take nuc degenerate sequence into array of possible sequences

js/Store/Util.js

@@ -0,0 +1,40 @@
+define('NucleotideDensityPlugin/Store/Util',[
+ 'dojo/_base/declare',
+ 'dojo/_base/array',
+ 'dojo/_base/lang',
+ 'dojo/json',
+ 'dojo/text!plugins/NucleotideDensityPlugin/nucleotide_table.json'
+],
+function(
+ declare,
+ array,
+ lang,
+ JSON,
+ nucleotidetable
+){
+var Util;
+ var ntable = JSON.parse(nucleotidetable);
+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;
+ }
+}
+return Util;
+});

nucleotide_table.json

@@ -0,0 +1,18 @@
+{
+ "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"]
+}