Update JBrowse track height config

Author: bbimber

jbrowse/resources/external/mGAPSession.json

@@ -57,7 +57,8 @@
         {
           "type": "ExtendedVariantDisplay",
           "displayId": "mgap_hg38-ExtendedVariantDisplay",
-          "maxDisplayedBpPerPx": 5000,
+          "maxFeatureScreenDensity": 100,
+          "height": 400,
           "mouseover": "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))",
           "renderer": {
             "type": "ExtendedVariantRenderer"

jbrowse/resources/web/jbrowse/window/ModifyJsonConfigWindow.js

@@ -65,6 +65,12 @@ Ext4.define('JBrowse.window.ModifyJsonConfigWindow', {
                         handler: function (gridBtn) {
                             this.addAttribute('chunkSizeLimit', null, 'INT');
                         }
+                    },{
+                        text: 'Track Height',
+                        scope: this,
+                        handler: function (gridBtn) {
+                            this.addAttribute('trackHeight', 400, 'INT');
+                        }
                     },{
                         text: 'Max Track Height',
                         scope: this,

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -531,7 +531,7 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
             put(new JSONObject(){{
                 put("type", "ExtendedVariantDisplay");
                 put("displayId", getJsonTrackId() + "-ExtendedVariantDisplay");
-                put("maxDisplayedBpPerPx", 2000);
+                put("maxFeatureScreenDensity", 100);
                 put("mouseover", "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))");
                 put("renderer", new JSONObject(){{
                     put("type", "ExtendedVariantRenderer");
@@ -550,6 +550,11 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
                 {
                     getJSONObject("renderer").put("message", json.getString("additionalFeatureMsg"));
                 }
+
+                if (json != null && json.has("trackHeight"))
+                {
+                    put("height", json.getInt("trackHeight"));
+                }
             }});
         }});