private void AddMarker(ZedGraphControl gc, DateTime date, Color color, GraphMarkerType markerType)
{
var ymax = gc.GraphPane.YAxis.Scale.Max;
LineObj line = new LineObj(color, (double)new XDate(date), (double)0, (double)new XDate(date), ymax);
line.Tag = markerType;
line.ZOrder = ZOrder.E_BehindCurves;
gc.GraphPane.GraphObjList.Add(line);
}
public static void AddLabel(this GraphPane pane, double x, int n)
{
var yScale = pane.YAxis.Scale;
double yMin = yScale.Min;
double yMax = yScale.Max;
var line = new LineObj(x, yMin, x, yMax) { IsClippedToChartRect = true };
//line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
line.Line.Color = Color.DarkGreen;
pane.GraphObjList.Add(line);
if (n > 0) {
var text = new TextObj(n.ToString(), x, yMax - 0.02 * (yMax - yMin)) { IsClippedToChartRect = true };
text.FontSpec.Border.IsVisible = true;
pane.GraphObjList.Add(text);
}
}
/// <summary>
/// Render legend
/// </summary>
/// <param name="gp"></param>
/// <param name="dataResults"></param>
protected override void RenderLegend(GraphPane gp, IEnumerable<RequestDataResults> dataResults)
{
int fontSize = 6;
int offset = 0;
int unit = (int) gp.YAxis.Scale.Max/10;
// Average time
var avgLegendBox = new BoxObj(-4, unit, 1, unit)
{
Fill = new Fill(Color.FromArgb(75, Color.YellowGreen))
};
gp.GraphObjList.Add(avgLegendBox);
var avgLegendText = new TextObj("125", -3.5, (double)unit / 2).Style(Color.Black, fontSize);
gp.GraphObjList.Add(avgLegendText);
var avgLegendLabel = new TextObj("Average time", -4, (double)unit / 2).Style(Color.Black, fontSize, AlignH.Right);
gp.GraphObjList.Add(avgLegendLabel);
offset += unit*2;
// Min/Max
var minMaxLine = new LineObj(Color.Black, -3.5, offset, -3.5, offset + 2*unit);
gp.GraphObjList.Add(minMaxLine);
var minMaxLabel = new TextObj("Min/Max", -4, offset + unit).Style(Color.Black, fontSize, AlignH.Right);
gp.GraphObjList.Add(minMaxLabel);
offset += 3*unit;
// Min/Max excluding extreme deciles
var minMaxExclLine = new LineObj(Color.Black, -3.5, offset, -3.5, offset + 2*unit);
minMaxExclLine.Line.Width = 3;
minMaxExclLine.Line.Color = Color.DarkGray;
gp.GraphObjList.Add(minMaxExclLine);
var avgExclLine = new LineObj(Color.Black, -3.8, offset + unit, -3.2, offset + unit);
avgExclLine.Line.Width = 3;
avgExclLine.Line.Color = Color.DarkGray;
gp.GraphObjList.Add(avgExclLine);
var avgExclLabel1 = new TextObj("Min/Max/Avg", -4, offset + 1.2 *unit).Style(Color.Black, fontSize, AlignH.Right);
gp.GraphObjList.Add(avgExclLabel1);
var avgExclLabel2 = new TextObj("excluding extremes", -4, offset + 0.8 * unit).Style(Color.Black, fontSize, AlignH.Right);
gp.GraphObjList.Add(avgExclLabel2);
}
public CurveItemTypePair(CurveItem curve, CurveType type, String name, int nC)
{
Curve = curve;
Type = type;
Scale = GlobalVars.DEFAULTSCALE(type);
CurrCoordinates = new CurveItemTypePair.CurrentCoordinates();
DrawCursorDot = true;
DrawCursorLines = true;
HorizontalCursorLine = new LineObj();
VerticalCursorLine = new LineObj();
SymbolsOn = true;
Name = name;
ComputeInterestingValues();
CurveObj = new CurveObject((PointPairList)curve.Points, nC);
CurveObj.XMAX = this.XMax;
CurveObj.YMAX = this.YMax;
NCurves = nC;
}
private void CreateThreshold()
{
GraphPane pane = this.graph.PaneList[0];
double num = 0.0;
LineObj item = new LineObj(Color.Green, 0.0, num, 1.0, num);
item.Location.CoordinateFrame = CoordType.XChartFractionYScale;
item.IsVisible = true;
pane.GraphObjList.Add(item);
pane.AxisChange();
this.graph.Invalidate();
}
private void CreateGraph_RadarPlot( ZedGraphControl z1 )
{
GraphPane myPane = z1.GraphPane;
RadarPointList rpl = new RadarPointList();
Random rand = new Random();
for ( int i = 0; i < 10; i++ )
{
double r = rand.NextDouble() * 10.0 + 10.0;
PointPair pt = new PointPair( PointPair.Missing, r, "r = " + r.ToString( "f1" ) );
rpl.Add( pt );
}
LineItem curve = myPane.AddCurve( "test", rpl, Color.Blue, SymbolType.Default );
for ( int i = 0; i < 10; i++ )
{
LineObj line = new LineObj( 0, 0, (float) rpl[i].X, (float) rpl[i].Y );
line.Line.Color = Color.LightBlue;
line.ZOrder = ZOrder.E_BehindCurves;
myPane.GraphObjList.Add( line );
}
myPane.XAxis.MajorTic.IsAllTics = true;
myPane.XAxis.MinorTic.IsAllTics = true;
myPane.XAxis.Title.IsTitleAtCross = false;
myPane.XAxis.Cross = 0;
myPane.XAxis.Scale.IsSkipFirstLabel = true;
myPane.XAxis.Scale.IsSkipLastLabel = true;
myPane.XAxis.Scale.IsSkipCrossLabel = true;
myPane.YAxis.MajorTic.IsAllTics = true;
myPane.YAxis.MinorTic.IsAllTics = true;
myPane.YAxis.Title.IsTitleAtCross = false;
myPane.YAxis.Cross = 0;
myPane.YAxis.Scale.IsSkipFirstLabel = true;
myPane.YAxis.Scale.IsSkipLastLabel = true;
myPane.YAxis.Scale.IsSkipCrossLabel = true;
}
// Build the Chart
private void CreateGraph_ImageObj( ZedGraphControl zg1 )
{
// get a reference to the GraphPane
GraphPane myPane = zg1.GraphPane;
// Set the Titles
myPane.Title.Text = "My Test Bar Graph";
myPane.XAxis.Title.Text = "Label";
myPane.YAxis.Title.Text = "My Y Axis";
myPane.X2Axis.Title.Text = "The Top X Axis";
myPane.Y2Axis.Title.Text = "Y2 Axis";
myPane.X2Axis.IsVisible = true;
myPane.X2Axis.Scale.IsReverse = true;
myPane.Y2Axis.IsVisible = true;
// Make up some random data points
string[] labels = { "Panther", "Lion", "Cheetah",
"Cougar", "Tiger", "Leopard" };
double[] x = { 1, 2, 3, 4, 5, 6 };
double[] y = { 100, 115, 75, 22, 98, 40 };
double[] y2 = { 90, 100, 95, 35, 80, 35 };
double[] y3 = { 80, 110, 65, 15, 54, 67 };
double[] y4 = { 120, 125, 100, 40, 105, 75 };
// Generate a red bar with "Curve 1" in the legend
//BarItem myBar = myPane.AddBar( "Curve 1 label is long\nsecond line", null, y, Color.Red );
BarItem myBar = myPane.AddBar( "Curve 1", null, y, Color.Red );
myBar.Bar.Fill = new Fill( Color.Red, Color.White, Color.Red );
// Generate a blue bar with "Curve 2" in the legend
myBar = myPane.AddBar( "Curve 2", null, y2, Color.Blue );
myBar.Bar.Fill = new Fill( Color.Blue, Color.White, Color.Blue );
// Generate a green bar with "Curve 3" in the legend
//myBar = myPane.AddBar( "Curve 3\ntwo lines", null, y3, Color.Green );
myBar = myPane.AddBar( "Curve 3", null, y3, Color.Green );
myBar.Bar.Fill = new Fill( Color.Green, Color.White, Color.Green );
// Generate a black line with "Curve 4" in the legend
LineItem myCurve = myPane.AddCurve( "Curve 4",
x, y4, Color.Black, SymbolType.Circle );
myCurve.IsX2Axis = true;
myCurve.Line.Fill = new Fill( Color.White,
Color.LightSkyBlue, -45F );
// Fix up the curve attributes a little
myCurve.Symbol.Size = 8.0F;
myCurve.Symbol.Fill = new Fill( Color.White );
myCurve.Line.Width = 2.0F;
// Draw the X tics between the labels instead of
// at the labels
myPane.XAxis.MajorTic.IsBetweenLabels = true;
// Set the XAxis labels
myPane.XAxis.Scale.TextLabels = labels;
// Set the XAxis to Text type
myPane.XAxis.Type = AxisType.Text;
// Fill the Axis and Pane backgrounds
myPane.Chart.Fill = new Fill( Color.White,
Color.FromArgb( 255, 255, 166 ), 90F );
myPane.Fill = new Fill( Color.FromArgb( 250, 250, 255 ) );
myPane.XAxis.MajorGrid.IsVisible = true;
myPane.YAxis.MajorGrid.IsVisible = true;
LineObj line = new LineObj( Color.Black, 2.3, 0, 2.3, 1 );
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.Line.Width = 2.0f;
myPane.GraphObjList.Add( line );
//Image image = Image.FromFile( @"c:\temp\vtx1330.jpg" );
Image image = Bitmap.FromFile( @"c:\temp\vtx1300crop.jpg" );
ImageObj imageObj = new ImageObj( image, new RectangleF( 3, 120, 2, 100 ) );
imageObj.IsScaled = false;
// imageObj.IsVisible = true;
imageObj.ZOrder = ZOrder.E_BehindCurves;
// imageObj.Location.CoordinateFrame = CoordType.ChartFraction;
myPane.GraphObjList.Add( imageObj );
// myPane.Chart.Fill = new Fill( image, WrapMode.Tile );
// myPane.Title.Text = null;
// GraphPane newOne = myPane.Clone();
// Tell ZedGraph to refigure the
// axes since the data have changed
zg1.AxisChange();
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="LineObj"/> object from which to copy</param>
public LineObj(LineObj rhs)
: base(rhs)
{
_color = rhs.Color;
_penWidth = rhs.PenWidth;
_style = rhs._style;
}
private void GoToSample(int SampleID, bool movemap, bool movegraph, bool movegrid)
{
bool zoomgraph = false;
m_currSampleID = SampleID;
markeroverlay.Markers.Clear();
PointLatLng pt1;
if (GetGPSFromRow(SampleID, out pt1))
{
MissionPlanner.Utilities.PointLatLngAlt pt3 = new MissionPlanner.Utilities.PointLatLngAlt(pt1);
GMapMarker pos3 = new GMarkerGoogle(pt3, GMarkerGoogleType.pink_dot);
markeroverlay.Markers.Add(pos3);
}
if (movemap)
{
myGMAP1.Position = pt1;
}
//move the graph "cursor"
if (m_cursorLine != null)
{
zg1.GraphPane.GraphObjList.Remove(m_cursorLine);
}
m_cursorLine = new LineObj(Color.Black, SampleID, 0, SampleID, 1);
m_cursorLine.Location.CoordinateFrame = CoordType.XScaleYChartFraction; // This do the trick !
