Commit 0b53fa81 authored by Marc Duez's avatar Marc Duez
Browse files

segmenter.js : can do AA sequence + align

parent cdb25ed4
......@@ -671,13 +671,13 @@ Sequence.prototype = {
var clone = this.m.clone(this.id);
if (typeof clone.seg != "undefined" && typeof clone.seg["cdr3"] != "undefined"){
start = clone.seg["cdr3"].start
stop = clone.seg["cdr3"].stop
start = this.pos[clone.seg["cdr3"].start];
stop = this.pos[clone.seg["cdr3"].stop];
}else if (typeof clone["_sequence.JUNCTION.raw nt seq"] != "undefined"){
// .clntab. TODO: move this to fuse.py
var junc = clone["_sequence.JUNCTION.raw nt seq"][0]
start = clone.sequence.indexOf(junc)
stop = start + junc.length
var junc = clone["_sequence.JUNCTION.raw nt seq"][0];
start = this.pos[clone.sequence.indexOf(junc)];
stop = this.pos[start + junc.length-1];
}
for (var i=0; i<this.seq.length; i++) this.seqAA[i] =this.seq[i]; // "&nbsp";
......
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