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ajax calls for fasta files
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@csw11004
csw11004 committed Sep 17, 2015
1 parent 0f81a93 commit cbe57b8
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Showing 3 changed files with 69 additions and 83 deletions.
142 changes: 61 additions & 81 deletions VQI_GenomeBrowser.js
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Expand Up @@ -696,7 +696,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
} }


var addOneTrack = function (data, name, type, fileHandle) { var addOneTrack = function (data, name, type, args) {


var trackIndex = trackList.length; var trackIndex = trackList.length;


Expand All @@ -721,11 +721,11 @@ function VQI_GenomeBrowser(id, serviceURL) {
name = name || "track-" + (trackIndex + 1); name = name || "track-" + (trackIndex + 1);


if(type == "cpg") if(type == "cpg")
trackList.push(new CpgTrack(name, fileHandle, graphRegion.append("g"))); trackList.push(new CpgTrack(name, graphRegion.append("g"), args));
if(type == "bed") if(type == "bed")
trackList.push(new BedTrack(name, fileHandle, graphRegion.append("g"))); trackList.push(new BedTrack(name, graphRegion.append("g"), args));
if(type == "fasta") if(type == "fasta")
trackList.push(new FastaTrack(name, graphRegion.append("g"))); trackList.push(new FastaTrack(name, graphRegion.append("g"), args));


clipPath.attr("height", Number(svg.attr("height"))); clipPath.attr("height", Number(svg.attr("height")));
zoomOnly = true; zoomOnly = true;
Expand Down Expand Up @@ -788,21 +788,21 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


}).success(function (returnData) { }).success(function (returnData) {
thisObj.addTrack(returnData[0], name, type, fileHandle); thisObj.addTrack(returnData[0], name, type, {"fileHandle" : fileHandle});
isready = true; isready = true;
updateTrack(); updateTrack();
}).error(function (req, status, error) { }).error(function (req, status, error) {
$("body").append(status + ": " + error); $("body").append(status + ": " + error);
}); });
} }


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


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, fileHandle); data = addOneTrack(data, name, type, args);


reorderTracks(); reorderTracks();
updateAllTracksSelectBoxes(); updateAllTracksSelectBoxes();
Expand Down Expand Up @@ -1120,11 +1120,11 @@ function VQI_GenomeBrowser(id, serviceURL) {
this.getData = function(){}; this.getData = function(){};
} }


function CpgTrack(name, fileHandle, group) { function CpgTrack(name, group, args) {
Track.call(this, name, group); Track.call(this, name, group);
var trackGroup = this.trackGroup; var trackGroup = this.trackGroup;


this.fileHandle = fileHandle; var fileHandle = args.fileHandle;
var tempHandles = fileHandle.split(","); var tempHandles = fileHandle.split(",");
var cpgFileHandle = tempHandles[0]; var cpgFileHandle = tempHandles[0];
var shelveFileHandle = tempHandles[1]; var shelveFileHandle = tempHandles[1];
Expand Down Expand Up @@ -1341,12 +1341,11 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
} }


function BedTrack(name, fileHandle, group) { function BedTrack(name, group, args) {
Track.call(this, name, group) Track.call(this, name, group)
var trackGroup = this.trackGroup; var trackGroup = this.trackGroup;


this.fileHandle = fileHandle; var fileHandle = args.fileHandle;
var tempHandles = fileHandle.split(",");
var data; var data;
var redrawCutoff = 1000; //Scale at which rectangles will be drawn individually var redrawCutoff = 1000; //Scale at which rectangles will be drawn individually


Expand Down Expand Up @@ -1594,16 +1593,12 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
} }


var faFile; function FastaTrack(name, group, args) {
var faiData;

function FastaTrack(name, group) {
Track.call(this, name, group); Track.call(this, name, group);
var trackGroup = this.trackGroup; var trackGroup = this.trackGroup;


var data; var file = args.file;

var indexFile = args.indexFile
var reader = new FileReader();


var drawTrack = function(data) var drawTrack = function(data)
{ {
Expand Down Expand Up @@ -1668,74 +1663,59 @@ function VQI_GenomeBrowser(id, serviceURL) {
.attr("x", function (d) { .attr("x", function (d) {
return xScale(d[1]) - 2; return xScale(d[1]) - 2;
}) })
}; }


this.updateTrack = function(){ this.updateTrack = function(){
if(faFile) if( zoom.scale() >= (panExtent[1] - panExtent[0]) / 100/ initialZoom)
{ {
if( zoom.scale() >= (panExtent[1] - panExtent[0]) / 100/ initialZoom) var LoadingText = group.append("g")
{ LoadingText.append("rect")
var offset; .attr("x", 450)
for(var i = 0; i < faiData.length; i++) .attr("width", 100)
.attr("y", -10)
.attr("height", 20)
.attr("rx", 6)
.attr("ry", 6)
.style("fill-opacity", .6)
.style("fill", "white")

