Adding Phylocanvas visualization for the Galaxy charts

config/plugins/visualizations/charts/static/repository/build/registry.tmp.js

@@ -1 +1 @@
-define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_basic:require( "visualizations/cytoscape/basic/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );
+define( [], function() { return {nvd3_bar:require( "visualizations/nvd3/bar/config" ), nvd3_bar_horizontal:require( "visualizations/nvd3/bar_horizontal/config" ), nvd3_bar_horizontal_stacked:require( "visualizations/nvd3/bar_horizontal_stacked/config" ), nvd3_bar_stacked:require( "visualizations/nvd3/bar_stacked/config" ), nvd3_line:require( "visualizations/nvd3/line/config" ), nvd3_line_focus:require( "visualizations/nvd3/line_focus/config" ), nvd3_scatter:require( "visualizations/nvd3/scatter/config" ), nvd3_stackedarea:require( "visualizations/nvd3/stackedarea/config" ), nvd3_stackedarea_full:require( "visualizations/nvd3/stackedarea_full/config" ), nvd3_stackedarea_stream:require( "visualizations/nvd3/stackedarea_stream/config" ), nvd3_pie:require( "visualizations/nvd3/pie/config" ), nvd3_histogram:require( "visualizations/nvd3/histogram/config" ), nvd3_histogram_discrete:require( "visualizations/nvd3/histogram_discrete/config" ), jqplot_bar:require( "visualizations/jqplot/bar/config" ), jqplot_boxplot:require( "visualizations/jqplot/boxplot/config" ), jqplot_histogram_discrete:require( "visualizations/jqplot/histogram_discrete/config" ), jqplot_line:require( "visualizations/jqplot/line/config" ), jqplot_scatter:require( "visualizations/jqplot/scatter/config" ), biojs_msa:require( "visualizations/biojs/msa/config" ), biojs_drawrnajs:require( "visualizations/biojs/drawrnajs/config" ), biojs_phylocanvas:require( "visualizations/biojs/phylocanvas/config" ), others_example:require( "visualizations/others/example/config" ), others_heatmap:require( "visualizations/others/heatmap/config" ), others_heatmap_cluster:require( "visualizations/others/heatmap_cluster/config" ), cytoscape_basic:require( "visualizations/cytoscape/basic/config" ), pv_viewer:require( "visualizations/pv/viewer/config" ), benfred_venn:require( "visualizations/benfred/venn/config" ), ngl_viewer:require( "visualizations/ngl/viewer/config" ),} } );

config/plugins/visualizations/charts/static/repository/registry.json

@@ -1,7 +1,7 @@
 {
     "nvd3"      : [ "bar", "bar_horizontal", "bar_horizontal_stacked", "bar_stacked", "line", "line_focus", "scatter", "stackedarea", "stackedarea_full", "stackedarea_stream", "pie", "histogram", "histogram_discrete" ],
     "jqplot"    : [ "bar", "boxplot", "histogram_discrete", "line", "scatter" ],
-    "biojs"     : [ "msa", "drawrnajs" ],
+    "biojs"     : [ "msa", "drawrnajs", "phylocanvas" ],
     "others"    : [ "example", "heatmap", "heatmap_cluster" ],
     "cytoscape" : [ "basic" ],
     "pv"        : [ "viewer" ],

config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js

@@ -0,0 +1,37 @@
+define( [], function() {
+    return {
+        title       : 'Phylogenetic tree visualization',
+        library     : 'BioJS',
+        datatypes   : [ 'txt', 'nwk' ],
+        keywords    : 'biojs phylogenetic tree',
+        description : 'A performant, reusable, and extensible tree visualisation library for the web at: http://biojs.io/d/phylocanvas',
+        settings    : {
+           tree_type : {
+                label   : 'Tree types',
+                help    : 'Select a tree type.',
+                type    : 'select',
+                display : 'radio',
+                value   : 'radial',
+                data    : [ { label : 'Circular', value : 'circular' },
+                            { label : 'Diagonal', value: 'diagonal' },
+                            { label : 'Hierarchial', value : 'hierarchical' },
+                            { label : 'Radial', value : 'radial' },
+                            { label : 'Rectangular', value : 'rectangular' } ]
+            },
+            edge_color : {
+                label : 'Select a color for the tree',
+                type  : 'color',
+                value : '#548DB8'
+            },
+            show_label: {
+                label   : 'Show/Hide labels',
+                help    : 'Select false to hide labels',
+                type    : 'select',
+                display : 'radio',
+                value   : 'true',
+                data    : [ { label : 'True', value : 'true' },
+                            { label : 'False', value : 'false' } ]
+            },
+        }
+    }
+});

config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js

@@ -0,0 +1,32 @@
+define( [ 'utilities/utils', 'plugins/biojs/phylocanvas/phylocanvas' ], function( Utils, Phylocanvas ) {
+    return Backbone.Model.extend({
+        initialize: function( options ) {
+            var chart    = options.chart,
+                dataset  = options.dataset,
+                settings = options.chart.settings;
+
+            Utils.get( {
+                url     : dataset.download_url,
+                success : function( content ) {
+                    try {
+                        var tree = Phylocanvas.default.createTree( options.targets[ 0 ] );
+                        // Set different properties of the tree
+                        tree.setTreeType( settings.get( 'tree_type' ) );
+                        tree.branchColour = settings.get( 'edge_color' );
+                        tree.showLabels = settings.get( 'show_label' ) === "true" ? true : false;
+                        // Draw the phylogenetic tree
+                        tree.load( content );
+                        chart.state( 'ok', 'Done.' );
+                        options.process.resolve();
+                    } catch( err ) {
+                        chart.state( 'failed', err );
+                    }
+                },
+                error: function() {
+                    chart.state( 'failed', 'Failed to access dataset.' );
+                    options.process.resolve();
+                }
+            });
+        }
+    });
+});