" class="checkbox control" value="';c=m.entryAnimDuration;c=e["if"].call(m,c,{hash:{},inverse:n.noop,fn:n.program(1,d,k)});if(c||c===0){i+=c}i+='" />\n <p class="form-help help-text-small">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id="width" class="form-input numeric-slider-input">\n <label for="width">Graph width: </label>\n <div class="slider-output">';h=e.width;if(h){c=h.call(m,{hash:{}})}else{c=m.width;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="height" class="form-input numeric-slider-input">\n <label for="height">Graph height: </label>\n <div class="slider-output">';h=e.height;if(h){c=h.call(m,{hash:{}})}else{c=m.height;c=typeof c===g?c():c}i+=j(c)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="';h=e.xLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.xLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <div id="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="';h=e.yLabel;if(h){c=h.call(m,{hash:{}})}else{c=m.yLabel;c=typeof c===g?c():c}i+=j(c)+'" />\n <p class="form-help help-text-small"></p>\n </div>\n\n <input id="render-button" type="button" value="Draw" />';return i})})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/templates/compiled/template-visualization-statsTable.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-visualization-statsTable.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-statsTable"]=b(function(f,l,e,k,j){e=e||f.helpers;var h="",c,g="function",i=this.escapeExpression,m=this;function d(r,q){var o="",p,n;o+="\n <tr><td>";n=e.name;if(n){p=n.call(r,{hash:{}})}else{p=r.name;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.xval;if(n){p=n.call(r,{hash:{}})}else{p=r.xval;p=typeof p===g?p():p}o+=i(p)+"</td><td>";n=e.yval;if(n){p=n.call(r,{hash:{}})}else{p=r.yval;p=typeof p===g?p():p}o+=i(p)+"</td></tr>\n </tr>\n ";return o}h+='<p class="help-text">By column:</p>\n <table id="chart-stats-table">\n <thead><th></th><th>X</th><th>Y</th></thead>\n ';c=l.stats;c=e.each.call(l,c,{hash:{},inverse:m.noop,fn:m.program(1,d,j)});if(c||c===0){h+=c}h+="\n </table>";return h})})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/viz/phyloviz.js --- a/static/scripts/packed/viz/phyloviz.js +++ b/static/scripts/packed/viz/phyloviz.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/visualization"],function(l,f){var k=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,m){var n=this,r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>m){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(m){if(m.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). 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B=A.dist||o;B=B>1?1:B;A.dist=B;if(y!==null){A.y0=y.y0+B*r}else{A.y0=m}if(!x){A.x0=s++*z}else{x.forEach(function(D){D.parent=A;w+=n(D,C,z,A)});A.x0=w/x.length}A.x=A.x0;A.y=A.y0;return A.x0}return v}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},root:{},toggle:function(m){if(typeof m==="undefined"){return}if(m.children){m._children=m.children;m.children=null}else{m.children=m._children;m._children=null}},toggleAll:function(m){if(m.children&&m.children.length!==0){m.children.forEach(this.toggleAll);toggle(m)}},getData:function(){return this.root},save:function(){var m=this.root;n(m);this.set("root",m);function n(p){delete p.parent;if(p._selected){delete p._selected}if(p.children){p.children.forEach(n)}if(p._children){p._children.forEach(n)}}var o=jQuery.extend(true,{},this.attributes);o.selectedNode=null;show_message("Saving to 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t=s.enter().insert("svg:g","g.node").attr("class","completeLink");t.append("svg:path").attr("class","link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1});var r=s.transition().duration(500);r.select("path.link").attr("d",function(w){u(w);return"M "+w.pos0+" L "+w.pos1+" L "+w.pos2});var p=s.exit().remove()},selectNode:function(n){var m=this;l.selectAll("g.node").classed("selectedHighlight",function(o){if(n.id===o.id){if(n._selected){delete n._selected;return false}else{n._selected=true;return true}}return false});m.model.set("selectedNode",n);$("#phyloVizSelectedNodeName").val(n.name);$("#phyloVizSelectedNodeDist").val(n.dist);$("#phyloVizSelectedNodeAnnotation").val(n.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var n=this.__data__,m=n.annotation||"None";return n?(n.name?n.name+"<br/>":"")+"Dist: "+n.dist+" <br/>Annotation: "+m:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(n){var m=this;m.margins=n.margins;m.layoutMode="Linear";m.stdInit(n);m.layout();m.updateAndRender(m.model.root)},layout:function(){var m=this;m.tree=new g().layoutMode("Linear");m.diagonal=l.svg.diagonal().projection(function(n){return[n.y,n.x]})},renderNodes:function(m){var t=this,u=t.model.get("fontSize")+"px";t.tree.separation(t.model.get("separation")).leafHeight(t.model.get("leafHeight"));var p=500,n=t.tree.separation(t.model.get("separation")).nodes(t.model.root);var o=t.vis.selectAll("g.node").data(n,function(v){return v.name+v.id||(v.id=++t.i)});t.nodes=n;t.duration=p;var q=o.enter().append("svg:g").attr("class","node").on("dblclick",function(){l.event.stopPropagation()}).on("click",function(v){if(l.event.altKey){t.selectNode(v)}else{if(v.children&&v.children.length===0){return}t.model.toggle(v);t.updateAndRender(v)}});q.attr("transform",function(v){return"translate("+m.y0+","+m.x0+")"});q.append("svg:circle").attr("r",0.000001).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});q.append("svg:text").attr("class","nodeLabel").attr("x",function(v){return v.children||v._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(v){return v.children||v._children?"end":"start"}).style("fill-opacity",0.000001);var r=o.transition().duration(p);r.attr("transform",function(v){return"translate("+v.y+","+v.x+")"});r.select("circle").attr("r",t.defaults.nodeRadius).style("fill",function(v){return v._children?"lightsteelblue":"#fff"});r.select("text").style("fill-opacity",1).style("font-size",u).text(function(v){return v.name});var s=o.exit().transition().duration(p).remove();s.select("circle").attr("r",0.000001);s.select("text").style("fill-opacity",0.000001);n.forEach(function(v){v.x0=v.x;v.y0=v.y})}});var i=Backbone.View.extend({className:"phyloviz",initialize:function(n){var m=this;m.MIN_SCALE=0.05;m.MAX_SCALE=5;m.MAX_DISPLACEMENT=500;m.margins=[10,60,10,80];m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.radius=m.width;m.data=n.data;$(window).resize(function(){m.width=$("#PhyloViz").width();m.height=$("#PhyloViz").height();m.render()});m.phyloTree=new b(n.config);m.phyloTree.root=m.data;m.zoomFunc=l.behavior.zoom().scaleExtent([m.MIN_SCALE,m.MAX_SCALE]);m.zoomFunc.translate(m.phyloTree.get("translate"));m.zoomFunc.scale(m.phyloTree.get("scaleFactor"));m.navMenu=new c(m);m.settingsMenu=new h({phyloTree:m.phyloTree});m.nodeSelectionView=new e({phyloTree:m.phyloTree});m.search=new j();setTimeout(function(){m.zoomAndPan()},1000)},render:function(){var n=this;$("#PhyloViz").empty();n.mainSVG=l.select("#PhyloViz").append("svg:svg").attr("width",n.width).attr("height",n.height).attr("pointer-events","all").call(n.zoomFunc.on("zoom",function(){n.zoomAndPan()}));n.boundingRect=n.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",n.width).attr("height",n.height).attr("stroke","black").attr("fill","white");n.vis=n.mainSVG.append("svg:g").attr("class","vis");n.layoutOptions={model:n.phyloTree,width:n.width,height:n.height,vis:n.vis,margins:n.margins};$("#title").text("Phylogenetic Tree from "+n.phyloTree.get("title")+":");var m=new a(n.layoutOptions)},zoomAndPan:function(m){var s,o;if(typeof m!=="undefined"){s=m.zoom;o=m.translate}var v=this,q=v.zoomFunc.scale(),u=v.zoomFunc.translate(),r="",t="";switch(s){case"reset":q=1;u=[0,0];break;case"+":q*=1.1;break;case"-":q*=0.9;break;default:if(typeof s==="number"){q=s}else{if(l.event!==null){q=l.event.scale}}}if(q<v.MIN_SCALE||q>v.MAX_SCALE){return}v.zoomFunc.scale(q);r="translate("+v.margins[3]+","+v.margins[0]+") scale("+q+")";if(l.event!==null){t="translate("+l.event.translate+")"}else{if(typeof o!=="undefined"){var p=o.split(",")[0];var n=o.split(",")[1];if(!isNaN(p)&&!isNaN(n)){u=[u[0]+parseFloat(p),u[1]+parseFloat(n)]}}v.zoomFunc.translate(u);t="translate("+u+")"}v.phyloTree.set("scaleFactor",q);v.phyloTree.set("translate",u);v.vis.attr("transform",t+r)},reloadViz:function(){var n=this,p=$("#phylovizNexSelector :selected").val(),m=n.phyloTree.get("dataset_id"),o="phyloviz/getJsonData?dataset_id="+m+"&treeIndex="+String(p);$.getJSON(o,function(q){window.initPhyloViz(q.data,q.config)})}});var c=Backbone.View.extend({initialize:function(n){var m=this;m.phylovizView=n;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();m.initNavBtns();m.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){m.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var m=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();m.