improvements to inline documentation

js/FeatureTrack.js

@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function FeatureTrack( trackMeta, refSeq, browserParams ) {
     //trackMeta: object with:
     //            key:   display text track name

js/GenomeView.js

@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function Animation(subject, callback, time) {
     //subject: what's being animated
     //callback: function to call at the end of the animation
@@ -59,6 +62,9 @@ Animation.prototype.stop = function() {
     this.callback(this);
 };
 
+/**
+ * @class
+ */
 function Slider(view, callback, time, distance) {
     Animation.call(this, view, callback, time);
     this.slideStart = view.getX();
@@ -78,6 +84,9 @@ Slider.prototype.step = function(pos) {
     this.subject.setX(newX);
 };
 
+/**
+ * @class
+ */
 function Zoomer(scale, toScroll, callback, time, zoomLoc) {
     Animation.call(this, toScroll, callback, time);
     this.toZoom = toScroll.zoomContainer;
@@ -115,6 +124,9 @@ Zoomer.prototype.step = function(pos) {
     this.subject.updateTrackLabels(this.initialX - newLeft);
 };
 
+/**
+ * @class
+ */
 function GenomeView(elem, stripeWidth, refseq, zoomLevel, browserRoot) {
     //all coordinates are interbase
 

js/GridTrack.js

@@ -1,7 +1,12 @@
 // VIEW
 
-// This track draws vertical gridlines, which are divs with height:
-// 100%, absolutely positioned at the very top of all the tracks
+/**
+
+This track draws vertical gridlines, which are divs with height 100%,
+absolutely positioned at the very top of all the tracks.
+
+@class
+*/
 function GridTrack(name) {
     Track.call(this, name, name, true, function() {});
 }
@@ -46,4 +51,3 @@ GridTrack.prototype.renderGridlines = function(block,leftBase,rightBase) {
 
 };
 
-

js/ImageTrack.js

@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function ImageTrack(trackMeta, refSeq, browserParams) {
     Track.call(this, trackMeta.label, trackMeta.key,
                false, browserParams.changeCallback);

js/Layout.js

@@ -1,6 +1,6 @@
 // VIEW
 
-/*
+/**
  * Code for laying out rectangles, given that layout is also happening
  * in adjacent blocks at the same time
  *
@@ -10,6 +10,7 @@
  * contour spans and give up some packing closeness in exchange for speed
  * (the code already merges spans that have the same x-coord and are vertically
  * contiguous).
+ * @class
  */
 
 function Contour(top) {
@@ -183,6 +184,9 @@ Contour.prototype.getNextTop = function(fit) {
     return this.spans[fit.above].top + this.spans[fit.above].height;
 };
 
+/**
+ * @class
+ */
 function Layout(leftBound, rightBound) {
     this.leftBound = leftBound;
     this.rightBound = rightBound;

js/LazyArray.js

@@ -7,10 +7,10 @@
  */
 
 /**
- * Construct a new LazyArray
- * @class This class makes it easier to partially load a large JSON array
+ * Construct a new LazyArray, which partially loads large JSON arrays.
+ * @class
  * @constructor
- * @param lazyArrayParams object with:<br>
+ * @param lazyArrayParams {Object} as:
  * <ul>
  * <li><code>urlTemplate</code> - for each lazily-loaded array chunk, the chunk number will get substituted for {chunk} in this template, and the result will beused as the URL of the JSON for that array chunk</li>
  * <li><code>length</code> - length of the overall array</li>
@@ -56,7 +56,7 @@ LazyArray.prototype.range = function(start, end, callback, postFun, param) {
     var firstChunk = Math.floor(start / this.chunkSize);
     var lastChunk = Math.floor(end / this.chunkSize);
 
-    if (postFun === undefined) postFun = function() {};
+    if (postFun === undefined) /** @inner */ postFun = function() {};
     var finish = new Finisher(postFun);
 
     for (var chunk = firstChunk; chunk <= lastChunk; chunk++) {
@@ -124,4 +124,4 @@ LazyArray.prototype._processChunk = function(start, end, chunk,
     for (var i = chunkStart; i <= chunkEnd; i++) {
         callback(i + firstIndex, this.chunks[chunk][i], param);
     }
-};
+};

js/LazyPatricia.js

@@ -1,6 +1,7 @@
 // MODEL
 
-/*
+/**
+<pre>
   Implements a lazy PATRICIA tree.
 
