Fix tabix histogram for CanvasFeatuers

docs/tutorial/data_files/volvox.bw.gff3.gz.conf

@@ -0,0 +1,11 @@
+[ tracks . volvox_gff3_tabix_bw ]
+storeClass = JBrowse/Store/SeqFeature/GFF3Tabix
+histograms.storeClass = JBrowse/Store/SeqFeature/BigWig
+histograms.urlTemplate = ../../raw/volvox/volvox-sorted.bam.coverage.bw
+urlTemplate = ../../raw/volvox/volvox.sort.gff3.gz.1
+tbiUrlTemplate = ../../raw/volvox/volvox.sort.gff3.gz.tbi
+type = CanvasFeatures
+metadata.description = This is just all the features in the volvox.gff3 test file, displayed using GFF3 and tabix, but a BW histogram.
+category = Miscellaneous
+maxFeatureScreenDensity = 0.05
+key = GFF3Tabix - volvox.gff3 in-memory adaptor with BW historgram

docs/tutorial/data_files/volvox.sort.gff3.gz.conf

@@ -5,4 +5,5 @@ tbiUrlTemplate = ../../raw/volvox/volvox.sort.gff3.gz.tbi
 type = CanvasFeatures
 metadata.description = This is just all the features in the volvox.gff3 test file, displayed using GFF3 and tabix
 category = Miscellaneous
+maxFeatureScreenDensity = 0.05
 key = GFF3Tabix - volvox.gff3 in-memory adaptor

setup.sh

@@ -131,6 +131,7 @@ echo -n "Formatting Volvox example data ...";
     cat docs/tutorial/data_files/volvox.gff3.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/volvox.gtf.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/volvox.sort.gff3.gz.conf >> sample_data/json/volvox/tracks.conf
+    cat docs/tutorial/data_files/volvox.bw.gff3.gz.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/volvox.sort.bed.gz.conf >> sample_data/json/volvox/tracks.conf
     cat docs/tutorial/data_files/bookmarks.conf >> sample_data/json/volvox/tracks.conf
     bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json

src/JBrowse/QueryParamConfigMapper.js

@@ -1,3 +1,14 @@
+/**
+ * This library interprets options passed in via dot-notation instead of JSON in the Query URL.
+ * The implementation is both for readability and security in some systems, esp. tomcat where
+ * passing JSON in the Query URL is both bad-form and potentially insecure.
+ *
+ * This is the dot-object library: https://www.npmjs.com/package/dot-object
+ *
+ * Usage is depicted here:
+ * http://gmod.org/wiki/JBrowse_Configuration_Guide#addFeatures
+ *
+ */
 define(['dojo/_base/declare', 'JBrowse/Util/dot-object'], function (declare, dotObject) {
     return declare(null, {
 
@@ -59,7 +70,7 @@ define(['dojo/_base/declare', 'JBrowse/Util/dot-object'], function (declare, dot
             var storeTracks = {};
             var storeBookmarks = {};
             Object.keys(queryParams).forEach(function (queryParam) {
-                if (queryParam.indexOf('addStore\.') == 0) {
+                if (queryParam.indexOf('addStores\.') == 0) {
                     queryNameArray = queryParam.split("\.");
                     propertyName = queryNameArray.slice(1).join('.');
                     dotObject.str('stores.'+propertyName, queryParams[queryParam], config)

src/JBrowse/Store/SeqFeature/GFF3Tabix.js

@@ -134,6 +134,78 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, Gl
         }, errorCallback );
     },
 
+
+    getRegionFeatureDensities: function( query, successCallback, errorCallback ) {
+
+        var thisB = this ;
+
+        var numBins, basesPerBin;
+        if( query.numBins ) {
+            numBins = query.numBins;
+            basesPerBin = (query.end - query.start)/numBins;
+        }
+        else if( query.basesPerBin ) {
+            basesPerBin = query.basesPerBin || query.ref.basesPerBin;
+            numBins = Math.ceil( (query.end-query.start)/basesPerBin );
+        }
+        else {
+            throw new Error('numBins or basesPerBin arg required for getRegionFeatureDensities');
+        }
+
+        var statEntry = (function( basesPerBin, stats ) {
+            for (var i = 0; i < stats.length; i++) {
+                if( stats[i].basesPerBin >= basesPerBin ) {
+                    return stats[i];
+                }
+            }
+            return undefined;
+        })( basesPerBin, [] );
+
+        var stats = {};
+        stats.basesPerBin = basesPerBin ;
+
+        stats.scoreMax = 0 ;
+        stats.max = 0 ;
+        var firstServerBin = Math.floor( query.start / basesPerBin);
+        var histogram = [];
+        var binRatio = 1 / basesPerBin;
+
+        var binStart, binEnd ;
+
+		for(var bin = 0 ; bin < numBins ; bin++){
+			histogram[bin] = 0;
+		}
+
+
+        thisB.getHeader().then( function() {
+            thisB.indexedData.getLines(
+                query.ref || thisB.refSeq.name,
+                query.start,
+                query.end,
+                function( line ) {
+                    // var feat = thisB.lineToFeature(line);
+					// if(!feat.attributes.parent) // only count if has NO parent
+                    var start = line.start ;
+                    var binValue = Math.round( (start - query.start )* binRatio)   ;
+
+					// in case it extends over the end, just push it on the end
+					binValue = binValue >=0 ? binValue : 0 ;
+					binValue = binValue < histogram.length ? binValue : histogram.length -1  ;
+
+					histogram[binValue] += 1;
+					if(histogram[binValue] > stats.max){
+						stats.max = histogram[binValue];
+					}
+                },
+                function() {
+					successCallback({ bins: histogram, stats: stats});
+                },
+                errorCallback
+            );
+        }, errorCallback );
+
+    },
+
     lineToFeature: function( line ) {
         var attributes = GFF3.parse_attributes( line.fields[8] );
         var ref    = line.fields[0];

