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more lienent spraying format, program will account for missing or ext…
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…ra columns or missing values
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ivp08001 committed Jan 7, 2016
1 parent afff1b3 commit 1a78270
Showing 1 changed file with 70 additions and 28 deletions.
98 changes: 70 additions & 28 deletions VQI_PathwayEditor.js
Original file line number Diff line number Diff line change
Expand Up @@ -568,7 +568,7 @@ var VQI_PathwayEditor = function (parent) {
var list = this.result.split('\n');
var lines = [];

for (var line = 1; line < list.length; line++) {
for (var line = 0; line < list.length; line++) {
lines[line] = list[line].split('\t');
}
sprayColor(lines);
Expand All @@ -582,44 +582,86 @@ var VQI_PathwayEditor = function (parent) {
else
lookup[obj.elements.nodes[i].data.name] = [obj.elements.nodes[i].data];
}

var header = {};
for(var i = 0; i < lines[0].length; i++){
if(lines[0][i].toLowerCase() == "gene")
header["gene"] = i;
else if(lines[0][i].toLowerCase() == "mut")
header["mut"] = i;
else if(lines[0][i].toLowerCase() == "cnv")
header["cnv"] = i;
else if(lines[0][i].toLowerCase() == "rna")
header["rna"] = i;
}

for(var line = 1; line < lines.length; line++) {
var target = lines[line][0];
var target = lines[line][header["gene"]];
if (typeof (lookup[target]) != "undefined") {
for(entry in lookup[target]){
var mut = "0";
var cnv = "0";
var rna = "0";
if(lines[line][1] != "")
mut = lines[line][1];
if(lines[line][2] != "")
cnv = lines[line][2];
if(lines[line][3] != "")
rna = lines[line][3];
lookup[target][entry].mut = mut;
lookup[target][entry].cnv = cnv;
lookup[target][entry].rna = rna;
if(typeof(header["mut"]) != "undefined"){
mut = lines[line][header["mut"]];
if(!isNaN(mut))
lookup[target][entry].mut = mut;
else
lookup[target][entry].mut = "0";
}
if(typeof(header["cnv"]) != "undefined"){
cnv = lines[line][header["cnv"]];
if(!isNaN(cnv))
lookup[target][entry].cnv = cnv;
else
lookup[target][entry].cnv = "0";
}
if(typeof(header["rna"]) != "undefined"){
rna = lines[line][header["rna"]];
if(!isNaN(rna))
lookup[target][entry].rna = rna;
else
lookup[target][entry].rna = "0";
}
}
}
}
}

function sprayColor(lines) {
var cy = $('#' + parent + '-cy').cytoscape('get');
for (var line = 1; line < lines.length; line++) {
var target = cy.elements("node[name = \"" + lines[line][0] + "\"]");
var mut = "0";
var cnv = "0";
var rna = "0";
if(lines[line][1] != "")
mut = lines[line][1];
if(lines[line][2] != "")
cnv = lines[line][2];
if(lines[line][3] != "")
rna = lines[line][3];
target.data('rna', rna);
target.data('cnv', cnv);
target.data('mut', mut);
var header = {};
for(var i = 0; i < lines[0].length; i++){
if(lines[0][i].toLowerCase() == "gene")
header["gene"] = i;
else if(lines[0][i].toLowerCase() == "mut")
header["mut"] = i;
else if(lines[0][i].toLowerCase() == "cnv")
header["cnv"] = i;
else if(lines[0][i].toLowerCase() == "rna")
header["rna"] = i;
}

for (var line = 1; line < lines.length; line++) {
var target = cy.elements("node[name = \"" + lines[line][header["gene"]] + "\"]");
if(typeof(header["mut"]) != "undefined"){
mut = lines[line][header["mut"]];
if(!isNaN(mut))
target.data('mut', mut);
else
target.data('mut', '0');
}
if(typeof(header["cnv"]) != "undefined"){
cnv = lines[line][header["cnv"]];
if(!isNaN(cnv))
target.data('cnv', cnv);
else
target.data('cnv', '0');
}
if(typeof(header["rna"]) != "undefined"){
rna = lines[line][header["rna"]];
if(!isNaN(rna))
target.data('rna', rna);
else
target.data('rna', '0');
}
}
}

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