Commit ba13fdc5 authored by Marc Duez's avatar Marc Duez

segmenter.js : toIgBlast/toImgt debug + handle all system (not only TRG nad IGH)

parent acda0b93
...@@ -87,10 +87,10 @@ igBlastInput["seqtype"] = "TCR"; ...@@ -87,10 +87,10 @@ igBlastInput["seqtype"] = "TCR";
function imgtPost(data, system) { function imgtPost(data, system) {
imgtInput["l01p01c10"] = data; imgtInput["l01p01c10"] = data;
if (system == "IGH") { if (system[0] == "I") {
imgtInput["l01p01c04"] = "IG"; imgtInput["l01p01c04"] = "IG";
} }
if (system == "TRG") { if (system[0] == "T") {
imgtInput["l01p01c04"] = "TR"; imgtInput["l01p01c04"] = "TR";
} }
var form = document.getElementById("form"); var form = document.getElementById("form");
...@@ -114,12 +114,12 @@ function imgtPost(data, system) { ...@@ -114,12 +114,12 @@ function imgtPost(data, system) {
function igBlastPost(data, system) { function igBlastPost(data, system) {
igBlastInput["queryseq"] = data; igBlastInput["queryseq"] = data;
if (system == "IGH") { if (system[0] == "I") {
igBlastInput["germline_db_V"] = "IG_DB/imgt.Homo_sapiens.V.f.orf.p"; igBlastInput["germline_db_V"] = "IG_DB/imgt.Homo_sapiens.V.f.orf.p";
igBlastInput["germline_db_D"] = "IG_DB/imgt.Homo_sapiens.D.f.orf"; igBlastInput["germline_db_D"] = "IG_DB/imgt.Homo_sapiens.D.f.orf";
igBlastInput["germline_db_J"] = "IG_DB/imgt.Homo_sapiens.J.f.orf"; igBlastInput["germline_db_J"] = "IG_DB/imgt.Homo_sapiens.J.f.orf";
} }
if (system == "TRG") { if (system[0] == "T") {
igBlastInput["germline_db_V"] = "IG_DB/imgt.TR.Homo_sapiens.V.f.orf.p"; igBlastInput["germline_db_V"] = "IG_DB/imgt.TR.Homo_sapiens.V.f.orf.p";
igBlastInput["germline_db_D"] = "IG_DB/imgt.TR.Homo_sapiens.D.f.orf"; igBlastInput["germline_db_D"] = "IG_DB/imgt.TR.Homo_sapiens.D.f.orf";
igBlastInput["germline_db_J"] = "IG_DB/imgt.TR.Homo_sapiens.J.f.orf.p"; igBlastInput["germline_db_J"] = "IG_DB/imgt.TR.Homo_sapiens.J.f.orf.p";
......
...@@ -336,7 +336,8 @@ Segment.prototype = { ...@@ -336,7 +336,8 @@ Segment.prototype = {
sendTo: function (address) { sendTo: function (address) {
var list = this.m.getSelected() var list = this.m.getSelected()
var request, system; var request = ""
var system;
var max=0; var max=0;
for (var i = 0; i < list.length; i++) { for (var i = 0; i < list.length; i++) {
...@@ -348,11 +349,10 @@ Segment.prototype = { ...@@ -348,11 +349,10 @@ Segment.prototype = {
request += ">" + c.getName() + "\n" + c.id + "\n"; request += ">" + c.getName() + "\n" + c.id + "\n";
} }
if (c.getSize()>max){ if (c.getSize()>max){
system=c.system system=c.getSystem()
max=c.getSize() max=c.getSize()
} }
} }
if (address == 'IMGT') imgtPost(request, system); if (address == 'IMGT') imgtPost(request, system);
if (address == 'igBlast') igBlastPost(request, system); if (address == 'igBlast') igBlastPost(request, system);
......
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