private void button1_Click(object sender, EventArgs e)
{
COL.MassLib.ThermoRawReader raw = new COL.MassLib.ThermoRawReader(@"E:\Dropbox\Chuan-Yih\PerMethQuant\RiboB_7plex_05302014.raw");
COL.MassLib.MSScan scan1 = raw.ReadScan(846);
//COL.MassLib.MSScan scan2 = raw.ReadScan(415);
GlycanCompound CP1 = new GlycanCompound(5, 6, 0, 2, false, false, false, false, true);
CP1.isHuman = true;
CP1.LabelingTag = enumLabelingTag.DRAG_Light;
double a = COL.MassLib.MassUtility.GetMassPPM(CP1.MonoMass, 2748.063);
}
public void SequenceCIDPeaks(ref Classes.MapRecord _glycoMap, ref Classes.Params _params, string sequencingFolder)
{
Classes.MapRecord _tempMap = new MapRecord();
_tempMap._AssociatedDatasetNames = _glycoMap._AssociatedDatasetNames;
_tempMap._IsCID = _glycoMap._IsCID;
_tempMap._IsETD = _glycoMap._IsETD;
_tempMap._IsHCD = _glycoMap._IsHCD;
Classes.FragEvents e = new FragEvents();
if (sequencingFolder == "")
sequencingFolder = @"c:\sequencing\";
for (int i = 0; i < _glycoMap._AllMLNRecords.Count; i++)
{
MultiAlignRecord m = new MultiAlignRecord();
m = _glycoMap._AllMLNRecords[i];
int num_records = m._AssociatedUMCRecords.Count;
if (m.ID == 2290)
{
bool test = true;
}
//for (int j = 0; j < num_records; j++)
//{
// for (int k = 0; k < m._AssociatedUMCRecords[j]._AssociatedFragEvents.Count; k++)
for (int k = 0; k < m._ClusterRepFragEvents.Count; k++)
{
e = new FragEvents();
e = m._ClusterRepFragEvents[k]; // m._AssociatedUMCRecords[j]._AssociatedFragEvents[k];
if (e.ETDScore > 0)
{
float PeptideMass = 0;
float GlcNAcMass = 0;
COL.MassLib.MSScan _msScan = new COL.MassLib.MSScan(e.CIDMzs, e.CIDIntensities, Convert.ToSingle(e.TransformResult.mdbl_mz),
Convert.ToSingle(e.TransformResult.mdbl_mono_mw), Convert.ToSingle(e.TransformResult.mdbl_average_mw), Convert.ToInt32(e.TransformResult.mshort_cs));
if (e.TransformResult.mdbl_average_mw > 0)
{
PeptideMass = Convert.ToSingle(e.GP_Record.SequenceAverageMass); // this means proper deisotoping has occured so use average compostion
GlcNAcMass = COL.GlycoLib.GlycanMass.GetGlycanAVGMass(COL.GlycoLib.Glycan.Type.HexNAc);
}
else
{
PeptideMass = Convert.ToSingle(e.GP_Record.SequenceMonoMass); // CS has been assigned, in which case both y1 and precursor should be just mono
GlcNAcMass = COL.GlycoLib.GlycanMass.GetGlycanMass(COL.GlycoLib.Glycan.Type.HexNAc);
}
short y1cs = e.TransformResult.mshort_cs;
y1cs--;
while (y1cs > 0)
{
float y1Mz = ((PeptideMass + GlcNAcMass) + (float)_utils._CC_MASS * y1cs) / y1cs;
COL.GlycoSequence.GlycanSequencing _Gs = new COL.GlycoSequence.GlycanSequencing(_msScan, y1Mz, y1cs, e.GP_Record.Glycan.numHex,
e.GP_Record.Glycan.numHexNAc, e.GP_Record.Glycan.numDeHex, e.GP_Record.Glycan.numNeuAc, 0, sequencingFolder, true, 0.8f, 60);
_Gs.NumbersOfPeaksForSequencing = 140;
_Gs.CreatePrecursotMZ = true;
_Gs.RewardForCompleteStructure = 3;
if (e.TransformResult.mdbl_average_mw > 0)
_Gs.UseAVGMass = true;
else
_Gs.UseAVGMass = false;
int structure_count = _Gs.StartSequencing();
if (structure_count > 0)
{
List<COL.GlycoLib.GlycanStructure> topstructures = _Gs.GetTopRankScoreStructre(1);
e.CIDSequencingScore = topstructures[0].Score;
e.GP_Record.GlycanSequence = topstructures[0].IUPACString;
// Printing out the sequences
string opfile = sequencingFolder + m.ID.ToString() + "_" + e.CIDScan.ToString() + ".txt";
Utils.CSVFileHandler cidString = new CSVFileHandler(opfile, CSVFileHandler.WRITE_ONLY);
cidString.openFile();
for (int zz = 0; zz < topstructures.Count; zz++)
{
cidString.writeLine(topstructures[zz].IUPACString);
/*COL.GlycoLib.GlycansDrawer _gdraw = new COL.GlycoLib.GlycansDrawer(topstructures[zz].IUPACString, false);
System.Drawing.Image img1 = _gdraw.GetImage();*/
}
cidString.closeFile();
break;
}
y1cs--;
}
}
}
}
}