m_cursorLine.IsClippedToChartRect = true;
m_cursorLine.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
m_cursorLine.Line.Width = 2f;
m_cursorLine.Line.Color = Color.LightGray;
m_cursorLine.ZOrder = ZOrder.E_BehindCurves;
zg1.GraphPane.GraphObjList.Add(m_cursorLine);
if (movegraph)
{
double delta = zg1.GraphPane.XAxis.Scale.Max - zg1.GraphPane.XAxis.Scale.Min;
if (zoomgraph)
{
delta = 2 * 60.0 / 20;
delta = Math.Max(100, delta);
}
zg1.GraphPane.XAxis.Scale.Min = SampleID - delta / 2;
zg1.GraphPane.XAxis.Scale.Max = SampleID + delta / 2;
zg1.AxisChange();
}
zg1.Invalidate();
if (movegrid)
{
try
{
scrollGrid(dataGridView1, SampleID);
dataGridView1.CurrentCell = dataGridView1.Rows[SampleID].Cells[1];
dataGridView1.ClearSelection();
dataGridView1.Rows[(int)SampleID].Selected = true;
dataGridView1.Rows[(int)SampleID].Cells[1].Selected = true;
}
catch { }
}
}
///<summary>Adds user requested ion series to the fragmentation summary.</summary>
private void addFragmentationSummary (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
{
int ionSeriesChargeState = min;
string sequence = peptide.sequence;
ModificationMap modifications = peptide.modifications();
// Select the color for the ion series.
Color topSeriesColor;
Color bottomSeriesColor;
switch (topSeries)
{
default: topSeriesColor = Color.Gray; break;
case "a": topSeriesColor = Color.YellowGreen; break;
case "b": topSeriesColor = Color.BlueViolet; break;
case "c": topSeriesColor = Color.Orange; break;
}
switch (bottomSeries)
{
default: bottomSeriesColor = Color.Gray; break;
case "x": bottomSeriesColor = Color.Green; break;
case "y": bottomSeriesColor = Color.Blue; break;
case "z": bottomSeriesColor = Color.OrangeRed; break;
case "z*": bottomSeriesColor = Color.Crimson; break;
}
// Ion series offsets. These offsets control where on the chart a particular ion series get displayed
double seriesTopLeftOffset = 0.2;
// Set the constants for starting the label paint
double topSeriesLeftPoint = 0.025;
double residueWidth = 0.5 / ((double) sequence.Length);
double topSeriesRightPoint = topSeriesLeftPoint + 0.5 - residueWidth;
double tickStart = residueWidth / 2.0;
// Process all the series except c and x
for (int i = 1; i <= sequence.Length; ++i)
{
double topSeriesFragmentMZ = 0.0;
double bottomSeriesFragmentMZ = 0.0;
switch (topSeries)
{
case "a": topSeriesFragmentMZ = fragmentation.a(i, ionSeriesChargeState); break;
case "b": topSeriesFragmentMZ = fragmentation.b(i, ionSeriesChargeState); break;
case "c": if (i < sequence.Length) topSeriesFragmentMZ = fragmentation.c(i, ionSeriesChargeState); break;
default: continue;
}
switch (bottomSeries)
{
case "x": if (i < sequence.Length) bottomSeriesFragmentMZ = fragmentation.x(i, ionSeriesChargeState); break;
case "y": bottomSeriesFragmentMZ = fragmentation.y(i, ionSeriesChargeState); break;
case "z": bottomSeriesFragmentMZ = fragmentation.z(i, ionSeriesChargeState); break;
case "z*": bottomSeriesFragmentMZ = fragmentation.zRadical(i, ionSeriesChargeState); break;
default: continue;
}
// Check if the top and bottom fragments have evidence
bool topSeriesHasMatch = false;
bool bottomSeriesHasMatch = false;
if (points != null)
{
topSeriesHasMatch = topSeriesFragmentMZ > 0 && findPointWithTolerance(points, topSeriesFragmentMZ, tolerance) > -1;
bottomSeriesHasMatch = bottomSeriesFragmentMZ > 0 && findPointWithTolerance(points, bottomSeriesFragmentMZ, tolerance) > -1;
}
// Build the label for the amino acid
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint, seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = false;
list.Add(text);
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.08), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesRightPoint + tickStart, seriesTopLeftOffset, topSeriesRightPoint + tickStart, seriesTopLeftOffset + 0.05);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesRightPoint + tickStart, seriesTopLeftOffset + 0.05, topSeriesRightPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.08);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
topSeriesRightPoint -= residueWidth;
}
}
public void MakeWindRose(List<int> nValues)
{
_nValues = nValues;
GraphPane pane = mainChart.GraphPane;
pane.Title.Text = "Роза ветров";
pane.IsFontsScaled = false;
pane.CurveList.Clear();
pane.XAxis.IsVisible = false;
pane.YAxis.IsVisible = false;
pane.XAxis.MajorGrid.IsVisible = false;
pane.YAxis.MajorGrid.IsVisible = false;
pane.YAxis.MajorGrid.IsZeroLine = false;
// Создаем список точек
var points = new RadarPointList {Clockwise = true};
var text = new TextObj[8];
var axText = new TextObj[8];
for (int i = 0; i < 8; i++)
points.Add(_nValues[i], 1);
int nMax = _nValues.Concat(new[] {0}).Max();
nMax += 1;
for (int i = 0; i < points.Count - 1; i++)
{
text[i] = new TextObj(_nValues[i].ToString(), points[i].X, points[i].Y);
text[i].FontSpec.Border.IsVisible = false;
Color color;
if (_nValues[i] < nMax / 3)
color = Color.GreenYellow;
else
if (_nValues[i] < (nMax / 3) * 2)
color = Color.Yellow;
else
color = Color.OrangeRed;
text[i].FontSpec.Fill = new Fill(color);
text[i].FontSpec.IsBold = true;
pane.GraphObjList.Add(text[i]);
}
// Добавляем кривую по этим четырем точкам
LineItem myCurve = pane.AddCurve("", points, Color.Blue, SymbolType.Triangle);
myCurve.Line.Width = 2.5F;
// Для наглядности нарисуем расстояния от начала координат до каждой из точек
var arrow = new LineObj[8];
arrow[0] = new LineObj(0, 0, 0, nMax);
arrow[1] = new LineObj(0, 0, -nMax, 0);
arrow[2] = new LineObj(0, 0, 0, -nMax);
arrow[3] = new LineObj(0, 0, nMax, 0);
arrow[4] = new LineObj(0, 0, nMax, nMax);
arrow[5] = new LineObj(0, 0, -nMax, nMax);
arrow[6] = new LineObj(0, 0, nMax, -nMax);
arrow[7] = new LineObj(0, 0, -nMax, -nMax);
axText[0] = new TextObj("с", 0, nMax);
axText[1] = new TextObj("з", -nMax, 0);
axText[2] = new TextObj("ю", 0, -nMax);
axText[3] = new TextObj("в", nMax, 0);
axText[4] = new TextObj("с/в", nMax, nMax);
axText[5] = new TextObj("с/з", -nMax, nMax);
axText[6] = new TextObj("ю/в", nMax, -nMax);
axText[7] = new TextObj("ю/з", -nMax, -nMax);
for (int i = 0; i < 8; i++)
{
pane.GraphObjList.Add(axText[i]);
pane.GraphObjList.Add(arrow[i]);
}
// Отметим начало координат черным квадратиком
var box = new BoxObj(-0.05, 0.05, 0.1, 0.1, Color.Black, Color.Black);
pane.GraphObjList.Add(box);
// Устанавливаем интересующий нас интервал по оси X
pane.XAxis.Scale.Min = -nMax;
pane.XAxis.Scale.Max = nMax;
// Устанавливаем интересующий нас интервал по оси Y
pane.YAxis.Scale.Min = -nMax;
pane.YAxis.Scale.Max = nMax;
mainChart.AxisChange();
mainChart.Invalidate();
}
private void UpdateGraph(List<Pair> PairList)
{
if (PairList.Count < hScrollBar.Value) return;
list.Clear();
double StartScan = 0;
double StartMask = 0;
double StartRetrigger = 0;
double StartAWin = 0.0;
double MaxReading = 0;
zedGraphControl.GraphPane.GraphObjList.Clear();
for (int i = hScrollBar.Value; i < hScrollBar.Value + WindowsSize; i++)
{
list.Add(PairList[i].X, PairList[i].Y);
if (StartAWin == 0 && PairList[i].AWindow > 0)
{
StartAWin = PairList[i].X;
}
if (StartAWin > 0 && (PairList[i].AWindow == 0 || i == hScrollBar.Value + WindowsSize - 1))
{
ZedGraph.BoxObj box = new BoxObj(StartAWin, 50, PairList[i].X - StartAWin, 50.0, Color.Black, Color.FromArgb(64, Color.Black));
box.ZOrder = ZOrder.D_BehindAxis;
box.IsClippedToChartRect = true;
zedGraphControl.GraphPane.GraphObjList.Add(box);
StartAWin = 0;
}
if (PairList[i].AWindow == 2)
{
ZedGraph.LineObj line = new LineObj(Color.Green, PairList[i].X, 1023, PairList[i].X, 0);
line.ZOrder = ZOrder.D_BehindAxis;
line.IsClippedToChartRect = true;
zedGraphControl.GraphPane.GraphObjList.Add(line);
}
if (StartScan == 0 && PairList[i].Status == 1)
{
StartScan = PairList[i].X;
}
if (StartScan > 0 && PairList[i].Y > MaxReading) MaxReading = PairList[i].Y;
if (StartScan > 0 && (PairList[i].Status != 1 || i == hScrollBar.Value + WindowsSize - 1))
{
ZedGraph.BoxObj box = new BoxObj(StartScan, /*PairList[i - 1].*/MaxReading, PairList[i].X - StartScan, MaxReading, Color.Black, Color.FromArgb(64, Color.Yellow));
box.ZOrder = ZOrder.D_BehindAxis;
box.IsClippedToChartRect = true;
zedGraphControl.GraphPane.GraphObjList.Add(box);
StartScan = 0;
MaxReading = 0;
}
if (StartMask == 0 && PairList[i].Status == 2)