   This class is a map where the keys are strings.  The map supports fast
@@ -49,7 +50,11 @@
   the wire (so, no type tags in the JSON to distinguish loaded nodes,
   lazy nodes, and leaves) while supporting lazy loading and reasonably
   fast lookups.
- */
+</pre>
+
+@class
+
+*/
 
 function LazyTrie(rootURL, chunkTempl) {
     this.rootURL = rootURL;

js/NCList.js

@@ -1,11 +1,22 @@
 // MODEL
 
-//After
-//Alekseyenko, A., and Lee, C. (2007).
-//Nested Containment List (NCList): A new algorithm for accelerating
-//   interval query of genome alignment and interval databases.
-//Bioinformatics, doi:10.1093/bioinformatics/btl647
-//http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1
+/**
+
+Nested containment list.
+
+@class
+
+After
+<pre>
+  Alekseyenko, A., and Lee, C. (2007).
+  Nested Containment List (NCList): A new algorithm for accelerating
+     interval query of genome alignment and interval databases.
+  Bioinformatics, doi:10.1093/bioinformatics/btl647
+</pre>
+
+<a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1">http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1</a>
+
+ */
 
 function NCList() {
 }

js/SeqFeatureStore/NCList.js

@@ -73,6 +73,7 @@ SeqFeatureStore.NCList.prototype.histogram = function() {
 SeqFeatureStore.NCList.prototype.iterate = function( startBase, endBase, origFeatCallback, finishCallback ) {
     var that = this;
     var accessors    = this.attrs.accessors(),
+        /** @inner */
         featCallBack = function( feature, path ) {
             that._add_getters( accessors.get, feature );
             return origFeatCallback( feature, path );

js/SequenceTrack.js

@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function SequenceTrack(trackMeta, refSeq, browserParams) {
     //trackMeta: object with:
     //  key:   display text track name
@@ -124,10 +127,12 @@ SequenceTrack.prototype.renderSeqDiv = function ( start, end, seq ) {
     return container;
 };
 
-SequenceTrack.prototype.getRange = function(start, end, callback) {
-    //start: start coord, in interbase
-    //end: end coord, in interbase
-    //callback: function that takes (start, end, seq)
+/**
+ * @param start start coord, in interbase
+ * @param end end coord, in interbase
+ * @param callback function that takes ( start, end, seq )
+ */
+SequenceTrack.prototype.getRange = function( /**Number*/ start, /**Number*/ end, /**Function*/ callback) {
     var firstChunk = Math.floor( Math.max(0,start) / this.chunkSize);
     var lastChunk = Math.floor((end - 1) / this.chunkSize);
     var chunkSize = this.chunkSize;

js/StaticTrack.js

@@ -1,7 +1,12 @@
 // VIEW
 
-//This track is for (e.g.) position and sequence information that should
-//always stay visible at the top of the view
+/**
+
+This track is for (e.g.) position and sequence information that should
+always stay visible at the top of the view.
+
+@class
+*/
 
 function StaticTrack(name, labelClass, posHeight) {
     Track.call(this, name, name, true, function() {});

js/Track.js

@@ -1,5 +1,8 @@
 // VIEW
 
+/**
+ * @class
+ */
 function Track(name, key, loaded, changeCallback) {
     this.name = name;
     this.key = key;

js/Util.js

@@ -1,5 +1,9 @@
 // MISC
 
+/**
+ * @namespace
+ */
+
 var Util = {};
 
 Util.is_ie = navigator.appVersion.indexOf('MSIE') >= 0;
@@ -364,6 +368,9 @@ if (!Array.prototype.indexOf)
   };
 }
 
+/**
+ * @class
+ */
 function Finisher(fun) {
     this.fun = fun;
     this.count = 0;