all files for v0.2

css/main.css

@@ -0,0 +1,15 @@
+
+div.nuc-dens-sublabel {
+ z-index: 10;
+ overflow: hidden;
+ cursor: default;
+ padding: 0px 1px 0px 1px;
+ border-left: 1px solid #999;
+ border-right: 1px solid #999;
+ border-top: 1px solid #999;
+ /*color: #111;*/
+ font-weight: bold;
+}
+div.nuc-dens-sublabel.last {
+ border-bottom: 1px solid #999;
+}

js/NucleotideDensityPlugin.profile.js

@@ -0,0 +1,62 @@
+function copyOnly(mid) {
+ return mid in {
+ // There are no modules right now that are copy-only. If you have some, though, just add
+ // them here like this:
+ // 'app/module': 1
+ };
+}
+
+var profile = {
+ action: 'release',
+ cssOptimize: 'comments',
+ mini: true,
+
+ basePath: '../../../src',
+ packages: [
+ {name: 'NucleotideDensityPlugin', location: '../plugins/NucleotideDensityPlugin/js' }
+ ],
+
+ layerOptimize: 'closure',
+ stripConsole: 'normal',
+ selectorEngine: 'acme',
+
+ layers: {
+ 'NucleotideDensityPlugin/main': {
+ include: [
+ 'NucleotideDensityPlugin',
+ ],
+ exclude: [ 'JBrowse' ]
+ }
+ },
+
+ staticHasFeatures: {
+ 'dojo-trace-api':0,
+ 'dojo-log-api':0,
+ 'dojo-publish-privates':0,
+ 'dojo-sync-loader':0,
+ 'dojo-xhr-factory':0,
+ 'dojo-test-sniff':0
+ },
+
+ resourceTags: {
+ // Files that contain test code.
+ test: function (filename, mid) {
+ return false;
+ },
+
+ // Files that should be copied as-is without being modified by the build system.
+ copyOnly: function (filename, mid) {
+ return copyOnly(mid);
+ },
+
+ // Files that are AMD modules.
+ amd: function (filename, mid) {
+ return !copyOnly(mid) && /.js$/.test(filename);
+ },
+
+ // Files that should not be copied when the “mini” compiler flag is set to true.
+ miniExclude: function (filename, mid) {
+ return ! ( /^NucleotideDensityPlugin/.test(mid) );
+ }
+ }
+};

js/Store/SeqFeature/NucContent.js

@@ -26,9 +26,10 @@ function(
  this.refSeq = this.store.refSeq;
  this.windowSize = args.windowSize;
  this.windowDelta = args.windowDelta;
+ this.bothStrands = args.bothStrands;
  this.nuc = args.nuc;
  this.nucLength = args.nuc.length;
- this.nucAr = StoreUtil.getPossibilities(this.nuc);
+ this.nucAr = StoreUtil.getPossibilities(this.nuc, this.bothStrands);
  this._deferred.features.resolve({success: true});
  },
 
@@ -82,6 +83,8 @@ function(
  }
  var pos = query.start;
  var score = nc / rn;
+ if(thisB.bothStrands)
+ score /= 2;
 
  // add to stats
  thisB.stats.count++;

js/Store/Util.js

@@ -12,6 +12,9 @@ function(
  JSON,
  nucleotidetable
 ){
+ /*
+ Utility class dealing with degenerate nucleotide sequences
+ */
  var Util;
  var ntable = JSON.parse(nucleotidetable);
 
@@ -51,15 +54,17 @@ function(
  return out;
  },
 
- getPossibilities: function(inStr){
+ getPossibilities: function(inStr, bothStrands){
  // first get forward possibilities
  var nucAr = Util._transformNuc(inStr);
  // get reverse
- /*var revAr = array.map(nucAr, function(x){
- return Util._reverseComplement(x);
- });
- // combine
- nucAr.push.apply(nucAr, revAr);*/
+ if(bothStrands){
+ var revAr = array.map(nucAr, function(x){
+ return Util._reverseComplement(x);
+ });
+ // combine
+ nucAr.push.apply(nucAr, revAr);
+ }
  return nucAr;
  }
 }

js/main.js

@@ -0,0 +1,36 @@
+define([
+ 'dojo/_base/declare',
+ 'JBrowse/Plugin',
+ 'NucleotideDensityPlugin/Store/Util'
+ ],
+ function(
+ declare,
+ JBrowsePlugin,
+ storeUtil
+ ) {
+return declare( JBrowsePlugin,
+{
+ constructor: function( args ) {
+ var browser = args.browser;
+
+ // do anything you need to initialize your plugin here
+ console.log( "NucleotideDensityPlugin plugin starting" );
+ // register new track type
+
+ browser.registerTrackType({
+ label: 'NucDensity',
+ type: 'NucleotideDensityPlugin/View/Track/NucDensityMulti'
+ });
+ /*var p = new ndstore({context:['CG'], windowDelta: 100, windowSize: 500, browser: browser, refSeq: 'stuff'});
+ console.log(p);*/
+ /*var m = 'chg';
+ var t = storeUtil._transformNuc(m);
+ //console.log(m,t);
+ m='whh';
+ var t = storeUtil._transformNuc(m);
+ //console.log(m,t);
+ //console.log('jls', storeUtil._reverseComplement('jls'));
+ console.log('chh',storeUtil.getPossibilities('chh'));*/
+ }
+});
+});

release_notes.txt

@@ -0,0 +1,6 @@
+# Release notes
+
+v0.2 - Nov 10, 2016
+- allows specifiying unlimited number of nucleotide contexts
+- multiple options to specify color of contexts default to random (not truly random but equidistant colors)
+- ability to compute density using forward strand or both strands