Bring data provided by data manager in line with Trackster's bigwig datatype. Also allow LinePainter to draw regions of variable length.

client/galaxy/scripts/libs/bbi/bigwig.js

@@ -807,7 +807,6 @@ define(["libs/bbi/spans", "libs/bbi/jszlib", "libs/bbi/jquery-ajax-native"], fun
         // If no zooming needed or available (common in bigbed), use unzoomed view.
         if (range <= MAX_DATA_POINTS || this.zoomLevels.length === 0) {
             view = this.getUnzoomedView();
-            console.log("zoomLevel unzoomed");
         }
         else {
             // Find reasonable zoom level. Reduction is the # of bases represented
@@ -815,7 +814,6 @@ define(["libs/bbi/spans", "libs/bbi/jszlib", "libs/bbi/jquery-ajax-native"], fun
             for (var i = 0; i < this.zoomLevels.length; i++) {
                 if (range/this.zoomLevels[i].reduction < MAX_DATA_POINTS) {
                     view = this.getZoomedView(i);
-                    console.log("zoomLevel", i);
                     break;
                 }
             }

client/galaxy/scripts/viz/bbi-data-manager.js

@@ -7,7 +7,7 @@ define( ["viz/visualization", "libs/bbi/bigwig"],
     var BBIDataManager = visualization.GenomeDataManager.extend({
 
         /**
-         * Load data from server and manages data entries. Adds a Deferred to manager
+         * Load data from server and manage data entries. Adds a Deferred to manager
          * for region; when data becomes available, replaces Deferred with data.
          * Returns the Deferred that resolves when data is available.
          */
@@ -20,22 +20,29 @@ define( ["viz/visualization", "libs/bbi/bigwig"],
                 var promise = new $.Deferred();
                 $.when(bigwig.makeBwg(url)).then(function(bb, err) {
                     $.when(bb.readWigData(region.get("chrom"), region.get("start"), region.get("end"))).then(function(data) {
-                    // Transform data into "bigwig" format. "bigwig" format is an array of 2-element arrays
-                    // where each array is [position, score].
-                    var result = [];
+                    // Transform data into "bigwig" format for LinePainter. "bigwig" format is an array of 2-element arrays
+                    // where each element is [position, score]; unlike real bigwig format, no gaps are allowed.
+                    var result = [],
+                        prev = { max: Number.MIN_VALUE };
                     data.forEach(function(d) {
-                        // Each data element includes a min and max. If min and max are the same,
-                        // then entry is single base-pair resolution and only a single data point
-                        // is added. Otherwise entry is multiple base pairs and two data points are
-                        // added, one for the start and one for the end.
-
-                        // Add data point for entry start.
-                        result.push([d.min, d.score]);
-
-                        if (d.min !== d.max) {
-                            // Multi base-pair entry, so two data points are generated.
-                            result.push([d.max, d.score]);
+                        // If there is a gap between prev and d, fill it with an interval with score 0.
+                        // This is necessary for LinePainter to draw correctly.
+                        if (prev.max !== d.min - 1) {
+                            // +1 to start after previous region.
+                            result.push([prev.max + 1, 0]);
+                            // -2 = -1 for converting from 1-based to 0-based coordinates,
+                            //      -1 for ending before current region.
+                            result.push([d.min - 2, 0]);
                         }
+
+                        // Add data point for entry start. -1 to convert from wiggle
+                        // 1-based coordinates to 0-based browser coordinates.
+                        result.push([d.min - 1, d.score]);
+
+                        // Add data point for entry end:
+                        result.push([d.max, d.score]);
+
+                        prev = d;
                     });
 
                     var entry = {

client/galaxy/scripts/viz/trackster/painters.js

@@ -194,12 +194,14 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
     }
 
     ctx.beginPath();
-    var x_scaled, y, delta_x_px;
+    var x_scaled, y, delta_x_pxs;
     if (data.length > 1) {
-        delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale);
+        delta_x_pxs = _.map(data.slice(0,-1), function(d, i) {
+            return Math.ceil((data[i+1][0] - data[i][0]) * w_scale);
+        });
     }
     else {
-        delta_x_px = 10;
+        delta_x_pxs = [10];
     }
 
     // Painter color can be in either block_color (FeatureTrack) or color pref (LineTrack).
@@ -214,12 +216,14 @@ LinePainter.prototype.draw = function(ctx, width, height, w_scale) {
 
 
     // Paint track.
+    var delta_x_px;
     for (var i = 0, len = data.length; i < len; i++) {
         // Reset attributes for next point.
         ctx.fillStyle = ctx.strokeStyle = painter_color;
         top_overflow = bot_overflow = false;
+        delta_x_px = delta_x_pxs[i];
 
