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@yuj12001
yuj12001 committed Jul 10, 2015
1 parent 68fe1a2 commit c98054d
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Showing 2 changed files with 295 additions and 101 deletions.
143 changes: 73 additions & 70 deletions VQI_GenomeBrowser.js
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Expand Up @@ -26,6 +26,10 @@ function VQI_GenomeBrowser(id) {
var isready = false;
var zoomOnly = false;

var trackInfo = [];
trackInfo[0] = {name: "HG19", type: "bed", fileHandle: "upload1436481988"};
trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", fileHandle: "upload1436411775"};

// $("#" + id).append("<div style='border : 1px solid; display : inline-block'>CPG:<input type='file' id='cpg'/>Shore:<input type='file' id='shore'/>Shelve:<input type='file' id='shelve'/><input id='submit' type='submit' /></div>");

// d3.select("#" + id).append("div").text("Chromosome: ")
Expand Down Expand Up @@ -471,6 +475,7 @@ function VQI_GenomeBrowser(id) {
};

var updateTrack = function(){

if (isready){

//console.log(trackList);
Expand All @@ -487,25 +492,35 @@ function VQI_GenomeBrowser(id) {
var chrom = "chr1";

$.ajax({
url: 'http://localhost/dynamic_loading.php',
url: 'dynamic_loading.php',
type: 'POST',
dataType: "json",
data: {
"getHG19Data": "",
"fileHandle": fileHandle,
"getTrackData": "",
"fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle],
"name": [trackInfo[0].name,trackInfo[1].name],
"chrom": chrom,
"start": start,
"end": end
}

}).success(function (returnData) {

console.log(returnData);
var i = getTrackIndexByName("HG19");
trackList[i] = returnData;
trackList[i] = returnData[0][0];
trackList[i]['name'] = "HG19";
trackList['type'] = "bed";
trackList[i]['type'] = "bed";
//console.log(trackList);
addBEDTrack(returnData[0][0], "HG19",returnData[0][1]);

var i = getTrackIndexByName("Tile2 Content Snp");
trackList[i] = returnData[1];
trackList[i]['name'] = "Tile2 Content Snp";
trackList[i]['type'] = "bed";
//console.log(trackList);
addBEDTrack(returnData, "HG19");
addBEDTrack(returnData[1], "Tile2 Content Snp");
//console.log(trackList);

zoomOnly = true;
zoomed();
zoomOnly = false;
Expand Down Expand Up @@ -909,7 +924,7 @@ function VQI_GenomeBrowser(id) {
});
}

var addBEDTrack = function (data, name) {
var addBEDTrack = function (data, name, exons) {
testdata = data;
//console.log(data);
/**
Expand Down Expand Up @@ -990,59 +1005,44 @@ function VQI_GenomeBrowser(id) {
.attr("class", "scalable")*/


// if (data[0].length >= indexArray.exonEnds)
// {
// var exons = [];
// $.each(data, function (index, value) {

// var exonStarts = value[indexArray.exonStarts].slice(1, value[indexArray.exonStarts].length - 2).split(",");
// var exonEnds = value[indexArray.exonEnds].slice(1, value[indexArray.exonEnds].length - 2).split(",");

// for (var i = 0; i < exonStarts.length; i++)
// {
// var exon = [];
// exon[indexArray.chr] = value[indexArray.chr];
// exon[indexArray.name] = value[indexArray.name] + " Exon " + (i + 1) + "/" + exonStarts.length;
// exon[indexArray.start] = parseInt(exonStarts[i]);
// exon[indexArray.end] = parseInt(exonEnds[i]);
// exons.push(exon);
// }
// });

// //console.log(exons[1]);

// trackScalableGroup.selectAll("rect")
// .data(data, function (d) {
// return d;
// })
// .exit()
// .remove();

// trackScalableGroup.selectAll("rect")
// .data(exons, function (d) {
// return d;
// })
// .enter()
// .append("rect");
// trackScalableGroup.selectAll("rect")
// .data(exons, function (d) {
// return d;
// })
// .attr("x", function (d) {
// return fullXScale(d[indexArray.start]);
// })
// .attr("y", -10)
// .attr("height", 20)
// .attr("width", function (d) {
// return fullXScale(d[indexArray.end]) - fullXScale(d[indexArray.start]);
// })
// .style("fill-opacity", ".8")
// .style("stroke", "black")
// .style("fill", "black")
// .style("vector-effect", "non-scaling-stroke")
// .attr("class", "scalable")

// }
if (exons)
{


//console.log(exons[1]);

trackScalableGroup.selectAll("rect")
.data(data, function (d) {
return d;
})
.exit()
.remove();

trackScalableGroup.selectAll("rect")
.data(exons, function (d) {
return d;
})
.enter()
.append("rect");
trackScalableGroup.selectAll("rect")
.data(exons, function (d) {
return d;
})
.attr("x", function (d) {
return fullXScale(d[0]);
})
.attr("y", -10)
.attr("height", 20)
.attr("width", function (d) {
return fullXScale(d[1]) - fullXScale(d[0]);
})
.style("fill-opacity", ".8")
.style("stroke", "black")
.style("fill", "black")
.style("vector-effect", "non-scaling-stroke")
.attr("class", "scalable")

}

// //addHeightTrack(thisData, name);

Expand Down Expand Up @@ -1185,22 +1185,27 @@ function VQI_GenomeBrowser(id) {
// var xScale = d3.scale.linear()
// .domain([-3953, 249241810])
// .range([0,1000]);
var fileHandle = "upload1435711655";
var fileHandle = "upload1436411775";
var chrom = "chr1";


$.ajax({
url: 'http://localhost/dynamic_loading.php',
url: 'dynamic_loading.php',
type: 'POST',
dataType: "json",
data: {
"getStartEndHG19Data": "",
"fileHandle": fileHandle,
"getStartEndTrackData": "",
"fileHandles": [trackInfo[0].fileHandle,trackInfo[1].fileHandle],
"name": [trackInfo[0].name, trackInfo[1].name],
"chrom": chrom
}

}).success(function (returnData) {
thisObj.addTrack(returnData, "HG19", "BED");
//console.log(returnData);
thisObj.addTrack(returnData[0], "HG19", "bed");
thisObj.addTrack(returnData[1], "Tile2 Content Snp", "bed");
isready = true;
updateTrack();
}).error(function (req, status, error) {
$("body").append(status + ": " + error);
});
Expand All @@ -1215,14 +1220,12 @@ function VQI_GenomeBrowser(id) {
data.unshift(["chrom", "chrom_start", "chrom_end", "name", "score", "strand"])
}
data = addOneTrack(data, name, type);
//console.log("haha");

trackList.push(data);

reorderTracks();
updateAllTracksSelectBoxes();
isready = true;
updateTrack();

}

this.addTrackFile = function (dataFile, name, type, header) {
Expand Down

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