/*private void PlotScan(MSScan argScan)
* {
*
* ZedGraph.PointPairList pplPeak = new ZedGraph.PointPairList();
* for (int i = 0; i < argScan.ScanMZs.Length; i++)
* {
* pplPeak.Add(argScan.ScanMZs[i], argScan.ScanIntensities[i]);
* }
* ZedGraph.GraphPane Pane = zedScan.GraphPane;
* Pane.XAxis.MajorTic.IsInside = false;
* Pane.XAxis.MinorTic.IsInside = false;
* Pane.CurveList.Clear();
* Pane.AddStick("Peaks", pplPeak, Color.Red);
* Pane.XAxis.Scale.Min = argScan.ScanMZs[0] - 10;
* Pane.XAxis.Scale.Max = argScan.ScanMZs[argScan.ScanMZs.Length - 1] - 10;
* Pane.Title.Text = "No. " + txtScanNo.Text;
* zedScan.AxisChange();
*
* }*/
private void dgView_CellClick(object sender, DataGridViewCellEventArgs e)
{
if (e.RowIndex < 0)
{
return;
}
GlycanStructure Structure = ReportStructure[Convert.ToInt32(dgView.Rows[e.RowIndex].Cells[0].Value)];
if (GS.FullSequencedStructures.Count != 0)
{
Structure = GS.FullSequencedStructures[Convert.ToInt32(dgView.Rows[e.RowIndex].Cells[0].Value)];
}
ListFragementStructure(Structure);
DrawsequencingGraph(Structure);
ListIDPeak(Structure);
float ParentMono = scan.ParentMonoMW;
float ParentAVGMono = scan.ParentAVGMonoMW;
/*lblPPM.Text = " Mono AVG\n" +
* " "+ParentMono.ToString() + " " + ParentAVGMono.ToString() + "\n" +
* "Hex: " + (GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.Hex)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.Hex), ParentMono).ToString("00000.000") + ") " +
* (GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.Hex)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.Hex), ParentAVGMono).ToString("00000.000") + ")\n" +
* "HexNAc: " + (GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.HexNAc)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.HexNAc), ParentMono).ToString("00000.000") + ") " +
* (GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.HexNAc)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.HexNAc), ParentAVGMono).ToString("00000.000") + ")\n" +
* "deHex: " + (GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.DeHex)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.DeHex), ParentMono).ToString("00000.000") + ") " +
* (GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.DeHex)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.DeHex), ParentAVGMono).ToString("00000.000") + ")\n" +
* "Sia: " + (GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.NeuAc)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanMonoMass + GlycanMass.GetGlycanMass(Glycan.Type.NeuAc), ParentMono).ToString("00000.000") + ") " +
* (GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuAc)).ToString("0000.000") + "(" + MassUtility.GetMassPPM(GS.PeptideMonoMass + Structure.GlycanAVGMonoMass + GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuAc), ParentAVGMono).ToString("00000.000") + ")\n";*/
}
private void ListFragementStructure(GlycanStructure argStructure)
{
//dgDetail
DataTable dtDetail = new DataTable();
DataColumn dcID = new DataColumn("ID", Type.GetType("System.Int32"));
DataColumn dcMass = new DataColumn("Mass", Type.GetType("System.Single"));
DataColumn dcScore = new DataColumn("Score", Type.GetType("System.Single"));
DataColumn dcStructure = new DataColumn("Structure", typeof(Image));
dtDetail.Columns.Add(dcID);
dtDetail.Columns.Add(dcMass);
dtDetail.Columns.Add(dcScore);
dtDetail.Columns.Add(dcStructure);
//dgDetail.DataSource = dtDetail;
//dgDetail.Columns[0].Width = 30;
//dgDetail.Columns[1].Width = 70;
//dgDetail.Columns[2].Width = 50;
//dgDetail.Columns[3].Width = 315;
