From b45a8326d33ad61f8490b6987aeb5b9002b18bbe Mon Sep 17 00:00:00 2001
From: jsmirob <jsmirob@gmail.com>
Date: Tue, 15 Jan 2013 16:29:12 -0500
Subject: [PATCH] Added new track type

---
 src/JBrowse/View/Track/BaseCoverage.js | 182 +++++++++++++++++++++++++
 1 file changed, 182 insertions(+)
 create mode 100644 src/JBrowse/View/Track/BaseCoverage.js

diff --git a/src/JBrowse/View/Track/BaseCoverage.js b/src/JBrowse/View/Track/BaseCoverage.js
new file mode 100644
index 0000000000..5e8b378f63
--- /dev/null
+++ b/src/JBrowse/View/Track/BaseCoverage.js
@@ -0,0 +1,182 @@
+define( ['dojo/_base/declare',
+         'dojo/_base/array',
+         'JBrowse/View/Track/Wiggle',
+         'JBrowse/Util'
+        ],
+        function( declare, array, Wiggle, Util ) {
+
+// feature class for the features we make for the calculated coverage
+// values
+var CoverageFeature = Util.fastDeclare(
+    {
+        get: function(f) { return this[f]; },
+        tags: function() { return [ 'start', 'end', 'score' ]; },
+        score: 0,
+        constructor: function( args ) {
+            this.start = args.start;
+            this.end = args.end;
+            this.score = args.score;
+        }
+    });
+
+return declare( Wiggle,
+{
+
+    _defaultConfig: function() {
+        return Util.deepUpdate(
+            dojo.clone( this.inherited(arguments) ),
+            {
+                min_score: 0,
+                max_score: 100
+            }
+        );
+    },
+
+    getGlobalStats: function() {
+        return {};
+    },
+
+    getFeatures: function( query, featureCallback, finishCallback, errorCallback ) {
+        var leftBase  = query.start;
+        var rightBase = query.end;
+        var scale = query.scale; // px/bp
+        var widthBp = rightBase-leftBase;
+        var widthPx = widthBp * ( query.scale || 1/query.basesPerSpan);
+
+        var binWidth = Math.ceil( query.basesPerSpan ); // in bp
+
+        var arraySize = Math.ceil( widthBp/binWidth );
+        var coverageBins = new Array( arraySize );
+        var aCoverage = new Array( arraySize );
+        var tCoverage = new Array( arraySize );
+        var cCoverage = new Array( arraySize );
+        var gCoverage = new Array( arraySize );
+        var bpToBin = function( bp ) {
+            return Math.floor( (bp-leftBase) / binWidth );
+        };
+
+        this.store.getFeatures(
+            query,
+            dojo.hitch( this, function( feature ) {
+                            var startBin = bpToBin( feature.get('start') );
+                            var endBin   = bpToBin( feature.get('end')-1 );
+                            for( var i = startBin; i <= endBin; i++ ) {
+                                coverageBins[i] = (coverageBins[i] || 0) + 1;
+                            }
+                            // Calculate SNP coverage
+                            var mdTag = feature.get('MD');
+                            if(mdTag) {
+                                var SNPs = this._mdToMismatches(feature, mdTag);
+                                // loops through mismatches and updates coverage variables accordingly.
