public void addModifiedResidue(ModifiedResidue ModifResidue)
{
this.ModifiedResidues.Add(ModifResidue);
}
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);
}