{
StartMask = PairList[i].X;
}
if (StartMask > 0 && (PairList[i].Status != 2 || i == hScrollBar.Value + WindowsSize - 1))
{
ZedGraph.BoxObj box = new BoxObj(StartMask, 100, PairList[i].X - StartMask, 100.0, Color.Black, Color.FromArgb(64, Color.Red));
box.ZOrder = ZOrder.D_BehindAxis;
box.IsClippedToChartRect = true;
zedGraphControl.GraphPane.GraphObjList.Add(box);
StartMask = 0;
}
if (StartRetrigger == 0 && PairList[i].Status == 3)
{
StartRetrigger = PairList[i].X;
}
if (StartRetrigger > 0 && (PairList[i].Status != 3 || i == hScrollBar.Value + WindowsSize - 1))
{
ZedGraph.BoxObj box = new BoxObj(StartRetrigger, 100, PairList[i].X - StartRetrigger, 100.0, Color.Black, Color.FromArgb(64, Color.Blue));
box.ZOrder = ZOrder.D_BehindAxis;
box.IsClippedToChartRect = true;
zedGraphControl.GraphPane.GraphObjList.Add(box);
StartRetrigger = 0;
}
}
if ((hScrollBar.Value + WindowsSize) < PairList.Count)
{
zedGraphControl.GraphPane.XAxis.Scale.Max = PairList[hScrollBar.Value + WindowsSize].X;
zedGraphControl.GraphPane.XAxis.Scale.Min = PairList[hScrollBar.Value].X;
zedGraphControl.Invoke(new EventHandler(delegate { zedGraphControl.AxisChange(); zedGraphControl.Refresh(); }));
}
}
private ScaledRetentionTime FindAnnotatedSpectrumRetentionTime(LineObj line)
{
foreach (var graphItem in GraphItems)
{
var spectrumRT = graphItem.FindSpectrumRetentionTime(line);
if (!spectrumRT.IsZero)
{
return spectrumRT;
}
}
return ScaledRetentionTime.ZERO;
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// ReSharper disable UseObjectOrCollectionInitializer
foreach (var rmi in SpectrumInfo.PeaksMatched)
{
if (!IsVisibleIon(rmi))
continue;
IonType type = IsVisibleIon(rmi.IonType, rmi.Ordinal, rmi.Charge) ?
rmi.IonType : rmi.IonType2;
Color color;
switch (type)
{
default: color = COLOR_NONE; break;
case IonType.a: color = COLOR_A; break;
case IonType.x: color = COLOR_X; break;
case IonType.b: color = COLOR_B; break;
case IonType.y: color = COLOR_Y; break;
case IonType.c: color = COLOR_C; break;
case IonType.z: color = COLOR_Z; break;
// FUTURE: Add custom ions when LibraryRankedSpectrumInfo can support them
case IonType.precursor: color = COLOR_PRECURSOR; break;
}
if (IsMatch(rmi.PredictedMz))
{
color = COLOR_SELECTED;
}
double mz = rmi.ObservedMz;
var stick = new LineObj(color, mz, rmi.Intensity, mz, 0);
stick.IsClippedToChartRect = true;
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = LineWidth + 1;
annotations.Add(stick);
}
//ReSharper restore UseObjectOrCollectionInitializer
}
private void addFragment( GraphObjList list, pwiz.MSGraph.MSPointList points, string series, int length, int charge, double mz )
{
string label = String.Format("{0}{1}{2}", series, length, (charge > 1 ? "+" + charge.ToString() : ""));
Color color;
double offset;
switch( series )
{
default: color = Color.Gray; offset = 0.1; break;
case "a": color = Color.YellowGreen; offset = 0.1; break;
case "x": color = Color.Green; offset = 0.12; break;
case "b": color = Color.BlueViolet; offset = 0.14; break;
case "y": color = Color.Blue; offset = 0.16; break;
case "c": color = Color.Orange; offset = 0.18; break;
case "z": color = Color.OrangeRed; offset = 0.2; break;
case "z*": color = Color.Crimson; offset = 0.4; break;
}
numFragmentsPredicted[series+(charge > 1 ? "+" + charge.ToString() : "")].Add(mz);
int index = -1;
if( points != null )
index = points.LowerBound( mz - 0.5 );
if( index == -1 || points.ScaledList[index].X > ( mz + 0.5 ) )
// no matching point: present a "missed" fragment annotation
{
if( !showMisses )
return;
color = Color.FromArgb( 115, color ); // transparent to emphasize miss
LineObj stick = new LineObj( color, mz, offset, mz, 1 );
stick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
stick.Line.Width = 2;
stick.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
list.Add( stick );
if( showLabels )
{
TextObj text = new TextObj( label, mz, offset, CoordType.XScaleYChartFraction,
AlignH.Center, AlignV.Bottom );
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec( "Arial", 12, color, false, false, false );
text.FontSpec.Border.IsVisible = false;
//text.IsClippedToChartRect = true;
list.Add( text );
}
} else
// matching point found: present the point as the fragment
{
numFragmentsMatched[series + (charge > 1 ? "+" + charge.ToString() : "")].Add(mz);
LineObj stick = new LineObj( color, mz, points.ScaledList[index].Y, mz, 0 );
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = 2;
list.Add( stick );
if( showLabels )
{
// use an existing text point annotation if possible
TextObj text = null;
foreach( GraphObj obj in list )
{
if( obj is TextObj &&
( obj.Location.CoordinateFrame == CoordType.AxisXYScale ||
obj.Location.CoordinateFrame == CoordType.XScaleYChartFraction ) &&
Math.Abs( obj.Location.X - mz ) < 0.5 )
{
text = obj as TextObj;
text.Text = String.Format( "{0}\n{1}", label, text.Text );
break;
}
}
if( text == null )
{
text = new TextObj( label, mz, points.ScaledList[index].Y, CoordType.AxisXYScale,
AlignH.Center, AlignV.Bottom );
list.Add( text );
}
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec( "Arial", 12, color, false, false, false );
text.FontSpec.Border.IsVisible = false;
//text.IsClippedToChartRect = true;
}
}
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="LineObj"/> object from which to copy</param>
public LineObj(LineObj rhs) : base(rhs)
{
_color = rhs.Color;
_penWidth = rhs.PenWidth;
_style = rhs._style;
}
private void addFragment (GraphObjList list, pwiz.MSGraph.MSPointList points, string series, int length, int charge, double mz)
{
string label = String.Format("{0}{1}{2}",
series,
(length > 0 ? length.ToString() : ""),
(charge > 1 ? "+" + charge.ToString() : ""));
Color color;
double offset;
switch (series)
{
default:
color = series.StartsWith("immonium") ? Color.Black : Color.Gray;
offset = 0.1;
break;
case "a": color = Color.YellowGreen; offset = 0.1; break;
case "x": color = Color.Green; offset = 0.12; break;
case "b": color = Color.BlueViolet; offset = 0.14; break;
case "y": color = Color.Blue; offset = 0.16; break;
case "c": color = Color.Orange; offset = 0.18; break;
case "z": color = Color.OrangeRed; offset = 0.2; break;
case "z*": color = Color.Crimson; offset = 0.4; break;
}
int index = -1;
if (points != null)
index = findPointWithTolerance(points, mz, tolerance);
if (index == -1)
// no matching point: present a "missed" fragment annotation
{
if (!showMisses)
return;
color = Color.FromArgb(115, color); // transparent to emphasize miss
if (list.Count(o => o.Location.X == mz) == 0)
{
LineObj stick = new LineObj(color, mz, offset, mz, 1);
stick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
stick.Line.Width = 2;
stick.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
stick.IsClippedToChartRect = true;
list.Add(stick);
if (showLabels)
{
TextObj text = new TextObj(label, mz, offset, CoordType.XScaleYChartFraction,
AlignH.Center, AlignV.Bottom);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
//text.IsClippedToChartRect = true;
list.Add(text);
}
}
}
else
// matching point found: present the point as the fragment
{
if (list.Count(o => o.Location.X == mz) == 0)
{
LineObj stick = new LineObj(color, mz, points.FullList[index].Y, mz, 0);
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = 2;
stick.IsClippedToChartRect = true;
list.Add(stick);
}
if (showLabels)
{
// use an existing text point annotation if possible
TextObj text = null;
double minError = Double.MaxValue;
foreach (GraphObj obj in list)
{
if (obj is TextObj &&
(obj.Location.CoordinateFrame == CoordType.AxisXYScale ||
obj.Location.CoordinateFrame == CoordType.XScaleYChartFraction))
{
double curError = Math.Abs(obj.Location.X - points.FullList[index].X);
if (curError < 1e-4 && curError < minError)
{
minError = curError;
text = obj as TextObj;
if (!text.Text.Contains(label))
text.Text = String.Format("{0}\n{1}", label, text.Text);
}
}
}
if (text == null)
{
text = new TextObj(label, mz, points.FullList[index].Y, CoordType.AxisXYScale,
AlignH.Center, AlignV.Bottom);
list.Add(text);
}
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
//text.IsClippedToChartRect = true;
}
}
}
/// <summary>
/// Update vertical line the marks current import time for progressively loaded files.
