diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index 63df9ef..c4fbb58 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -31,9 +31,9 @@ function VQI_GenomeBrowser(id, serviceURL) {
var trackInfo = [];
- trackInfo[0] = {name: "HG19", type: "bed", fileHandle: "upload1436481988"};
- trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", fileHandle: "upload1436411775"};
- trackInfo[2] = {name: "cpg", type: "cpg", fileHandle: "upload1437097194,upload1437098473,upload1437098556"};
+ trackInfo[0] = {name: "HG19", type: "bed", args: {fileHandle: "upload1436481988"}};
+ trackInfo[1] = {name: "Tile2 Content Snp", type: "bed", args: {fileHandle: "upload1436411775", exportable: true}};
+ trackInfo[2] = {name: "cpg", type: "cpg", args: {fileHandle: "upload1437097194,upload1437098473,upload1437098556"}};
var serviceURL = serviceURL;
@@ -76,7 +76,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
for (i in trackInfo){
if (trackInfo[i].name == track){
- self.addOneTrackFromDatabase(trackInfo[i].fileHandle,track,trackInfo[i].type);
+ self.addTrack([] , track , trackInfo[i].type , trackInfo[i].args);
break;
}
}
@@ -285,8 +285,8 @@ function VQI_GenomeBrowser(id, serviceURL) {
trackList.splice(i, 1);
}
}
- setPanExtent();
- graph(chrom_curr, xScale.domain()[0], xScale.domain()[1]);
+ //setPanExtent();
+ //graph(chrom_curr, xScale.domain()[0], xScale.domain()[1]);
reorderTracks();
updateAllTracksSelectBoxes();
}
@@ -555,7 +555,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
}
trackInfo.push({name: trackName, type: "bed", fileHandle: CurrentFileHandle});
updateRecentTrackDropDown();
- self.addOneTrackFromDatabase(CurrentFileHandle,trackName,"bed");
+ self.addTrack([] , trackName , "bed" , trackInfo[i].args);
}).error(function (req, status, error) {
$("body").append(status + ": " + error);
});
@@ -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) {
addOneTrack(data, name, type, args);
@@ -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.name = name;
@@ -973,27 +975,77 @@ function VQI_GenomeBrowser(id, serviceURL) {
group.append("foreignObject")
- .attr("width", 50)
+ .attr("width", 20)
.attr("height", 20)
.attr("x", width+5)
- .attr("y", -7.5)
+ .attr("y", -15)
.append("xhtml:div")
.html("")
.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("")
+ .on("click", function () {
+ exportTrack(name);
+ });
+ }
+
group.append("foreignObject")
- .attr("width", 50)
+ .attr("width", 20)
.attr("height", 20)
.attr("x", width+25)
- .attr("y", -7.5)
+ .attr("y", -10)
+ .attr("class", "checkbox")
+ .append("xhtml:div")
+ .html("")
+ .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("")
+ .on("click", function () {
+ removeTrack(name);
+ });
+
+ deleteConfirm.append("foreignObject")
+ .attr("width", 40)
+ .attr("height", 20)
+ .attr("x", width+5)
+ .attr("y", 0)
.append("xhtml:div")
- .html("")
+ .html("")
.on("click", function () {
- exportTrack(name);
+ deleteConfirm.style("visibility", "hidden");
});
-
group.append("path")
.attr("transform", function (d) {
@@ -1049,7 +1101,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
}
function CpgTrack(name, group, args) {
- Track.call(this, name, group);
+ Track.call(this, name, group, args);
var trackGroup = this.trackGroup;
var fileHandle = args.fileHandle;
@@ -1293,7 +1345,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
}
function BedTrack(name, group, args) {
- Track.call(this, name, group)
+ Track.call(this, name, group, args)
var trackGroup = this.trackGroup;
var fileHandle = args.fileHandle;
@@ -1540,6 +1592,22 @@ function VQI_GenomeBrowser(id, serviceURL) {
}
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;
}
@@ -1567,7 +1635,7 @@ function VQI_GenomeBrowser(id, serviceURL) {
}
function FastaTrack(name, group, args) {
- Track.call(this, name, group);
+ Track.call(this, name, group, args);
var trackGroup = this.trackGroup;
var file = args.file;
diff --git a/VQI_GenomeBrowserDemo.html b/VQI_GenomeBrowserDemo.html
index db6e2d0..ad9e717 100644
--- a/VQI_GenomeBrowserDemo.html
+++ b/VQI_GenomeBrowserDemo.html
@@ -29,13 +29,16 @@
var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php');
//insert path to file and indexfile
- obj.addTrack([[""],[""]], "fasta", "fasta",
- { "file" : "",
- "indexFile" : ""});
+ obj.addTrack([], "fasta", "fasta",
+ { file : "",
+ indexFile : ""});
- obj.addOneTrackFromDatabase("upload1437097194,upload1437098473,upload1437098556", "cpg", "cpg");
- obj.addOneTrackFromDatabase("upload1436481988", "HG19", "bed");
- obj.addOneTrackFromDatabase("upload1436411775", "Tile2 Content Snp", "bed");
+ obj.addTrack([], "cpg", "cpg",
+ {fileHandle : "upload1437097194,upload1437098473,upload1437098556"});
+ obj.addTrack([], "HG19", "bed", {fileHandle : "upload1436481988"});
+ obj.addTrack([], "Tile2 Content Snp", "bed",
+ { fileHandle : "upload1436411775",
+ exportable : true});
/*var data = [["chr1", "896004", "896005", ".", "0", "+"],
["chr1", "976170", "976171", ".", "-.4", "+"],
["chr1", "1198674", "1198675", ".", "0", "+"],
diff --git a/dynamic_loading.php b/dynamic_loading.php
index b871d60..959fbc0 100644
--- a/dynamic_loading.php
+++ b/dynamic_loading.php
@@ -62,6 +62,10 @@
$result = getFastaRange($_POST["chrom"],$_POST["indexFile"]);
ajaxReturn($result);
}
+ else if (isset($_POST["getFullTrackData"])){
+ $result = getFullTrackData($_POST["fileHandles"]);
+ ajaxReturn($result);
+ }
else {
loadTable();
}
@@ -512,6 +516,26 @@
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){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];