/// <summary>
/// Translates amino acid sequences into phantom sequences.
/// </summary>
/// <param name="inputChain">
/// Amino acid sequence.
/// </param>
/// <returns>
/// Phantom sequence of <see cref="BaseChain"/> type.
/// Elements are <see cref="ValuePhantom"/>.
/// </returns>
public static BaseChain Decode(BaseChain inputChain)
{
var resultChain = new BaseChain(inputChain.GetLength());
for (int i = 0; i < inputChain.GetLength(); i++)
{
string aminoAcid = inputChain[i].ToString();
var element = new ValuePhantom();
switch (aminoAcid)
{
case "F":
element.Add(new ValueString("TTT"));
element.Add(new ValueString("TTC"));
break;
case "L":
element.Add(new ValueString("TTA"));
element.Add(new ValueString("TTG"));
element.Add(new ValueString("CTT"));
element.Add(new ValueString("CTC"));
element.Add(new ValueString("CTA"));
element.Add(new ValueString("CTG"));
break;
case "S":
element.Add(new ValueString("TCT"));
element.Add(new ValueString("TCC"));
element.Add(new ValueString("TCA"));
element.Add(new ValueString("TCG"));
element.Add(new ValueString("AGT"));
element.Add(new ValueString("AGC"));
break;
case "Y":
element.Add(new ValueString("TAT"));
element.Add(new ValueString("TAC"));
break;
case "X":
element.Add(new ValueString("TAA"));
element.Add(new ValueString("TAG"));
element.Add(new ValueString("TGA"));
break;
case "C":
element.Add(new ValueString("TGT"));
element.Add(new ValueString("TGC"));
break;
case "W":
element.Add(new ValueString("TGG"));
break;
case "P":
element.Add(new ValueString("CCT"));
element.Add(new ValueString("CCC"));
element.Add(new ValueString("CCA"));
element.Add(new ValueString("CCG"));
break;
case "H":
element.Add(new ValueString("CAT"));
element.Add(new ValueString("CAC"));
break;
case "Q":
element.Add(new ValueString("CAA"));
element.Add(new ValueString("CAG"));
break;
case "R":
element.Add(new ValueString("CGT"));
element.Add(new ValueString("CGC"));
element.Add(new ValueString("CGA"));
element.Add(new ValueString("CGG"));
element.Add(new ValueString("AGA"));
element.Add(new ValueString("AGG"));
break;
case "I":
element.Add(new ValueString("ATT"));
element.Add(new ValueString("ATC"));
element.Add(new ValueString("ATA"));
break;
case "M":
element.Add(new ValueString("ATG"));
break;
case "T":
element.Add(new ValueString("ACT"));
element.Add(new ValueString("ACC"));
element.Add(new ValueString("ACA"));
element.Add(new ValueString("ACG"));
break;
case "N":
element.Add(new ValueString("AAT"));
element.Add(new ValueString("AAC"));
break;
case "K":
element.Add(new ValueString("AAA"));
element.Add(new ValueString("AAG"));
break;
case "V":
element.Add(new ValueString("GTT"));
element.Add(new ValueString("GTC"));
element.Add(new ValueString("GTA"));
element.Add(new ValueString("GTG"));
break;
case "A":
element.Add(new ValueString("GCT"));
element.Add(new ValueString("GCC"));
element.Add(new ValueString("GCA"));
element.Add(new ValueString("GCG"));
break;
case "D":
element.Add(new ValueString("GAT"));
element.Add(new ValueString("GAC"));
break;
case "E":
element.Add(new ValueString("GAA"));
element.Add(new ValueString("GAG"));
break;
case "G":
element.Add(new ValueString("GGT"));
element.Add(new ValueString("GGC"));
element.Add(new ValueString("GGA"));
element.Add(new ValueString("GGG"));
break;
default:
throw new ArgumentException("Unknown amino acid");
}
resultChain[i] = element;
}
return resultChain;
}
/// <summary>
/// Translates dna sequence into triplet sequence.
/// </summary>
/// <param name="inputChain">
/// Nucleotide sequence.
/// </param>
/// <returns>
/// Triplet sequence of <see cref="BaseChain"/> type.
/// Elements are of <see cref="ValueString"/> type.
/// </returns>
public static BaseChain EncodeTriplets(BaseChain inputChain)
{
DnaProcessor.CheckDnaAlphabet(inputChain.Alphabet);
var resultLength = (int)Math.Floor((double)inputChain.GetLength() / 3);
var resultChain = new BaseChain(resultLength);
for (int i = 0; i < resultLength * 3; i += 3)
{
resultChain[i / 3] = new ValueString(inputChain[i].ToString() + inputChain[i + 1] + inputChain[i + 2]);
}
return resultChain;
}
/// <summary>
/// Translates DNA sequence into amino acids.
/// </summary>
/// <param name="inputChain">
/// DNA sequence.
/// </param>
/// <returns>
/// Amino acid sequence of type <see cref="BaseChain"/>.
/// Elements are of <see cref="ValueString"/> type.
/// </returns>
public static BaseChain EncodeAmino(BaseChain inputChain)
{
DnaProcessor.CheckDnaAlphabet(inputChain.Alphabet);
var count = (int)Math.Floor((double)inputChain.GetLength() / 3);
var outChain = new BaseChain(count);
for (int i = 0; i < count * 3; i += 3)
{
string first = inputChain[i].ToString();
string second = inputChain[i + 1].ToString();
string third = inputChain[i + 2].ToString();
switch (first)
{
case "T":
switch (second)
{
case "T":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('F');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('L');
}
else
{
throw new Exception();
}
}
break;
case "C":
outChain[i / 3] = new ValueString('S');
break;
case "A":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('Y');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('X');
}
else
{
throw new Exception();
}
}
break;
case "G":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('C');
}
else
{
if (third == "A")
{
outChain[i / 3] = new ValueString('X');
}
else
{
if (third == "G")
{
outChain[i / 3] = new ValueString('W');
}
else
{
throw new Exception();
}
}
}
break;
default:
throw new Exception();
}
break;
case "C":
switch (second)
{
case "T":
outChain[i / 3] = new ValueString('L');
break;
case "C":
outChain[i / 3] = new ValueString('P');
break;
case "A":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('H');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('Q');
}
else
{
throw new Exception();
}
}
break;
case "G":
outChain[i / 3] = new ValueString('R');
break;
default:
throw new Exception();
}
break;
case "A":
switch (second)
{
case "T":
if ((third == "T") || (third == "C") || (third == "A"))
{
outChain[i / 3] = new ValueString('I');
}
else
{
if (third == "G")
{
outChain[i / 3] = new ValueString('M');
}
else
{
throw new Exception();
}
}
break;
case "C":
outChain[i / 3] = new ValueString('T');
break;
case "A":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('N');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('K');
}
else
{
throw new Exception();
}
}
break;
case "G":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('S');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('R');
}
else
{
throw new Exception();
}
}
break;
default:
throw new Exception();
}
break;
case "G":
switch (second)
{
case "T":
outChain[i / 3] = new ValueString('V');
break;
case "C":
outChain[i / 3] = new ValueString('A');
break;
case "A":
if ((third == "T") || (third == "C"))
{
outChain[i / 3] = new ValueString('D');
}
else
{
if ((third == "A") || (third == "G"))
{
outChain[i / 3] = new ValueString('E');
}
else
{
throw new Exception();
}
}
break;
case "G":
outChain[i / 3] = new ValueString('G');
break;
default:
throw new Exception();
}
break;
default:
throw new Exception();
}
}
return outChain;
}
