public static Peptide getPeptide(AminoAcid[] StandardProteinSequence, int ModificationSite)
{
AminoAcid[] PeptAminoAcids = new AminoAcid[9];
int PeptIndex, SeqncIndex;
for (int i = 0; i < StandardProteinSequence.Length; i++)
{
if ((i + 1) == ModificationSite)
{
PeptAminoAcids[4] = StandardProteinSequence.ElementAt(i);
PeptIndex = 3;
SeqncIndex = (i - 1);
while (PeptIndex != -1)
{
if (SeqncIndex < 0)
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex--;
SeqncIndex--;
}
PeptIndex = 5;
SeqncIndex = (i + 1);
while (PeptIndex != 9)
{
if (SeqncIndex > (StandardProteinSequence.Length - 1))
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex++;
SeqncIndex++;
}
break;
}
}
return(new Peptide(PeptAminoAcids));
}
public static AminoAcid[] getStandardProteinSequence(String ProteinSequence)
{
#region Amino Acid List
List <AminoAcid> AminoAcidList = new List <AminoAcid>();
AminoAcidList.Add(new AminoAcid("Alanine", 'A'));
AminoAcidList.Add(new AminoAcid("Arginine", 'R'));
AminoAcidList.Add(new AminoAcid("Asparagine", 'N'));
AminoAcidList.Add(new AminoAcid("Aspartic Acid", 'D'));
AminoAcidList.Add(new AminoAcid("Cystein", 'C'));
AminoAcidList.Add(new AminoAcid("Glutamine", 'Q'));
AminoAcidList.Add(new AminoAcid("Glutamic Acid", 'E'));
AminoAcidList.Add(new AminoAcid("Glycine", 'G'));
AminoAcidList.Add(new AminoAcid("Histidine", 'H'));
AminoAcidList.Add(new AminoAcid("Isoleucine", 'I'));
AminoAcidList.Add(new AminoAcid("Leucine", 'L'));
AminoAcidList.Add(new AminoAcid("Lysine", 'K'));
AminoAcidList.Add(new AminoAcid("Methionine", 'M'));
AminoAcidList.Add(new AminoAcid("Phenylalanine", 'F'));
AminoAcidList.Add(new AminoAcid("Proline", 'P'));
AminoAcidList.Add(new AminoAcid("Serine", 'S'));
AminoAcidList.Add(new AminoAcid("Threonine", 'T'));
AminoAcidList.Add(new AminoAcid("Tryptophan", 'W'));
AminoAcidList.Add(new AminoAcid("Tyrosine", 'Y'));
AminoAcidList.Add(new AminoAcid("Valine", 'V'));
#endregion
AminoAcid[] StandardProteinSequence = new AminoAcid[ProteinSequence.Length];
char SequenceChar;
for (int i = 0; i < ProteinSequence.Length; i++)
{
SequenceChar = ProteinSequence.ElementAt(i);
for (int j = 0; j < AminoAcidList.Count; j++)
{
if (AminoAcidList.ElementAt(j).getSymbol().Equals(SequenceChar))
{
StandardProteinSequence[i] = AminoAcidList.ElementAt(j);
break;
}
}
}
return(StandardProteinSequence);
}
public void setModifAminoAcid(AminoAcid ModifAminoAcid)
{
this.ModifAminoAcid = ModifAminoAcid;
}
public static List <Peptide> getPeptideList(AminoAcid[] StandardProteinSequence, Boolean SerineChecked, Boolean ThreonineChecked, Boolean TyrosineChecked, Boolean AllChecked)
{
List <Peptide> peptides = new List <Peptide>();
int PeptIndex, SeqncIndex;
for (int i = 0; i < StandardProteinSequence.Length; i++)
{
AminoAcid[] PeptAminoAcids = new AminoAcid[9];
if (SerineChecked == true)
{
if (StandardProteinSequence.ElementAt(i).getSymbol().Equals('S'))
{
PeptAminoAcids[4] = StandardProteinSequence.ElementAt(i);
PeptIndex = 3;
SeqncIndex = (i - 1);
while (PeptIndex != -1)
{
if (SeqncIndex < 0)
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex--;
SeqncIndex--;
}
PeptIndex = 5;
SeqncIndex = (i + 1);
while (PeptIndex != 9)
{
if (SeqncIndex > (StandardProteinSequence.Length - 1))
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex++;
SeqncIndex++;
}
Peptide peptide = new Peptide(PeptAminoAcids);
peptides.Add(peptide);
}
}
else if (ThreonineChecked == true)
{
if (StandardProteinSequence.ElementAt(i).getSymbol().Equals('T'))
{
PeptAminoAcids[4] = StandardProteinSequence.ElementAt(i);
PeptIndex = 3;
SeqncIndex = (i - 1);
while (PeptIndex != -1)
{
if (SeqncIndex < 0)
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex--;
SeqncIndex--;
}
PeptIndex = 5;
SeqncIndex = (i + 1);
while (PeptIndex != 9)
{
if (SeqncIndex > (StandardProteinSequence.Length - 1))
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex++;
SeqncIndex++;
}
Peptide peptide = new Peptide(PeptAminoAcids);
peptides.Add(peptide);
}
}
