private void btnBrowseRaw_Click(object sender, EventArgs e)
{
openFileDialog1.Filter = "RAW Files (*.raw; *.mzXML)|*.raw;*.mzxml";
openFileDialog1.Filter = "RAW Files (*.raw)|*.raw";
openFileDialog1.FileName = "";
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
txtRawFile.Text = openFileDialog1.FileName;
if (Path.GetExtension(openFileDialog1.FileName) == ".raw")
{
raw = new COL.MassLib.ThermoRawReader(txtRawFile.Text);
_endScan = raw.NumberOfScans;
}
//else
//{
// COL.MassLib.RawReader raw = new COL.MassLib.RawReader(txtRawFile.Text,"mzxml");
// _endScan = raw.NumberOfScans;
//}
lblLastScanTime.Text = "Last Scan Time:" + raw.ReadScan(raw.NumberOfScans).Time.ToString();
txtEndScan.Text = _endScan.ToString();
txtLCTime.Text = raw.ReadScan(raw.NumberOfScans).Time.ToString("0");
}
}
private void btnLoadRawCSMSL_Click(object sender, EventArgs e)
{
if(openFileDialog1.ShowDialog () == System.Windows.Forms.DialogResult.OK)
{
COL.MassLib.ThermoRawReader raw = new ThermoRawReader(openFileDialog1.FileName);
}
}
public Form1()
{
InitializeComponent();
//StreamReader SR = new StreamReader(@"D:\Data\Jacobson Tang Meeting\bkdsub_smooth_centroid RNASE5.txt");
//List<double> mzs = new List<double>();
//List<double> intensities = new List<double>();
//do
//{
// string tmp = SR.ReadLine();
// mzs.Add(Convert.ToDouble(tmp.Split('\t')[0]));
// intensities.Add(Convert.ToDouble(tmp.Split('\t')[1]));
//} while (!SR.EndOfStream);
//SR.Close();
//GraphPane gp = zedGraphControl1.GraphPane;
//PointPairList ppl = new PointPairList(mzs.ToArray(), intensities.ToArray());
//gp.AddBar("X-Y", ppl, Color.Black);
//gp.AxisChange();
//zedGraphControl1.Refresh();
//List<Protease.Type> proteasList = new List<Protease.Type>();
//proteasList.Add(Protease.Type.Trypsin);
//List<ProteinInfo> PInfos = FastaReader.ReadFasta(@"E:\Dropbox\@Paper\MyPaper\GlycanSeq_AC\Data\H1N1\H1N1.fasta");
//List<string> Peptides = PInfos[0].NGlycopeptide(0, proteasList, enumPeptideMutation.NoMutation);
//List<string> MutaPeptides = PInfos[0].NGlycopeptide(0, proteasList,enumPeptideMutation.DtoN);
//Console.WriteLine(Peptides.Count);
//Console.WriteLine(MutaPeptides.Count);
COL.GlycoLib.ReadGlycanListFromFile.ReadGlycanList(@"D:\!Git\MultiGlycan\lib\Default_Combination.csv", true,
false, false, true, true);
COL.MassLib.ThermoRawReader Raw = new ThermoRawReader(@"E:\Dropbox\@Paper\MyPaper\GlycanSeq_AC\Data\H1N1\P-Glu-C_IU_090710_HCD.RAW");
List<MSScan> Scan = Raw.ReadScanWMSLevel(13107, 13127, 1);
Console.WriteLine(Raw.NumberOfScans.ToString());
List<MSScan> MS1 = Raw.ReadScanWMSLevel(1,Raw.NumberOfScans,1);
List<MSScan> MS2 = Raw.ReadScanWMSLevel(1, Raw.NumberOfScans, 2);
int CIDCount = 0;
int HCDCount = 0;
foreach (var m in MS2)
{
if (m.IsCIDScan)
{
CIDCount++;
}
if (m.IsHCDScan)
{
HCDCount++;
}
}
