예제 #1
0
        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;
        }
예제 #2
0
        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();
        }