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Util.js
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Util.js
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define('NucleotideDensityPlugin/Store/Util',[
'dojo/_base/declare',
'dojo/_base/array',
'dojo/_base/lang'
],
function(
declare,
array,
lang
){
/*
Utility class dealing with degenerate nucleotide sequences
*/
var Util;
var ntable = {
"A": ["A"],
"C": ["C"],
"G": ["G"],
"T": ["T"],
"U": ["T"],
"R": ["A", "G"],
"Y": ["C", "T"],
"S": ["C", "G"],
"W": ["A", "T"],
"K": ["G", "T"],
"M": ["A", "C"],
"B": ["C", "G", "T"],
"D": ["A", "G", "T"],
"H": ["A", "C", "T"],
"V": ["A", "C", "G"],
"N": ["A", "C", "G", "T"]
}
Util = {
_transformNuc: function(inStr){
var n = inStr.length;
var outAr = [''];
var i;
for(i=0; i < n; i++){
var p = inStr.charAt(i).toUpperCase();
var v=ntable[p];
var newAr= [];
array.forEach(outAr, function(item){
var m = array.map(v,function(nuc){
return item+nuc;
});
newAr.push.apply(newAr, m);
});
outAr = newAr;
}
return outAr;
},
_reverseComplement: function(inStr){
var baseAr = ['A','C','G','T'];
var out = '';
var i,k;
for(i=0; i < inStr.length; i++){
k = array.indexOf(baseAr, inStr.charAt(i).toUpperCase());
if(k===-1)
out = 'X'+out;
else
out = baseAr[3-k] + out;
}
return out;
},
getPossibilities: function(inStr, bothStrands){
// first get forward possibilities
var nucAr = Util._transformNuc(inStr);
// get reverse
if(bothStrands){
var revAr = array.map(nucAr, function(x){
return Util._reverseComplement(x);
});
// combine
nucAr.push.apply(nucAr, revAr);
}
return nucAr;
}
}
return Util;
});