/**
* Method to generate decoy sequence according to a given input sequence and other options like
* decoy type and whether to exclude N-terminus.
**/
private static string GenerateDecoySequence(string sequence, DecoyDatabaseMethod decoyType, bool excludeNTerminus, bool onlyIfNTerminusIsMethionine)
{
char[] temp = new char[sequence.Length];
bool keepNTerminus = excludeNTerminus && (!onlyIfNTerminusIsMethionine || sequence[0] == 'M');
switch (decoyType)
{
case DecoyDatabaseMethod.Reverse:
temp = sequence.ToCharArray();
if (keepNTerminus)
{
Array.Reverse(temp, 1, temp.Length - 1);
}
else
{
Array.Reverse(temp);
}
break;
case DecoyDatabaseMethod.Shuffle:
temp = sequence.ToCharArray();
if (keepNTerminus)
{
Shuffle(temp, 1, temp.Length - 1);
}
else
{
Shuffle(temp);
}
break;
case DecoyDatabaseMethod.Random:
int index = 0;
if (keepNTerminus)
{
temp[index++] = sequence[0];
}
// Generate Random Characters
while (index < sequence.Length)
{
temp[index++] = AminoAcids[Random.Next(AminoAcids.Count)];
}
break;
case DecoyDatabaseMethod.None:
break;
}
// Create decoy sequence string from temporary char array.
return(new string(temp));
}
/// <summary>
/// Generate a decoy version of the given fasta
/// </summary>
/// <param name="preText">The pretext to add to the description to indicated this is a decoy fasta</param>
/// <param name="method">The decoy generation type</param>
/// <param name="excludeNTerminus">Exclude the n-terminal amino acid</param>
/// <param name="onlyIfNTerminusIsMethionine">Exclude the n-terminal amino aicd only if it is a Methionine</param>
/// <returns>The generated decoy fasta</returns>
public Fasta ToDecoy(string preText = "DECOY_", DecoyDatabaseMethod method = DecoyDatabaseMethod.Reverse, bool excludeNTerminus = true, bool onlyIfNTerminusIsMethionine = true)
{
return(new Fasta(GenerateDecoySequence(Sequence, method, excludeNTerminus, onlyIfNTerminusIsMethionine), preText + Description));
}