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var n=$("#phylovizNexSelector option:selected").text();if(n){m.phylovizView.phyloTree.set("title",n)}m.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz 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m=this;m.phyloTree=n.phyloTree;m.el=$("#SettingsMenu");m.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){m.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){m.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){m.apply()})},apply:function(){var m=this;if(!m.isAcceptableValue(m.inputs.separation,50,2500)||!m.isAcceptableValue(m.inputs.leafHeight,5,30)||!m.isAcceptableValue(m.inputs.fontSize,5,20)){return}$.each(m.inputs,function(n,o){m.phyloTree.set(n,o.val())})},updateUI:function(){var m=this;$.each(m.inputs,function(n,o){o.val(m.phyloTree.get(n))})},resetToDefaults:function(){$(".bs-tooltip").remove();var m=this;$.each(m.phyloTree.defaults,function(n,o){m.phyloTree.set(n,o)});m.updateUI()},render:function(){}});var e=k.extend({className:"Settings",initialize:function(n){var m=this;m.el=$("#nodeSelectionView");m.phyloTree=n.phyloTree;m.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};m.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){m.el.hide()});m.UI.saveChanges.off().on("click",function(){m.updateNodes()});m.UI.cancelChanges.off().on("click",function(){m.cancelChanges()});(function(o){o.fn.enable=function(p){return o(this).each(function(){if(p){o(this).removeAttr("disabled")}else{o(this).attr("disabled","disabled")}})}})(jQuery);m.UI.enableEdit.off().on("click",function(){m.toggleUI()})},toggleUI:function(){var m=this,n=m.UI.enableEdit.is(":checked");if(!n){m.cancelChanges()}$.each(m.valuesOfConcern,function(o,p){m.UI[o].enable(n)});if(n){m.UI.saveChanges.show();m.UI.cancelChanges.show()}else{m.UI.saveChanges.hide();m.UI.cancelChanges.hide()}},cancelChanges:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){$.each(m.valuesOfConcern,function(o,p){m.UI[o].val(n[o])})}},updateNodes:function(){var m=this,n=m.phyloTree.get("selectedNode");if(n){if(!m.isAcceptableValue(m.UI.dist,0,1)||m.hasIllegalJsonCharacters(m.UI.name)||m.hasIllegalJsonCharacters(m.UI.annotation)){return}$.each(m.valuesOfConcern,function(o,p){(n[o])=m.UI[o].val()});m.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var j=k.extend({initialize:function(){var m=this;$("#phyloVizSearchBtn").on("click",function(){var o=$("#phyloVizSearchTerm"),p=$("#phyloVizSearchCondition").val().split("-"),n=p[0],q=p[1];m.hasIllegalJsonCharacters(o);if(n==="dist"){m.isAcceptableValue(o,0,1)}m.searchTree(n,q,o.val())})},searchTree:function(m,o,n){l.selectAll("g.node").classed("searchHighlight",function(q){var p=q[m];if(typeof p!=="undefined"&&p!==null){if(m==="dist"){switch(o){case"greaterEqual":return p>=+n;case"lesserEqual":return p<=+n;default:return}}else{if(m==="name"||m==="annotation"){return p.toLowerCase().indexOf(n.toLowerCase())!==-1}}}})}});return{PhylovizView:i}}); \ No newline at end of file +define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(r,p,n){var o=this,s=r.val(),t=r.attr("displayLabel")||r.attr("id").replace("phyloViz","");function q(u){return !isNaN(parseFloat(u))&&isFinite(u)}if(!q(s)){alert(t+" is not a number!");return false}if(s>n){alert(t+" is too large.");return false}else{if(s<p){alert(t+" is 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C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t++*A}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);this.set("root",n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(p)},success:function(q){var r=q.url.split("id=")[1].split("&")[0],s="/visualization?id="+r;window.history.pushState({},"",s+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".bs-tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("http://wiki.g2.bx.psu.edu/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".bs-tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;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 x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);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;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=w;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+w+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+w+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-w});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+w});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new e(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new aa.Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};q(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};q(j.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{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:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ac,x,l,u,L,aa,i){var q=ac.extend;var Q=l.get_random_color;var ad=function(ae,ag,af){$.ajax({url:ae,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(ah){show_modal("Select datasets for new tracks",ah,{Cancel:function(){hide_modal()},Add:function(){var ai=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var aj={data_type:"track_config",hda_ldda:"hda"},ak=$(this).val();if($(this).attr("name")!=="id"){aj.hda_ldda="ldda"}ai[ai.length]=$.ajax({url:ag+"/"+ak,data:aj,dataType:"json"})});$.when.apply($,ai).then(function(){var aj=(arguments[0] instanceof Array?$.map(arguments,function(ak){return ak[0]}):[arguments[0]]);af(aj)});hide_modal()}})}})};var W=function(ae){return("isResolved" in ae)};var n={};var k=function(ae,af){n[ae.attr("id")]=af};var m=function(ae,ag,ai,ah){ai=".group";var af={};n[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=n[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=n[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}n[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);n[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));n[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=m;var ab=16,G=9,D=20,A=100,I=12000,T=400,K=5000,w=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",R=10,H=20;function X(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var r=function(af,ae,ah){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){r.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=p(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){q(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new i.FiltersManager(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof c){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new i.NumberFilter({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new f(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var Z=function(ae){q(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;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 x.CanvasManager(this.container.get(0).ownerDocument);this.reset()};ac.extend(Z.prototype,Backbone.Events);q(Z.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);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;k(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){ad(add_datasets_url,add_track_async_url,function(ai){ac.each(ai,function(aj){ae.add_drawable(p(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom 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af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var 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ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div 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O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new x.GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?X(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(af,ae,ag){q(ag,{drag_handle_class:"draghandle"});r.call(this,af,ae,ag);this.dataset=new aa.Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ac.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ac.map($(".bookmark"),function(ao){return new x.GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof U){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(v);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(V);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){g.call(this,ag,af,ah);var ae=this;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new i.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new s(this,ah.tool,ah.tool_state):null);this.tile_cache=new x.Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();q(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(W(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(W(al)){an=false}}if(an){q(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,aj,ak){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ai=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}ae.css({position:"absolute",top:0,left:ai});if(ae.hasClass("remove")){ae.removeClass("remove")}else{aj.append(ae)}ag.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ag.html_elt.height());ag.html_elt.parent().children().css("height",this.max_height_px+"px");var ah=this.max_height_px;if(this.visible_height_px!