tests/js_tests/spec/QueryParamConfigMapper.spec.js

@@ -1,10 +1,10 @@
 require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryParamConfigMapper, ioQuery) {
 
     describe("QueryParamConfigMapper", function () {
-        it("should interpret addStore properly", function () {
+        it("should interpret addStores properly", function () {
             var mapper = QueryParamConfigMapper();
             expect(mapper).toBeTruthy();
-            var queryString = 'addStore.store1.type=HMLFeatures&addStore.store1.urlTemplate=http://abc.com/test.gff';
+            var queryString = 'addStores.store1.type=HMLFeatures&addStores.store1.urlTemplate=http://abc.com/test.gff';
             var config = {};
             var queryParams = ioQuery.queryToObject(queryString);
             runs(function () {
@@ -14,10 +14,10 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
             })
         });
 
-        it("tests bookmarks, addStore, and addTracks", function () {
+        it("tests addBookmarks, addStores, and addTracks", function () {
             var mapper = QueryParamConfigMapper();
             expect(mapper).toBeTruthy();
-            var queryString = 'addStore.store1.type=JBrowse/Store/SeqFeature/GFF3&addStore.store1.urlTemplate=http://localhost/volvox.gff3&addTracks.store1.label=genes&addTracks.store1.type=JBrowse/View/Track/HTMLFeatures&highlight=&addBookmarks.bookmark1.start=3000&addBookmarks.bookmark1.end=4000&addBookmarks.bookmark1.ref=ctgA';
+            var queryString = 'addStores.store1.type=JBrowse/Store/SeqFeature/GFF3&addStores.store1.urlTemplate=http://localhost/volvox.gff3&addTracks.store1.label=genes&addTracks.store1.type=JBrowse/View/Track/HTMLFeatures&highlight=&addBookmarks.bookmark1.start=3000&addBookmarks.bookmark1.end=4000&addBookmarks.bookmark1.ref=ctgA';
             var config = {};
             var queryParams = ioQuery.queryToObject(queryString);
             runs(function () {
@@ -53,7 +53,7 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
             var mapper = QueryParamConfigMapper();
             expect(mapper).toBeTruthy();
             var inputJson = {
-                'addStore': {
+                'addStores': {
                     'stores': {
                         'store1': {
                             'type': 'HMLFeatures',
@@ -64,7 +64,7 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
             };
             runs(function () {
                 var generatedUrl = mapper.generateUrl(inputJson);
-                var answer = 'addStore.stores.store1.type=HMLFeatures&addStore.stores.store1.urlTemplate=http://abc.com/test.gff';
+                var answer = 'addStores.stores.store1.type=HMLFeatures&addStores.stores.store1.urlTemplate=http://abc.com/test.gff';
                 expect(generatedUrl).toEqual(answer);
             })
         });
@@ -73,10 +73,10 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
         it("test multiple nested ingest", function () {
             var mapper = QueryParamConfigMapper();
             expect(mapper).toBeTruthy();
-            var queryString = 'addStore.stores.store1.type=HMLFeatures&addStore.stores.store1.urlTemplate=http://abc.com/test.gff';
+            var queryString = 'addStores.stores.store1.type=HMLFeatures&addStores.stores.store1.urlTemplate=http://abc.com/test.gff';
             var config = {};
             var answer = {
-                'addStore': {
+                'addStores': {
                     'stores': {
                         'store1': {
                             'type': 'HMLFeatures',
@@ -94,7 +94,7 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
         it("test multiple nested views", function () {
             var mapper = QueryParamConfigMapper();
             expect(mapper).toBeTruthy();
-            var queryString = 'addStore.store1.type=HMLFeatures&addStore.store1.urlTemplate=http://abc.com/test.gff';
+            var queryString = 'addStores.store1.type=HMLFeatures&addStores.store1.urlTemplate=http://abc.com/test.gff';
             var config = {};
             var answer = {
                 'stores': {
@@ -136,4 +136,4 @@ require(['JBrowse/QueryParamConfigMapper', 'dojo/io-query'], function (QueryPara
         });
 
     });
-});
+});