/// </summary>
private void UpdateProgressLine(double time)
{
// Remove old progressive loading indicators.
if (_unfinishedBox != null)
{
_graphPane.GraphObjList.Remove(_unfinishedBox);
_graphPane.GraphObjList.Remove(_unfinishedLine);
_unfinishedBox = null;
}
// If we're still loading, create a white rectangle which blocks the fill background, indicating data yet to be loaded.
if (time < _status.Transitions.MaxRetentionTime)
{
_graphPane.Chart.Fill = new Fill(_backgroundGradientColor1, _backgroundGradientColor2, 45.0f);
_unfinishedBox = new BoxObj(
time,
_graphPane.YAxis.Scale.Max,
_graphPane.XAxis.Scale.Max - time,
_graphPane.YAxis.Scale.Max - _graphPane.YAxis.Scale.Min,
Color.White, Color.White)
{
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.F_BehindGrid
};
_graphPane.GraphObjList.Add(_unfinishedBox);
// Place a vertical line after the last loaded data.
_unfinishedLine = new LineObj(
_unfinishedLineColor,
time,
_graphPane.YAxis.Scale.Max,
time,
_graphPane.YAxis.Scale.Min)
{
Location = { CoordinateFrame = CoordType.AxisXYScale },
Line = { Width = PROGRESS_LINE_WIDTH },
ZOrder = ZOrder.D_BehindAxis
};
_graphPane.GraphObjList.Add(_unfinishedLine);
}
}
///<summary>Adds user requested ion series on top of the chart.</summary>
private void addIonSeries (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
{
int ionSeriesChargeState = min;
string sequence = peptide.sequence;
ModificationMap modifications = peptide.modifications();
// Select the color for the ion series.
Color topSeriesColor;
Color bottomSeriesColor;
switch (topSeries)
{
default: topSeriesColor = Color.Gray; break;
case "a": topSeriesColor = Color.YellowGreen; break;
case "b": topSeriesColor = Color.BlueViolet; break;
case "c": topSeriesColor = Color.Orange; break;
}
switch (bottomSeries)
{
default: bottomSeriesColor = Color.Gray; break;
case "x": bottomSeriesColor = Color.Green; break;
case "y": bottomSeriesColor = Color.Blue; break;
case "z": bottomSeriesColor = Color.OrangeRed; break;
case "z*": bottomSeriesColor = Color.Crimson; break;
}
// Ion series offsets. These offsets control where on the chart a particular ion series
// get displayed
double topSeriesOffset = 0.025;
double bottomSeriesOffset = 0.1;
if (topSeries.Length == 0)
bottomSeriesOffset = topSeriesOffset;
double topSeriesLeftPoint = 0.0;
double bottomSeriesLeftPoint = 0.0;
// Step through each fragmentation site
for (int i = 1; i <= sequence.Length; ++i)
{
// Paint the top series first
double rightPoint = 0.0;
// Figure out the right mz for this fragmentaion site
switch (topSeries)
{
case "a": rightPoint = fragmentation.a(i, ionSeriesChargeState); break;
case "b": rightPoint = fragmentation.b(i, ionSeriesChargeState); break;
case "c": if (i < sequence.Length) rightPoint = fragmentation.c(i, ionSeriesChargeState); break;
default: continue;
}
// If the left mz and right mz are different
if (rightPoint > 0 && topSeriesLeftPoint != rightPoint)
{
LineObj line;
// Use a dashed line format if there are fragment ions supporting this
// amino acid
if (!aminoAcidHasFragmentEvidence(points, topSeriesLeftPoint, rightPoint))
{
// Draw the line from previous mz to site to this mz in trasparent color.
line = new LineObj(Color.FromArgb(115, topSeriesColor), topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
}
else
{
// Draw the line from previous mz to site to this mz in solid color.
line = new LineObj(topSeriesColor, topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
}
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.Line.Width = 2;
line.ZOrder = ZOrder.F_BehindGrid;
line.IsClippedToChartRect = true;
list.Add(line);
// Add a tick demarking the fragmentation site.
LineObj tick = new LineObj(topSeriesColor, rightPoint, (topSeriesOffset - 0.015), rightPoint, (topSeriesOffset + 0.015));
tick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), (topSeriesLeftPoint + rightPoint) / 2.0,
topSeriesOffset, CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = true;
list.Add(text);
topSeriesLeftPoint = rightPoint;
}
// Time to paint the bottom series
// Get the right mz for this series
switch (bottomSeries)
{
case "x": if (i < sequence.Length) rightPoint = fragmentation.x(i, ionSeriesChargeState); break;
case "y": rightPoint = fragmentation.y(i, ionSeriesChargeState); break;
case "z": rightPoint = fragmentation.z(i, ionSeriesChargeState); break;
case "z*": rightPoint = fragmentation.zRadical(i, ionSeriesChargeState); break;
default: rightPoint = 0.0; break;
}
// If the left and right mz are different
if (rightPoint > 0 && bottomSeriesLeftPoint != rightPoint)
{
LineObj line;
// Use a dashed line format if there are fragment ions supporting this
// amino acid
if (!aminoAcidHasFragmentEvidence(points, bottomSeriesLeftPoint, rightPoint))
{
// Draw the line from previous mz to site to this mz in trasparent color.
line = new LineObj(Color.FromArgb(115, bottomSeriesColor), bottomSeriesLeftPoint, bottomSeriesOffset, rightPoint, bottomSeriesOffset);
line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
}
else
{
// Draw the line from previous mz to site to this mz in solid color.
line = new LineObj(bottomSeriesColor, bottomSeriesLeftPoint, bottomSeriesOffset, rightPoint, bottomSeriesOffset);
}
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.Line.Width = 2;
line.ZOrder = ZOrder.F_BehindGrid;
line.IsClippedToChartRect = true;
list.Add(line);
// Draw a tick mark demarking the fragmentation site
LineObj tick = new LineObj(bottomSeriesColor, rightPoint, (bottomSeriesOffset - 0.015), rightPoint, (bottomSeriesOffset + 0.015));
tick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Add the text label containing the amino acid
StringBuilder label = new StringBuilder(sequence[sequence.Length - i].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[sequence.Length - i].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), (bottomSeriesLeftPoint + rightPoint) / 2.0,
bottomSeriesOffset, CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = true;
list.Add(text);
bottomSeriesLeftPoint = rightPoint;
}
}
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations)
{
if (Chromatogram == null)
return;
// Calculate maximum y for potential retention time indicators
PointF ptTop = new PointF(0, graphPane.Chart.Rect.Top);
if (GraphChromatogram.ShowRT != ShowRTChrom.none)
{
if (RetentionMsMs != null)
{
foreach (double retentionTime in RetentionMsMs)
{
Color color = COLOR_MSMSID_TIME;
if (SelectedRetentionMsMs.HasValue && Equals((float) retentionTime, (float) SelectedRetentionMsMs))
{
color = ColorSelected;
}
AddRetentionTimeAnnotation(graphPane, g, annotations, ptTop,
Resources.ChromGraphItem_AddAnnotations_ID, GraphObjType.ms_ms_id, color,
ScaleRetentionTime(retentionTime));
}
}
if (AlignedRetentionMsMs != null)
{
foreach (var time in AlignedRetentionMsMs)
{
var scaledTime = ScaleRetentionTime(time);
var line = new LineObj(COLOR_ALIGNED_MSMSID_TIME, scaledTime.DisplayTime, 0,
scaledTime.DisplayTime, 1)
{
