add LRU caching to XHRBlobs, providing a big speedup to both BAM and …

…BigWig backends. woot!

src/JBrowse/Model/XHRBlob.js

@@ -1,7 +1,8 @@
 define( [ 'dojo/_base/declare',
-          'JBrowse/Model/FileBlob'
+          'JBrowse/Model/FileBlob',
+          'JBrowse/Store/LRUCache'
         ],
-        function( declare, FileBlob ) {
+        function( declare, FileBlob, LRUCache ) {
 var XHRBlob = declare( FileBlob,
 /**
  * @lends JBrowse.Model.XHRBlob.prototype
@@ -32,6 +33,12 @@ var XHRBlob = declare( FileBlob,
             this.end = end;
         }
         this.opts = opts;
+
+        this.cache = opts.cache
+            || new LRUCache({
+                                fillCallback: dojo.hitch(this, '_fetch')
+                            });
+        this.opts.cache = this.cache;
     },
 
     slice: function(s, l) {
@@ -49,7 +56,25 @@ var XHRBlob = declare( FileBlob,
         return new XHRBlob(this.url, ns, ne, this.opts);
     },
 
-    fetch: function(callback, attempt, truncatedLength) {
+    fetch: function( callback ) {
+        var url = this.url,
+            end = this.end,
+            start = this.start;
+
+        var request = {
+            url: url,
+            end: end,
+            start: start,
+            toString: function() {
+                return url+" (bytes "+start+".."+end+")";
+            }
+        };
+
+        // note that the cache has `_fetch` configured as its fill callback
+        this.cache.get( request, callback );
+    },
+
+    _fetch: function( request, callback, attempt, truncatedLength) {
         var thisB = this;
 
         attempt = attempt || 1;
@@ -60,12 +85,12 @@ var XHRBlob = declare( FileBlob,
 
         var req = new XMLHttpRequest();
         var length;
-        req.open('GET', this.url, true);
+        req.open('GET', request.url, true);
         if( req.overrideMimeType )
             req.overrideMimeType('text/plain; charset=x-user-defined');
-        if (this.end) {
-            req.setRequestHeader('Range', 'bytes=' + this.start + '-' + this.end);
-            length = this.end - this.start + 1;
+        if (request.end) {
+            req.setRequestHeader('Range', 'bytes=' + request.start + '-' + request.end);
+            length = request.end - request.start + 1;
         }
         req.responseType = 'arraybuffer';
         req.onreadystatechange = function() {
@@ -88,7 +113,7 @@ var XHRBlob = declare( FileBlob,
                         try{
                             var r = req.responseText;
                             if (length && length != r.length && (!truncatedLength || r.length != truncatedLength)) {
-                                return thisB.fetch( callback, attempt + 1, r.length );
+                                return thisB._fetch( request, callback, attempt + 1, r.length );
                             } else {
                                 return callback.call( thisB, thisB._stringToBuffer(req.responseText) );
                             }
@@ -98,7 +123,7 @@ var XHRBlob = declare( FileBlob,
                         }
                     }
                 } else {
-                    return thisB.fetch(callback, attempt + 1);
+                    return thisB._fetch( request, callback, attempt + 1);
                 }
             }
             return null;

src/JBrowse/Store/LRUCache.js

@@ -21,7 +21,7 @@ return declare( null,
      */
     constructor: function( args ) {
         this.fill = args.fillCallback;
-        this.maxSize = args.maxSize || 100000;
+        this.maxSize = args.maxSize || 1000000;
 
         this._size = args.sizeFunction || this._size;
         this._keyString = args.keyFunction || this._keyString;
@@ -36,20 +36,34 @@ return declare( null,
         this._cacheNewest = null;
     },
 
-    get: function( inKey ) {
+    _log: function() {
+        //console.log.apply( console, arguments );
+    },
+
+    get: function( inKey, callback ) {
         var key = this._keyString( inKey );
 
         var record = this._cacheByKey[ key ];
         if( !record ) {
             // call our fill callback if necessary
+            this._log( 'cache miss', key );
+
             if( this.fill ) {
-                var val = this.fill( inKey );
-                if( val )
-                    return this.set( inKey, val );
+                this.fill( inKey, dojo.hitch(this, function( value ) {
+                    if( value ) {
+                        this.set( inKey, value );
+                    }
+                    callback( value );
+                }));
             }
-            return null;
+            else {
+                callback( null );
+            }
+            return;
         }
 
+        this._log( 'cache hit', key, record.value );
+
         // take it out of the linked list
         if( record.prev )
             record.prev.next = record.next;
@@ -63,14 +77,15 @@ return declare( null,
             this._cacheNewest.next = record;
         this._cacheNewest = record;
 
-        return record.value;
+        callback( record.value );
     },
 
     set: function( inKey, value ) {
         var key = this._keyString( inKey );
         if( this._cacheByKey[key] ) {
-            return this.get( inKey );
+            return;
         }
+        this._log( 'cache fill', key, value );
 
         // make a cache record for it
         var record = {
@@ -83,11 +98,12 @@ return declare( null,
         this._prune( record.size );
 
         // put it in the byKey structure
-        this._cacheByKey[key] = value;
+        this._cacheByKey[key] = record;
 
         // put it in the doubly-linked list
         record.prev = this._cacheNewest;
-        this._cacheNewest.next = record;
+        if( this._cacheNewest )
+            this._cacheNewest.next = record;
         this._cacheNewest = record;
         if( ! this._cacheOldest )
             this._cacheOldest = record;
@@ -96,7 +112,7 @@ return declare( null,
         this.size += record.size;
         this.itemCount++;
 
-        return value;
+        return;
     },
 
     _keyString: function( key ) {
@@ -110,9 +126,23 @@ return declare( null,
     },
 
     _size: function( value ) {
-        var type = typeof key;
-        if( typeof value == 'object' ) {
-            throw 'not implemented';
+        var type = typeof value;
+        if( type == 'object' ) {
+            var sizeType = typeof value.size;
+            if( sizeType == 'number' ) {
+                return sizeType;
+            }
+            else if( sizeType == 'function' ) {
+                return value.size();
+            } else {
+                var sum = 0;
+                for( var k in value ) {
+                    if( value.hasOwnProperty( k ) ) {
+                        sum += this._size( value[k] );
+                    }
+                }
+            }
+            return sum;
         } else {
             return 1;
         }