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Commit 8661d297 authored by Mikaël Salson's avatar Mikaël Salson

scatterplot: Plot CDR3 length

The cdr3 field in seg is not anymore a string field but is similar to the
other fields in seg. And we use the start and stop field to know
the length of the CDR3 in nt.
parent cd34ebf1
......@@ -174,6 +174,17 @@ Clone.prototype = {
}
}, //end getCode
getCDR3length: function() {
if (typeof(this.seg) != 'undefined'
&& typeof (this.seg['cdr3']) != 'undefined'
&& typeof (this.seg['cdr3'].start) != 'undefined'
&& typeof (this.seg['cdr3'].stop) != 'undefined') {
return this.seg["cdr3"].stop - this.seg["cdr3"].start + 1
} else {
return 0;
}
},
/**
* change/add custom name
......
......@@ -140,7 +140,7 @@ function ScatterPlot(id, model) {
},
"lengthCDR3": {
label: "CDR3 length",
fct: function(cloneID) {return self.m.clone(cloneID).seg["cdr3"].length}
fct: function(cloneID) {return self.m.clone(cloneID).getCDR3length()}
},
"coverage": {
label: "clone consensus coverage",
......
......@@ -294,6 +294,8 @@ In the .analysis file, this section is intended to describe some specific clones
// any feature to be highligthen in the sequenc
// the optional "seq" element gives a sequence that corresponds to this feature
// CDR3 should be stored that way (in a field called "cdr3"), this is similar
// for the other regions of interest.
"somefeature": { "start": 0, "stop": 0, "seq": "" }
}
......
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