ZOrder = ZOrder.F_BehindGrid,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
Tag = new GraphObjTag(this, GraphObjType.aligned_ms_id, scaledTime),
};
annotations.Add(line);
}
}
if (UnalignedRetentionMsMs != null)
{
foreach (var time in UnalignedRetentionMsMs)
{
var scaledTime = ScaleRetentionTime(time);
var line = new LineObj(COLOR_UNALIGNED_MSMSID_TIME, scaledTime.DisplayTime, 0,
scaledTime.DisplayTime, 1)
{
ZOrder = ZOrder.F_BehindGrid,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
Tag = new GraphObjTag(this, GraphObjType.unaligned_ms_id, scaledTime),
};
annotations.Add(line);
}
}
}
// Draw retention time indicator, if set
if (RetentionPrediction.HasValue)
{
double time = RetentionPrediction.Value;
// Create temporary label to calculate positions
if (GraphChromatogram.ShowRT != ShowRTChrom.none)
{
AddRetentionTimeAnnotation(graphPane,
g,
annotations,
ptTop,
Resources.ChromGraphItem_AddAnnotations_Predicted,
GraphObjType.predicted_rt_window,
COLOR_RETENTION_TIME,
ScaleRetentionTime(time));
}
// Draw background for retention time window
if (RetentionWindow > 0)
{
double x1 = ScaleRetentionTime(time - RetentionWindow/2).DisplayTime;
double x2 = ScaleRetentionTime(time + RetentionWindow/2).DisplayTime;
BoxObj box = new BoxObj(x1, 0, x2-x1, 1,
COLOR_RETENTION_WINDOW, COLOR_RETENTION_WINDOW)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
};
annotations.Add(box);
}
}
if (RetentionExplicit != null && GraphChromatogram.ShowRT != ShowRTChrom.none)
{
// Create temporary label to calculate positions
AddRetentionTimeAnnotation(graphPane,
g,
annotations,
ptTop,
Resources.ChromGraphItem_AddAnnotations_Explicit,
GraphObjType.predicted_rt_window,
COLOR_RETENTION_TIME,
ScaleRetentionTime(RetentionExplicit.RetentionTime));
}
for (int i = 0, len = Chromatogram.NumPeaks; i < len; i++)
{
if (_arrayLabelIndexes[i] == -1)
continue;
double maxIntensity = _intensities[_arrayLabelIndexes[i]];
// Show peak extent indicators, if they are far enough apart
ChromPeak peak = Chromatogram.GetPeak(i);
AddPeakBoundaries(graphPane, annotations, false,
ScaleRetentionTime(peak.StartTime), ScaleRetentionTime(peak.EndTime), maxIntensity);
}
}
private void btnBrowse_Click(object sender, EventArgs e)
{
OpenFileDialog oFD1 = new OpenFileDialog();
oFD1.Multiselect = true;
if (oFD1.ShowDialog() == System.Windows.Forms.DialogResult.OK)
{
files = oFD1.SafeFileNames; //Save only the names
paths = oFD1.FileNames; //Save the full paths
for (int i = 0; i < files.Length; i++)
{
//listBox1.Items.Add(files[i]); //Add songs to the listbox
ext = Path.GetExtension(oFD1.FileName);
if (ext == ".avi")
{
//Convert Avi to wav
AviManager aviManager = new AviManager(oFD1.FileName, true);
AudioStream audioStream = aviManager.GetWaveStream();
audioStream.ExportStream(oFD1.FileName + ".wav");
filepath = oFD1.FileName + ".wav";
aviManager.Close();
listBox1.Items.Add(files[i]); //Add songs to the listbox
}
else if (ext == ".wav")
{
filepath = oFD1.FileName;
listBox1.Items.Add(files[i]); //Add songs to the listbox
}
}
}
NAudio.Wave.WaveChannel32 wave = new NAudio.Wave.WaveChannel32(new NAudio.Wave.WaveFileReader(filepath));
WaveFileReader wavFile = new WaveFileReader(filepath);
byte[] mainBuffer = new byte[wave.Length];
float fileSize = (float)wavFile.Length / 1048576;
if (fileSize < 2)
window = 8;
else if (fileSize > 2 && fileSize < 4)
window = 16;
else if (fileSize > 4 && fileSize < 8)
window = 32;
else if (fileSize > 8 && fileSize < 12)
window = 128;
else if (fileSize > 12 && fileSize < 20)
window = 256;
else if (fileSize > 20 && fileSize < 30)
window = 512;
else
window = 2048;
float[] fbuffer = new float[mainBuffer.Length / window];
wave.Read(mainBuffer, 0, mainBuffer.Length);
for (int i = 0; i < fbuffer.Length; i++)
{
fbuffer[i] = (BitConverter.ToSingle(mainBuffer, i * window));
}
double time = wave.TotalTime.TotalSeconds;
GraphPane myPane1 = zedGraphControl2.GraphPane;
PointPairList list1 = new PointPairList();
PointPairList list2 = new PointPairList();
for (int i = 0; i < fbuffer.Length; i++)
{
list1.Add(i, fbuffer[i]);
}
list2.Add(0, 0);
list2.Add(time, 0);
if (myCurve1 != null && myCurve2 != null)
{
myCurve1.Clear();
myCurve2.Clear();
}
GraphPane myPane2 = zedGraphControl2.GraphPane;
myPane2.Title.Text = "Audio Sound Wave";
myPane2.XAxis.Title.Text = "Time, Seconds";
myPane2.YAxis.Title.Text = "Sound Wave Graph";
myCurve1 = myPane1.AddCurve(null, list1, System.Drawing.Color.Blue, SymbolType.None);
myCurve1.IsX2Axis = true;
myCurve2 = myPane1.AddCurve(null, list2, System.Drawing.Color.Black, SymbolType.None);
myPane1.XAxis.Scale.MaxAuto = true;
myPane1.XAxis.Scale.MinAuto = true;
//Threshold Line
double threshHoldY = -1.2;
double threshHoldX = 1.2;
LineObj threshHoldLine = new LineObj(System.Drawing.Color.Red, myPane2.XAxis.Scale.Min, threshHoldY, myPane2.XAxis.Scale.Max, threshHoldY);
LineObj threshHoldLine2 = new LineObj(System.Drawing.Color.Red, myPane2.XAxis.Scale.Min, threshHoldX, myPane2.XAxis.Scale.Max, threshHoldX);
myPane2.GraphObjList.Add(threshHoldLine);
myPane2.GraphObjList.Add(threshHoldLine2);
// Add a text box with instructions
TextObj text = new TextObj(
"Ratio Conversion: 1:100\nRed Lines: Threshold\nZoom: left mouse & drag\nContext Menu: right mouse",
0.05f, 0.95f, CoordType.ChartFraction, AlignH.Left, AlignV.Bottom);
text.FontSpec.StringAlignment = StringAlignment.Near;
myPane2.GraphObjList.Add(text);
// Show the x axis grid
myPane2.XAxis.MajorGrid.IsVisible = true;
myPane2.YAxis.MajorGrid.IsVisible = true;
// Just manually control the X axis range so it scrolls continuously
// instead of discrete step-sized jumps
//myPane2.XAxis.Scale.Format = @"00:00:00";
myPane2.XAxis.Scale.IsSkipCrossLabel = true;
myPane2.XAxis.Scale.IsPreventLabelOverlap = true;
myPane2.XAxis.Type = ZedGraph.AxisType.Linear;
myPane2.XAxis.Scale.Min = 0;
myPane2.XAxis.Scale.Max = 1.2;
myPane2.AxisChange();
// turn off the opposite tics so the Y tics don't show up on the Y2 axis
myPane2.YAxis.MajorTic.IsOpposite = false;
myPane2.YAxis.MinorTic.IsOpposite = false;
// Don't display the Y zero line
myPane2.YAxis.MajorGrid.IsZeroLine = false;
// Align the Y axis labels so they are flush to the axis
myPane2.YAxis.Scale.Align = AlignP.Inside;
// Manually set the axis range
myPane2.YAxis.Scale.Min = -1.5;
myPane2.YAxis.Scale.Max = 1.5;
zedGraphControl2.AxisChange();
zedGraphControl2.Invalidate();
}
private void AddPeakBoundaries(GraphPane graphPane, ICollection<GraphObj> annotations,
bool best, ScaledRetentionTime startTime, ScaledRetentionTime endTime, double maxIntensity)
{
// Only show boundaries for dragging when boundaries turned off
if (!Settings.Default.ShowPeakBoundaries && (!best || DragInfo == null))
return;
float xStart = graphPane.XAxis.Scale.Transform(startTime.DisplayTime);
float xEnd = graphPane.XAxis.Scale.Transform(endTime.DisplayTime);
// Hide boundaries, if they are too close together
if (xEnd - xStart <= MIN_BOUNDARY_DISPLAY_WIDTH)
{
// But not if they are currently part of a drag operation.
