public void ExtractPeptides()
{
if (PeptideExtractionStarted != null)
{
PeptideExtractionStarted(this);
}
totalRows = _SourceDataTable.Rows.Count;
#region Peptide Extraction Loop
for (rowIndex = 0; rowIndex < totalRows; rowIndex++)
{
row = _SourceDataTable.Rows[rowIndex];
sequence = row[_NameOfSequenceFeildName].ToString();
position = int.Parse(row[_NameOfPositionFeildName].ToString());
if (_IsExtendedSequence == true)
{
pd = PeptideCutter.ToPeptideFromExtendedSequence(sequence, position, _SizeOfOneSide);
}
else
{
pd = PeptideCutter.ToPeptideFromStandardSequence(sequence, position, _SizeOfOneSide);
}
peptideID = row[_NamePIDFeildName].ToString() + "-" + position.ToString();
peptideRow = _PeptideDataTable.NewRow();
peptideRow["PeptideID"] = peptideID;
peptideRow["ExtendedSequence"] = pd.ExtendedPeptideSequence;
if (_MarkClassificationLabel == true)
{
peptideRow["Class"] = _ClassificationLabel;
}
ctr = 0;
for (index = (-1 * _SizeOfOneSide); index <= _SizeOfOneSide; index++)
{
peptideRow["P" + index.ToString()] = pd.PeptideSequence[ctr];
ctr++;
}
_PeptideDataTable.Rows.Add(peptideRow);
if (PeptideExtractionProgress != null)
{
progress = (((float)(rowIndex + 1) / (float)totalRows) * 100);
PeptideExtractionProgressEventArg.AssociatedData = null;
PeptideExtractionProgressEventArg.ProgressPercentage = progress;
PeptideExtractionProgress(this, PeptideExtractionProgressEventArg);
}
}
#endregion Peptide Extraction Loop
if (PeptideExtractionCompleted != null)
{
PeptideExtractionCompletedEventArg.UserStateMessage = "";
PeptideExtractionCompletedEventArg.Result = PeptideDataTable;
PeptideExtractionCompleted(this, PeptideExtractionCompletedEventArg);
}
}
public static DataTable ExtractPeptide(string sequence, List <string> listOfTargetResidues, int sizeOfOneSide, bool isExtendedSequence)
{
List <int> listOfTargetPositions = new List <int>();
int aminoIndex, totalAminoAcids;
string aminoAcid;
_SizeOfOneSide = sizeOfOneSide;
peptideDataTable = new DataTable("PeptideDataTable");
peptideDataTable.Columns.Add("ExtendedSequence");
peptideDataTable.Columns.Add("Position");
int index;
for (index = (-1 * sizeOfOneSide); index <= sizeOfOneSide; index++)
{
peptideDataTable.Columns.Add("P" + index.ToString());
}
if (isExtendedSequence == true)
{
char[] sep = { ',' };
string[] aminoAcidArray = sequence.Split(sep);
totalAminoAcids = aminoAcidArray.Length;
for (aminoIndex = 0; aminoIndex < totalAminoAcids; aminoIndex++)
{
aminoAcid = aminoAcidArray[aminoIndex];
if (listOfTargetResidues.Contains(aminoAcid) == true)
{
peptideData = PeptideCutter.ToPeptideFromExtendedSequence(sequence, aminoIndex + 1, sizeOfOneSide);
UpdatePeptideDataTable(aminoIndex + 1);
}
}
}
else
{
totalAminoAcids = sequence.Length;
for (aminoIndex = 0; aminoIndex < totalAminoAcids; aminoIndex++)
{
aminoAcid = sequence[aminoIndex].ToString();
if (listOfTargetResidues.Contains(aminoAcid) == true)
{
peptideData = PeptideCutter.ToPeptideFromStandardSequence(sequence, aminoIndex + 1, sizeOfOneSide);
UpdatePeptideDataTable(aminoIndex + 1);
}
}
}
return(peptideDataTable);
}
public void Dispose()
{
if (_SourceDataTable != null)
{
_SourceDataTable.Clear();
_SourceDataTable.Dispose();
_SourceDataTable = null;
}
if (_PeptideDataTable != null)
{
_PeptideDataTable.Clear();
_PeptideDataTable.Dispose();
_PeptideDataTable = null;
}
if (pd != null)
{
pd.Dispose();
pd = null;
}
}