==0){ah=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ah+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new l.ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var Y=function(af,ae){var ag={resize:false};g.call(this,af,ae,ag);this.container_div.addClass("label-track")};q(Y.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var f=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=p(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(W(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(W(ap)){ar=false}}an.push(ap)}if(ar){q(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof h){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var h=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{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:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(X(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(X(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var t=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var c=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof j){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (u.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ab,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new j(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){c.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(S.prototype,r.prototype,M.prototype,c.prototype);var U=function(ag,af,ai){c.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{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:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(U.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:S,ReadTrack:U,CompositeTrack:f,DrawableGroup:P};var p=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new d[ah](af,ae,ag)}};return{View:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:U,VcfTrack:S,CompositeTrack:f,object_from_template:p,add_datasets:ad}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"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.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}var x;if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",tracks:null},relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{bookmarks:null,viewport:null})});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util"],function(q,h,j){var i=function(s){return("isResolved" in s)};var e=function(s){this.default_font=s!==undefined?s:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};q.extend(e.prototype,{load_pattern:function(s,w){var t=this.patterns,u=this.dummy_context,v=new Image();v.src=galaxy_paths.attributes.image_path+w;v.onload=function(){t[s]=u.createPattern(v,"repeat")}},get_pattern:function(s){return this.patterns[s]},new_canvas:function(){var s=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(s)}s.manager=this;return s}});var o=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(s){this.clear()},get_elt:function(t){var u=this.attributes.obj_cache,v=this.attributes.key_ary,s=v.indexOf(t);if(s!==-1){if(u[t].stale){v.splice(s,1);delete u[t]}else{this.move_key_to_end(t,s)}}return u[t]},set_elt:function(t,v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=this.attributes.num_elements;if(!w[t]){if(x.length>=u){var s=x.shift();delete w[s]}x.push(t)}w[t]=v;return v},move_key_to_end:function(t,s){this.attributes.key_ary.splice(s,1);this.attributes.key_ary.push(t)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var c=o.extend({defaults:q.extend({},o.prototype.defaults,{dataset:null,filters_manager:null,data_type:"data",data_mode_compatible:function(s,t){return true},can_subset:function(s){return false}}),data_is_ready:function(){var u=this.get("dataset"),t=$.Deferred(),s=new j.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:u.get("hda_ldda"),data_type:"state"},dataType:"json"},interval:5000,success_fn:function(v){return v!=="pending"}});$.when(s.go()).then(function(v){t.resolve(v==="ok"||v==="data")});return t},search_features:function(s){var t=this.get("dataset"),u={query:s,hda_ldda:t.get("hda_ldda"),data_type:"features"};return $.getJSON(t.url(),u)},load_data:function(A,z,t,y){var w=this.get("dataset"),v={data_type:this.get("data_type"),chrom:A.get("chrom"),low:A.get("start"),high:A.get("end"),mode:z,resolution:t,hda_ldda:w.get("hda_ldda")};$.extend(v,y);var C=this.get("filters_manager");if(C){var D=[];var s=C.filters;for(var x=0;x<s.length;x++){D.push(s[x].name)}v.filter_cols=JSON.stringify(D)}var u=this,B=$.getJSON(w.url(),v,function(E){u.set_data(A,E)});this.set_data(A,B);return B},get_data:function(y,x,u,w){var z=this.get_elt(y);if(z&&(i(z)||this.get("data_mode_compatible")(z,x))){return z}var A=this.get("key_ary"),t=this.get("obj_cache"),B,s;for(var v=0;v<A.length;v++){B=A[v];s=new f({from_str:B});if(s.contains(y)){z=t[B];if(i(z)||(this.get("data_mode_compatible")(z,x)&&this.get("can_subset")(z))){this.move_key_to_end(B,v);return z}}}return this.load_data(y,x,u,w)},set_data:function(t,s){this.set_elt(t,s)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(A,z,v,y,w){var C=this._mark_stale(A);if(!(C&&this.get("data_mode_compatible")(C,z))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var u=A.get("start");if(w===this.DEEP_DATA_REQ){$.extend(y,{start_val:C.data.length+1})}else{if(w===this.BROAD_DATA_REQ){u=(C.max_high?C.max_high:C.data[C.data.length-1][2])+1}}var B=A.copy().set("start",u);var t=this,x=this.load_data(B,z,v,y),s=$.Deferred();this.set_data(A,s);$.when(x).then(function(D){if(D.data){D.data=C.data.concat(D.data);if(D.max_low){D.max_low=C.max_low}if(D.message){D.message=D.message.replace(/[0-9]+/,D.data.length)}}t.set_data(A,D);s.resolve(D)});return s},get_more_detailed_data:function(v,x,t,w,u){var s=this._mark_stale(v);if(!s){console.log("ERROR getting more detailed data: no current data");return}if(!u){u={}}if(s.dataset_type==="bigwig"){u.num_samples=s.data.length*w}else{if(s.dataset_type==="summary_tree"){u.level=Math.min(s.level-1,2)}}return this.load_data(v,x,t,u)},_mark_stale:function(t){var s=this.get_elt(t);if(!s){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),t.toString())}s.stale=true;return s},get_elt:function(s){return o.prototype.get_elt.call(this,s.toString())},set_elt:function(t,s){return o.prototype.set_elt.call(this,t.toString(),s)}});var m=c.extend({initialize:function(s){var t=new Backbone.Model();t.urlRoot=s.data_url;this.set("dataset",t)},load_data:function(u,v,s,t){console.log(u,v,s);if(s>1){return{data:null}}return c.prototype.load_data.call(this,u,v,s,t)}});var b=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(s){this.id=s.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(s){var t=q.find(this.get_chroms_info(),function(u){return u.chrom==s});return new f({chrom:t.chrom,end:t.len})}});var f=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(t){if(t.from_str){var v=t.from_str.split(":"),u=v[0],s=v[1].split("-");this.set({chrom:u,start:parseInt(s[0],10),end:parseInt(s[1],10)})}},copy:function(){return new f({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(z){var t=this.get("chrom"),y=z.get("chrom"),x=this.get("start"),v=z.get("start"),w=this.get("end"),u=z.get("end"),s;if(t&&y&&t!==y){return this.get("DIF_CHROMS")}if(x<v){if(w<v){s=this.get("BEFORE")}else{if(w<=u){s=this.get("OVERLAP_START")}else{s=this.get("CONTAINS")}}}else{if(x>u){s=this.get("AFTER")}else{if(w<=u){s=this.get("CONTAINED_BY")}else{s=this.get("OVERLAP_END")}}}return s},contains:function(s){return this.compute_overlap(s)===this.get("CONTAINS")},overlaps:function(s){return q.intersection([this.compute_overlap(s)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var l=Backbone.Collection.extend({model:f});var d=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:f}]});var p=Backbone.Collection.extend({model:d});var r=h.Dataset.extend({initialize:function(s){this.set("id",s.dataset_id);var t=new c({dataset:this});this.set("data_manager",t);var u=this.get("preloaded_data");if(u){t.set("num_elements",u.data.length);q.each(u.data,function(v){t.set_data(v.region,v)})}},get_genome_wide_data:function(s){var t=this.get("data_manager");return q.map(s.get("chroms_info").chrom_info,function(u){return t.get_elt(new f({chrom:u.chrom,start:0,end:u.len}))})}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:q.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:r}],add_track:function(s){this.get("tracks").push(s)}});var a=Backbone.Model.extend({});var g=Backbone.Router.extend({initialize:function(t){this.view=t.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var s=this;s.view.on("navigate",function(u){s.navigate(u)})},change_location:function(s){this.view.go_to(s)}});return{BackboneTrack:r,BrowserBookmark:d,BrowserBookmarkCollection:p,Cache:o,CanvasManager:e,Genome:b,GenomeDataManager:c,GenomeRegion:f,GenomeRegionCollection:l,GenomeVisualization:k,ReferenceTrackDataManager:m,TrackBrowserRouter:g,TrackConfig:a,Visualization:n}}); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-chartSettings.