/// <summary>
///
/// </summary>
/// <param name="seq1">The peptide to be queried</param>
/// <param name="theDB">The sequence database</param>
/// <returns></returns>
public List <List <int[]> > SwapAlignBulk(char[] seq1, List <FastaItem> theDB)
{
List <char[]> seq1Swapped = Swapper.Swap(seq1);
Console.WriteLine("------------------------------- Swap solutions ---------------------------------");
for (int i = 0; i < seq1Swapped.Count; i++)
{
Console.WriteLine("{0}:{1}", i, new string(seq1Swapped[i]));
}
Console.WriteLine("\n-------------------------------------------------------------------------------\n");
List <List <int[]> > returnResult = new List <List <int[]> >(seq1Swapped.Count);
int counter = 0;
foreach (FastaItem fi in theDB)
{
counter++;
if (counter % 100 == 0)
{
Console.WriteLine("DB item " + counter);
}
List <int[]> alignmentResult = SWAPAlign2(seq1, fi.Sequence.ToCharArray());
if (alignmentResult != null)
{
returnResult.Add(alignmentResult);
}
}
return(returnResult);
}
public double SimilarityScore(KeyValuePair <int, List <List <int> > > PBSA, List <FastaItem> DB, List <List <int[]> > swapBulk, char [] seq1)
{
List <char[]> seq1Swapped = Swapper.Swap(seq1);
double score = 0;
int cont = 0;
for (int i = 0; i < PBSA.Value[0].Count; i++)
{
for (int j = 0; j < swapBulk[0].Count; j++)
{
for (int k = 0; k < seq1Swapped[0].Length; k++)
{
if (DB[PBSA.Value[0][i]].Sequence[k].ToString() != seq1Swapped[j][k].ToString())
{
score = swapBulk[i][j][k] + score;
cont++;
}
}
}
}
score = score / cont;
return(score);
}
public List <int[]> SWAPAlign2(char[] seq1, char[] seq2)
{
List <char[]> seq1Swapped = Swapper.Swap(seq1);
List <int[]> returnResult = new List <int[]>(seq1Swapped.Count);
for (int y = 0; y < seq1Swapped.Count; y++)
{
Debug.Write(new string (seq1Swapped[y]) + "\n");
int[] result = Align(seq1Swapped[y], seq2);
returnResult.Add(result);
}
return(returnResult);
}
public int IdentitylScore(KeyValuePair <int, List <List <int> > > PBSA, List <FastaItem> DB, List <List <int[]> > swapBulk, char[] seq1)
{
List <char[]> seq1Swapped = Swapper.Swap(seq1);
int score = 0;
for (int i = 0; i < PBSA.Value[0].Count; i++)
{
for (int j = 0; j < swapBulk[0].Count; j++)
{
for (int k = 0; k < seq1Swapped[0].Length; k++)
{
if (DB[PBSA.Value[0][i]].Sequence[k].ToString() == seq1Swapped[j][k].ToString())
{
score = swapBulk[i][j][k] + score;
}
}
}
}
return(score);
}