dtDetail.DefaultView.Sort = "Mass";
int idx = 0;
float TotalScore = 0.0f;
GlycansDrawer GDRaw;
foreach (GlycanTreeNode frm in argStructure.TheoreticalFragment)
{
DataRow row = dtDetail.NewRow();
row[0] = idx;
float glycanmass = COL.GlycoLib.GlycanMass.GetGlycanMasswithCharge(frm.GlycanType, argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
int closepeakidx = MassUtility.GetClosestMassIdx(scan.MSPeaks, glycanmass);
row[1] = glycanmass;
if (MassUtility.GetMassPPM(glycanmass, scan.MSPeaks[closepeakidx].MonoisotopicMZ) < _torelance)
{
row[2] = scan.MSPeaks[closepeakidx].MonoIntensity / scan.MaxIntensity;
}
else
{
row[2] = 0.0f;
}
GDRaw = new GlycansDrawer(frm.GetIUPACString(), false);
row[3] = GDRaw.GetImage();
idx++;
dtDetail.Rows.Add(row);
TotalScore = TotalScore + Convert.ToSingle(row[2]);
}
DataRow dtrow = dtDetail.NewRow();
dtrow[0] = idx;
dtrow[1] = GlycanMass.GetGlycanMasswithCharge(argStructure.Root.GlycanType, argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
dtrow[2] = TotalScore;
GDRaw = new GlycansDrawer(argStructure.IUPACString, false);
dtrow[3] = GDRaw.GetImage();
dtDetail.Rows.Add(dtrow);
}
public static float GetGlycopeptideMZ(string argPeptide, GlycanStructure argGlycan, int argCharge)
{
float TotalMZ = 0.0f;
AminoAcidMass AAMS = new AminoAcidMass();
float PeptideMonoMass = AAMS.GetAVGMonoMW(argPeptide, true);
float GlycanMass = 0.0f;
GlycanMass = GlycanMass + argGlycan.NoOfHex*GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.Hex);
GlycanMass = GlycanMass + argGlycan.NoOfHexNac * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.HexNAc);
GlycanMass = GlycanMass + argGlycan.NoOfDeHex * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.DeHex);
GlycanMass = GlycanMass + argGlycan.NoOfNeuAc * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuAc);
GlycanMass = GlycanMass + argGlycan.NoOfNeuGc * GlycoLib.GlycanMass.GetGlycanAVGMass(Glycan.Type.NeuGc);
TotalMZ = (PeptideMonoMass + GlycanMass + MassLib.Atoms.ProtonMass*argCharge)/argCharge;
return TotalMZ;
}
private string GetRepresentStructure(GlycanStructure argCompleteGS, int argNodeID)
{
int ID = argNodeID;
GlycanStructure Clone = (GlycanStructure)argCompleteGS.Clone();
List <GlycanTreeNode> removelist = new List <GlycanTreeNode>();
foreach (GlycanTreeNode node in Clone.Root.FetchAllGlycanNode())
{
if (node.NodeID > argNodeID)
{
removelist.Add(node);
}
}
removelist.Sort(delegate(GlycanTreeNode t1, GlycanTreeNode t2) { return(t2.NodeID.CompareTo(t1.NodeID)); });
foreach (GlycanTreeNode node in removelist)
{
Clone.Root.RemoveGlycan(node);
}
return(Clone.Root.GetIUPACString());
}
private void ListIDPeak(GlycanStructure argStructure)
{
DataTable dtIDPeak = new DataTable();
DataColumn dcMass = new DataColumn("Glycopeptide m/z", Type.GetType("System.Single"));
DataColumn dcScore = new DataColumn("Score", Type.GetType("System.Single"));
DataColumn dcStructure = new DataColumn("Structure", typeof(Image));
dtIDPeak.Columns.Add(dcMass);
dtIDPeak.Columns.Add(dcScore);
dtIDPeak.Columns.Add(dcStructure);
dgIDPeak.DataSource = dtIDPeak;
dgIDPeak.Columns[0].Width = 70;
dgIDPeak.Columns[1].Width = 50;
dgIDPeak.Columns[2].Width = 315;
dtIDPeak.DefaultView.Sort = "Glycopeptide m/z";
GlycansDrawer GDraw;
foreach (GlycanTreeNode GT in argStructure.Root.FetchAllGlycanNode())
{
DataRow row = dtIDPeak.NewRow();
row[0] = GT.IDMass;
row[1] = GT.IDIntensity;
string tmp = argStructure.GetSequqncedIUPACwNodeID(GT.NodeID);
GDraw = new GlycansDrawer(tmp);
row[2] = GDraw.GetImage();
dtIDPeak.Rows.Add(row);