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-chartSettings.js @@ -0,0 +1,42 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-chartSettings'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + + return "checked";} + + buffer += "<p class=\"help-text\">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n <div id=\"maxDataPoints\" class=\"form-input numeric-slider-input\">\n <label for=\"maxDataPoints\">Maximum data points allowed on graph: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.maxDataPoints; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.maxDataPoints; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Change the maximum number of data points displayable on this graph (higher values will\n load significantly slower)\n </p>\n </div>\n\n <div id=\"datapointSize\" class=\"form-input numeric-slider-input\">\n <label for=\"datapointSize\">Size of data point: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.datapointSize; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.datapointSize; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n Size of the graphic representation of each data point\n </p>\n </div>\n\n <div id=\"entryAnimDuration\" class=\"form-input checkbox-input\">\n <label for=\"animated\">Animate graph transitions?: </label>\n <input type=\"checkbox\" id=\"animated\" class=\"checkbox control\" value=\""; + stack1 = depth0.entryAnimDuration; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\" />\n <p class=\"form-help help-text-small\">\n Uncheck this to disable the animations used on the graph\n </p>\n </div>\n\n <div id=\"width\" class=\"form-input numeric-slider-input\">\n <label for=\"width\">Graph width: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.width; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.width; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"height\" class=\"form-input numeric-slider-input\">\n <label for=\"height\">Graph height: </label>\n <div class=\"slider-output\">"; + foundHelper = helpers.height; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.height; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</div>\n <div class=\"slider\"></div>\n <p class=\"form-help help-text-small\">\n (not including graph margins and axes)\n </p>\n </div>\n\n <div id=\"X-axis-label\"class=\"text-input form-input\">\n <label for=\"X-axis-label\">Re-label the X axis: </label>\n <input type=\"text\" name=\"X-axis-label\" id=\"X-axis-label\" value=\""; + foundHelper = helpers.xLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <div id=\"Y-axis-label\" class=\"text-input form-input\">\n <label for=\"Y-axis-label\">Re-label the Y axis: </label>\n <input type=\"text\" name=\"Y-axis-label\" id=\"Y-axis-label\" value=\""; + foundHelper = helpers.yLabel; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yLabel; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\" />\n <p class=\"form-help help-text-small\"></p>\n </div>\n\n <input id=\"render-button\" type=\"button\" value=\"Draw\" />"; + return buffer;}); +})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js @@ -32,20 +32,45 @@ buffer += escapeExpression(stack1) + "</option>\n "; return buffer;} +function program5(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <option value=\""; + foundHelper = helpers.index; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.index; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\">"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</option>\n "; + return buffer;} + + buffer += "\n\n<ul class=\"nav nav-tabs\">\n <li class=\"active\">\n <a data-toggle=\"tab\" href=\"#data-settings\">Data Controls</a>\n </li>\n <li><a data-toggle=\"tab\" href=\"#chart-settings\">Plot Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-stats\">Statistics</a></li>\n</ul>\n\n"; + buffer += "\n<div class=\"tab-content\">\n<div id=\"data-settings\" class=\"tab-pane active\">\n\n <p class=\"help-text\">\n Use the following controls to change the data used by the chart.\n Use the 'Draw' button to render (or re-render) the chart with the current settings.\n </p>\n \n "; + buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n <div class=\"column-select\">\n <label for=\"Y-select\">Data column for Y: </label>\n <select name=\"Y\" id=\"Y-select\">\n "; + stack1 = depth0.numericColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n \n "; + buffer += "\n <div id=\"include-id\">\n <label for=\"include-id-checkbox\">Include a third column as data point IDs?</label>\n <input type=\"checkbox\" name=\"include-id\" id=\"include-id-checkbox\" />\n <p class=\"help-text-small\">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n </div>\n <div class=\"column-select\" style=\"display: none\">\n <label for=\"ID-select\">Data column for IDs: </label>\n <select name=\"ID\" id=\"ID-select\">\n "; + stack1 = depth0.allColumns; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <input id=\"save-button\" type=\"button\" value=\"Download Plot as SVG\" style=\"display: none;\" />\n <div class=\"clear\"></div>\n</div>\n\n<div id=\"chart-settings\" class=\"tab-pane\">\n</div>\n\n<div id=\"chart-stats\" class=\"tab-pane\">\n</div>\n</div>"; + buffer += "\n\n"; buffer += "\n<div id=\"loading-indicator\" style=\"display: none;\">\n <img class=\"loading-img\" src=\""; foundHelper = helpers.loadingIndicatorImagePath; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } else { stack1 = depth0.loadingIndicatorImagePath; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\"></span>\n</div>\n\n"; - buffer += "\n<div id=\"chart-settings\">\n\n "; - buffer += "\n <div id=\"x-column-input\">\n <label for=\"\">Data column for X: </label>\n <select name=\"x-column\">\n "; - stack1 = depth0.availableColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n <div id=\"y-column-input\">\n <label for=\"\">Data column for Y: </label>\n <select name=\"y-column\">\n "; - stack1 = depth0.availableColumns; - stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </select>\n </div>\n \n <input id=\"render-button\" type=\"button\" value=\"Draw\" />\n <div class=\"clear\"></div>\n</div>"; + buffer += escapeExpression(stack1) + "\" />\n <span class=\"loading-message\">"; + foundHelper = helpers.message; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</span>\n</div>"; return buffer;}); })(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/compiled/template-visualization-statsTable.js --- /dev/null +++ b/static/scripts/templates/compiled/template-visualization-statsTable.js @@ -0,0 +1,31 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-visualization-statsTable'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <tr><td>"; + foundHelper = helpers.name; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.xval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.xval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td><td>"; + foundHelper = helpers.yval; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.yval; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "</td></tr>\n </tr>\n "; + return buffer;} + + buffer += "<p class=\"help-text\">By column:</p>\n <table id=\"chart-stats-table\">\n <thead><th></th><th>X</th><th>Y</th></thead>\n "; + stack1 = depth0.stats; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </table>"; + return buffer;}); +})(); \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -1,33 +1,155 @@ <script type="text/template" class="template-visualization" id="template-visualization-scatterplotControlForm"> +{{! main controls }} -{{! loading indicator - initially hidden }} -<div id="loading-indicator" style="display: none;"> - <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> - <span class="loading-message"></span> -</div> +<ul class="nav nav-tabs"> + <li class="active"> + <a data-toggle="tab" href="#data-settings">Data Controls</a> + </li> + <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li> + <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li> +</ul> -{{! main controls }} -<div id="chart-settings"> +{{! data settings }} +<div class="tab-content"> +<div id="data-settings" class="tab-pane active"> + <p class="help-text"> + Use the following controls to change the data used by the chart. + Use the 'Draw' button to render (or re-render) the chart with the current settings. + </p> + {{! column selector containers }} - <div id="x-column-input"> - <label for="">Data column for X: </label> - <select name="x-column"> - {{#each availableColumns}} + <div class="column-select"> + <label for="X-select">Data column for X: </label> + <select name="X" id="X-select"> + {{#each numericColumns}} <option value="{{index}}">{{name}}</option> {{/each}} </select></div> - <div id="y-column-input"> - <label for="">Data column for Y: </label> - <select name="y-column"> - {{#each availableColumns}} + <div class="column-select"> + <label for="Y-select">Data column for Y: </label> + <select name="Y" id="Y-select"> + {{#each numericColumns}} + <option value="{{index}}">{{name}}</option> + {{/each}} + </select> + </div> + + {{! optional id column }} + <div id="include-id"> + <label for="include-id-checkbox">Include a third column as data point IDs?