dialog box to change some parameters

css/main.css

@@ -13,3 +13,8 @@ div.nuc-dens-sublabel {
 div.nuc-dens-sublabel.last {
  border-bottom: 1px solid #999;
 }
+
+div#nuc-dens-parameters{
+ border-bottom: 1px solid lightgray;
+ padding-bottom: 3px;
+}

js/View/Dialog/NucleotideDensityDialog.js

@@ -0,0 +1,93 @@
+define([
+ 'dojo/_base/declare',
+ 'dojo/dom-construct',
+ 'dojo/on',
+ 'dijit/focus',
+ 'dijit/form/NumberSpinner',
+ 'dijit/form/Button',
+ 'JBrowse/View/Dialog/WithActionBar'
+],
+function(
+ declare,
+ dom,
+ on,
+ focus,
+ NumberSpinner,
+ Button,
+ ActionBarDialog
+) {
+ return declare(ActionBarDialog, {
+ title: 'Set Nucleotide Density Track Options',
+
+ constructor: function(args) {
+ this.windowSize = args.windowSize || 100;
+ this.windowDelta = args.windowDelta || 10;
+ this.browser = args.browser;
+ this.setCallback = args.setCallback || function() {};
+ this.cancelCallback = args.cancelCallback || function() {};
+ },
+
+ _fillActionBar: function(actionBar) {
+ new Button({
+ label: 'OK',
+ onClick: dojo.hitch(this, function() {
+ var windowSize = +this.windowSizeSpinner.getValue();
+ var windowDelta = +this.windowDeltaSpinner.getValue();
+ if (isNaN(windowSize) || isNaN(windowDelta)) {
+ return;
+ }
+ this.setCallback && this.setCallback(windowSize, windowDelta);
+ this.hide();
+ })
+ }).placeAt(actionBar);
+
+ new Button({
+ label: 'Cancel',
+ onClick: dojo.hitch(this, function() {
+ this.cancelCallback && this.cancelCallback();
+ this.hide();
+ })
+ }).placeAt(actionBar);
+ },
+
+ show: function(/* callback */) {
+ dojo.addClass(this.domNode, 'nuc-dens-dialog');
+
+
+ var topPane = dom.create('div',{id:'nuc-dens-parameters'});
+ this._createTopPane(topPane);
+
+ this.set('content', [
+ topPane
+ ]);
+
+ this.inherited(arguments);
+ },
+
+ _createTopPane: function(obj){
+ var thisB = this;
+ this.windowSizeSpinner = new NumberSpinner({
+ value: thisB.windowSize,
+ smallDelta: 10,
+ id: 'nuc-dens-window-size'
+ });
+ dom.create('label', { for: 'nuc-dens-window-size', innerHTML: 'Window size (bp)', style: {display: 'inline-block', width: '100px'} }, obj);
+ this.windowSizeSpinner.placeAt(obj);
+ dom.create('br',{},obj);
+
+ this.windowDeltaSpinner = new NumberSpinner({
+ value: thisB.windowDelta,
+ smallDelta: 10,
+ id: 'nuc-dens-window-delta'
+ });
+ dom.create('label', { for: 'nuc-dens-window-delta', innerHTML: 'Window delta (bp)', style: {display: 'inline-block', width: '100px'} }, obj);
+ this.windowDeltaSpinner.placeAt(obj);
+ dom.create('br',{},obj);
+ },
+
+ hide: function() {
+ this.inherited(arguments);
+ window.setTimeout(dojo.hitch(this, 'destroyRecursive'), 500);
+ }
+ });
+});

js/View/Track/NucleotideDensity.js

@@ -4,10 +4,10 @@ define([
  'dojo/_base/lang',
  'dojo/_base/Color',
  'dojox/color',
- 'NucleotideDensityPlugin/Store/SeqFeature/NucContentMulti',
+ 'NucleotideDensityPlugin/Store/SeqFeature/NucDensityMulti',
  'JBrowse/View/Track/Wiggle/Density',
  'JBrowse/Util',
- 'dijit/Tooltip'
+ 'NucleotideDensityPlugin/View/Dialog/NucleotideDensityDialog'
 ],
 function(
  declare,
@@ -18,7 +18,7 @@ function(
  NucContent,
  WiggleDensity,
  Util,
-  Tooltip
+ NucDensDialog
 ) {
  return declare(WiggleDensity, {
  constructor: function() {
@@ -225,34 +225,28 @@ function(
  }
  }, this);
  }
- }
- /*_trackMenuOptions: function() {
+ },
+ _trackMenuOptions: function() {
  var track = this;
  var options = this.inherited(arguments);
- options.push({
- label: 'GC Track Options',
+ options.push(
+ { type: 'dijit/MenuSeparator' },
+ {
+ label: 'Track options',
+ iconClass: 'dijitIconFunction',
  onClick: function() {
- new WindowSize({
+ new NucDensDialog({
  setCallback: function(ws, wd, mode) {
  track.config.windowSize = ws;
  track.config.windowDelta = wd;
- track.config.gcMode = mode;
- if (mode === 'skew') {
- track.config.min_score = -1;
- track.config.bicolor_pivot = 0;
- } else {
- track.config.min_score = 0;
- track.config.bicolor_pivot = 0.5;
- }
  track.browser.publish('/jbrowse/v1/c/tracks/replace', [track.config]);
  },
  windowSize: track.config.windowSize,
  windowDelta: track.config.windowDelta,
- gcMode: track.config.gcMode
  }).show();
  }
  });
  return options;
- }*/
+ }
  });
 });