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load track from server fixed
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@yuj12001
yuj12001 committed Aug 6, 2015
1 parent e5c22a0 commit 6fa59af
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Showing 2 changed files with 52 additions and 24 deletions.
66 changes: 42 additions & 24 deletions VQI_GenomeBrowser.js
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Expand Up @@ -26,6 +26,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
var isready = false; var isready = false;
var zoomOnly = false; var zoomOnly = false;
var waitTime; var waitTime;
var loadCount = 0;




var trackInfo = []; var trackInfo = [];
Expand Down Expand Up @@ -59,7 +60,6 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
}; };
var addRecentTrack = function(){ var addRecentTrack = function(){
console.log(trackInfo);
var track = $("#" + divId + " #RecentTracks").val(); var track = $("#" + divId + " #RecentTracks").val();
for (i in trackList){ for (i in trackList){
if (trackList[i]['name'] == track){ if (trackList[i]['name'] == track){
Expand Down Expand Up @@ -421,17 +421,19 @@ function VQI_GenomeBrowser(id, serviceURL) {
"font-size": "11px"}); "font-size": "11px"});


if (! zoomOnly){ if (! zoomOnly){
//updateTrack();
if (waitTime != undefined) if (waitTime != undefined)
{ {
clearTimeout(waitTime); clearTimeout(waitTime);
} }
waitTime = setTimeout(updateTrack, 100); } waitTime = setTimeout(updateTrack, 100);
}
$("#" + divId + " #navigate").val(chrom_curr + ":" + Math.round(xScale.domain()[0]) + "-" + Math.round(xScale.domain()[1])); $("#" + divId + " #navigate").val(chrom_curr + ":" + Math.round(xScale.domain()[0]) + "-" + Math.round(xScale.domain()[1]));
}; };


var uploadFile = function(data){ var uploadFile = function(data,name,genome){
var rows = data.split("\n"); //var rows = data.split("\n");
headerArray = rows[0].split("\t"); headerArray = ["CHROM","CHROM_START","CHROM_END","GENESYMBOL","SCORE","STRAND"];


for (i in headerArray) { for (i in headerArray) {
indexArray[headerArray[i]] = i; indexArray[headerArray[i]] = i;
Expand All @@ -449,17 +451,28 @@ function VQI_GenomeBrowser(id, serviceURL) {


}).success(function (data) { }).success(function (data) {
var CurrentFileHandle = data; var CurrentFileHandle = data;
console.log(CurrentFileHandle); var trackName = CurrentFileHandle;
trackInfo.push({name: CurrentFileHandle, type: "bed", fileHandle: CurrentFileHandle}); if(name !== undefined){
var trackName = name+" "+genome;
}
trackInfo.push({name: trackName, type: "bed", fileHandle: CurrentFileHandle});
updateRecentTrackDropDown(); updateRecentTrackDropDown();
self.addOneTrackFromDatabase(CurrentFileHandle,CurrentFileHandle,"bed"); self.addOneTrackFromDatabase(CurrentFileHandle,trackName,"bed");
}).error(function (req, status, error) { }).error(function (req, status, error) {
$("body").append(status + ": " + error); $("body").append(status + ": " + error);
}); });
} }


var updateTrack = function(){ this.uploadFileFromServer = function(data,name,genome){
var temp = [];
for (i in data) {
temp.push(data[i].join('\t'));
}
trackData = temp.join('\n');
uploadFile(trackData,name,genome);
}


var updateTrack = function(){
if (isready){ if (isready){
var start = (Math.round(xScale.domain()[0])).toString(); var start = (Math.round(xScale.domain()[0])).toString();
var end = (Math.round(xScale.domain()[1])).toString(); var end = (Math.round(xScale.domain()[1])).toString();
Expand Down Expand Up @@ -491,21 +504,22 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


