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Export track for all chromosomes and delete confirmation
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@csw11004
csw11004 committed Sep 19, 2015
1 parent 3b56814 commit 2bf102c
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Showing 3 changed files with 124 additions and 29 deletions.
114 changes: 91 additions & 23 deletions VQI_GenomeBrowser.js
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Original file line number Original file line Diff line number Diff line change
Expand Up @@ -31,9 +31,9 @@ function VQI_GenomeBrowser(id, serviceURL) {




var trackInfo = []; var trackInfo = [];
trackInfo[0] = {name: "HG19", type: "bed", fileHandle: "upload1436481988"}; trackInfo[0] = {name: "HG19", type: "bed", args: {fileHandle: "upload1436481988"}};
trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", fileHandle: "upload1436411775"}; trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", args: {fileHandle: "upload1436411775", exportable: true}};
trackInfo[2] = {name: "cpg", type: "cpg", fileHandle: "upload1437097194,upload1437098473,upload1437098556"}; trackInfo[2] = {name: "cpg", type: "cpg", args: {fileHandle: "upload1437097194,upload1437098473,upload1437098556"}};


var serviceURL = serviceURL; var serviceURL = serviceURL;


Expand Down Expand Up @@ -76,7 +76,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
for (i in trackInfo){ for (i in trackInfo){


if (trackInfo[i].name == track){ if (trackInfo[i].name == track){
self.addOneTrackFromDatabase(trackInfo[i].fileHandle,track,trackInfo[i].type); self.addTrack([] , track , trackInfo[i].type , trackInfo[i].args);
break; break;
} }
} }
Expand Down Expand Up @@ -285,8 +285,8 @@ function VQI_GenomeBrowser(id, serviceURL) {
trackList.splice(i, 1); trackList.splice(i, 1);
} }
} }
setPanExtent(); //setPanExtent();
graph(chrom_curr, xScale.domain()[0], xScale.domain()[1]); //graph(chrom_curr, xScale.domain()[0], xScale.domain()[1]);
reorderTracks(); reorderTracks();
updateAllTracksSelectBoxes(); updateAllTracksSelectBoxes();
} }
Expand Down Expand Up @@ -555,7 +555,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
trackInfo.push({name: trackName, type: "bed", fileHandle: CurrentFileHandle}); trackInfo.push({name: trackName, type: "bed", fileHandle: CurrentFileHandle});
updateRecentTrackDropDown(); updateRecentTrackDropDown();
self.addOneTrackFromDatabase(CurrentFileHandle,trackName,"bed"); self.addTrack([] , trackName , "bed" , trackInfo[i].args);
}).error(function (req, status, error) { }).error(function (req, status, error) {
$("body").append(status + ": " + error); $("body").append(status + ": " + error);
}); });
Expand Down Expand Up @@ -722,10 +722,6 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }
} }


this.addOneTrackFromDatabase = function(fileHandle,name,type) {
thisObj.addTrack([], name, type, {"fileHandle" : fileHandle});
}

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


addOneTrack(data, name, type, args); addOneTrack(data, name, type, args);
Expand Down Expand Up @@ -951,7 +947,13 @@ function VQI_GenomeBrowser(id, serviceURL) {
}); });
} }


function Track(name, group) { function Track(name, group, args) {
//Perhaps I need a better structure if I'm just going to pass custom arguments through args as a json object
//Possible value pairs:
//filehandle : string
//exportable : boolean
//file : string
//indexFile : string
this.group = group; this.group = group;
this.name = name; this.name = name;


Expand All @@ -973,27 +975,77 @@ function VQI_GenomeBrowser(id, serviceURL) {




group.append("foreignObject") group.append("foreignObject")
.attr("width", 50) .attr("width", 20)
.attr("height", 20) .attr("height", 20)
.attr("x", width+5) .attr("x", width+5)
.attr("y", -7.5) .attr("y", -15)
.append("xhtml:div") .append("xhtml:div")
.html("<form><input type=image src=DeleteTrack.png width=15 height=15 onclick='return false;'></form>") .html("<form><input type=image src=DeleteTrack.png width=15 height=15 onclick='return false;'></form>")
.on("click", function () { .on("click", function () {
removeTrack(name); deleteConfirm.style("visibility", "visible");
}); });


if(args.exportable)
{
group.append("foreignObject")
.attr("width", 20)
.attr("height", 20)
.attr("x", width+5)
.attr("y", 0)
.append("xhtml:div")
.html("<form><input type=image src=ExportTrack.png width=15 height=15 onclick='return false;'></form>")
.on("click", function () {
exportTrack(name);
});
}

group.append("foreignObject") group.append("foreignObject")
.attr("width", 50) .attr("width", 20)
.attr("height", 20) .attr("height", 20)
.attr("x", width+25) .attr("x", width+25)
.attr("y", -7.5) .attr("y", -10)
.attr("class", "checkbox")
.append("xhtml:div")
.html("<form><input type=checkbox id='check'/></form>")
.on("click", function () {
xAxisSelection.call(xAxis)});//I have no idea why it won't redraw the checkbox unless I call this

var deleteConfirm = group.append("g")
.style("visibility", "hidden");

deleteConfirm.append("rect")
.attr("width", 40)
.attr("height", 50)
.attr("x", width+5)
.attr("y", -25)
.style("fill", "white")

deleteConfirm.append("text")
.attr("x", width+5)
.attr("y", -25)
.text("Delete?")

