[galaxy-commits] commit/galaxy-central: 3 new changesets

10 Sep 2012

3 new commits in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/ef7f11e99547/
changeset:   ef7f11e99547
user:        james_taylor
date:        2012-09-10 23:09:09
summary:     circster: Allow data_standalone types to work; phyloviz: add tree datatypes to sample conf
affected #:  2 files

diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 datatypes_conf.xml.sample

--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -198,6 +198,10 @@
       <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype>
+    <!-- Phylogenetic tree datatypes -->
+    <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" />
+    <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" />
+    <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><!-- Start RGenetics Datatypes --><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/><!-- eigenstrat pedigree input file -->


diff -r 6e79399b38d22512d8438522d26945c53f95b11a -r ef7f11e995473293a2e45f5517a627ad7177a3b1 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -553,11 +553,14 @@
             # Get dataset and indexed datatype.
             dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] )
             data_sources = self._get_datasources( trans, dataset )
-            indexed_type = data_sources['index']['name']
-
-            # Get converted dataset and append track's genome data.
-            converted_dataset = dataset.get_converted_dataset( trans, indexed_type )
-            data_provider = get_data_provider( indexed_type )( converted_dataset, dataset )
+            if 'data_standalone' in data_sources:
+                indexed_type = data_sources['data_standalone']['name']
+                data_provider = get_data_provider( indexed_type )( dataset )
+            else:
+                indexed_type = data_sources['index']['name']
+                # Get converted dataset and append track's genome data.
+                converted_dataset = dataset.get_converted_dataset( trans, indexed_type )
+                data_provider = get_data_provider( indexed_type )( converted_dataset, dataset )
             # HACK: pass in additional params, which are only used for summary tree data, not BBI data.
             track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=3, detail_cutoff=0, draw_cutoff=0 ) }
         



https://bitbucket.org/galaxy/galaxy-central/changeset/c71026b3d7ac/
changeset:   c71026b3d7ac
user:        james_taylor
date:        2012-09-10 23:40:56
summary:     circster: render in entire window, ensure initially entire plot fits in view and is centered
affected #:  2 files

diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -823,26 +823,27 @@
     className: 'circster',
     
     initialize: function(options) {
-        this.width = options.width;
-        this.height = options.height;
         this.total_gap = options.total_gap;
         this.genome = options.genome;
         this.dataset_arc_height = options.dataset_arc_height;
         this.track_gap = 5;
-
-        // Compute radius start based on model.
-        this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap);
     },
     
     render: function() {
         var self = this,
-            dataset_arc_height = this.dataset_arc_height;
+            dataset_arc_height = this.dataset_arc_height,
+            width = self.$el.width(),
+            height = self.$el.height(),
+            // Compute radius start based on model, will be centered 
+            // and fit entirely inside element by default
+            init_radius_start = ( Math.min(width,height)/2 
+                - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) );
 
         // Set up SVG element.
         var svg = d3.select(self.$el[0])
               .append("svg")
-                .attr("width", self.width)
-                .attr("height", self.height)
+                .attr("width", width)
+                .attr("height", height)
                 .attr("pointer-events", "all")
               // Set up zooming, dragging.
               .append('svg:g')
@@ -851,14 +852,14 @@
                       "translate(" + d3.event.translate + ")"
                       + " scale(" + d3.event.scale + ")");
                 }))
-                .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")")
+                .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
               .append('svg:g')
                 
 
         // -- Render each dataset in the visualization. --
         this.model.get('tracks').each(function(track, index) {
             var dataset = track.get('genome_wide_data'),
-                radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap),
+                radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
                 // Layout chromosome arcs.
                 layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ),
                 arcs_layout = new layout_class({


diff -r ef7f11e995473293a2e45f5517a627ad7177a3b1 -r c71026b3d7ac3c01ed6ee5350962de96b6ca47dd templates/visualization/circster.mako
--- a/templates/visualization/circster.mako
+++ b/templates/visualization/circster.mako
@@ -69,8 +69,7 @@
             var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }'))
                 visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')),
                 viz_view = new CircsterView({
-                    width: 700,
-                    height: 700,
+                    el: $('#vis'),
                     // Gap is difficult to set because it very dependent on chromosome size and organization.
                     total_gap: 2 * Math.PI * 0.1,
                     genome: genome,
@@ -81,7 +80,7 @@
             // -- Render viz. --
                 
             viz_view.render();
-            $('#vis').append(viz_view.$el);
+
         });
     </script></%def>



https://bitbucket.org/galaxy/galaxy-central/changeset/6568368038dc/
changeset:   6568368038dc
user:        james_taylor
date:        2012-09-10 23:41:20
summary:     Automated merge with https://bitbucket.org/galaxy/galaxy-central
affected #:  4 files

diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -198,6 +198,10 @@
       <display file="igv/vcf.xml" /><converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/></datatype>
+    <!-- Phylogenetic tree datatypes -->
+    <datatype extension="phyloxml" type="galaxy.datatypes.xml:Phyloxml" display_in_upload="true" />
+    <datatype extension="nhx" type="galaxy.datatypes.data:Newick" display_in_upload="true" />
+    <datatype extension="nex" type="galaxy.datatypes.data:Nexus" display_in_upload="true" /><!-- Start RGenetics Datatypes --><datatype extension="affybatch" type="galaxy.datatypes.genetics:Affybatch" display_in_upload="true"/><!-- eigenstrat pedigree input file -->


diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -553,11 +553,14 @@
             # Get dataset and indexed datatype.
             dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] )
             data_sources = self._get_datasources( trans, dataset )
-            indexed_type = data_sources['index']['name']
-
-            # Get converted dataset and append track's genome data.
-            converted_dataset = dataset.get_converted_dataset( trans, indexed_type )
-            data_provider = get_data_provider( indexed_type )( converted_dataset, dataset )
+            if 'data_standalone' in data_sources:
+                indexed_type = data_sources['data_standalone']['name']
+                data_provider = get_data_provider( indexed_type )( dataset )
+            else:
+                indexed_type = data_sources['index']['name']
+                # Get converted dataset and append track's genome data.
+                converted_dataset = dataset.get_converted_dataset( trans, indexed_type )
+                data_provider = get_data_provider( indexed_type )( converted_dataset, dataset )
             # HACK: pass in additional params, which are only used for summary tree data, not BBI data.
             track[ 'genome_wide_data' ] = { 'data': data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) }
         


diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -823,26 +823,27 @@
     className: 'circster',
     
     initialize: function(options) {
-        this.width = options.width;
-        this.height = options.height;
         this.total_gap = options.total_gap;
         this.genome = options.genome;
         this.dataset_arc_height = options.dataset_arc_height;
         this.track_gap = 5;
-
-        // Compute radius start based on model.
-        this.radius_start = this.width/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap);
     },
     
     render: function() {
         var self = this,
-            dataset_arc_height = this.dataset_arc_height;
+            dataset_arc_height = this.dataset_arc_height,
+            width = self.$el.width(),
+            height = self.$el.height(),
+            // Compute radius start based on model, will be centered 
+            // and fit entirely inside element by default
+            init_radius_start = ( Math.min(width,height)/2 
+                - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) );
 
         // Set up SVG element.
         var svg = d3.select(self.$el[0])
               .append("svg")
-                .attr("width", self.width)
-                .attr("height", self.height)
+                .attr("width", width)
+                .attr("height", height)
                 .attr("pointer-events", "all")
               // Set up zooming, dragging.
               .append('svg:g')
@@ -851,14 +852,14 @@
                       "translate(" + d3.event.translate + ")"
                       + " scale(" + d3.event.scale + ")");
                 }))
-                .attr("transform", "translate(" + self.width / 2 + "," + self.height / 2 + ")")
+                .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
               .append('svg:g')
                 
 
         // -- Render each dataset in the visualization. --
         this.model.get('tracks').each(function(track, index) {
             var dataset = track.get('genome_wide_data'),
-                radius_start = self.radius_start + index * (dataset_arc_height + self.track_gap),
+                radius_start = init_radius_start + index * (dataset_arc_height + self.track_gap),
                 // Layout chromosome arcs.
                 layout_class = (dataset instanceof GenomeWideBigWigData ? CircsterBigWigLayout : CircsterSummaryTreeLayout ),
                 arcs_layout = new layout_class({


diff -r 04cd4894e8406028c6acfd521cbcef7a396748b2 -r 6568368038dc220ce1f66d5566570f32633055d9 templates/visualization/circster.mako
--- a/templates/visualization/circster.mako
+++ b/templates/visualization/circster.mako
@@ -69,8 +69,7 @@
             var genome = new Genome(JSON.parse('${ h.to_json_string( genome ) }'))
                 visualization = new GenomeVisualization(JSON.parse('${ h.to_json_string( viz_config ) }')),
                 viz_view = new CircsterView({
-                    width: 700,
-                    height: 700,
+                    el: $('#vis'),
                     // Gap is difficult to set because it very dependent on chromosome size and organization.
                     total_gap: 2 * Math.PI * 0.1,
                     genome: genome,
@@ -81,7 +80,7 @@
             // -- Render viz. --
                 
             viz_view.render();
-            $('#vis').append(viz_view.$el);
+
         });
     </script></%def>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 3 new changesets

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