else if (TyrosineChecked == true)
{
if (StandardProteinSequence.ElementAt(i).getSymbol().Equals('Y'))
{
PeptAminoAcids[4] = StandardProteinSequence.ElementAt(i);
PeptIndex = 3;
SeqncIndex = (i - 1);
while (PeptIndex != -1)
{
if (SeqncIndex < 0)
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex--;
SeqncIndex--;
}
PeptIndex = 5;
SeqncIndex = (i + 1);
while (PeptIndex != 9)
{
if (SeqncIndex > (StandardProteinSequence.Length - 1))
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex++;
SeqncIndex++;
}
Peptide peptide = new Peptide(PeptAminoAcids);
peptides.Add(peptide);
}
}
else if (AllChecked == true)
{
if (StandardProteinSequence.ElementAt(i).getSymbol().Equals('S') || StandardProteinSequence.ElementAt(i).getSymbol().Equals('T') || StandardProteinSequence.ElementAt(i).getSymbol().Equals('Y'))
{
PeptAminoAcids[4] = StandardProteinSequence.ElementAt(i);
PeptIndex = 3;
SeqncIndex = (i - 1);
while (PeptIndex != -1)
{
if (SeqncIndex < 0)
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex--;
SeqncIndex--;
}
PeptIndex = 5;
SeqncIndex = (i + 1);
while (PeptIndex != 9)
{
if (SeqncIndex > (StandardProteinSequence.Length - 1))
{
PeptAminoAcids[PeptIndex] = new AminoAcid("Null", 'X');
}
else
{
PeptAminoAcids[PeptIndex] = StandardProteinSequence[SeqncIndex];
}
PeptIndex++;
SeqncIndex++;
}
Peptide peptide = new Peptide(PeptAminoAcids);
peptides.Add(peptide);
}
}
}
return(peptides);
}
public static List <Protein> getProteinRecordsFromTestingDataset(String Dataset_File_Path)
{
Excel.Application ExcelApplication = new Excel.Application();
Excel.Workbook ExcelWorkbook = ExcelApplication.Workbooks.Open(Dataset_File_Path);
Excel.Worksheet ExcelWorksheet = ExcelWorkbook.Sheets[2];
Excel.Range ExcelSheetRange = ExcelWorksheet.UsedRange;
int NumberOfRows = ExcelSheetRange.Rows.Count;
int NumberOfColumn = ExcelSheetRange.Columns.Count;
String ProteinID = "", ModifiedResidueName = "", AminoAcidName = "", KineaseName = "", ProteinSequence = "";
int ModificationSite = 0, SequenceLength = 0;
char Symbol = '\0';
List <Protein> Proteins = new List <Protein>();
for (int RowCount = 2; RowCount <= NumberOfRows; RowCount++)
{
for (int ColumnCount = 1; ColumnCount <= NumberOfColumn; ColumnCount++)
{
if (ExcelSheetRange.Cells[RowCount, ColumnCount] != null && ExcelSheetRange.Cells[RowCount, ColumnCount].Value2 != null)
{
switch (ColumnCount)
{
case 1:
{
ProteinID = ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString();
break;
}
case 2:
{
ModificationSite = Int32.Parse(ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString());
break;
}
case 3:
{
ModifiedResidueName = ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString();
break;
}
case 4:
{
AminoAcidName = ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString();
break;
}
case 5:
{
Symbol = char.Parse(ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString());
break;
}
case 6:
{
KineaseName = ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString();
break;
}
case 7:
{
ProteinSequence = ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString();
break;
}
case 8:
{
SequenceLength = Int32.Parse(ExcelSheetRange.Cells[RowCount, ColumnCount].Value2.ToString());
break;
}
}
}
}
AminoAcid ModifAminoAcid = new AminoAcid(AminoAcidName, Symbol);
AminoAcid[] StandardProteinSequence = getStandardProteinSequence(ProteinSequence);
Peptide ModifPeptide = getPeptide(StandardProteinSequence, ModificationSite);
ModifiedResidue ModifResidue = new ModifiedResidue(ModificationSite, ModifiedResidueName, ModifAminoAcid, KineaseName, ModifPeptide);
Protein protein = new Protein(ProteinID, ProteinSequence, SequenceLength);
protein.addModifiedResidue(ModifResidue);
Proteins.Add(protein);
}
GC.Collect();
GC.WaitForPendingFinalizers();
Marshal.ReleaseComObject(ExcelSheetRange);
Marshal.ReleaseComObject(ExcelWorksheet);
ExcelWorkbook.Close();
Marshal.ReleaseComObject(ExcelWorkbook);
ExcelApplication.Quit();
Marshal.ReleaseComObject(ExcelApplication);
return(Proteins);
}