+                                for (var i = 0; i<SNPs.length; i++) {
+                                    var pos = feature.get('start') + SNPs[i].start - leftBase;
+                                    switch (SNPs[i].bases) {
+                                        case "A": aCoverage[pos] = (aCoverage[pos] || 0) + 1; break;
+                                        case "T": tCoverage[pos] = (tCoverage[pos] || 0) + 1; break;
+                                        case "C": cCoverage[pos] = (cCoverage[pos] || 0) + 1; break;
+                                        case "G": gCoverage[pos] = (gCoverage[pos] || 0) + 1; break;
+                                        default: alert("Unknown base encountered: " + SNPs[i].bases);
+                                    }
+                                }
+                            }
+                        }),
+            function () {
+                // make fake features from the coverage
+                for( var i = 0; i < coverageBins.length; i++ ) {
+                    // score contains [non-SNP coverage, a SNPs, t SNPs, c SNPs, g SNPs]
+                    var nonSNP = (coverageBins[i] || 0) - (aCoverage[i] || 0) - (tCoverage[i] || 0) - (cCoverage[i] || 0) - (gCoverage[i] || 0);
+                    var score = [nonSNP, aCoverage[i] || 0, tCoverage[i] || 0, cCoverage[i] || 0, gCoverage[i] || 0];
+                    var bpOffset = leftBase+binWidth*i;
+                    featureCallback( new CoverageFeature({
+                        start: bpOffset,
+                        end:   bpOffset+binWidth,
+                        score: score
+                     }));
+                }
+                finishCallback();
+            }
+        );
+    },
+
+    /***********************************************************************************************************************
+     * Draw a set of features on the canvas.
+     * @private
+     */
+    _drawFeatures: function( scale, leftBase, rightBase, block, canvas, features, featureRects, dataScale ) {
+        var context = canvas.getContext('2d');
+        var canvasHeight = canvas.height;
+        var toY = dojo.hitch( this, function( val ) {
+           return canvasHeight * ( 1-dataScale.normalize.call(this, val) );
+        });
+        var originY = toY( dataScale.origin );
+
+        var barColor  = ['#777', 'green', 'red', 'blue', 'yellow'];
+        var clipColor = this.config.style.clip_marker_color;
+        var bgColor   = this.config.style.bg_color;
+        var disableClipMarkers = this.config.disable_clip_markers;
+
+        dojo.forEach( features, function(f,i) {
+
+            var fRect = featureRects[i];
+
+            var score = f.get('score');
+
+            for (var j = 0; j<5; j++) {
+
+                fRect.t = toY(score.slice(j,5).reduce(function(a,b){return a+b;})); // makes progressively shorter rectangles.
+
+                // draw the background color if we are configured to do so
+                if( bgColor && fRect.t >= 0 ) {
+                    context.fillStyle = bgColor;
+                    context.fillRect( fRect.l, 0, fRect.w, canvasHeight );
+                }
+
+                if( fRect.t <= canvasHeight ) { // if the rectangle is visible at all
+
+                    if( fRect.t <= originY ) {
+                        // bar goes upward
+                        context.fillStyle = barColor[j];
+                        context.fillRect( fRect.l, fRect.t, fRect.w, originY-fRect.t+1);
+                        if( !disableClipMarkers && fRect.t < 0 ) { // draw clip marker if necessary
+                            context.fillStyle = clipColor || negColor;
+                            context.fillRect( fRect.l, 0, fRect.w, 2 );
+                        }
+                    }
+                    else {
+                        alert('Invalid data used. Negative values are not possible.');
+                    }
+                }
+            }
+        }, this );
+    },
+    //*******************************************************************************************************************************
+
+    // a method blatently stolen from "Alignments.js" Perhaps it would be better just to include the file...
+    _mdToMismatches: function( feature, mdstring ) {
+        var mismatchRecords = [];
+        var curr = { start: 0, bases: '' };
+        var seq = feature.get('seq');
+        var nextRecord = function() {
+              mismatchRecords.push( curr );
+              curr = { start: curr.start + curr.bases.length, bases: ''};
+        };
+        array.forEach( mdstring.match(/(\d+|\^[a-z]+|[a-z])/ig), function( token ) {
+          if( token.match(/^\d/) ) { // matching bases
+              curr.start += parseInt( token );
+          }
+          else if( token.match(/^\^/) ) { // insertion in the template
+              var i = token.length-1;
+              while( i-- ) {
+                  curr.bases += '*';
+              }
+              nextRecord();
+          }
+          else if( token.match(/^[a-z]/i) ) { // mismatch
+              curr.bases = seq.substr( curr.start, token.length );
+              nextRecord();
+          }
+        });
+        return mismatchRecords;
+    }
+});
+});
\ No newline at end of file