if (DragInfo == null)
return;
}
// Make sure the best borders are visible
if (best)
{
float yMax = graphPane.YAxis.Scale.Transform(maxIntensity);
float yZero = graphPane.YAxis.Scale.Transform(0);
if (yZero - yMax < MIN_BEST_BOUNDARY_HEIGHT)
maxIntensity = graphPane.YAxis.Scale.ReverseTransform(yZero - MIN_BEST_BOUNDARY_HEIGHT);
}
// Summary graphs show only the best peak boundaries
else if (_isSummary)
{
return;
}
Color colorBoundaries = (best ? COLOR_BOUNDARIES_BEST : COLOR_BOUNDARIES);
GraphObjType graphObjType = best ? GraphObjType.best_peak : GraphObjType.peak;
// Make sure to get maximum intensity within the peak range,
// as this is not guaranteed to be the center of the peak
LineObj stickStart = new LineObj(colorBoundaries, startTime.DisplayTime, maxIntensity, startTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, startTime),
};
annotations.Add(stickStart);
LineObj stickEnd = new LineObj(colorBoundaries, endTime.DisplayTime, maxIntensity, endTime.DisplayTime, 0)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.B_BehindLegend,
Line = { Width = 1, Style = DashStyle.Dash },
Tag = new GraphObjTag(this, graphObjType, endTime),
};
annotations.Add(stickEnd);
}
// Basic curve test - Date Axis
private void CreateGraph_DateAxis( ZedGraphControl z1 )
{
GraphPane myPane = z1.GraphPane;
PointPairList list = new PointPairList();
PointPairList list2 = new PointPairList();
for ( int i = 0; i < 50; i++ )
{
double x = new XDate( 2005, 12 + i, 15 );
double y = Math.Sin( i / 8.0 ) * 1000 + 1001;
list.Add( x, y, 1500 );
list2.Add( x, y * 1.2, 1500 );
}
LineItem line = myPane.AddCurve( "Line", list, Color.Blue, SymbolType.Diamond );
//myPane.XAxis.Scale.Format = "MMM\nyyyy";
myPane.XAxis.Type = AxisType.Date;
//myPane.XAxis.Scale.MajorStep = 1;
//myPane.XAxis.Scale.MajorUnit = DateUnit.Year;
myPane.XAxis.Scale.MinorStep = 1;
myPane.XAxis.Scale.MinorUnit = DateUnit.Month;
/*
BarItem myBar = myPane.AddBar( "Bar", list, Color.Blue );
BarItem myBar2 = myPane.AddBar( "Bar2", list2, Color.Green );
//LineItem myCurve = myPane.AddCurve( "curve", list, Color.Blue, SymbolType.Diamond );
myPane.BarSettings.Type = BarType.ClusterHiLow;
myPane.BarSettings.ClusterScaleWidth = 20.0;
*/
z1.IsAutoScrollRange = true;
z1.IsShowHScrollBar = true;
z1.IsShowVScrollBar = true;
XDate now = new XDate( DateTime.Now );
ArrowObj arrow = new ArrowObj( Color.Black,
2.0f, (float) now.XLDate, 0.0f, (float) now.XLDate, 1.0f );
arrow.IsArrowHead = false;
arrow.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
arrow.IsClippedToChartRect = true;
myPane.GraphObjList.Add( arrow );
// Make the first year line
double xDate = new XDate( 2006, 1, 1 ).XLDate;
LineObj myLine = new LineObj();
myLine.Location.X1 = xDate;
myLine.Location.Y1 = 0.0;
myLine.Location.Width = 0.0;
myLine.Location.Height = 1.0;
myLine.IsClippedToChartRect = true;
myLine.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
myLine.Line.Width = 2.0f;
myLine.Line.Color = Color.Red;
myPane.GraphObjList.Add( myLine );
// Repeat for each Grid by cloning
xDate = new XDate( 2007, 1, 1 ).XLDate;
;
myLine = new LineObj( myLine );
myLine.Location.X1 = xDate;
myPane.GraphObjList.Add( myLine );
}
private void AddRetentionTimeAnnotation(MSGraphPane graphPane, Graphics g, GraphObjList annotations,
PointF ptTop, string title, GraphObjType graphObjType, Color color, ScaledRetentionTime retentionTime)
{
string label = string.Format("{0}\n{1:F01}", title, retentionTime.DisplayTime); // Not L10N
FontSpec fontLabel = CreateFontSpec(color, _fontSpec.Size);
SizeF sizeLabel = fontLabel.MeasureString(g, label, graphPane.CalcScaleFactor());
PointF realTopPoint = ptTop;
ptTop = new PointF(0, ptTop.Y + sizeLabel.Height + 15);
float chartHeightWithLabel = graphPane.Chart.Rect.Height + sizeLabel.Height + 15;
double intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
LineObj stick = new LineObj(color, retentionTime.DisplayTime, intensityChartFraction, retentionTime.DisplayTime, 1)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
ZOrder = ZOrder.E_BehindCurves,
Line = { Width = 1 },
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(stick);
ptTop = new PointF(0, ptTop.Y - 5);
intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
TextObj text = new TextObj(label, retentionTime.DisplayTime, intensityChartFraction,
CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Bottom)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = CreateFontSpec(color, _fontSpec.Size),
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(text);
}
private void CreateGraph_NegativeHorizontalBars( ZedGraphControl z1 )
{
GraphPane myPane = z1.GraphPane;
PointPairList list = new PointPairList();
Random rand = new Random();
for ( int i = 0; i < 20; i++ )
{
list.Add( rand.NextDouble() * 200.0 - 100.0, (double) i + 1.0, 50.0 );
}
list.Sort( SortType.XValues );
HiLowBarItem myBar = myPane.AddHiLowBar( "histogram", list, Color.Blue );
myBar.Bar.Fill = new Fill( Color.Blue );
myPane.BarSettings.MinClusterGap = 0.0f;
myPane.YAxis.MajorGrid.IsZeroLine = false;
myPane.BarSettings.Base = BarBase.Y;
LineObj line = new LineObj( Color.Black, 0, 50, 1, 50 );
line.Location.CoordinateFrame = CoordType.XChartFractionYScale;
myPane.GraphObjList.Add( line );
z1.AxisChange();
}
private void CreateThreshold()
{
GraphPane graphPane = graph.PaneList[0];
double num = 0.0;
LineObj lineObj = new LineObj(Color.Green, 0.0, num, 1.0, num);
lineObj.Location.CoordinateFrame = CoordType.XChartFractionYScale;
lineObj.IsVisible = true;
graphPane.GraphObjList.Add((GraphObj)lineObj);
graphPane.AxisChange();
graph.Invalidate();
}
void GenerateGraphData()
{
PointPairList stab = new PointPairList();
stab.Add(0, MainV2.comPort.MAV.param["IM_STAB_COL_1"].Value);
stab.Add(40, MainV2.comPort.MAV.param["IM_STAB_COL_2"].Value);
stab.Add(60, MainV2.comPort.MAV.param["IM_STAB_COL_3"].Value);
stab.Add(100, MainV2.comPort.MAV.param["IM_STAB_COL_4"].Value);
PointPairList acro = new PointPairList();
double _acro_col_expo = MainV2.comPort.MAV.param["IM_ACRO_COL_EXP"].Value;
// 100 point curve
for (int a = 0; a <= 100; a++)
{
double col_in = (a-50.0)/50.0;
double col_in3 = col_in*col_in*col_in;
double col_out = (_acro_col_expo*col_in3) + ((1 - _acro_col_expo)*col_in);
double acro_col_out = 500 + col_out*500;
acro.Add(a, acro_col_out);
}
zedGraphControl1.GraphPane.CurveList.Clear();
zedGraphControl1.GraphPane.GraphObjList.Clear();
var myCurve = zedGraphControl1.GraphPane.AddCurve("Stabalize Collective", stab, Color.DodgerBlue, SymbolType.Circle);
foreach (PointPair pp in stab)
{
// Add a another text item to to point out a graph feature
TextObj text = new TextObj(pp.X.ToString(), pp.X, pp.Y);
// rotate the text 90 degrees
text.FontSpec.Angle = 0;
text.FontSpec.FontColor = Color.White;
// Align the text such that the Right-Center is at (700, 50) in user scale coordinates
text.Location.AlignH = AlignH.Right;
text.Location.AlignV = AlignV.Center;
// Disable the border and background fill options for the text
text.FontSpec.Fill.IsVisible = false;
text.FontSpec.Border.IsVisible = false;
zedGraphControl1.GraphPane.GraphObjList.Add(text);
}
zedGraphControl1.GraphPane.AddCurve("Acro Collective", acro, Color.Yellow, SymbolType.None);
double posx = map(MainV2.comPort.MAV.cs.ch6out, MainV2.comPort.MAV.param["H_COL_MIN"].Value,
MainV2.comPort.MAV.param["H_COL_MAX"].Value, 0, 100);
// set current marker
var m_cursorLine = new LineObj(Color.Black, posx, 0, posx, 1);
m_cursorLine.Location.CoordinateFrame = CoordType.XScaleYChartFraction; // This do the trick !
m_cursorLine.IsClippedToChartRect = true;
m_cursorLine.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
m_cursorLine.Line.Width = 2f;
m_cursorLine.Line.Color = Color.Red;
m_cursorLine.ZOrder = ZOrder.E_BehindCurves;
zedGraphControl1.GraphPane.GraphObjList.Add(m_cursorLine);
try
{
//zedGraphControl1.AxisChange();
}
catch
{
}
// Force a redraw
zedGraphControl1.Invalidate();
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="LineObj"/> object from which to copy</param>
public LineObj( LineObj rhs ) : base( rhs )
{
_line = new LineBase( rhs._line );
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="LineObj"/> object from which to copy</param>
public LineObj(LineObj rhs) : base(rhs)
{
_line = new LineBase(rhs._line);
}
private void addFragment(GraphObjList list, pwiz.MSGraph.MSPointList points, string series, int length, int charge, double mz)
{
///<summary>
/// IMPORTANT: INORDER TO ADAPT TO ORBI-ORBI DATA, I NEED TO CHANGE THE TOLERANCE TO 30PPM!