</label> + <input type="checkbox" name="include-id" id="include-id-checkbox" /> + <p class="help-text-small"> + These will be displayed (along with the x and y values) when you hover over + a data point. + </p> + </div> + <div class="column-select" style="display: none"> + <label for="ID-select">Data column for IDs: </label> + <select name="ID" id="ID-select"> + {{#each allColumns}} <option value="{{index}}">{{name}}</option> {{/each}} </select></div><input id="render-button" type="button" value="Draw" /> + <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" /><div class="clear"></div></div> + +<div id="chart-settings" class="tab-pane"> +</div> + +<div id="chart-stats" class="tab-pane"> +</div> +</div>{{! class="tab-content" }} + +{{! loading indicator - initially hidden }} +<div id="loading-indicator" style="display: none;"> + <img class="loading-img" src="{{loadingIndicatorImagePath}}" /> + <span class="loading-message">{{message}}</span> +</div> + </script> + +<script type="text/template" class="template-visualization" id="template-visualization-statsTable"> + <p class="help-text">By column:</p> + <table id="chart-stats-table"> + <thead><th></th><th>X</th><th>Y</th></thead> + {{#each stats}} + <tr><td>{{name}}</td><td>{{xval}}</td><td>{{yval}}</td></tr> + </tr> + {{/each}} + </table> +</script> + +<script type="text/template" class="template-visualization" id="template-visualization-chartSettings"> + + <p class="help-text"> + Use the following controls to how the chart is displayed. + The slide controls can be moved by the mouse or, if the 'handle' is in focus, your keyboard's arrow keys. + Move the focus between controls by using the tab or shift+tab keys on your keyboard. + Use the 'Draw' button to render (or re-render) the chart with the current settings. + </p> + + <div id="maxDataPoints" class="form-input numeric-slider-input"> + <label for="maxDataPoints">Maximum data points allowed on graph: </label> + <div class="slider-output">{{maxDataPoints}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + Change the maximum number of data points displayable on this graph (higher values will + load significantly slower) + </p> + </div> + + <div id="datapointSize" class="form-input numeric-slider-input"> + <label for="datapointSize">Size of data point: </label> + <div class="slider-output">{{datapointSize}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + Size of the graphic representation of each data point + </p> + </div> + + <div id="entryAnimDuration" class="form-input checkbox-input"> + <label for="animated">Animate graph transitions?: </label> + <input type="checkbox" id="animated" class="checkbox control" value="{{#if entryAnimDuration}}checked{{/if}}" /> + <p class="form-help help-text-small"> + Uncheck this to disable the animations used on the graph + </p> + </div> + + <div id="width" class="form-input numeric-slider-input"> + <label for="width">Graph width: </label> + <div class="slider-output">{{width}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + (not including graph margins and axes) + </p> + </div> + + <div id="height" class="form-input numeric-slider-input"> + <label for="height">Graph height: </label> + <div class="slider-output">{{height}}</div> + <div class="slider"></div> + <p class="form-help help-text-small"> + (not including graph margins and axes) + </p> + </div> + + <div id="X-axis-label"class="text-input form-input"> + <label for="X-axis-label">Re-label the X axis: </label> + <input type="text" name="X-axis-label" id="X-axis-label" value="{{xLabel}}" /> + <p class="form-help help-text-small"></p> + </div> + + <div id="Y-axis-label" class="text-input form-input"> + <label for="Y-axis-label">Re-label the Y axis: </label> + <input type="text" name="Y-axis-label" id="Y-axis-label" value="{{yLabel}}" /> + <p class="form-help help-text-small"></p> + </div> + + <input id="render-button" type="button" value="Draw" /> +</script> \ No newline at end of file diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,54 +1,66 @@ define([ + //"../libs/jquery/jquery", + "../libs/underscore", + "../mvc/base-mvc", + "../templates/compiled/template-visualization-scatterplotControlForm", + "../templates/compiled/template-visualization-statsTable", + "../templates/compiled/template-visualization-chartSettings", + "../libs/d3", - "../mvc/base-mvc", - "../templates/compiled/template-visualization-scatterplotControlForm" + "../libs/bootstrap", + "../libs/jquery/jquery-ui-1.8.23.custom.min" ], function(){ + + + /* ============================================================================= todo: outside this: BUG: visualization menu doesn't disappear - BUG?: get column_names (from datatype if necessary) + BUG?: get metadata_column_names (from datatype if necessary) BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' - ??: maybe better to do this with a canvas... + wire label setters, anim setter - move renderScatter plot to obj, possibly view? + TwoVarScatterplot: + ??: maybe better to do this with a canvas... + save as visualization + to seperate file? + remove underscore dependencies + add interface to change values (seperate)? + download svg -> base64 encode + incorporate glyphs, glyph state renderers + + ScatterplotSettingsForm: + some css bug that lowers the width of settings form when plot-controls tab is open + causes chart to shift + what can be abstracted/reused for other graphs? + avoid direct manipulation of this.plot + allow option to put plot into seperate tab of interface (for small multiples) - fix x axis - adjust ticks when tick labels are long - move odds down and extend tick line - - provide callback in view to load data incrementally - for large sets - - paginate - handle rerender - use endpoint (here and on the server (fileptr)) - fetch (new?) data - handle rerender + provide callback in view to load data incrementally - for large sets + paginate + handle rerender + use endpoint (here and on the server (fileptr)) + fetch (new?) data + handle rerender + use d3.TSV? + render warning on long data (> maxDataPoints) + adjust endpoint - selectable list of preset column comparisons (rnaseq etc.) - multiple plots on one page (small multiples) - - where are bad dataprovider params handled? api/datasets? + selectable list of preset column comparisons (rnaseq etc.) + how to know what sort of Tabular the data is? + smarter about headers + validate columns selection (here or server) - config changes to the graph - render stats on the data (max, min, count) - render warning on long data (> maxDataPoints) - adjust endpoint - - loading indicator - - download svg -> base64 encode - dress up ui - - incorporate glyphs, glyph state renderers - - validate columns selection (here or server) - - ?? ensure svg styles thru d3 or css? - d3: configable (easily) - css: standard - better maintenance - ? override at config + Scatterplot.mako: + multiple plots on one page (small multiples) + ?? ensure svg styles thru d3 or css? + d3: configable (easily) + css: standard - better maintenance + ? override at config ============================================================================= */ /** @@ -61,8 +73,7 @@ * depends on: d3, underscore */ function TwoVarScatterplot( config ){ - var plot = this, - TICK_LINE_AND_PADDING = 10, + var TICK_LINE_AND_PADDING = 10, GUESS_AT_SVG_CHAR_WIDTH = 7, GUESS_AT_SVG_CHAR_HEIGHT = 10, PADDING = 8, @@ -73,7 +84,7 @@ if( this.debugging && console && console.debug ){ var args = Array.prototype.slice.call( arguments ); args.unshift( this.toString() ); - console.debug.apply( null, args ); + console.debug.apply( console, args ); } }; this.log( 'new TwoVarScatterplot:', config ); @@ -84,10 +95,10 @@ this.defaults = { id : 'TwoVarScatterplot', containerSelector : 'body', - maxDataPoints : 30000, - bubbleRadius : 4, + maxDataPoints : 10000, + datapointSize : 4, entryAnimDuration : 500, - //TODO: no effect? + //TODO: variable effect (not always exactly # of ticks set to) xNumTicks : 10, yNumTicks : 10, xAxisLabelBumpY : 40, @@ -99,10 +110,12 @@ marginRight : 50, marginBottom : 50, marginLeft : 50, + xMin : null, xMax : null, yMin : null, yMax : null, + xLabel : "X", yLabel : "Y" }; @@ -126,8 +139,9 @@ // ........................................................ initial element creation //NOTE: called on new this.svg = d3.select( this.config.containerSelector ) - .append( "svg:svg" ).attr( "class", "chart" ).style( 'display', 'none' ); - this.content = this.svg.append( "svg:g" ).attr( "class", "content" ); + .append( "svg:svg" ).attr( "class", "chart" ); + + this.content = this.svg.append( "svg:g" ).attr( "class", "content" ).attr( 'id', this.config.id ); this.xAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'x-axis' ); this.xAxisLabel = this.xAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'x-axis-label' ); @@ -157,7 +171,9 @@ }; // ........................................................ data and scales - this.preprocessData = function( data ){ + this.preprocessData = function( data, min, max ){ + //TODO: filter by min, max if set + // set a cap on the data, limit to first n points return ( data.length > this.config.maxDataPoints )? ( data.slice( 0, this.config.maxDataPoints ) ): ( data ); }; @@ -313,63 +329,110 @@ }; - this.renderDatapoints = function( xCol, yCol ){ + this.renderDatapoints = function( xCol, yCol, ids ){ + // initial render, complete re-render (REPLACE datapoints) - var xPosFn = function( d, i ){ - return plot.xScale( xCol[ i ] ); - }; - var yPosFn = function( d, i ){ - return plot.yScale( yCol[ i ] ); - }; - - // select all existing glyphs and compare to incoming data - // enter() will yield those glyphs that need to be added - // exit() will yield existing glyphs that need to be removed - this.datapoints = this.content.selectAll( ".glyph" ) - .data( xCol ); - - // enter - new data to be added as glyphs: give them a 'entry' position and style - this.datapoints.enter() - .append( "svg:circle" ).attr( "class", "glyph" ) - // start all bubbles at corner... - .attr( "cx", xPosFn ) - .attr( "cy", 0 ) - .attr( "r", 0 ); - - // for all existing glyphs and those that need to be added: transition anim to final state - this.datapoints - // ...animate to final position - .transition().duration( this.config.entryAnimDuration ) - .attr( "cx", xPosFn ) - .attr( "cy", yPosFn ) - .attr( "r", this.config.bubbleRadius ); + this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM this.datapoints.exit() .transition().duration( this.config.entryAnimDuration ) .attr( "cy", this.config.height ) .attr( "r", 0 ) - .style( "fill-opacity", 0 ) .remove(); - //this.log( this.datapoints, 'glyphs rendered' ); + this.log( this.datapoints, 'glyphs rendered' ); + }; + + this.addDatapoints = function( newXCol, newYCol, ids, selectorForExisting ){ + // ADD datapoints to plot that's already rendered + // if selectorForExisting === undefined (as in not passed), addDatapoints won't update existing + // pass in the class ( '.glyph' ) to update exising datapoints + var plot = this, + xPosFn = function( d, i ){ + return plot.xScale( newXCol[ i ] ); + }, + yPosFn = function( d, i ){ + return plot.yScale( newYCol[ i ] ); + }; + + // select all existing glyphs and compare to incoming data + // enter() will yield those glyphs that need to be added + var newDatapoints = this.content.selectAll( selectorForExisting ).data( newXCol ); + + // enter - new data to be added as glyphs: give them a 'entry' position and style + newDatapoints.enter() + .append( "svg:circle" ) + .classed( "glyph", true ) + // start all bubbles small... + .attr( "cx", xPosFn ) + .attr( "cy", yPosFn ) + .attr( "r", 0 ); + + // for all existing glyphs and those that need to be added: transition anim to final state + newDatapoints + // ...animate to final position + .transition().duration( this.config.entryAnimDuration ) + .attr( "r", this.config.datapointSize ); + + // attach ids + if( ids ){ + newDatapoints.attr( 'data', function( d, i ){ return ( ids[ i ] ); } ); + } + + // titles + newDatapoints.attr( 'title', function( d, i ){ + return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; + }); + + // events + newDatapoints + //TODO: remove magic numbers + .on( 'mouseover', function(){ + var datapoint = d3.select( this ); + datapoint + .style( 'fill', 'red' ) + .style( 'fill-opacity', 1 ); + + // create horiz, vert lines to axis + plot.content.append( 'line' ) + .attr( 'stroke', 'red' ) + .attr( 'stroke-width', 1 ) + .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) + .attr( 'x2', 0 ).attr( 'y2', datapoint.attr( 'cy' ) ) + .classed( 'hoverline', true ); + plot.content.append( 'line' ) + .attr( 'stroke', 'red' ) + .attr( 'stroke-width', 1 ) + .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) + .attr( 'x2', datapoint.attr( 'cx' ) ).attr( 'y2', plot.config.height ) + .classed( 'hoverline', true ); + }) + .on( 'mouseout', function(){ + d3.select( this ) + .style( 'fill', 'black' ) + .style( 'fill-opacity', 0.2 ); + + d3.selectAll( '.hoverline' ).remove(); + }); + + return newDatapoints; }; this.render = function( columnData, meta ){ //pre: columns passed are numeric //pre: at least two columns are passed - //assume: first column is x, second column is y, any remaining aren't used + //assume: first column is x, second column is y, any remaining aren't used var xCol = columnData[0], - yCol = columnData[1]; + yCol = columnData[1], + ids = ( columnData.length > 2 )?( columnData[2] ):( undefined ); this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); //pre: xCol.len == yCol.len - //TODO: ^^ isn't necessarily true with current ColumnDataProvider xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); - //TODO: compute min, max on server. this.setUpDomains( xCol, yCol, meta ); this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); @@ -380,28 +443,31 @@ this.setUpYAxis(); this.renderGrid(); - this.renderDatapoints( xCol, yCol ); - //TODO: on hover red line to axes, display values + this.renderDatapoints( xCol, yCol, ids ); }; } //============================================================================== /** * Scatterplot control UI as a backbone view - * + * handles: + * getting the desired data + * configuring the plot display */ var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ //logger : console, tagName : 'form', className : 'scatterplot-settings-form', - loadingIndicatorImagePath : ( galaxy_paths.get( 'image_path' ) + '/loading_large_white_bg.gif' ), + loadingIndicatorImage : 'loading_large_white_bg.gif', events : { - 'click #render-button' : 'renderScatterplot' + 'click #render-button' : 'renderPlot', + 'click #include-id-checkbox' : 'toggleThirdColumnSelector' }, initialize : function( attributes ){ + if( !attributes || !attributes.dataset ){ throw( "ScatterplotView requires a dataset" ); } else { @@ -414,106 +480,230 @@ // set up the basic chart infrastructure with config (if any) this.chartConfig = attributes.chartConfig || {}; - this.log( 'this.chartConfig:', this.chartConfig ); + this.log( 'initial chartConfig:', this.chartConfig ); this.plot = new TwoVarScatterplot( this.chartConfig ); + this.chartConfig = this.plot.config; + + this.$statsPanel = null; + this.$chartSettingsPanel = null; + this.$dataSettingsPanel = null; + this.dataFetch = null; }, render : function(){ var view = this, - html = ''; + formData = { + config : this.chartConfig, + allColumns : [], + numericColumns : [], + loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage + }; + + // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) + _.each( this.dataset.metadata_column_types.split( ', ' ), function( type, index ){ + //TODO: using 0-based indeces + // label with the name if available (fall back on 'column <index>') + var name = 'column ' + ( index + 1 ); + if( view.dataset.metadata_column_names ){ + name = view.dataset.metadata_column_names[ index ]; + } - // build column select controls for each x, y (based on name if available) - var formData = { - loadingIndicatorImagePath : this.loadingIndicatorImagePath, - config : this.chartConfig, - availableColumns : [] - }; - _.each( this.dataset.metadata_column_types.split( ', ' ), function( type, index ){ - // use only numeric columns + // filter numeric columns to their own list if( type === 'int' || type === 'float' ){ - //TODO: using 0-based indeces - var name = 'column ' + index; - // label with the name if available - if( view.dataset.metadata_column_names ){ - name = view.dataset.metadata_column_names[ index ]; - } - formData.availableColumns.push({ index: index, name: name }); + formData.numericColumns.push({ index: index, name: name }); } + formData.allColumns.push({ index: index, name: name }); }); - //TODO: other vals: max_vals, start_val, pagination - html = ScatterplotControlForm.templates.form( formData ); - this.$el.append( html ); + //TODO: other vals: max_vals, start_val, pagination (plot-settings) + + this.$el.append( ScatterplotControlForm.templates.form( formData ) ); + this.$dataSettingsPanel = this.$el.find( '.tab-pane#data-settings' ); + this.$chartSettingsPanel = this._render_chartSettings(); + this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); + + this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); return this; }, - showLoadingIndicator : function( message ){ + _render_chartSettings : function(){ + var chartControl = this, + $chartSettingsPanel = this.