private void button1_Click(object sender, EventArgs e)
{
//GlycansDraw GS = new GlycansDraw();
COL.GlycoLib.GlycansDrawer GS = new COL.GlycoLib.GlycansDrawer(comboBox1.Text.ToString(), false);
Image a = GS.GetImage();
a.Save(@"D:\!SVN\GlycanSequencing\Code\bin\x86\Debug\aaa.jpg", System.Drawing.Imaging.ImageFormat.Jpeg);
pictureBox1.Image = a;
}
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 btnConvert_Click(object sender, EventArgs e)
{
if (openFileDialog1.ShowDialog() == DialogResult.OK)
{
if (folderBrowserDialog1.ShowDialog() == DialogResult.OK)
{
if (!Directory.Exists(folderBrowserDialog1.SelectedPath))
{
Directory.CreateDirectory(folderBrowserDialog1.SelectedPath);
}
if (!Directory.Exists(folderBrowserDialog1.SelectedPath + "\\Pics"))
{
Directory.CreateDirectory(folderBrowserDialog1.SelectedPath + "\\Pics");
}
StringBuilder sb = new StringBuilder();
sb.AppendLine("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">");
sb.AppendLine("<html xmlns=\"http://www.w3.org/1999/xhtml\">");
sb.AppendLine("<head>");
sb.AppendLine("<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />");
sb.AppendLine("<title>GlycoSeq</title>\n</head>\n<body>");
GlycansDrawer Draw;
StreamReader SR = new StreamReader(openFileDialog1.FileName);
sb.AppendLine("<table border=\"1\">");
sb.AppendLine("<tr><td>ID</td><td>Orignal Glycan</td><td>Add Glycan</td><td>Result</td></tr>");
int idx = 1;
do
{
string[] tmp = SR.ReadLine().Split(',');
sb.AppendLine("<tr>");
sb.AppendLine("<td>");
sb.AppendLine(idx.ToString());
sb.AppendLine("</td>");
Draw = new GlycansDrawer(tmp[0], false);
Image tmpImg = Draw.GetImage();
tmpImg.Save(folderBrowserDialog1.SelectedPath + "\\Pics\\PreStructure_" + idx.ToString("000") + ".png");
tmpImg.Dispose();
tmpImg = null;
sb.AppendLine("<td><img src=\".\\Pics\\PreStructure_" + idx.ToString("000") + ".png\"/><br>" + tmp[0]+ "</td>");
Draw = new GlycansDrawer(tmp[1], false);
tmpImg = Draw.GetImage();
tmpImg.Save(folderBrowserDialog1.SelectedPath + "\\Pics\\AddStructure_" + idx.ToString("000") + ".png");
tmpImg.Dispose();
tmpImg = null;
sb.AppendLine("<td><img src=\".\\Pics\\AddStructure_" + idx.ToString("000") + ".png\"/><br>"+tmp[1] + "</td>");
sb.AppendLine("<td>");
for (int i = 2; i < tmp.Length; i++)
{
Draw = new GlycansDrawer(tmp[i], false);
tmpImg = Draw.GetImage();
tmpImg.Save(folderBrowserDialog1.SelectedPath + "\\Pics\\AddedStructure_" + idx.ToString("000")+"-"+(i-1).ToString("000") + ".png");
tmpImg.Dispose();
tmpImg = null;
sb.AppendLine("<img src=\".\\Pics\\AddedStructure_" + idx.ToString("000")+"-"+(i-1).ToString("000")+ ".png\"/>" );
}
sb.AppendLine("</td>");
sb.AppendLine("</tr>");
idx++;
} while (!SR.EndOfStream);
sb.AppendLine("</table><br>-----------------------------------------------------------<br>");
sb.AppendLine("</body>\n</html>");
StreamWriter Sw = new StreamWriter(folderBrowserDialog1.SelectedPath + "\\Result.htm");
Sw.Write(sb.ToString());
Sw.Flush();
Sw.Close();
MessageBox.Show("Done");
}
}
}
private void button1_Click(object sender, EventArgs e)
{
//GlycansDraw GS = new GlycansDraw();
COL.GlycoLib.GlycansDrawer GS = new COL.GlycoLib.GlycansDrawer(comboBox1.Text.ToString(), false);
Image a = GS.GetImage();
a.Save(@"D:\!SVN\GlycanSequencing\Code\bin\x86\Debug\aaa.jpg", System.Drawing.Imaging.ImageFormat.Jpeg);
pictureBox1.Image = a;
}
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 btnGlycanDraw_Click(object sender, EventArgs e)
{
GlycansDrawer draw = new GlycansDrawer("HexNAc-(Hex-)HexNAc", false);
picGlycan.Image = draw.GetImage();
GlycansDrawer draw = new GlycansDrawer();
picGlycan.Image = draw.GlycanCartoon(Glycan.Type.DeHex);
}