///<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;
}
}
}
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>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;
}
}
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
}
}
///<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
}
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);
}
public override void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations)
{
if (Chromatogram == null)
return;
// Give priority to showing the best peak text object above all other annotations
if (DragInfo != null || (!HideBest && TransitionChromInfo != null) || CurveAnnotation != null)
{
// Show text and arrow for the best peak
double intensityBest = 0;
if (_bestPeakTimeIndex != -1)
{
ScaledRetentionTime timeBest = new ScaledRetentionTime(_measuredTimes[_bestPeakTimeIndex], _displayTimes[_bestPeakTimeIndex]);
float xBest = graphPane.XAxis.Scale.Transform(timeBest.DisplayTime);
intensityBest = _intensities[_bestPeakTimeIndex];
float yBest = graphPane.YAxis.Scale.Transform(intensityBest);
if (GraphChromatogram.ShowRT != ShowRTChrom.none || DragInfo != null)
{
// Best peak gets its own label to avoid curve overlap detection
double intensityLabel = graphPane.YAxis.Scale.ReverseTransform(yBest - 5);
float? massError = Settings.Default.ShowMassError && TransitionChromInfo != null
? TransitionChromInfo.MassError
: null;
double dotProduct = _dotProducts != null ? _bestProduct : 0;
TextObj text;
if (CurveAnnotation != null)
{
// Darken peptide name a little so light colors stand out against the white background.
var color = FontSpec.FontColor;
if (!GraphInfo.IsSelected)
color = Color.FromArgb(color.R*7/10, color.G*7/10, color.B*7/10);
var fontSpec = new FontSpec(FontSpec) { FontColor = color, Angle = 90 };
if (GraphInfo.IsSelected)
fontSpec = new FontSpec(fontSpec) {IsBold = true, Size = fontSpec.Size + 2, IsAntiAlias = true};
// Display peptide name label using vertical text.
text = new TextObj(CurveAnnotation, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Left, AlignV.Center)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = fontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
else
{
string label = FormatTimeLabel(timeBest.DisplayTime, massError, dotProduct);
text = new TextObj(label, timeBest.DisplayTime, intensityLabel,
CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
ZOrder = ZOrder.A_InFront,
IsClippedToChartRect = true,
FontSpec = FontSpec,
Tag = new GraphObjTag(this, GraphObjType.best_peak, timeBest),
};
}
annotations.Add(text);
}
// If showing multiple peptides, skip the best peak arrow indicator.
if (CurveAnnotation == null)
{
// Show the best peak arrow indicator
double timeArrow = graphPane.XAxis.Scale.ReverseTransform(xBest - 4);
double intensityArrow = graphPane.YAxis.Scale.ReverseTransform(yBest - 2);
ArrowObj arrow = new ArrowObj(COLOR_BEST_PEAK, 12f,
timeArrow, intensityArrow, timeArrow, intensityArrow)
{
Location = {CoordinateFrame = CoordType.AxisXYScale},
IsArrowHead = true,
IsClippedToChartRect = true,
ZOrder = ZOrder.A_InFront
};
annotations.Add(arrow);
}
}
// Show the best peak boundary lines
if (CurveAnnotation == null)
{
double startTime = 0, endTime = 0;
if (DragInfo != null)
{
startTime = DragInfo.StartTime.MeasuredTime;
endTime = DragInfo.EndTime.MeasuredTime;
}
else if (TransitionChromInfo != null)
{
var tranPeakInfo = TransitionChromInfo;
startTime = tranPeakInfo.StartRetentionTime;
endTime = tranPeakInfo.EndRetentionTime;
}
AddPeakBoundaries(graphPane, annotations, true,
ScaleRetentionTime(startTime), ScaleRetentionTime(endTime), intensityBest);
}
}
}
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);
}
}
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;
}
}
}