$el.find( '.tab-pane#chart-settings' ), + // limits for controls (by control/chartConfig id) + controlRanges = { + 'maxDataPoints' : { min: 1000, max: 30000, step: 100 }, + 'datapointSize' : { min: 2, max: 10, step: 1 }, + 'width' : { min: 200, max: 800, step: 20 }, + 'height' : { min: 200, max: 800, step: 20 } + }; + + // render the html + $chartSettingsPanel.append( ScatterplotControlForm.templates.chartSettings( this.chartConfig ) ); + + // set up js on controls + // sliders + $chartSettingsPanel.find( '.numeric-slider-input' ).each( function(){ + var $this = $( this ), + $output = $this.find( '.slider-output' ), + $slider = $this.find( '.slider' ), + id = $this.attr( 'id' ); + chartControl.log( 'slider set up', 'this:', $this, 'slider:', $slider, 'id', id ); + + // what to do when the slider changes: update display and update chartConfig + function onSliderChange(){ + var $this = $( this ), + newValue = $this.slider( 'value' ); + //chartControl.log( 'slider change', 'this:', $this, 'output:', $output, 'value', newValue ); + $output.text( newValue ); + chartControl.chartConfig[ id ] = newValue; + } + + $slider.slider( _.extend( controlRanges[ id ], { + value : chartControl.chartConfig[ id ], + change : onSliderChange, + slide : onSliderChange + })); + }); + + //TODO: anim checkbox + //TODO: labels -> renderPlot + + return $chartSettingsPanel; + }, + + toggleThirdColumnSelector : function(){ + this.$el.find( 'select[name="ID"]' ).parent().toggle(); + }, + + showLoadingIndicator : function( message, callback ){ message = message || ''; - this.$el.find( 'div#loading-indicator' ).children( '.loading-message' ).text( message ); - this.$el.find( 'div#loading-indicator' ).show( 'fast' ); + var indicator = this.$el.find( 'div#loading-indicator' ); + messageBox = indicator.find( '.loading-message' ); + + if( indicator.is( ':visible' ) ){ + if( message ){ + messageBox.fadeOut( 'fast', function(){ + messageBox.text( message ); + messageBox.fadeIn( 'fast', callback ); + }); + } else { + callback(); + } + + } else { + if( message ){ messageBox.text( message ); } + indicator.fadeIn( 'fast', callback ); + } }, - hideLoadingIndicator : function(){ - this.$el.find( 'div#loading-indicator' ).hide( 'fast' ); + hideLoadingIndicator : function( callback ){ + this.$el.find( 'div#loading-indicator' ).fadeOut( 'fast', callback ); }, - renderScatterplot : function(){ + getColumnVals : function(){ + // returns a map: { column-select name (eg. X) : { colIndex : column-selector val, + // colName : selected option text }, ... } + var selections = {}; + this.$el.find( 'div.column-select select' ).each( function(){ + var $this = $( this ), + val = $this.val(); + selections[ $this.attr( 'name' ) ] = { + colIndex : val, + colName : $this.children( '[value="' + val + '"]' ).text() + }; + }); + return selections; + }, + + fetchData : function( params, callbackFn ){ + var view = this, + url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&' + jQuery.param( params ); + this.log( 'url:', url ); + + this.showLoadingIndicator( 'Fetching data...', function(){ + jQuery.ajax({ + url : url, + dataType : 'json', + success : callbackFn, + error : function( xhr, status, error ){ + view.hideLoadingIndicator(); + alert( 'ERROR:' + status + '\n' + error ); + } + }); + }); + }, + + renderPlot : function(){ // parse the column values for both // indeces (for the data fetch) and names (for the graph) var view = this, - url = this.apiDatasetsURL + '/' + this.dataset.id + '?data_type=raw_data&', + columnSelections = this.getColumnVals(), + columns = []; + this.log( 'columnSelections:', columnSelections ); - xSelector = this.$el.find( '[name="x-column"]' ), - xVal = xSelector.val(), - xName = xSelector.children( '[value="' + xVal + '"]' ).text(), - - ySelector = this.$el.find( '[name="y-column"]' ), - yVal = ySelector.val(), - yName = ySelector.children( '[value="' + yVal + '"]' ).text(); - this.log( xName, yName ); - - this.chartConfig.xLabel = xName; - this.chartConfig.yLabel = yName; + //TODO: ?? could be moved into getColumnVals; + this.log( columnSelections.X.val, columnSelections.Y.val ); + this.xColIndex = columnSelections.X.colIndex; + this.yColIndex = columnSelections.Y.colIndex; + columns = [ this.xColIndex, this.yColIndex ]; + + // include the desired ID column + if( $( '#include-id-checkbox' ).attr( 'checked' ) ){ + columns.push( columnSelections.ID.colIndex ); + } + + this.log( columnSelections.X.colName, columnSelections.Y.colName ); + this.plot.xLabel = this.chartConfig.xLabel = columnSelections.X.colName; + this.plot.xLabel = this.chartConfig.yLabel = columnSelections.Y.colName; //TODO: alter directly - view.plot.updateConfig( this.chartConfig ); - + view.plot.updateConfig( this.chartConfig, false ); //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string //TODO: other vals: max, start, page //TODO: chart config // fetch the data, sending chosen columns to the server - url += jQuery.param({ - columns : '[' + [ xVal, yVal ] + ']' + var params = { + columns : '[' + columns + ']' + }; + + //TODO: prob. better to use events rather than callback chains like this + this.fetchData( params, function( response ){ + // save the endpoint (number of next line, fileptr) for this object + //TODO: server sends back an endpoint, cache for next pagination request + view.dataFetch = response; + view.showLoadingIndicator( 'Rendering...', function(){ + view.plot.render( response.data, response.meta ); + + view.renderStats( response.data, response.meta ); + view.$el.find( 'ul.nav' ).find( 'a[href="#chart-stats"]' ).tab( 'show' ); + + view.hideLoadingIndicator(); + }); }); - this.log( 'url:', url ); - - this.showLoadingIndicator( 'Fetching data...' ); - jQuery.ajax({ - url : url, - dataType : 'json', - success : function( response ){ - // save the endpoint (number of next line, fileptr) for this object - //TODO: server sends back an endpoint, cache for next pagination request - view.endpoint = response.endpoint; - - view.showLoadingIndicator( 'Rendering...' ); - view.plot.render( response.data, response.meta ); - view.hideLoadingIndicator(); - }, - - error : function( xhr, status, error ){ - view.hideLoadingIndicator(); - alert( 'ERROR:' + status + '\n' + error ); - } - }); + }, + + renderStats : function(){ + this.$statsPanel.html( ScatterplotControlForm.templates.statsTable({ + stats: [ + { name: 'Count', xval: this.dataFetch.meta[0].count, yval: this.dataFetch.meta[1].count }, + { name: 'Min', xval: this.dataFetch.meta[0].min, yval: this.dataFetch.meta[1].min }, + { name: 'Max', xval: this.dataFetch.meta[0].max, yval: this.dataFetch.meta[1].max }, + { name: 'Mean', xval: this.dataFetch.meta[0].mean, yval: this.dataFetch.meta[1].mean }, + { name: 'Median', xval: this.dataFetch.meta[0].median, yval: this.dataFetch.meta[1].median } + ] + })); + }, + + toString : function(){ + return 'ScatterplotControlForm(' + attributes.dataset.id + ')'; } }); -ScatterplotControlForm.templates = CompiledTemplateLoader.getTemplates({ - 'visualization-templates.html' : { - form : 'template-visualization-scatterplotControlForm' - } -}); +ScatterplotControlForm.templates = { + form : Handlebars.templates[ 'template-visualization-scatterplotControlForm' ], + statsTable : Handlebars.templates[ 'template-visualization-statsTable' ], + chartSettings : Handlebars.templates[ 'template-visualization-chartSettings' ] +}; //============================================================================== return { diff -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 -r 0684f69e527da908b27fc78e0f0d15ddef5ea33b templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -2,18 +2,45 @@ <%def name="stylesheets()"> ${parent.stylesheets()} +${h.css( + "base", + "autocomplete_tagging", + "jquery-ui/smoothness/jquery-ui-1.8.23.custom" +)} <style type="text/css"> /*TODO: use/move into base.less*/ * { margin: 0px; padding: 0px; } + +/* -------------------------------------------- layout */ +.column { + position:relative; + overflow: auto; +} + +.left-column { + float: left; + width: 30%; +} + +.right-column { + margin-left: 32%; +} + +div.tab-pane { + padding: 8px; +} + +/* -------------------------------------------- header */ +.header { + margin-bottom: 8px; +} + #chart-header { padding : 8px; background-color: #ebd9b2; } -.title { -} - #chart-header .subtitle { margin: -4px 0px 0px 4px; padding : 0; @@ -21,33 +48,121 @@ font-size: small; } +/* -------------------------------------------- all controls */ #chart-settings-form { /*from width + margin of chart?