Exemple #1
0
        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;
        }
Exemple #2
0
        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;
        }
Exemple #3
0
        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");
                }
            }
        }
Exemple #4
0
        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;
        }
Exemple #5
0
        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);
        }
Exemple #6
0
 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);
 }