/// <summary>
/// Cloning method.
/// </summary>
/// <returns>
/// Phantom value clone.
/// </returns>
public new IBaseObject Clone()
{
var clone = new ValuePhantom();
foreach (IBaseObject element in Elements)
{
clone.Add(element);
}
return clone;
}
/// <summary>
/// Adds phantom value by merging.
/// All not duplicated elements from second phantom value are added to this phantom value.
/// </summary>
/// <param name="phantomValue">
/// Phantom value to add.
/// </param>
public void Add(ValuePhantom phantomValue)
{
if (phantomValue != null)
{
for (int i = 0; i < phantomValue.Cardinality; i++)
{
if (!Contains(phantomValue[i]))
{
Add(phantomValue[i]);
}
}
}
}
/// <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>
/// The equals as phantom.
/// </summary>
/// <param name="phantomValue">
/// The phantom value.
/// </param>
/// <returns>
/// The <see cref="bool"/>.
/// </returns>
private bool EqualsAsPhantom(ValuePhantom phantomValue)
{
return base.Equals(phantomValue);
}