*/ - float: right; - width: 100%; - margin: 0px; padding-top: 1em; } -#chart-settings > * { - margin: 8px; +#chart-settings-form input[type=button], +#chart-settings-form select { + width: 100%; + max-width: 256px; + margin-bottom: 8px; } -#chart-settings-form input, #chart-settings-form select { - width: 30%; - max-width: 256px; +#chart-settings-form .help-text, +#chart-settings-form .help-text-small { + color: grey; } -#chart-holder { - overflow: auto; +#chart-settings-form .help-text { + padding-bottom: 16px; +} + +#chart-settings-form .help-text-small { + padding: 4px; + font-size: smaller; +} + +#chart-settings-form > * { +} + +#chart-settings-form input[value=Draw] { + display: block; + margin-top: 16px; +} + +/* -------------------------------------------- data controls */ + +/* -------------------------------------------- chart controls */ +#chart-settings .form-input { + /*display: table-row;*/ +} + +#chart-settings label { + /*text-align: right;*/ + margin-bottom: 8px; + /*display: table-cell;*/ +} + +#chart-settings .slider { + /*display: table-cell;*/ + height: 8px; + display: block; + margin: 8px 0px 0px 8px; +} + +#chart-settings .slider-output { + /*display: table-cell;*/ + float: right; +} + +#chart-settings input[type="text"] { + border: 1px solid lightgrey; +} + + +/* -------------------------------------------- statistics */ +#chart-stats table#chart-stats-table { + width: 100%; +} + +#chart-stats #chart-stats-table th { + width: 30%; + padding: 4px; + font-weight: bold; + color: grey; +} + +#chart-stats #chart-stats-table td { + border: solid lightgrey; + border-width: 1px 0px 0px 1px; + padding: 4px; +} + +#chart-stats #chart-stats-table td:nth-child(1) { + border-width: 1px 0px 0px 0px; + padding-right: 1em; + text-align: right; + font-weight: bold; + color: grey; +} + +/* -------------------------------------------- load indicators */ +#loading-indicator { + z-index: 2; + position: absolute; + top: 0; + bottom: 0; + left: 0; + right: 0; + background-color: white; + padding: 32px 0 0 32px; } #chart-settings-form #loading-indicator .loading-message { - margin-left: 16px; + margin-left: 10px; font-style: italic; color: grey; } +/* -------------------------------------------- chart area */ +#chart-holder { + overflow: auto; + margin-left: 8px; +} + svg .grid-line { fill: none; stroke: lightgrey; @@ -94,8 +209,6 @@ var hda = ${h.to_json_string( hda )}, historyID = '${historyID}' apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; - //?? hmmmm - //kwargs = ${h.to_json_string( kwargs )}; var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, @@ -113,10 +226,20 @@ </%def><%def name="body()"> - <div id="chart-header"> +  + <div id="chart-header" class="header"><h2 class="title">Scatterplot of '${hda['name']}'</h2><p class="subtitle">${hda['misc_info']}</p></div> - <div id="chart-holder"></div> - <div id="chart-settings-form"></div> + <div class="outer-container"> +  + <div id="chart-settings-form" class="column left-column"></div> +  + <div class="column right-column"> + <div id="chart-holder" class="inner-container"></div> + </div> + <div style="clear: both;"></div> + </div> + <div id="test"></div> + </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 6 new changesets
by Bitbucket 10 Oct '12

10 Oct '12

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/87641aaefe47/ changeset: 87641aaefe47 user: chapmanb date: 2012-10-08 11:32:54 summary: Consistently return list of users from users/index for case where API user is not an admin affected #: 1 file diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -33,7 +33,7 @@ if not trans.user_is_admin(): item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) - return item + return [item] for user in query: item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) https://bitbucket.org/galaxy/galaxy-central/changeset/9abbec24c356/ changeset: 9abbec24c356 user: chapmanb date: 2012-10-08 12:25:49 summary: Provide retrieval of the current user and user history via the API affected #: 2 files diff -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c -r 9abbec24c3566393b05a0744941361fbfba1a968 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,6 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} + GET /api/histories/current Displays information about a history. """ history_id = id @@ -65,8 +66,13 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) + if history_id == "current" and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: + raise return str( e ) try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) diff -r 87641aaefe47d1892bbbd4a7ea56cc21cab9d68c -r 9abbec24c3566393b05a0744941361fbfba1a968 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -45,11 +45,15 @@ """ GET /api/users/{encoded_user_id} GET /api/users/deleted/{encoded_user_id} + GET /api/users/current Displays information about a user. """ deleted = util.string_as_bool( deleted ) try: - user = self.get_user( trans, id, deleted=deleted ) + if id == "current": + user = trans.user + else: + user = self.get_user( trans, id, deleted=deleted ) if not trans.user_is_admin(): assert trans.user == user assert not user.deleted https://bitbucket.org/galaxy/galaxy-central/changeset/f5772000c6d9/ changeset: f5772000c6d9 user: chapmanb date: 2012-10-08 12:27:29 summary: Remove extra debugging statement affected #: 1 file diff -r 9abbec24c3566393b05a0744941361fbfba1a968 -r f5772000c6d9ea5d15b1332f2ea42330e645371d lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -72,7 +72,6 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: - raise return str( e ) try: item = history.get_api_value(view='element', value_mapper={'id':trans.security.encode_id}) https://bitbucket.org/galaxy/galaxy-central/changeset/2bfdbe09caf7/ changeset: 2bfdbe09caf7 user: chapmanb date: 2012-10-09 11:39:15 summary: Defensively check for user and histories before retrieving current history from API affected #: 1 file diff -r f5772000c6d9ea5d15b1332f2ea42330e645371d -r 2bfdbe09caf7fd1e49fb5fcdfbb1665764ed39ed lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -66,9 +66,12 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - if history_id == "current" and len(trans.user.galaxy_sessions) > 0: - # Most recent active history for user sessions, not deleted - history = trans.user.galaxy_sessions[0].histories[-1].history + if history_id == "current": + if trans.user and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = None else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: https://bitbucket.org/galaxy/galaxy-central/changeset/e7178dd7f9db/ changeset: e7178dd7f9db user: chapmanb date: 2012-10-10 12:53:33 summary: Rename history retrieval to reflect multiple sessions: most_recently_used affected #: 1 file diff -r 2bfdbe09caf7fd1e49fb5fcdfbb1665764ed39ed -r e7178dd7f9dbb22c880627c2fb9c05cb696392cf lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,7 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} - GET /api/histories/current + GET /api/histories/most_recently_used Displays information about a history. """ history_id = id @@ -66,7 +66,7 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - if history_id == "current": + if history_id == "most_recently_used": if trans.user and len(trans.user.galaxy_sessions) > 0: # Most recent active history for user sessions, not deleted history = trans.user.galaxy_sessions[0].histories[-1].history https://bitbucket.org/galaxy/galaxy-central/changeset/666e873a21a0/ changeset: 666e873a21a0 user: jgoecks date: 2012-10-10 15:43:15 summary: Merged in chapmanb/galaxy-central-apicurrent (pull request #77) affected #: 2 files diff -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -48,6 +48,7 @@ """ GET /api/histories/{encoded_history_id} GET /api/histories/deleted/{encoded_history_id} + GET /api/histories/most_recently_used Displays information about a history. """ history_id = id @@ -65,7 +66,14 @@ rval[item['state']] = rval[item['state']] + 1 return rval try: - history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) + if history_id == "most_recently_used": + if trans.user and len(trans.user.galaxy_sessions) > 0: + # Most recent active history for user sessions, not deleted + history = trans.user.galaxy_sessions[0].histories[-1].history + else: + history = None + else: + history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True, deleted=deleted ) except Exception, e: return str( e ) try: diff -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 -r 666e873a21a0f8032a2f7b39204b5edb6ee47797 lib/galaxy/webapps/galaxy/api/users.py --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -33,7 +33,7 @@ if not trans.user_is_admin(): item = trans.user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) - return item + return [item] for user in query: item = user.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) item['url'] = url_for( route, id=item['id'] ) @@ -45,11 +45,15 @@ """ GET /api/users/{encoded_user_id} GET /api/users/deleted/{encoded_user_id} + GET /api/users/current Displays information about a user. """ deleted = util.string_as_bool( deleted ) try: - user = self.get_user( trans, id, deleted=deleted ) + if id == "current": + user = trans.user + else: + user = self.get_user( trans, id, deleted=deleted ) if not trans.user_is_admin(): assert trans.user == user assert not user.deleted Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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