-        x_scaled = Math.ceil((data[i][0] - view_start) * w_scale);
+        x_scaled = Math.ceil((data[i][0] - view_start - 0.5) * w_scale);
         y = data[i][1];
 
         // Process Y (scaler) value.

client/galaxy/scripts/viz/trackster/tracks.js

@@ -3614,6 +3614,8 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
 var LineTrack = function (view, container, obj_dict) {
     this.mode = "Histogram";
     TiledTrack.call(this, view, container, obj_dict);
+    // Need left offset for drawing overlap near tile boundaries.
+    this.left_offset = 30;
 
     // var self = this;
     // $.when(supportsByteRanges(galaxy_config.root + 'datasets/' + this.dataset.id + '/display'))

static/maps/viz/bbi-data-manager.js.map

@@ -1 +1 @@
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+{"version":3,"file":"bbi-data-manager.js","sources":["../../src/viz/bbi-data-manager.js"],"names":["define","visualization","bigwig","BBIDataManager","GenomeDataManager","extend","load_data","region","deferred","$","Deferred","this","set_data","url","galaxy_config","root","get","id","self","when","makeBwg","then","bb","readWigData","data","result","prev","max","Number","MIN_VALUE","forEach","d","min","push","score","entry","dataset_type","resolve"],"mappings":"AAAAA,QAAS,oBAAqB,mBACtB,SAASC,EAAeC,GAK5B,GAAIC,GAAiBF,EAAcG,kBAAkBC,QAOjDC,UAAW,SAASC,GAChB,GAAIC,GAAWC,EAAEC,UACjBC,MAAKC,SAASL,EAAQC,EAEtB,EAAA,GAAIK,GAAMC,cAAcC,KAAO,YAAcJ,KAAKK,IAAI,WAAWC,GAAK,WAClEC,EAAOP,IACO,IAAIF,GAAEC,SAuCxB,MAtCID,GAAEU,KAAKjB,EAAOkB,QAAQP,IAAMQ,KAAK,SAASC,GACtCb,EAAEU,KAAKG,EAAGC,YAAYhB,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAAUT,EAAOS,IAAI,SAASK,KAAK,SAASG,GAGlG,GAAIC,MACAC,GAASC,IAAKC,OAAOC,UACzBL,GAAKM,QAAQ,SAASC,GAGdL,EAAKC,MAAQI,EAAEC,IAAM,IAErBP,EAAOQ,MAAMP,EAAKC,IAAM,EAAG,IAG3BF,EAAOQ,MAAMF,EAAEC,IAAM,EAAG,KAK5BP,EAAOQ,MAAMF,EAAEC,IAAM,EAAGD,EAAEG,QAG1BT,EAAOQ,MAAMF,EAAEJ,IAAKI,EAAEG,QAEtBR,EAAOK,GAGX,IAAII,IACIX,KAAMC,EACNlB,OAAQA,EACR6B,aAAc,SAGtBlB,GAAKN,SAASL,EAAQ4B,GACtB3B,EAAS6B,QAAQF,OAIlB3B,IAIf,QACIL,eAAgBA"}

static/scripts/viz/bbi-data-manager.js

@@ -1,2 +1,2 @@
-define(["viz/visualization","libs/bbi/bigwig"],function(a,b){var c=a.GenomeDataManager.extend({load_data:function(a){var c=$.Deferred();this.set_data(a,c);{var d=galaxy_config.root+"datasets/"+this.get("dataset").id+"/display",e=this;new $.Deferred}return $.when(b.makeBwg(d)).then(function(b){$.when(b.readWigData(a.get("chrom"),a.get("start"),a.get("end"))).then(function(b){var d=[];b.forEach(function(a){d.push([a.min,a.score]),a.min!==a.max&&d.push([a.max,a.score])});var f={data:d,region:a,dataset_type:"bigwig"};e.set_data(a,f),c.resolve(f)})}),c}});return{BBIDataManager:c}});
+define(["viz/visualization","libs/bbi/bigwig"],function(a,b){var c=a.GenomeDataManager.extend({load_data:function(a){var c=$.Deferred();this.set_data(a,c);{var d=galaxy_config.root+"datasets/"+this.get("dataset").id+"/display",e=this;new $.Deferred}return $.when(b.makeBwg(d)).then(function(b){$.when(b.readWigData(a.get("chrom"),a.get("start"),a.get("end"))).then(function(b){var d=[],f={max:Number.MIN_VALUE};b.forEach(function(a){f.max!==a.min-1&&(d.push([f.max+1,0]),d.push([a.min-2,0])),d.push([a.min-1,a.score]),d.push([a.max,a.score]),f=a});var g={data:d,region:a,dataset_type:"bigwig"};e.set_data(a,g),c.resolve(g)})}),c}});return{BBIDataManager:c}});
 //# sourceMappingURL=../../maps/viz/bbi-data-manager.js.map