deleteConfirm.append("foreignObject")
.attr("width", 40)
.attr("height", 20)
.attr("x", width+5)
.attr("y", -20)
.append("xhtml:div")
.html("<form><input type=button value='Yes' onclick='return false;'></form>")
.on("click", function () {
removeTrack(name);
});

deleteConfirm.append("foreignObject")
.attr("width", 40)
.attr("height", 20)
.attr("x", width+5)
.attr("y", 0)
.append("xhtml:div") .append("xhtml:div")
.html("<form><input type=image src=ExportTrack.png width=15 height=15 onclick='return false;'></form>") .html("<form><input type=button value='No' onclick='return false;'></form>")
.on("click", function () { .on("click", function () {
exportTrack(name); deleteConfirm.style("visibility", "hidden");
}); });



group.append("path") group.append("path")
.attr("transform", function (d) { .attr("transform", function (d) {
Expand Down Expand Up @@ -1049,7 +1101,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


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


var fileHandle = args.fileHandle; var fileHandle = args.fileHandle;
Expand Down Expand Up @@ -1293,7 +1345,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


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


var fileHandle = args.fileHandle; var fileHandle = args.fileHandle;
Expand Down Expand Up @@ -1540,6 +1592,22 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


this.getData = function(){ this.getData = function(){
var data;
$.ajax({
url: serviceURL,
type: 'POST',
dataType: "json",
async : false,
data: {
"getFullTrackData": "",
"fileHandles": [fileHandle]
}
}).success(function (returnData) {
data = returnData;
}).error(function (req, status, error) {
$("body").append(status + ": " + error);
});

return data; return data;
} }


Expand Down Expand Up @@ -1567,7 +1635,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
} }


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


var file = args.file; var file = args.file;
Expand Down
15 changes: 9 additions & 6 deletions VQI_GenomeBrowserDemo.html
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Original file line number Original file line Diff line number Diff line change
Expand Up @@ -29,13 +29,16 @@
var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php'); var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php');


//insert path to file and indexfile //insert path to file and indexfile
obj.addTrack([[""],[""]], "fasta", "fasta", obj.addTrack([], "fasta", "fasta",
{ "file" : "", { file : "",
"indexFile" : ""}); indexFile : ""});


obj.addOneTrackFromDatabase("upload1437097194,upload1437098473,upload1437098556", "cpg", "cpg"); obj.addTrack([], "cpg", "cpg",
obj.addOneTrackFromDatabase("upload1436481988", "HG19", "bed"); {fileHandle : "upload1437097194,upload1437098473,upload1437098556"});
obj.addOneTrackFromDatabase("upload1436411775", "Tile2 Content Snp", "bed"); obj.addTrack([], "HG19", "bed", {fileHandle : "upload1436481988"});
obj.addTrack([], "Tile2 Content Snp", "bed",
{ fileHandle : "upload1436411775",
exportable : true});
/*var data = [["chr1", "896004", "896005", ".", "0", "+"], /*var data = [["chr1", "896004", "896005", ".", "0", "+"],
["chr1", "976170", "976171", ".", "-.4", "+"], ["chr1", "976170", "976171", ".", "-.4", "+"],
["chr1", "1198674", "1198675", ".", "0", "+"], ["chr1", "1198674", "1198675", ".", "0", "+"],
Expand Down
24 changes: 24 additions & 0 deletions dynamic_loading.php
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Original file line number Original file line Diff line number Diff line change
Expand Up @@ -62,6 +62,10 @@
$result = getFastaRange($_POST["chrom"],$_POST["indexFile"]); $result = getFastaRange($_POST["chrom"],$_POST["indexFile"]);
ajaxReturn($result); ajaxReturn($result);
} }
else if (isset($_POST["getFullTrackData"])){
$result = getFullTrackData($_POST["fileHandles"]);
ajaxReturn($result);
}
else { else {
loadTable(); loadTable();
} }
Expand Down Expand Up @@ -512,6 +516,26 @@ function getTrackData($fileHandles,$name,$chrom,$start,$end){
return $returnArray; return $returnArray;
} }


function getFullTrackData($fileHandles){
$returnArray = [];
foreach ($fileHandles as $key => $value) {
$fileHandle = $value;

$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];

$sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
$sql .= " ORDER BY LENGTH(`CHROM`), `CHROM`, `CHROM_START` * 1 ASC";

$res = mysqli_query ($link,$sql);

while($row = mysqli_fetch_row($res)){
array_push($returnArray, [$row[0],$row[1],$row[2],$row[3],$row[4]]);
}
}
return $returnArray;
}

function getRange($fileHandles,$name,$chrom){ function getRange($fileHandles,$name,$chrom){
$db_name = $GLOBALS['db_name']; $db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink']; $link = $GLOBALS['DBlink'];
Expand Down

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