///</summary>
double basePeakIntensity = 0;
double cutoff = 0;
foreach (var pointlist in points)
{
if (basePeakIntensity < pointlist.Y)
basePeakIntensity = pointlist.Y;
}
cutoff = basePeakIntensity * basePeakPercentage * 0.01;
double tolerance = mz * 30 * Math.Pow(10.0, -6);
//define the max of scaled list
//double maxScaledIntensity = 0;
//foreach (var pointlist in points.ScaledList)
//{
// if (maxScaledIntensity < pointlist.Y)
// maxScaledIntensity = pointlist.Y;
//}
//test neutral loss
string label = String.Format("{0}{1}{2}", series, length, (charge > 1 ? "+" + charge.ToString() : ""));
Color color;
double offset;
switch (series)
{
default: color = Color.Gray; offset = 0.1; break;
case "a": color = Color.YellowGreen; offset = 0.1; break;
case "x": color = Color.Green; offset = 0.12; break;
case "b": color = Color.Red; offset = 0.14; break;
case "y": color = Color.Blue; offset = 0.16; break;
case "c": color = Color.Orange; offset = 0.18; break;
case "z": color = Color.OrangeRed; offset = 0.2; break;
case "z*": color = Color.Crimson; offset = 0.4; break;
//test neutral loss
case "a-water": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "x-water": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "b-water": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "y-water": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "c-water": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "z-water": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
case "z*-water": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H2O"); break;
//test neutral loss
case "a-ammonium": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "x-ammonium": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "b-ammonium": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "y-ammonium": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "c-ammonium": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "z-ammonium": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "z*-ammonium": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-NH3"); break;
case "a-1phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "x-1phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "b-1phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "y-1phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "c-1phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "z-1phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "z*-1phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-H3PO4"); break;
case "a-2phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "x-2phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "b-2phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "y-2phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "c-2phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "z-2phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "z*-2phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)2"); break;
case "a-3phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "x-3phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "b-3phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "y-3phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "c-3phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "z-3phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "z*-3phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)3"); break;
case "a-4phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "x-4phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "b-4phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "y-4phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "c-4phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "z-4phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "z*-4phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)4"); break;
case "a-5phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "x-5phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "b-5phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "y-5phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "c-5phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "z-5phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "z*-5phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)5"); break;
case "a-6phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "x-6phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "b-6phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "y-6phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "c-6phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "z-6phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "z*-6phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)6"); break;
case "a-7phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "x-7phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "b-7phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "y-7phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "c-7phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "z-7phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "z*-7phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)7"); break;
case "a-8phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "x-8phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "b-8phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "y-8phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "c-8phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "z-8phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "z*-8phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)8"); break;
case "a-9phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "x-9phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "b-9phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "y-9phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "c-9phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "z-9phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "z*-9phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)9"); break;
case "a-10phos": color = Color.YellowGreen; offset = 0.1; label = String.Format("{0}{1}{2}{3}", "a", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "x-10phos": color = Color.Green; offset = 0.12; label = String.Format("{0}{1}{2}{3}", "x", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "b-10phos": color = Color.Red; offset = 0.14; label = String.Format("{0}{1}{2}{3}", "b", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "y-10phos": color = Color.Blue; offset = 0.16; label = String.Format("{0}{1}{2}{3}", "y", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "c-10phos": color = Color.Orange; offset = 0.18; label = String.Format("{0}{1}{2}{3}", "c", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "z-10phos": color = Color.OrangeRed; offset = 0.2; label = String.Format("{0}{1}{2}{3}", "z", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
case "z*-10phos": color = Color.Crimson; offset = 0.4; label = String.Format("{0}{1}{2}{3}", "z*", length, (charge > 1 ? "+" + charge.ToString() : ""), "-(H3PO4)10"); break;
}
int index = -1;
if (points != null)
index = points.ScaledLowerBound(mz - tolerance);
///
#region regular ion series a/b/c/x/y/z/z* keep unchanged
if (series == "a" || series == "b" || series == "c" || series == "x" || series == "y" || series == "z" || series == "z*")
{
if (index == -1 || points.ScaledList[index].X > (mz + tolerance))
// no matching point: present a "missed" fragment annotation
{
if (!showMisses)
return;
color = Color.FromArgb(115, color); // transparent to emphasize miss
LineObj stick = new LineObj(color, mz, offset, mz, 1);
stick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
stick.Line.Width = 2;
stick.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
list.Add(stick);
if (showLabels)
{
TextObj text = new TextObj(label, mz, offset, CoordType.XScaleYChartFraction,
AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Angle = 90;
//text.IsClippedToChartRect = true;
list.Add(text);
}
}
else
// matching point found: present the point as the fragment
{
LineObj stick = new LineObj(color, mz, points.ScaledList[index].Y, mz, 0);
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = 2;
list.Add(stick);
if (showLabels)
{
// use an existing text point annotation if possible
TextObj text = null;
foreach (GraphObj obj in list)
{
if (obj is TextObj &&
(obj.Location.CoordinateFrame == CoordType.AxisXYScale ||
obj.Location.CoordinateFrame == CoordType.XScaleYChartFraction) &&
Math.Abs(obj.Location.X - mz) < tolerance)
{
text = obj as TextObj;
text.Text = String.Format("{0}\n{1}", label, text.Text);
break;
}
}
if (text == null)
{
text = new TextObj(label, mz, points.ScaledList[index].Y, CoordType.AxisXYScale,
AlignH.Left, AlignV.Center);
list.Add(text);
}
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.FontSpec.Angle = 90;
//SizeF size = text.LayoutArea;
//float width = size.Width;
//pwiz.MSGraph.MSGraphPane g = new pwiz.MSGraph.MSGraphPane();
//YAxis y = g.YAxis;
//double scaled2pixel = width + y.Scale.Transform(points.ScaledList[index].Y) ;
//double width2Scale = width / 0.75 * maxScaledIntensity*1.1;
//text.IsClippedToChartRect = true;
//if (charge > 1)
//{
// //calculate the Y value to actual size in CharFraction
// TextObj chargeLabel = new TextObj("+" + charge, mz, 1-scaled2pixel, CoordType.XScaleYChartFraction,
// AlignH.Left, AlignV.Bottom);
// chargeLabel.ZOrder = ZOrder.A_InFront;
// chargeLabel.FontSpec = new FontSpec("Arial", 8, color, false, false, false);
// chargeLabel.FontSpec.Border.IsVisible = false;
// chargeLabel.FontSpec.Fill.IsVisible = false;
// chargeLabel.FontSpec.Angle = 90;
// list.Add(chargeLabel);
//}
}
}
}
#endregion
else //if neutral loss ion series
{
///
#region basepeakthresholding is false
if (basePeakThresholding == false)
{
if (index == -1 || points.ScaledList[index].X > (mz + 0.5))
// no matching point: present a "missed" fragment annotation
{
if (!showMisses)
return;
color = Color.FromArgb(115, color); // transparent to emphasize miss
LineObj stick = new LineObj(color, mz, offset, mz, 1);
stick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
stick.Line.Width = 2;
stick.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
list.Add(stick);
if (showLabels)
{
TextObj text = new TextObj(label, mz, offset, CoordType.XScaleYChartFraction,
AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Angle = 90;
//text.IsClippedToChartRect = true;
list.Add(text);
}
}
else
// matching point found: present the point as the fragment
{
LineObj stick = new LineObj(color, mz, points.ScaledList[index].Y, mz, 0);
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = 2;
list.Add(stick);
if (showLabels)
{
// use an existing text point annotation if possible
TextObj text = null;
foreach (GraphObj obj in list)
{
if (obj is TextObj &&
(obj.Location.CoordinateFrame == CoordType.AxisXYScale ||
obj.Location.CoordinateFrame == CoordType.XScaleYChartFraction) &&
Math.Abs(obj.Location.X - mz) < 0.5)
{
text = obj as TextObj;
text.Text = String.Format("{0}\n{1}", label, text.Text);
break;
}
}
if (text == null)
{
text = new TextObj(label, mz, points.ScaledList[index].Y, CoordType.AxisXYScale,
AlignH.Left, AlignV.Center);
list.Add(text);
}
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.FontSpec.Angle = 90;
//text.IsClippedToChartRect = true;
}
}
}
#endregion
///
#region basepeakthresholding is true
else //if basepeakthresholding is true
{
if (index == -1 || points.ScaledList[index].X > (mz + 0.5) || points.FullList[index].Y < cutoff)
// no matching point: present a "missed" fragment annotation
{
if (!showMisses)
return;
color = Color.FromArgb(115, color); // transparent to emphasize miss
LineObj stick = new LineObj(color, mz, offset, mz, 1);
stick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
stick.Line.Width = 2;
stick.Line.Style = System.Drawing.Drawing2D.DashStyle.Dot;
list.Add(stick);
if (showLabels)
{
TextObj text = new TextObj(label, mz, offset, CoordType.XScaleYChartFraction,
AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Angle = 90;
//text.IsClippedToChartRect = true;
list.Add(text);
}
}
else
// matching point found: present the point as the fragment
{
LineObj stick = new LineObj(color, mz, points.ScaledList[index].Y, mz, 0);
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = 2;
list.Add(stick);
if (showLabels)
{
// use an existing text point annotation if possible
TextObj text = null;
foreach (GraphObj obj in list)
{
if (obj is TextObj &&
(obj.Location.CoordinateFrame == CoordType.AxisXYScale ||
obj.Location.CoordinateFrame == CoordType.XScaleYChartFraction) &&
Math.Abs(obj.Location.X - mz) < 0.5)
{
text = obj as TextObj;
text.Text = String.Format("{0}\n{1}", label, text.Text);
break;
}
}
if (text == null)
{
text = new TextObj(label, mz, points.ScaledList[index].Y, CoordType.AxisXYScale,
AlignH.Left, AlignV.Center);
list.Add(text);
}
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 12, color, false, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.FontSpec.Angle = 90;
//text.IsClippedToChartRect = true;
}
}
}
#endregion
}
}
private static void AddLine(GraphPane g, double val, Color color, string label = null)
{
var line = new LineObj(0, val, 1, val);
line.IsClippedToChartRect = true;
line.Location.CoordinateFrame = CoordType.XChartFractionYScale;
line.Line.Color = color;
line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
g.GraphObjList.Add(line);
if (!string.IsNullOrWhiteSpace(label))
{
var text = new TextObj(label, 0.01, val);
text.IsClippedToChartRect = true;
text.Location.CoordinateFrame = CoordType.XChartFractionYScale;
text.Location.AlignH = AlignH.Left;
text.Location.AlignV = AlignV.Bottom;
text.FontSpec.FontColor = color;
text.FontSpec.Fill.IsVisible = false;
text.FontSpec.Size = 18.0f;
text.FontSpec.Border.IsVisible = false;
g.GraphObjList.Add(text);
}
}
///<summary>Adds user requested ion series to the fragmentation summary.</summary>
private void addFragmentationSummary(GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
{
///cutoff definition for neutral loss
double basePeakIntensity = 0;
double cutoff = 0;
foreach (var pointlist in points)
{
if (basePeakIntensity < pointlist.Y)
basePeakIntensity = pointlist.Y;
}
cutoff = basePeakIntensity * basePeakPercentage * 0.01;
///
int ionSeriesChargeState = min;
string sequence = peptide.sequence;
int sequenceLength = peptide.sequence.Length;
ModificationMap modifications = peptide.modifications();
// Select the color for the ion series.
Color topSeriesColor;
Color bottomSeriesColor;
switch (topSeries)
{
default: topSeriesColor = Color.Gray; break;
case "a": topSeriesColor = Color.YellowGreen; break;
case "b": topSeriesColor = Color.Red; break;
case "c": topSeriesColor = Color.Orange; break;
}
switch (bottomSeries)
{
default: bottomSeriesColor = Color.Gray; break;
case "x": bottomSeriesColor = Color.Green; break;
case "y": bottomSeriesColor = Color.Blue; break;
case "z": bottomSeriesColor = Color.OrangeRed; break;
case "z*": bottomSeriesColor = Color.Crimson; break;
}
// Ion series offsets. These offsets control where on the chart a particular ion series
// get displayed
//change the seriesTopLeftOffset value to 0.1 to make the label higher in the image.
