//This function reads datagridview4 and obtain its data.
private List<Peptide> GetPeptidesFromTable()
{
List<Peptide> PP = new List<Peptide>();
for (int i = 0; i < PeptideGridView.Rows.Count; i++)
{
//if (Convert.ToInt32(dataGridView4.Rows[c].Cells[0].Value) == 0)
// continue;
Peptide pp = new Peptide();
pp.Selected = Convert.ToBoolean((PeptideGridView.Rows[i].Cells[0].Value));
pp.Mass = Convert.ToDouble(PeptideGridView.Rows[i].Cells[1].Value);
pp.Modifications = Convert.ToString(PeptideGridView.Rows[i].Cells[2].Value);
pp.StartAA = Convert.ToInt32(PeptideGridView.Rows[i].Cells[3].Value);
pp.EndAA = Convert.ToInt32(PeptideGridView.Rows[i].Cells[4].Value);
pp.MissedCleavages = Convert.ToInt32(PeptideGridView.Rows[i].Cells[5].Value);
pp.Sequence = Convert.ToString(PeptideGridView.Rows[i].Cells[6].Value);
pp.NumGlycosylations = Convert.ToInt32(PeptideGridView.Rows[i].Cells[7].Value);
pp.ProteinID = Convert.ToString(PeptideGridView.Rows[i].Cells[8].Value);
PP.Add(pp);
}
return PP;
}
//This function reads tab delimited file.
private List<Peptide> ReadTabDelimitedProteinProspecter(String currentpath)
{
List<Peptide> data = new List<Peptide>();
FileStream FS = new FileStream(currentpath, FileMode.Open, FileAccess.Read );
StreamReader read = new StreamReader(FS);
//skip title line:
read.ReadLine();
while (read.Peek() >= 0)
{
Peptide pp = new Peptide();
String line = read.ReadLine();
String[] Lines = line.Split('\t');
pp.PeptideIndex = Convert.ToInt32(Lines[0]);
pp.Mass = Convert.ToDouble(Lines[1]);
pp.Charge = Convert.ToInt32(Lines[3]);
pp.Modifications = Convert.ToString(Lines[4]);
pp.StartAA = Convert.ToInt32(Lines[5]);
pp.EndAA = Convert.ToInt32(Lines[6]);
pp.MissedCleavages = Convert.ToInt32(Lines[7]);
pp.PreviousAA = Convert.ToString(Lines[8]);
pp.Sequence = Convert.ToString(Lines[9]);
pp.NextAA = Convert.ToString(Lines[10]);
data.Add(pp);
}
read.Close();
FS.Close();
return data;
}
private List<Peptide> genFalsePPMSD(String path)
{
Features fea = new Features();
List<Peptide> PP = fea.readtablim(path);
CompositionHypothesisTabbedForm comp = new CompositionHypothesisTabbedForm();
String sequence = comp.GetSequenceFromCleavedPeptides(PP);
List<int> forRandom = new List<int>
{
{0},{1},{2}
};
List<int> forlength = new List<int>
{
{4},{5},{6},{7},{8},{9},{10},{11}
};
List<Peptide> finalAns = new List<Peptide>();
Int32 StartAA = 0;
Int32 EndAA = 0;
while (EndAA != sequence.Count())
{
forRandom.Shuffle();
if (forRandom[0] == 1)
{
//add in this fragment
Peptide Ans = new Peptide();
forlength.Shuffle();
Int32 length = forlength[0];
EndAA = StartAA + length;
if (EndAA > sequence.Count())
EndAA = sequence.Count();
String Fra = "";
Ans.StartAA = Convert.ToInt32(StartAA + 1);
Ans.EndAA = Convert.ToInt32(EndAA + 1);
for (int i = StartAA; i < EndAA; i++)
{
Fra = Fra + sequence[i];
}
StartAA = StartAA + length;
Ans.Selected = true;
Ans.PeptideIndex = 1;
Ans.Mass = getFragmentMass(Fra);
Ans.Charge = 0;
Ans.Modifications = "";
Ans.MissedCleavages = 0;
Ans.PreviousAA = "";
Ans.NextAA = "";
forRandom.Shuffle();
Ans.NumGlycosylations = Convert.ToInt32(forRandom[0]);
finalAns.Add(Ans);
}
else
{
//Skip this fragment
forlength.Shuffle();
Int32 length = forlength[0];
EndAA = StartAA + length;
if (EndAA > sequence.Count())
EndAA = sequence.Count();
StartAA = StartAA + length;
}
if (EndAA == sequence.Count() && finalAns.Count() == 0)
{
EndAA = 0;
StartAA = 0;
}
}
return finalAns;
}