}).success(function (returnData) { }).success(function (returnData) {

for (i in trackList){ for (i in trackList){
var name = trackList[i]['name']; var name = trackList[i]['name'];
var type = trackList[i]['type']; var type = trackList[i]['type'];
trackList[i] = returnData[name]; if(returnData[name] != undefined){
trackList[i]['name'] = name; trackList[i] = returnData[name];
trackList[i]['type'] = type; trackList[i]['name'] = name;
if (name == "HG19"){ trackList[i]['type'] = type;
addBEDTrack(returnData[name][0], name, returnData[name][1]); if (name == "HG19"){
} addBEDTrack(returnData[name][0], name, returnData[name][1]);
else if (name == "cpg"){ }
addCpgTrack(returnData[name], name); else if (name == "cpg"){
} addCpgTrack(returnData[name], name);
else{ }
addBEDTrack(returnData[name], name); else{
addBEDTrack(returnData[name], name);
}
} }
} }


Expand Down Expand Up @@ -577,7 +591,9 @@ function VQI_GenomeBrowser(id, serviceURL) {
zoom.translate([zoomWidth, 0]) zoom.translate([zoomWidth, 0])
.scale(scale); .scale(scale);


zoomOnly = true;
zoomed(); zoomed();
zoomOnly = false;
} }


var setPanExtent = function (min, max) { var setPanExtent = function (min, max) {
Expand Down Expand Up @@ -631,6 +647,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


var addOneTrack = function (data, name, type, i) { var addOneTrack = function (data, name, type, i) {
//console.log("addonetrack");
i = Number(i); i = Number(i);
var trackIndex; var trackIndex;
if (!isNaN(i)) { if (!isNaN(i)) {
Expand Down Expand Up @@ -670,6 +687,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


data['name'] = name; data['name'] = name;
//console.log(data);
clipPath.attr("height", Number(svg.attr("height"))); clipPath.attr("height", Number(svg.attr("height")));
zoomOnly = true; zoomOnly = true;
zoomed(); zoomed();
Expand Down Expand Up @@ -975,7 +993,6 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


this.addTrackFromDatabase = function(){ this.addTrackFromDatabase = function(){

var chrom = "chr1"; var chrom = "chr1";
var fileHandles = []; var fileHandles = [];
var name = []; var name = [];
Expand Down Expand Up @@ -1010,7 +1027,6 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


this.addOneTrackFromDatabase = function(fileHandle,name,type){ this.addOneTrackFromDatabase = function(fileHandle,name,type){

var chrom = "chr1"; var chrom = "chr1";


$.ajax({ $.ajax({
Expand All @@ -1034,13 +1050,15 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


this.addTrack = function (data, name, type) { this.addTrack = function (data, name, type) {

if(data[0][0] != "chrom") if(data[0][0] != "chrom")
{ {
data.unshift(["chrom", "chrom_start", "chrom_end", "name", "score", "strand"]) data.unshift(["chrom", "chrom_start", "chrom_end", "name", "score", "strand"])
} }
data = addOneTrack(data, name, type); data = addOneTrack(data, name, type);

//console.log("addtrack");
trackList.push(data); trackList.push(data);



reorderTracks(); reorderTracks();
updateAllTracksSelectBoxes(); updateAllTracksSelectBoxes();
Expand Down
10 changes: 10 additions & 0 deletions VQI_GenomeBrowserDemo.html
View file
Expand Up @@ -32,6 +32,16 @@
//obj.addTrackFile(genomeFile, "base", 'bed'); //obj.addTrackFile(genomeFile, "base", 'bed');


obj.addTrackFromDatabase(); obj.addTrackFromDatabase();
var data = [["chr1", "896004", "896005", ".", "0", "+"],
["chr1", "976170", "976171", ".", "-.4", "+"],
["chr1", "1198674", "1198675", ".", "0", "+"],
["chr1", "1250433", "1250434", ".", "1", "+"],
["chr1", "1597292", "1597293", "rs79791328", "0", "+"],
["chr1", "1597292", "1597293", "rs79791328", "0", "+"]];

obj.uploadFileFromServer(data,"test","testgenome");
obj.uploadFileFromServer(data,"tests","testgenomes");
//setTimeout(function(){ obj.uploadFileFromServer(data,"test","testgenome"); }, 3000);


// var snpFile = file_dir + "./Tile2contentsnpplotter.txt"; // var snpFile = file_dir + "./Tile2contentsnpplotter.txt";
//obj.addTrackFile(snpFile, "Tile2 Content Snp", 'bed'); //obj.addTrackFile(snpFile, "Tile2 Content Snp", 'bed');
Expand Down

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