private void GeneratedYxPeak()
{
_YxMz = new float[5];
_YxMz[1] = _y1;
_YxMz[2] = _YxMz[1] + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, _charge);
_YxMz[3] = _YxMz[2] + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, _charge);
_YxMz[4] = _YxMz[3] + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, _charge);
}
private List <float> GetPeakCluster(float argPeptideMono, int argCharge)
{
List <float> peakmz = new List <float>();
//Y1
peakmz.Add((argPeptideMono + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, 1) + 1.0078f * argCharge) / argCharge);
//Y2
peakmz.Add((argPeptideMono + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, 1) * 2 + 1.0078f * argCharge) / argCharge);
//Y3
peakmz.Add((argPeptideMono + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, 1) * 2 + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, 1) + 1.0078f * argCharge) / argCharge);
//Y4
peakmz.Add((argPeptideMono + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.HexNAc, 1) * 2 + GlycanMass.GetGlycanMasswithCharge(Glycan.Type.Hex, 1) * 2 + 1.0078f * argCharge) / argCharge);
return(peakmz);
}
public List <float> GetFragmentMassList()
{
if (_fragment == null)
{
_fragment = FragementGlycanTree(_tree);
}
List <float> _fragmentMz = new List <float>();
foreach (GlycanTreeNode t in _fragment)
{
GlycanCompound comp = new GlycanCompound(t.NoOfHexNac, t.NoOfHex, t.NoOfDeHex, t.NoOfNeuAc);
if (!_fragmentMz.Contains(GlycanMass.GetGlycanMasswithCharge(comp, _tree.Charge)))
{
_fragmentMz.Add(GlycanMass.GetGlycanMasswithCharge(t.GlycanType, _tree.Charge));
}
}
return(_fragmentMz);
}
public static List <GlycanTreeNode> FragementGlycanTree(GlycanTreeNode argTree)
{
List <GlycanTreeNode> _fragment = new List <GlycanTreeNode>();
Queue ChildQueue = new Queue();
GlycanTreeNode CurrentTree = argTree;
do
{
GlycanTreeNode tmpTree = (GlycanTreeNode)argTree.Clone();
if (CurrentTree.GetChildren() != null)
{
if (CurrentTree.GetChildren().Count == 1)
{
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
_fragment.Add(tmpTree);
CurrentTree = CurrentTree.GetChildren()[0];
}
else if (CurrentTree.GetChildren().Count == 2)
{
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
ChildQueue.Enqueue(CurrentTree.GetChildren()[1]);
CurrentTree = CurrentTree.GetChildren()[0];
}
else if (CurrentTree.GetChildren().Count == 3)
{
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
ChildQueue.Enqueue(CurrentTree.GetChildren()[1]);
ChildQueue.Enqueue(CurrentTree.GetChildren()[2]);
CurrentTree = CurrentTree.GetChildren()[0];
}
else if (CurrentTree.GetChildren().Count == 4)
{
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[0]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
tmpTree = (GlycanTreeNode)argTree.Clone();
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[1]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[2]);
tmpTree.RemoveGlycan(CurrentTree.GetChildren()[3]);
_fragment.Add(tmpTree);
ChildQueue.Enqueue(CurrentTree.GetChildren()[1]);
ChildQueue.Enqueue(CurrentTree.GetChildren()[2]);
ChildQueue.Enqueue(CurrentTree.GetChildren()[3]);
CurrentTree = CurrentTree.GetChildren()[0];
}
}
else
{
if (ChildQueue.Count != 0)
{
CurrentTree = (GlycanTreeNode)ChildQueue.Dequeue();
}
else
{
break;
}
}
} while (true);
//Filter out duplicate tree
List <GlycanTreeNode> tmpGlycanTree = new List <GlycanTreeNode>();
foreach (GlycanTreeNode t in _fragment)
{
if (!tmpGlycanTree.Contains(t))
{
tmpGlycanTree.Add(t);
}
}
tmpGlycanTree.Sort(delegate(GlycanTreeNode T1, GlycanTreeNode T2)
{
return(GlycanMass.GetGlycanMasswithCharge(new GlycanCompound(T1.NoOfHexNac, T1.NoOfHex, T1.NoOfDeHex, T1.NoOfNeuAc), argTree.Charge).CompareTo(
GlycanMass.GetGlycanMasswithCharge(new GlycanCompound(T2.NoOfHexNac, T2.NoOfHex, T2.NoOfDeHex, T2.NoOfNeuAc), argTree.Charge)));
});
return(tmpGlycanTree);
}
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);
}