GT.GetIUPACString();
}
dgIDPeak.Sort(dgIDPeak.Columns[0], ListSortDirection.Descending);
for (int i = 0; i < dtIDPeak.Rows.Count; i++)
{
this.dgIDPeak.AutoResizeRow(i);
}
this.dgIDPeak.Columns[2].DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleLeft;
}
public static Image GetAnnotatedImage(string argPeptide, MSScan argScan, List<MSPoint> argPeaks, GlycanStructure argStructure)
{
float MaxX = argStructure.Root.FetchAllGlycanNode().OrderByDescending(o => o.IDMass).ToList()[0].IDMass;
if (MaxX + 100 > 2000.0)
{
MaxX = 2000.0f;
}
else
{
MaxX = MaxX + 100;
}
ZedGraph.GraphPane Pane = new ZedGraph.GraphPane(new RectangleF(0.0f, 0.0f, 2000.0f, 1500.0f), argScan.ScanNo.ToString(), "Mass", "Intensity");
//ZedGraph.MasterPane Pane = new ZedGraph.MasterPane(argTitle,new RectangleF(0.0f, 0.0f, 2400.0f, 1800.0f) );
Pane.XAxis.MajorTic.IsInside = false;
Pane.XAxis.MinorTic.IsInside = false;
Pane.Legend.IsVisible = false;
ZedGraph.PointPairList Peaks = new ZedGraph.PointPairList();
double MaxIntensity = 0.0;
/////////////////
//Peaks
////////////////
foreach (MSPoint p in argPeaks)
{
if (p.Intensity > MaxIntensity && p.Mass<=MaxX)
{
MaxIntensity = p.Intensity;
}
}
foreach (MSPoint p in argPeaks)
{
if (p.Mass <= MaxX)
{
Peaks.Add(p.Mass, (p.Intensity/MaxIntensity)*100.0);
}
}
Pane.AddStick("Peaks", Peaks, Color.Red);
//////////////////
//Y1 text object
//////////////////
/* ZedGraph.TextObj txtY1 = new ZedGraph.TextObj("Y1", argStructure.Y1.MZ, 102);
txtY1.FontSpec.Size = txtY1.FontSpe.cSize*0.5f;
txtY1.FontSpec.Border.IsVisible = false;
Pane.GraphObjList.Insert(0, txtY1);*/
/////////////////
//Structure
////////////////
GlycansDrawer GS;
double previousBoundary = 0;
foreach (GlycanTreeNode t in argStructure.Root.FetchAllGlycanNode().OrderBy(o => o.IDMass).ToList())
{
GS = new GlycansDrawer(t.IUPACFromRoot, false);
double glycopeptideMZ = t.IDMass;
//double glycopeptideMZ =argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfHexNac * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.HexNAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfHex*GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.Hex, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfDeHex * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.DeHex, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfNeuAc * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.NeuAc, FGS.Charge);
//glycopeptideMZ = glycopeptideMZ +
// FGS.NoOfNeuGc * GlycanMass.GetGlycanAVGMasswithCharge(Glycan.Type.NeuGc, FGS.Charge);
Image imgStructure = GlycanImage.RotateImage(GS.GetImage(), 270);
ZedGraph.TextObj txtGlycanMz = new ZedGraph.TextObj(glycopeptideMZ.ToString("0.000"), 100, 131);
double PositionX = glycopeptideMZ;
if (previousBoundary >= PositionX)
{
PositionX = previousBoundary + 20;
}
if (imgStructure.Width > txtGlycanMz.Location.Width)
{
previousBoundary = imgStructure.Width + PositionX;
}
else
{
previousBoundary = (float)txtGlycanMz.Location.Width + PositionX;
}
ZedGraph.ImageObj glycan = new ZedGraph.ImageObj(imgStructure, PositionX, 130, imgStructure.Width + 20, imgStructure.Height);
glycan.IsScaled = false;
glycan.Location.AlignV = ZedGraph.AlignV.Bottom;
txtGlycanMz.Location.X = glycan.Location.X + (float)glycan.Image.Width / 2 - (float)txtGlycanMz.Location.Width / 2;
txtGlycanMz.FontSpec.Size = txtGlycanMz.FontSpec.Size * 0.3f;
txtGlycanMz.FontSpec.Border.IsVisible = false;
Pane.GraphObjList.Add(txtGlycanMz);
Pane.GraphObjList.Add(glycan);
double interval = 100000;
int idx = 0;
for (int i = 0; i < Peaks.Count; i++)