Console.WriteLine(CIDCount.ToString());
}
private void button3_Click(object sender, EventArgs e)
{
MassLib.ThermoRawReader Raw = new ThermoRawReader(@"E:\Dropbox\Chuan-Yih\PerMethQuant\RiboB_7plex_05302014.raw");
List<MSScan> scans = Raw.ReadScans(766, 1066);
List<MSPeak> Peaks = new List<MSPeak>();
foreach (MSScan s in scans)
{
foreach (MSPeak p in s.MSPeaks)
{
if (p.ChargeState == 2)
{
Peaks.Add(p);
;
}
//if (p.MonoisotopicMZ >= 834.62 && p.MonoisotopicMZ <= 834.65)
//{
// Peaks.Add(p);
//}
}
}
}
private void btnBrowseRaw_Click(object sender, EventArgs e)
{
openFileDialog1.Filter = "RAW Files (*.raw; *.mzXML)|*.raw;*.mzxml";
openFileDialog1.Filter = "RAW Files (*.raw)|*.raw";
openFileDialog1.FileName = "";
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
txtRawFile.Text = openFileDialog1.FileName;
if (Path.GetExtension(openFileDialog1.FileName) == ".raw")
{
raw = new COL.MassLib.ThermoRawReader(txtRawFile.Text);
_endScan = raw.NumberOfScans;
}
//else
//{
// COL.MassLib.RawReader raw = new COL.MassLib.RawReader(txtRawFile.Text,"mzxml");
// _endScan = raw.NumberOfScans;
//}
lblLastScanTime.Text = "Last Scan Time:" + raw.ReadScan(raw.NumberOfScans).Time.ToString() ;
txtEndScan.Text = _endScan.ToString();
txtLCTime.Text = raw.ReadScan(raw.NumberOfScans).Time.ToString("0");
}
}
private void btnLoad_Click(object sender, EventArgs e)
{
openFileDialog1.Filter = "Raw files (*.RAW,*.mzXML)|*.RAW;*.mzXML";
openFileDialog1.RestoreDirectory = true;
if (txtScanNo.Text == "" || txtPeptideSeq.Text == "")
{
MessageBox.Show("Please fill the information");
return;
}
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
_torelance = Convert.ToSingle(txtPeaKTol.Text);
_precursorTorelance = Convert.ToSingle(txtPrecusorTol.Text);
dtTrees.Rows.Clear();
int ScanNo = 0;
if (Int32.TryParse(txtScanNo.Text, out ScanNo) == false)
{
MessageBox.Show("Input Scan Number Error");
return;
}
if (Path.GetExtension(openFileDialog1.FileName).ToLower() == ".raw")
{
ThermoRawReader RawReader = new COL.MassLib.ThermoRawReader(openFileDialog1.FileName);
/*GlypID.Peaks.clsPeakProcessorParameters clsParameters = new GlypID.Peaks.clsPeakProcessorParameters();
* clsParameters.SignalToNoiseThreshold = 0.0f;
* clsParameters.PeakBackgroundRatio = 0.01f;*/
//RawReader.SetPeakProcessorParameter(2, 2);
scan = RawReader.ReadScan(ScanNo);
}
else
{
//scan = new mzXMLReader(openFileDialog1.FileName).ReadScan(ScanNo);
}
int NoNeuAc = 0;
int NoNeuGc = 0;
if (rdoNeuAc.Checked)
{
NoNeuAc = Convert.ToInt32(txtSia.Text);
}
else
{
NoNeuGc = Convert.ToInt32(txtSia.Text);
}
List <int> SequenceParameters = new List <int>();
SequenceParameters.Add(Convert.ToInt32(txtTopPeaks_i.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopDiagPeaks_j.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopCorePeaks_k.Text));
