private int findPointWithTolerance(pwiz.MSGraph.MSPointList points, double mz, MZTolerance tolerance, bool scaled = false)
{
double lowestMatchMz = mz - tolerance;
double highestMatchMz = mz + tolerance;
var pointPairList = scaled ? points.ScaledList : points.FullList;
int index = scaled ? points.ScaledLowerBound(mz) : points.FullLowerBound(mz);
// if index is below the tolerance threshold, bump it to the next one or set to -1 if doing so would exceed the list size
if (index > -1 && pointPairList[index].X < lowestMatchMz)
index = index + 1 == pointPairList.Count ? -1 : index + 1;
if (index == -1 || pointPairList[index].X > highestMatchMz)
return -1;
return index;
}
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
}
}