{
if (Math.Abs(Peaks[i].X - glycopeptideMZ) < interval)
{
interval = Math.Abs((float)Peaks[i].X - glycopeptideMZ);
idx = i;
}
}
string mzLabelwPPM = Peaks[idx].X.ToString("0.000");// + "\n(" + Math.Abs(glycopeptideMZ - (float)Peaks[idx].X).ToString("0") + "da)";
ZedGraph.TextObj PeakLabel = new ZedGraph.TextObj(mzLabelwPPM, Peaks[idx].X, Peaks[idx].Y + 3.0);
PeakLabel.FontSpec.Size = PeakLabel.FontSpec.Size * 0.3f;
PeakLabel.FontSpec.Border.IsVisible = false;
PeakLabel.FontSpec.Fill.IsVisible = false;
Pane.GraphObjList.Add(PeakLabel);
}
Pane.AxisChange();
Pane.YAxis.Scale.Max = 145;
Pane.XAxis.Scale.Min = Convert.ToInt32(argStructure.Y1.Mass - 100);
Pane.XAxis.Scale.Max = Peaks[Peaks.Count - 1].X + 100;
////////////
//Glycan Structure
////////////
GS = new GlycansDrawer(argStructure.IUPACString, false);
Image imgStruc = RotateImage( GS.GetImage() ,180);
ZedGraph.ImageObj fullStructure = new ZedGraph.ImageObj(imgStruc, Pane.XAxis.Scale.Min + 20, 140, imgStruc.Width + 20, imgStruc.Height);
fullStructure.IsScaled = false;
Pane.GraphObjList.Add(fullStructure);
///////////////
//Glycan M/Z
//////////////
double glycopeptidemz = GlycanMass.GetGlycanMasswithCharge(argStructure.Root.GlycanType,argStructure.Charge) + argStructure.Y1.Mass - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, argStructure.Charge);
ZedGraph.TextObj txtGlycanMZ = new ZedGraph.TextObj("\n Precursor:" + argScan.ParentMZ.ToString("0.000")+"(" +argScan.ParentCharge.ToString()+")"+
"\nPeptide Sequence:" + argPeptide
, Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X2, 140);
txtGlycanMZ.FontSpec.Size = txtGlycanMZ.FontSpec.Size * 0.3f;
txtGlycanMZ.FontSpec.Border.IsVisible = false;
txtGlycanMZ.FontSpec.Fill.IsVisible = false;
Pane.GraphObjList.Add(txtGlycanMZ);
Image tmp = (Image)Pane.GetImage();
return tmp;
}
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;
}
}
}
}
public void DrawsequencingGraph(GlycanStructure argStructure)
{
zedSequence.GraphPane.GraphObjList.Clear();
zedSequence.GraphPane.Legend.IsVisible = false;
List <String> tmp = argStructure.Root.GetSequencingMapList();
if (tmp.Count == 0)
{
return;
}
float Xmin = Convert.ToSingle(tmp[0].Split('-')[0]);
float Xmax = Convert.ToSingle(tmp[tmp.Count - 1].Split('-')[2]);
if (Xmax == 0.0f)
{
Xmax = scan.MSPeaks[scan.MSPeaks.Count - 1].MonoMass;
}
double YMax = 0.0;
ZedGraph.PointPairList pplPeak = new ZedGraph.PointPairList();
for (int i = 0; i < GS.FilteredPeaks.Count; i++)
{
if (GS.FilteredPeaks[i].Mass >= Xmin + 10.0f && GS.FilteredPeaks[i].Mass <= Xmax + 10.0f)
{
if (GS.FilteredPeaks[i].Intensity > YMax)
{
YMax = GS.FilteredPeaks[i].Intensity;
}
}
}
for (int i = 0; i < GS.FilteredPeaks.Count; i++)
{
if (GS.FilteredPeaks[i].Mass >= Xmin + 10.0f && GS.FilteredPeaks[i].Mass <= Xmax + 10.0f)
{
pplPeak.Add(GS.FilteredPeaks[i].Mass, GS.FilteredPeaks[i].Intensity / YMax * 100.0f);
}
}
ZedGraph.GraphPane Pane = zedSequence.GraphPane;
Pane.XAxis.MajorTic.IsInside = false;
Pane.XAxis.MinorTic.IsInside = false;
Pane.CurveList.Clear();
Pane.AddStick("Peaks", pplPeak, Color.Red);
//Pane.XAxis.Scale.Min = Xmin - 10;
//Pane.XAxis.Scale.Max = Xmax + 10;
Pane.Title.Text = "No. " + txtScanNo.Text + "; Y1 m/z:" + argStructure.Y1.Mass.ToString("0.000");//+ " Structure:" + Convert.ToString(dgView.Rows[e.RowIndex].Cells[0].Value);
Pane.AxisChange();
double YLevel = YMax;
double outX, outY, outY2, diff;
Pane.ReverseTransform(new Point(100, 100), out outX, out outY);
Pane.ReverseTransform(new Point(100, 110), out outX, out outY2);
diff = outY - outY2;
