From c44f9a9a4b2be6f0c287fbd58fea3b4bc0f04244 Mon Sep 17 00:00:00 2001
From: corywang <cory.wang@uconn.edu>
Date: Fri, 13 Mar 2015 11:10:25 -0400
Subject: [PATCH] Fixed rest of currently known zoom and exon bugs

---
 VQI_GenomeBrowser.js | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index 20d3eba..2c4fef4 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -293,8 +293,6 @@ function VQI_GenomeBrowser(id) {
                 xScale.domain()[1] > panExtent[1] ? 
                     maxX : 
                     zoom.translate()[0];
-
-        console.log(tx);
         return tx;
 
     }
@@ -320,20 +318,18 @@ function VQI_GenomeBrowser(id) {
 
         zoom.scale(scale);
 
+
+        //translates scale with regards to the middle of xMin and xMax
         var divisor = (width) / ((xScale.domain()[1]-xScale.domain()[0])*scale);
         var diff = margin - scale* margin;
         var minX = -(((xScale.domain()[0]-xScale.domain()[1])*scale)+(panExtent[1]-(panExtent[1]-(width/divisor)))) + diff;
         var maxX = -(((xScale.domain()[0]-xScale.domain()[1]))+(panExtent[1]-panExtent[0]))*divisor*scale + diff;
 
         var midScale = d3.scale.linear()
-                        .domain([panExtent[0], panExtent[1]])
+                        .domain([panExtent[0] + (xMax - xMin) / 2, panExtent[1] - (xMax - xMin) / 2])
                         .range([minX,maxX]);
 
-        //TODO: Need to figure out actual translation
-        var zoomWidth = midScale(xMin);
-
-        /*console.log(diff);
-        console.log(zoomWidth);*/
+        var zoomWidth = midScale((xMax + xMin)/2);
 
         zoom.translate([zoomWidth,0])
             .scale(scale);
@@ -490,24 +486,26 @@ function VQI_GenomeBrowser(id) {
                     .text(name);
         }
 //        test.addTrack({start:20000000, end:20000100})
-        var tracks = svg.selectAll("line")
-                .data(thisData)
+        svg.selectAll("line")
+                .data(thisData, function (d){return d;})
                 .enter()
                 .append("line");
+        var tracks = svg.selectAll("line")
+                .data(thisData, function (d){return d;})
         var lineAttributes = tracks
                 .attr("x1", function (d) {
                     return xScale(d[index.start]);
                 })
                 .attr("y1", function (d) {
 
-                    return height / 2 + margin + 20 + ySpace;
+                    return thisY;
                 })
                 .attr("x2", function (d) {
                     return xScale(d[index.end]);
                 })
                 .attr("y2", function (d) {
 //                    return 50;
-                    return height / 2 + margin + 20 + ySpace;
+                    return thisY;
                 })
                 .style("stroke", "black")
                 .style("stroke-width", "2px")
@@ -566,7 +564,7 @@ function VQI_GenomeBrowser(id) {
                 return name + " (" + d[indexArray.chr] + " : " + d[indexArray.start] + " - " + d[indexArray.end] + ")";
             }
         });
-        $('svg line').tipsy({
+        $(tracks[0]).tipsy({
             gravity: 'n',
             html: true,
             title: function () {