LoadingText.append("text")
.text("Loading...")
.attr("x", 475)
.attr("y", 5);

var xStart = Math.floor(xScale.domain()[0]);
var length = Math.ceil(xScale.domain()[1]) - xStart;
$.ajax({
url: serviceURL,
type: 'POST',
dataType: "json",
data: {
"loadFastaData": "",
"chrom" : chrom_curr,
"start": xStart,
"length": length,
"file": file,
"indexFile": indexFile
}
}).success(function (returnData) {
var data = returnData.split("");
for(var i = 0; i < returnData.length; i++)
{ {
if(faiData[i][0] == chrom_curr) data[i] = [data[i], xStart + i]
{
offset = Number(faiData[i][2]);
break;
}
}
xStart = Math.floor(xScale.domain()[0]);
var blob = faFile.slice(xStart+offset ,Math.ceil(xScale.domain()[1])+offset);
var data;
reader.onload = function (e) {
data = reader.result;
data = data.split("");
for(var i = 0; i < data.length; i++)
{
data[i] = [data[i], xStart + i]
}
drawTrack(data);
} }
reader.readAsText(blob); drawTrack(data);
} data = returnData;
else LoadingText.remove();
{ }).error(function (req, status, error) {
clearTrack(); $("body").append(status + ": " + error);
} });
} }
}; else

{
} clearTrack();

}
this.makeTempForm = function() { //just for putting in .fa and .fai files for now }

var fileInput = document.createElement('input');
fileInput.type = 'file';


fileInput.addEventListener('change', function (e) {
var file = fileInput.files[0];
if (file.name == "mm9.fa.txt") {
faFile = file;
}
if (file.name == "mm9.fa.fai.txt") {
var reader = new FileReader();
reader.onload = function (e) {
data = reader.result;
data = data.split("\n");
for(var i = 0; i < data.length; i++)
{
data[i] = data[i].split("\t");
}
faiData = data;
}
reader.readAsText(file);
}
});
$("#" + divId).append(fileInput);
} }

this.makeTempForm();

} }


6 changes: 4 additions & 2 deletions VQI_GenomeBrowserDemo.html
View file
Expand Up @@ -27,8 +27,10 @@
<script type="text/javascript"> <script type="text/javascript">
var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php'); var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php');


//just choose the .fa file then the .fai file in file select at bottom to load //insert path to file and indexfile
obj.addTrack([[""],[""]], "fasta", "fasta"); obj.addTrack([[""],[""]], "fasta", "fasta",
{ "file" : "",
"indexFile" : ""});


obj.addOneTrackFromDatabase("upload1437097194,upload1437098473,upload1437098556", "cpg", "cpg"); obj.addOneTrackFromDatabase("upload1437097194,upload1437098473,upload1437098556", "cpg", "cpg");
obj.addOneTrackFromDatabase("upload1436481988", "HG19", "bed"); obj.addOneTrackFromDatabase("upload1436481988", "HG19", "bed");
Expand Down
4 changes: 4 additions & 0 deletions dynamic_loading.php
View file
Expand Up @@ -54,6 +54,10 @@
$result = loadTooltip($_POST["chrom"],$_POST["trackName"], $_POST["type"], $_POST["min"],$_POST["max"],$_POST["fileHandle"]); $result = loadTooltip($_POST["chrom"],$_POST["trackName"], $_POST["type"], $_POST["min"],$_POST["max"],$_POST["fileHandle"]);
ajaxReturn($result); ajaxReturn($result);
} }
else if (isset($_POST["loadFastaData"])){
$result = loadFastaData($_POST["chrom"],$_POST["start"], $_POST["length"], $_POST["file"],$_POST["indexFile"]);
ajaxReturn($result);
}
else { else {
loadTable(); loadTable();
} }
Expand Down

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