From a7c854743951fc6da24d2e4d35e3f525db970ffc Mon Sep 17 00:00:00 2001
From: Yuchen Jiang <yuchen.jiang@uconn.edu>
Date: Sun, 11 Oct 2015 16:02:17 -0400
Subject: [PATCH] fixed add recent track

---
 VQI_GenomeBrowser.js       | 81 ++++++++++++++++++++++----------------
 VQI_GenomeBrowserDemo.html |  5 ++-
 dynamic_loading.php        |  1 +
 3 files changed, 51 insertions(+), 36 deletions(-)

diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index cd3ddca..557ded5 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -73,7 +73,8 @@ function VQI_GenomeBrowser(id, serviceURL) {
         for (i in trackInfo){
 
             if (trackInfo[i].name == track){
-                self.addTrack(track[i].name , trackInfo[i].type , trackInfo[i].args);
+                console.log([trackInfo[i].name,trackInfo[i].type , trackInfo[i].args]);
+                self.addTrack(trackInfo[i].name , trackInfo[i].type , trackInfo[i].args);
                 break;
             }           
         }
@@ -539,6 +540,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
     };
 
     var uploadFile = function(data,name,genome){
+        //console.log(data);
         headerArray = ["CHROM","CHROM_START","CHROM_END","GENESYMBOL","SCORE","STRAND"];
 
         for (i in headerArray) {
@@ -559,9 +561,9 @@ function VQI_GenomeBrowser(id, serviceURL) {
             var CurrentFileHandle = data;
             var trackName = CurrentFileHandle;
             if(name !== undefined){
-                var trackName = name+" "+genome;
+                var trackName = name;
             }
-            trackInfo.push({name: trackName, type: "custom", args: {fileHandle: CurrentFileHandle, exportable: true}});
+            trackInfo.push({name: trackName, type: "custom", args: {table_name: CurrentFileHandle, exportable: true}});
             updateRecentTrackDropDown();
             self.addTrack(trackName , "custom" , {table_name: CurrentFileHandle});
         }).error(function (req, status, error) {
@@ -772,42 +774,51 @@ function VQI_GenomeBrowser(id, serviceURL) {
             });
     }
 
-    this.addTrack = function (name, type, args) {
-
-        var trackIndex = trackList.length;
+    this.addTrack = function (name, type, args, fromServer) {
+        if(fromServer){
+            var temp = [];
+            for (i in args) {
+                temp.push(args[i].join('\t'));
+            }
+            trackData = temp.join('\n');
+            uploadFile(trackData,name);
+        }
+        else{
+            var trackIndex = trackList.length;
 
-        var trackCount = trackIndex + 1;
-        //name of track
-        name = name || "track-" + (trackIndex + 1);
+            var trackCount = trackIndex + 1;
+            //name of track
+            name = name || "track-" + (trackIndex + 1);
 
-        if(type == "cpg")
-        {
-            trackList.push(new CpgTrack(name, graphRegion.append("g"), args));
-        }
-        else if(type == "genes")
-        {
-            trackList.push(new BedTrack(name, graphRegion.append("g"), args));
-        }
-        else if(type == "fasta")
-        {
-            trackList.push(new FastaTrack(name, graphRegion.append("g"), args));
-        }
-        else
-        {
-            args.exportable = true;
-            trackList.push(new CustomTrack(name, graphRegion.append("g"), args));
-        }
+            if(type == "cpg")
+            {
+                trackList.push(new CpgTrack(name, graphRegion.append("g"), args));
+            }
+            else if(type == "genes")
+            {
+                trackList.push(new BedTrack(name, graphRegion.append("g"), args));
+            }
+            else if(type == "fasta")
+            {
+                trackList.push(new FastaTrack(name, graphRegion.append("g"), args));
+            }
+            else
+            {
+                args.exportable = true;
+                trackList.push(new CustomTrack(name, graphRegion.append("g"), args));
+            }
 
-        setPanExtent();
-        graph(chrom_curr);
+            setPanExtent();
+            graph(chrom_curr);
 
-        clipPath.attr("height", Number(svg.attr("height")));
-        zoomOnly = true;
-        zoomed();
-        zoomOnly = false;
-        
-        reorderTracks();
-        updateAllTracksSelectBoxes();
+            clipPath.attr("height", Number(svg.attr("height")));
+            zoomOnly = true;
+            zoomed();
+            zoomOnly = false;
+            
+            reorderTracks();
+            updateAllTracksSelectBoxes();
+        }
         
     }
 
diff --git a/VQI_GenomeBrowserDemo.html b/VQI_GenomeBrowserDemo.html
index 718d021..beac1d1 100644
--- a/VQI_GenomeBrowserDemo.html
+++ b/VQI_GenomeBrowserDemo.html
@@ -46,6 +46,7 @@
                         genes: {file: "../../genome/hg19_genes.txt", table_name:'hg19_gene_annotation'},
                         cpg: {file: "../../genome/hg19_genes.txt", table_name:'hg19_cpg'},*/
                         //fasta: {fasta: "/Users/corywang/Downloads/hg19.fa.txt", index : "/Users/corywang/Downloads/hg19.fa.fai.txt"},
+                        
                         genes: {file: "hg19_refgene.txt", table_name: "hg19_refgene"},
                         cpg: {file: "cpg_site_hg19.txt,shelve_hg19.txt,shoer_hg19.txt", table_name: "cpg_site_hg19,shelve_hg19,shoer_hg19"},
                         //custom: {file: "", table_name:'upload1436411775'}
@@ -59,10 +60,12 @@
                 };
 
                 obj.loadGenomes(genomes);  //loads the genomes based on the datastructure described above
-                setTimeout(function(){ hs()}, 3000);
+                setTimeout(function(){ hs()}, 1000);
                 function hs (){
                     obj.setGenome("HG19");
                 }
+                // obj.addTrack("HG19_Custom","Custom",[["CHROM", "CHROM_START" ,"CHROM_END" ,  "GENESYMBOL",  "SCORE",   "STRAND"],["chr1" , "896004" , "896005" , "." ,  "0"  , "+"]],true);
+
                 //obj.setGenome("HG19");
              //   obj.setGenome("MM9"); //should set hg19 genome in dropdown and display fasta, cpg and genes tracks.
 
diff --git a/dynamic_loading.php b/dynamic_loading.php
index de38178..178ef60 100644
--- a/dynamic_loading.php
+++ b/dynamic_loading.php
@@ -18,6 +18,7 @@
 
     if (isset($_POST["upload"])){
         $timestamp = (new DateTime())->getTimestamp();
+        $timestamp = "upload".$timestamp;
         $data = parseData($_POST["upload"]);
         if(isset($_POST["tableName"])){
             $result = insertToDb($_POST["tableName"], $_POST["header"],$data);