GlycanTreeNode GT = argStructure.Root;//GS.GlycanTrees[e.RowIndex];
//Peak Interval
//List<string> SeqList = new List<string>();
//for (int i = 0; i < GT.GetSequencingMapList().Count; i++)
//{
// //Split the string
// string[] strArray = GT.GetSequencingMapList()[i].Split('-');
// ZedGraph.TextObj TxtObg = new ZedGraph.TextObj();
// TxtObg.Text = strArray[1];
// double Start = Convert.ToDouble(strArray[0]);
// double End = Convert.ToDouble(strArray[2]);
// System.Drawing.Drawing2D.DashStyle LineStyle = DashStyle.Solid;
// if (Start == 0)
// {
// if (strArray[1] == "HexNAc")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, GT.Charge);
// }
// else if (strArray[1] == "DeHex")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.DeHex, GT.Charge);
// }
// else if (strArray[1] == "Hex")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, GT.Charge);
// }
// else if (strArray[1] == "NeuAc")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuAc, GT.Charge);
// }
// else
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuGc, GT.Charge);
// }
// TxtObg.Text = TxtObg.Text + "?";
// LineStyle = DashStyle.Dash;
// }
// else
// {
// if (strArray[1] == "HexNAc")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, GT.Charge);
// }
// else if (strArray[1] == "DeHex")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.DeHex, GT.Charge);
// }
// else if (strArray[1] == "Hex")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, GT.Charge);
// }
// else if (strArray[1] == "NeuAc")
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuAc, GT.Charge);
// }
// else
// {
// Start = End - GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuGc, GT.Charge);
// }
// }
// if (End == 0)
// {
// if (strArray[1] == "HexNAc")
// {
// End = Start + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, GT.Charge);
// }
// else if (strArray[1] == "DeHex")
// {
// End = Start + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.DeHex, GT.Charge);
// }
// else if (strArray[1] == "Hex")
// {
// End = Start + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, GT.Charge);
// }
// else if (strArray[1] == "NeuAc")
// {
// End = Start + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuAc, GT.Charge);
// }
// else
// {
// End = Start + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.NeuGc, GT.Charge);
// }
// TxtObg.Text = TxtObg.Text + "?";
// LineStyle = DashStyle.Dash;
// }
// //Determine the Y level
// int Ylevel = 0;
// if (SeqList.Count == 0)
// {
// SeqList.Add(Start.ToString() + "," + End.ToString() + ",0");
// }
// else
// {
// for (int j = i - 1; j >= 0; j--)
// {
// double PreStart = Convert.ToDouble(SeqList[j].Split(',')[0]);
// double PreEnd = Convert.ToDouble(SeqList[j].Split(',')[1]);
// int Prelevel = Convert.ToInt32(SeqList[j].Split(',')[2]);
// if ((PreStart <= Start && Start <= PreEnd))
// {
// if (Math.Abs(PreEnd - Start) <= 10.0)
// {
// Ylevel = Prelevel;
// break;
// }
// else
// {
// Ylevel = Prelevel + 1;
// break;
// }
// }
// }
// SeqList.Add(Start.ToString() + "," + End.ToString() + "," + Ylevel.ToString());
// }
// TxtObg.FontSpec.Size = TxtObg.FontSpec.Size * 0.8f;
// YLevel = YMax + diff * Ylevel;
// ZedGraph.LineObj Lne = new ZedGraph.LineObj(Start, YLevel + diff, Start, YLevel - diff); //Left V Line
// Pane.GraphObjList.Add(Lne);
// Lne = new ZedGraph.LineObj(End, YLevel + diff, End, YLevel - diff); //Right V Line
// Pane.GraphObjList.Add(Lne);
// Lne = new ZedGraph.LineObj(Start, YLevel, End, YLevel); //Add Line
// Lne.Line.Style = LineStyle;