//original is 0.031
double seriesTopLeftOffset = 0.05;
// Set the constants for starting the label paint
double topSeriesLeftPoint = 0.025;
//test and looks reasonalbe
double residueWidth = 0.031;
//double residueWidth = 0.25 / ((double)sequence.Length);
// Process all the series except c and x
//small block modified
//here is a big bug: if go like orignal code, then the y ions is just the like the order of b ions, which are not right.
//My modification is to seperate a/b/c and x/y/z ions, and then it will solve this problem.
//it seems works well.
///
#region Process a/b ions
//first we are going to touch only a/b ions
///
for (int i = 1; i <= sequence.Length; ++i)
{
double tickStart = residueWidth * 4 / 5.0;
double topSeriesFragmentMZ = 0.0;
//test neutral loss
//this block is to give clear clue for phospate loss
//exact number of phosphated amino acids are counted.
string Nseq = peptide.sequence.Substring(0, i);
char[] Nseqchars = Nseq.ToCharArray();
int Nphosmodi = 0;
for (int k = 0; k < i; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (Nseqchars[k] == 'S' || Nseqchars[k] == 'T' || Nseqchars[k] == 'Y'))
{
Nphosmodi++;
}
}
//correct the bug:
//when multiple charges allowed for fragmentation, then there is no tick thing showing the existance of the fragment
//what I did is: make top/bottomSeriesHasMatch true if there is fragment of any charges matched.
//bug fixed
bool topSeriesHasMatch = false;
for (int z = min; z <= max; z++)
{
switch (topSeries)
{
case "a": topSeriesFragmentMZ = fragmentation.a(i, z); break;
case "b": topSeriesFragmentMZ = fragmentation.b(i, z); break;
default: topSeriesFragmentMZ = 0.0; break;
}
// Check if the top and bottom fragments have evidence
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
//test neutral loss
#region water loss a/b top series
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
// Check if the top and bottom fragments have evidence
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - WATERMONOMASS/z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y >= cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region ammonium loss a/b top series
if (ammoniumLoss == true)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region phosphate loss a/b top series
if (phosphateLoss == true)
{
//need to judge qualified number of AAs;
int minPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
//first need to judge if there are as many as phos AAs
//then if AA <= phos, then deal with AA;
//if AA > phos, then deal with phos.
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
}
#endregion
}
// Build the label for the amino acid
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
string deltaMassString = deltaMass.ToString();
TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.E_BehindCurves;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.IsClippedToChartRect = true;
list.Add(text);
SizeF size = text.LayoutArea;
float width = size.Width;
if (deltaMass > 0.0)
{
deltaMassString = "+" + Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.011,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.A_InFront;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false ;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
else if (deltaMass < 0.0)
{
deltaMassString = Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false ;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.03), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.03);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
// Reset the series starting point
topSeriesLeftPoint = 0.025;
#endregion
///
#region Process y/z ions
//then for y/z ions:
//note: since the fragmentsummary starts the ticking/lining from left to right,
//so we need to adjust the starting point of bottoms series from the highest to lowest.
///
for (int i = sequence.Length; i >= 1; --i)
{
double tickStart = residueWidth / 5.0;
double bottomSeriesFragmentMZ = 0.0;
bool bottomSeriesHasMatch = false;
//test neutral
string Cseq = peptide.sequence.Substring(sequenceLength - i, i);
char[] seqchars = peptide.sequence.ToCharArray();
int Cphosmodi = 0;
for (int k = sequenceLength - i; k < sequenceLength; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
{
Cphosmodi++;
}
}
for (int z = min; z <= max; z++)
{
switch (bottomSeries)
{
case "y": bottomSeriesFragmentMZ = fragmentation.y(i, z); break;
case "z": bottomSeriesFragmentMZ = fragmentation.z(i, z); break;
case "z*": bottomSeriesFragmentMZ = fragmentation.zRadical(i, z); break;
default: bottomSeriesFragmentMZ = 0.0; break;
}
// Check if the top and bottom fragments have evidence
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
//test neutral loss
#region water loss y/z bottom series
if (waterLoss == true)
{
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
#endregion
//test neutral loss
#region ammonium loss y/z bottom series
if (ammoniumLoss == true)
{
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
#endregion
//test neutral loss
#region phosphate loss y/z bottom series
if (phosphateLoss == true)
{
int minPhosphate = Math.Min(Cphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
}
#endregion
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesLeftPoint - tickStart, seriesTopLeftOffset, topSeriesLeftPoint - tickStart, seriesTopLeftOffset + 0.03);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesLeftPoint - tickStart, seriesTopLeftOffset + 0.03, topSeriesLeftPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
// Reset the series starting point
topSeriesLeftPoint = 0.025;
#endregion
///
#region Process x/c series
///
//the reason that I didn't split c/x as ab/yz, is that c/x doesn't have to deal with the termini. so good to go.
//disable the function of neutral losses
for (int i = 1; i < sequence.Length; ++i)
{
double tickStart = residueWidth *4 / 5.0;
double topSeriesFragmentMZ = 0.0;
double bottomSeriesFragmentMZ = 0.0;
// Check if the top and bottom fragments have evidence
bool topSeriesHasMatch = false;
bool bottomSeriesHasMatch = false;
///
//test neutral loss
//test neutral
//adjust the "i" accordingly, must let the C ions be left=>right.
//if it goes from left to right, then N series is i;
//C series is more tricky. Get a NTempSeq from 0 to sequenceLength-i; then get C from total.
///
string Nseq = peptide.sequence.Substring(0, i);
string NTempSeq = peptide.sequence.Substring(0, sequenceLength - i);
string Cseq = peptide.sequence.Substring(i, sequenceLength-i);
char[] Nseqchars = Nseq.ToCharArray();
char[] seqchars = peptide.sequence.ToCharArray();
char[] NTempSeqChars = NTempSeq.ToCharArray();
int Nphosmodi = 0;
int NTempPhosmodi = 0;
int Cphosmodi = 0;
int phosmodi = 0;
for (int k = 0; k < i; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (Nseqchars[k] == 'S' || Nseqchars[k] == 'T' || Nseqchars[k] == 'Y'))
{
Nphosmodi++;
}
}
for (int k = 0; k < sequenceLength - i; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (NTempSeqChars[k] == 'S' || NTempSeqChars[k] == 'T' || NTempSeqChars[k] == 'Y'))
{
NTempPhosmodi++;
}
}
for (int k = 0; k < sequenceLength; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
{
phosmodi++;
}
}
Cphosmodi = phosmodi - NTempPhosmodi;
for (int z = min; z <= max; z++)
{
switch (topSeries)
{
case "c": topSeriesFragmentMZ = fragmentation.c(i, z); break;
default: topSeriesFragmentMZ = 0.0; break;
}
switch (bottomSeries)
{
case "x": bottomSeriesFragmentMZ = fragmentation.x(sequence.Length - i, z); break;
default: bottomSeriesFragmentMZ = 0.0; break;
}
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ + 0.5))
topSeriesHasMatch = true;
// Reset the search index
index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - 0.5);
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ + 0.5))
bottomSeriesHasMatch = true;
}
//disable neutral losses for c/x series
//test neutral loss
#region water loss c/x
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
topSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
topSeriesHasMatch = true;
}
}
}
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - WATERMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5))
bottomSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - WATERMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
bottomSeriesHasMatch = true;
}
}
}
}
#endregion
////test neutral loss
#region ammonium loss c/x
if (ammoniumLoss == true)
{
if (points != null)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
topSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
topSeriesHasMatch = true;
}
}
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
{
// Reset the search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5))
bottomSeriesHasMatch = true;
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - AMMONIUMMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
bottomSeriesHasMatch = true;
}
}
}
}
#endregion
////test neutral loss
#region phosphate loss c/x
if (phosphateLoss == true)
{
int minPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
topSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (topSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
topSeriesHasMatch = true;
break;
}
}
}
}
}
minPhosphate = Math.Min(Cphosmodi, numPhosphate);
{
if (minPhosphate > 0)
{
for (int k = 1; k <= minPhosphate; k++)
{
if (points != null)
{
// Search index
int index = -1;
// Find the left mz value using a mass tolerance of 0.5 da.
index = points.FullLowerBound(bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z - 0.5);
if (basePeakThresholding == false)
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5))
{
bottomSeriesHasMatch = true;
break;
}
}
else
{
if (index != -1 && points.FullList[index].X <= (bottomSeriesFragmentMZ - k * PHOSPHATEMONOMASS / z + 0.5) && points.FullList[index].Y > cutoff)
{
bottomSeriesHasMatch = true;
break;
}
}
}
}
}
}
}
#endregion
}
// Build the label for the amino acid
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
string deltaMassString = deltaMass.ToString();
// Round the mod mass and append it to the amino acid as a string
//if (deltaMass > 0.0)
//{
// label.Append("+" + Math.Round(deltaMass));
//}
//else if (deltaMass < 0.0)
//{
// label.Append(Math.Round(deltaMass));
//}
TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
text.ZOrder = ZOrder.B_BehindLegend;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
text.IsClippedToChartRect = true;
list.Add(text);
SizeF size = text.LayoutArea;
float width = size.Width;
if (deltaMass > 0.0)
{
deltaMassString = "+" + Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
else if (deltaMass < 0.0)
{
deltaMassString = Math.Round(deltaMass).ToString();
TextObj textModi = new TextObj(deltaMassString, topSeriesLeftPoint + 0.01,
seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Left, AlignV.Center);
textModi.ZOrder = ZOrder.B_BehindLegend;
textModi.FontSpec = new FontSpec("Arial", 8, Color.Black, true, false, false);
textModi.FontSpec.Border.IsVisible = false;
textModi.FontSpec.Fill.IsVisible = false;
textModi.IsClippedToChartRect = true;
list.Add(textModi);
}
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.03), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.03);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesLeftPoint + tickStart, seriesTopLeftOffset, topSeriesLeftPoint + tickStart, seriesTopLeftOffset + 0.03);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesLeftPoint + tickStart, seriesTopLeftOffset + 0.03, topSeriesLeftPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
}
#endregion
}