SequenceParameters.Add(Convert.ToInt32(txtTopBrancingPeaks_l.Text));
SequenceParameters.Add(Convert.ToInt32(txtMaxGlycansToCompleteStruct_m.Text));
GS = new GlycanSequencing_MultipleScoring(scan, scan.ParentCharge, Convert.ToInt32(txtHex.Text), Convert.ToInt32(txtHexNAc.Text), Convert.ToInt32(txtdeHex.Text), NoNeuAc, NoNeuGc, @"D:\tmp", true, 0.8f, 10, SequenceParameters, Peptides.ReadFastaFile(txtPeptideSeq.Text));
GS.NumbersOfPeaksForSequencing = 140;
GS.UseAVGMass = true;
//GS.DebugMode(@"E:\temp\SeqTmp\");
GS.CreatePrecursotMZ = true;
GS.RewardForCompleteStructure = 3;
GS.StartSequencing();
GS.GetTopRankScoreStructre(1);
//lstPeak.Items.Add("Top " + GS.FilteredPeaks.Count.ToString() + " peaks");
//lstPeak.Items.Add("m/z / normailzed intensity ");
//foreach (MSPoint p in GS.FilteredPeaks)
//{
// lstPeak.Items.Add(p.Mass.ToString("0.0000") +"/" + p.Intensity.ToString("0.0000"));
//}
bool isFullSeq = false;
ReportStructure = GS.SequencedStructures;
if (ReportStructure.Count == 0)
{
MessageBox.Show("No Structure Found");
return;
}
if (GS.FullSequencedStructures.Count != 0)
{
ReportStructure = GS.FullSequencedStructures;
isFullSeq = true;
}
AminoAcidMass AA = new AminoAcidMass();
for (int i = 0; i < ReportStructure.Count; i++)
{
GlycanStructure gt = ReportStructure[i];
DataRow row = dtTrees.NewRow();
//row.Add(new Object[] (gt.Mass.ToString("0.0000"), gt.Score.ToString("0.0000"),gt.GetIUPACString()));
row["ID"] = i.ToString();
row["Glycan Mass"] = gt.GlycanAVGMonoMass.ToString("0.0000");
row["Y1"] = gt.Y1.Mass.ToString("0.0000");;
row["Core Score"] = Convert.ToSingle((gt.CoreScore).ToString("0.00"));
row["Branch Score"] = Convert.ToSingle((gt.BranchScore).ToString("0.00"));
row["Append Glycan Score"] = Convert.ToSingle((gt.InCompleteScore).ToString("0.00"));
if (gt.IsCompleteByPrecursorDifference)
{
row["PPM"] =
Convert.ToSingle(
MassUtility.GetMassPPM(
gt.GlycanMonoMass + AA.GetMonoMW(gt.PeptideSequence, true) +
GetGlycanMassByGlycanString(gt.RestGlycanString), GS.PrecusorMonoMass)
.ToString("0.00"));
}
else
{
row["PPM"] =
Convert.ToSingle(
MassUtility.GetMassPPM(
gt.GlycanMonoMass + AA.GetMonoMW(gt.PeptideSequence, true), GS.PrecusorMonoMass).ToString("0.00"));
}
row["Peptide"] = gt.PeptideSequence;
row["Append Glycan"] = gt.RestGlycanString;
row["IUPAC"] = gt.IUPACString;
GlycansDrawer GDRaw = new GlycansDrawer(gt.IUPACString, false);
Image tmpImg = GDRaw.GetImage();
row["Structure"] = tmpImg;
dtTrees.Rows.Add(row);
}
////GS.SequencStructures[0].TheoreticalFragment
dtTrees.DefaultView.Sort = "Glycan Mass DESC";
for (int i = 0; i < dgView.Rows.Count; i++)
{
this.dgView.AutoResizeRow(i);
if (Convert.ToSingle(dgView.Rows[i].Cells["PPM"].Value) <= Convert.ToSingle(txtPrecusorTol.Text))
{
dgView.Rows[i].DefaultCellStyle.BackColor = Color.Red;
}
}
}
}