// Pane.GraphObjList.Add(Lne);
// //ZedGraph.ArrowObj arr= new ZedGraph.ArrowObj(Start, YLevel, End, YLevel);
// //arr.IsArrowHead = true;
// //arr.Line.Style = LineStyle;
// //Pane.GraphObjList.Add(arr);
// TxtObg.Location = new ZedGraph.Location(((Start + End) / 2), (double)YLevel, ZedGraph.CoordType.AxisXYScale);
// TxtObg.FontSpec.Border.IsVisible = false;
// TxtObg.Location.AlignH = ZedGraph.AlignH.Center;
// TxtObg.Location.AlignV = ZedGraph.AlignV.Center;
// Pane.GraphObjList.Insert(0, TxtObg);
//}
/////Annotation
GlycansDrawer GDraw;
double previousX2 = 0;
List <GlycanTreeNode> Fragements = argStructure.Root.FetchAllGlycanNode();
Fragements.Sort(delegate(GlycanTreeNode T1, GlycanTreeNode T2) { return(Comparer <float> .Default.Compare(T1.IDMass, T2.IDMass)); });
foreach (GlycanTreeNode FGS in Fragements)
{
string Exp = argStructure.GetIUPACfromParentToNodeID(FGS.NodeID);
//Queue<string> tmpQue = new Queue<string>();
//for (int i = 0; i < Exp.Length; i++)
//{
// int NodeID = 0;
// if (Exp[i].StartsWith("(") || Exp[i].StartsWith(")"))
// {
// NodeID = Convert.ToInt32(Exp[i].Split(',')[0].Substring(1));
// }
// else
// {
// NodeID = Convert.ToInt32(Exp[i].Split(',')[0]);
// }
// if (NodeID > FGS.NodeID)
// {
// if (Exp[i].StartsWith("(") || Exp[i].StartsWith(")"))
// {
// tmpQue.Enqueue(Exp[i].Substring(0, 1)); //
// }
// }
// else
// {
// tmpQue.Enqueue(Exp[i]);
// }
//}
//string IUPAC = "";
//do
//{
// string tmp =tmpQue.Dequeue();
// if(tmp == "(" && tmpQue.Peek() == ")" )
// {
// }
//}while(tmpQue.Count!=0)
string tmpIUPAC = argStructure.GetSequqncedIUPACwNodeID(FGS.NodeID);
GDraw = new GlycansDrawer(tmpIUPAC);
float glycopeptideMZ = FGS.IDMass;
if (double.IsNaN(glycopeptideMZ))
{
continue;
}
Image imgStructure = RotateImage(GDraw.GetImage(), 270);
double PositionX = glycopeptideMZ;
if (previousX2 >= PositionX)
{
PositionX = previousX2 + 20;
}
ZedGraph.ImageObj glycan = new ZedGraph.ImageObj(imgStructure, PositionX, 130, imgStructure.Width * 0.3f, imgStructure.Height * 0.3f);
glycan.IsScaled = true;
glycan.Location.AlignV = ZedGraph.AlignV.Bottom;
Pane.GraphObjList.Add(glycan);
ZedGraph.TextObj txtGlycanMz = new ZedGraph.TextObj(glycopeptideMZ.ToString("0.000"), 100, 140);
txtGlycanMz.Location.X = Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X1 + (Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X2 - Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X1) / 2;
txtGlycanMz.FontSpec.Size = txtGlycanMz.FontSpec.Size * 0.5f;
txtGlycanMz.FontSpec.Border.IsVisible = false;
Pane.GraphObjList.Add(txtGlycanMz);
if (Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X2 > Pane.GraphObjList[Pane.GraphObjList.Count - 2].Location.X2)
{
previousX2 = Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.X2;
}
else
{
previousX2 = Pane.GraphObjList[Pane.GraphObjList.Count - 2].Location.X2;
}
}
Pane.AxisChange();
Pane.YAxis.Scale.Max = 145;
Pane.XAxis.Scale.Min = Convert.ToInt32(argStructure.Y1.Mass - 100);
Pane.XAxis.Scale.Max = pplPeak[pplPeak.Count - 1].X + 100;
////////////
//Glycan Structure on the Right Top Header
////////////
GDraw = new GlycansDrawer(argStructure.IUPACString, false);
Image imgStruc = GDraw.GetImage();
ZedGraph.ImageObj fullStructure = new ZedGraph.ImageObj(imgStruc, 0.01f, 0.01f, imgStruc.Width, imgStruc.Height);
fullStructure.IsScaled = false;
Pane.GraphObjList.Add(fullStructure);
Pane.GraphObjList[Pane.GraphObjList.Count - 1].Location.CoordinateFrame = ZedGraph.CoordType.PaneFraction;
zedSequence.AxisChange();
zedSequence.Refresh();
}
