'use strict';

this.dnaSeq = dnaSeq.toUpperCase();

this.UNKNOWN = 'X';

this.translateTable = {'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'AGA': 'R', 'AGG': 'R', 'AAT': 'N', 'AAC': 'N', 'GAT': 'D', 'GAC': 'D', 'TGT': 'C', 'TGC': 'C', 'CAA': 'Q', 'CAG': 'Q', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G', 'CAT': 'H', 'CAC': 'H', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'TTA': 'L', 'TTG': 'L', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'AAA': 'K', 'AAG': 'K', 'ATG': 'M', 'TTT': 'F', 'TTC': 'F', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'AGT': 'S', 'AGC': 'S', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'TGG': 'W', 'TAT': 'Y', 'TAC': 'Y', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'TAG': '*', 'TGA': '*', 'TAA': '*'};

this.iupacAmbiCodes = {'A': ['A'], 'C': ['C'], 'G': ['G'], 'T': ['T'], 'U': ['U'], 'M': ['A', 'C'], 'R': ['A', 'G'], 'W': ['A', 'T'], 'S': ['C', 'G'], 'Y': ['C', 'T'], 'K': ['G', 'T'], 'V': ['A', 'C', 'G'], 'H': ['A', 'C', 'T'], 'D': ['A', 'G', 'T'], 'B': ['C', 'G', 'T'], 'X': ['G', 'A', 'T', 'C'], 'N': ['G', 'A', 'T', 'C']};

'use strict';

var codons = [],

first = this.iupacAmbiCodes[ambiguousCodon.charAt(0)],

lenFirst = first.length,

second = this.iupacAmbiCodes[ambiguousCodon.charAt(1)],

lenSecond = second.length,

third = this.iupacAmbiCodes[ambiguousCodon.charAt(2)],

lenThird = third.length,

nuc1,

nuc2,

nuc3,

codon,

i,

j,

k;

for (i = 0; i < lenFirst; i += 1) {

nuc1 = first[i];

for (j = 0; j < lenSecond; j += 1) {

nuc2 = second[j];

for (k = 0; k < lenThird; k += 1) {

nuc3 = third[k];

codon = nuc1 + nuc2 + nuc3;

codons.push(codon);

}

}

}

return codons;

'use strict';

var i = 0,

seqLen = this.dnaSeq.length,

triplets = [],

triplet;

for (i = 0; i < seqLen; i += 3) {

triplet = this.dnaSeq.slice(i, 3 + i);

triplets.push(triplet);

}

this.triplets = triplets;

'use strict';

if (!this.triplets) {

this.splitSequenceIntoTriplets();

}

return this.triplets;

'use strict';

var triplets = this.getTriplets(),

tripletCount = triplets.length,

aminoAcids = [],

aminoAcid,

mixedTriplets = [],

mixedAminoAcids = [],

i,

j;

for (i = 0; i < tripletCount; i += 1) {

//Match only triplets composed of the four standard DNA nucleotide bases.

if (triplets[i].match(/[ACGT]{3}/)) {

aminoAcid = this.translateTable[triplets[i]];

aminoAcids.push(aminoAcid);

} else {

//Allowable characters in input (four standard nucleotides A,C,G,T and all recognized IUPAC mixture codes).

if (triplets[i].match(/[ACGTUMRWSYKVHDBXN]{3}/)) {

mixedTriplets = this.getCodonsFromAmbiguous(triplets[i]);

for (j = 0; j < mixedTriplets.length; j += 1) {

aminoAcid = this.translateTable[mixedTriplets[j]];

if (mixedAminoAcids.indexOf(aminoAcid) === -1) {

mixedAminoAcids.push(aminoAcid);

}

}

aminoAcids.push(mixedAminoAcids);

} else {

aminoAcids.push(this.UNKNOWN);

}

}

}

return aminoAcids;