public AnnotationSettings()
{
labelToAliasAndColorMap = new Map <string, Pair <string, Color> >();
pointAnnotations = new PointDataMap <SeemsPointAnnotation>();
pointFontSpec = new ZedGraph.FontSpec("Arial", 10, Color.Gray, false, false, false);
pointFontSpec.Border.IsVisible = false;
}
public AnnotationEditForm(GraphForm graphForm)
{
InitializeComponent();
ownerGraphForm = graphForm;
PointDataMap <SeemsPointAnnotation> annotationMap = (ownerGraphForm.CurrentScan.IsMassSpectrum ? ownerGraphForm.AnnotationSettings.ScanPointAnnotations : ownerGraphForm.AnnotationSettings.ChromatogramPointAnnotations);
foreach (SeemsPointAnnotation annotation in annotationMap.Values)
{
annotationListBox.Items.Add(new AnnotationListItem(annotation));
}
}
public SeemsAnnotationSettings()
{
// ms-product-label -> (label alias, known color)
labelToAliasAndColorMap = new Map <string, Pair <string, Color> >();
labelToAliasAndColorMap["y"] = new Pair <string, Color>("y", Color.Blue);
labelToAliasAndColorMap["b"] = new Pair <string, Color>("b", Color.Red);
labelToAliasAndColorMap["y-NH3"] = new Pair <string, Color>("y^", Color.Green);
labelToAliasAndColorMap["y-H2O"] = new Pair <string, Color>("y*", Color.Cyan);
labelToAliasAndColorMap["b-NH3"] = new Pair <string, Color>("b^", Color.Orange);
labelToAliasAndColorMap["b-H2O"] = new Pair <string, Color>("b*", Color.Violet);
scanPointAnnotations = new PointDataMap <SeemsPointAnnotation>();
chromatogramPointAnnotations = new PointDataMap <SeemsPointAnnotation>();
}
private void okButton_Click(object sender, EventArgs e)
{
DialogResult = DialogResult.OK;
PointDataMap <SeemsPointAnnotation> annotationMap = (ownerGraphForm.CurrentScan.IsMassSpectrum ? ownerGraphForm.AnnotationSettings.ScanPointAnnotations : ownerGraphForm.AnnotationSettings.ChromatogramPointAnnotations);
annotationMap.Clear();
foreach (object itr in annotationListBox.Items)
{
AnnotationListItem item = (AnnotationListItem)itr;
annotationMap[item.annotation.Point] = item.annotation;
}
this.Close();
}
public override Spectrum spectrum(int index, bool getBinaryData)
{
Spectrum s = base.spectrum(index, true);
if (s.cvParam(CVID.MS_MSn_spectrum).empty() ||
(int)s.cvParam(CVID.MS_ms_level).value == 1)
{
if (!getBinaryData)
{
s.binaryDataArrays.Clear();
}
return(s);
}
PrecursorList pl = s.precursors;
BinaryData mzArray = s.getMZArray().data;
BinaryData intensityArray = s.getIntensityArray().data;
PointDataMap <double> mziMap = new PointDataMap <double>();
for (int i = 0; i < (int)s.defaultArrayLength; ++i)
{
mziMap.Insert(mzArray[i], intensityArray[i]);
}
Set <double> pointsToRemove = new Set <double>();
foreach (Precursor p in pl)
{
foreach (SelectedIon si in p.selectedIons)
{
double mz = (double)si.cvParam(CVID.MS_selected_ion_m_z).value;
PointDataMap <double> .Enumerator itr = mziMap.LowerBound(mz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - mz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
CVParam chargeParam = si.cvParam(CVID.MS_charge_state);
if (!chargeParam.empty())
{
int z = (int)chargeParam.value;
for (int i = 1; i < z; ++i)
{
double strippedMz = (mz * z) / (z - i);
itr = mziMap.LowerBound(strippedMz - 4.0);
if (itr != null && itr.IsValid)
{
while (itr.IsValid && itr.Current.Key - strippedMz < 4.0)
{
pointsToRemove.Add(itr.Current.Key);
itr.MoveNext();
}
}
}
}
}
}
if (getBinaryData)
{
mzArray.Clear();
intensityArray.Clear();
foreach (PointDataMap <double> .MapPair pair in mziMap)
{
if (pointsToRemove.Contains(pair.Key))
{
continue;
}
mzArray.Add(pair.Key);
intensityArray.Add(pair.Value);
}
s.defaultArrayLength = (ulong)mzArray.Count;
}
else
{
s.binaryDataArrays.Clear();
s.defaultArrayLength -= (ulong)pointsToRemove.Count;
}
return(s);
}
public void SetDataLabelsVisible(bool visible)
{
//zedGraphControl1.GraphPane.GraphObjList.Clear();
foreach (ZedGraph.GraphObj dataLabel in dataLabels)
{
zedGraphControl1.GraphPane.GraphObjList.Remove(dataLabel);
}
if (visible)
{
if (!(AnnotationSettings.ShowChromatogramPointTimes || AnnotationSettings.ShowScanPointMZs ||
AnnotationSettings.ShowChromatogramPointIntensities || AnnotationSettings.ShowScanPointIntensities ||
AnnotationSettings.ShowUnmatchedAnnotations || AnnotationSettings.ShowMatchedAnnotations))
{
return;
}
// set direct references
ZedGraph.GraphPane pane = zedGraphControl1.GraphPane;
ZedGraph.Axis xAxis = pane.XAxis;
ZedGraph.Axis yAxis = pane.YAxis;
yAxis.Scale.MinAuto = false;
yAxis.Scale.Min = 0;
// setup axes scales to enable the Transform method
xAxis.Scale.SetupScaleData(pane, xAxis);
yAxis.Scale.SetupScaleData(pane, yAxis);
Graphics g = zedGraphControl1.CreateGraphics();
//pane.Draw( g );
pane.CurveList.Draw(g, pane, 1.0f);
System.Drawing.Bitmap gmap = new Bitmap(Convert.ToInt32(pane.Rect.Width), Convert.ToInt32(pane.Rect.Height));
zedGraphControl1.DrawToBitmap(gmap, Rectangle.Round(pane.Rect));
Region chartRegion = new Region(pane.Chart.Rect);
Region clipRegion = new Region();
clipRegion.MakeEmpty();
g.SetClip(zedGraphControl1.MasterPane.Rect, CombineMode.Replace);
g.SetClip(chartRegion, CombineMode.Exclude);
/*Bitmap clipBmp = new Bitmap( Convert.ToInt32( pane.Rect.Width ), Convert.ToInt32( pane.Rect.Height ) );
* Graphics clipG = Graphics.FromImage( clipBmp );
* clipG.Clear( Color.White );
* clipG.FillRegion( new SolidBrush( Color.Black ), g.Clip );
* clipBmp.Save( "C:\\clip.bmp" );*/
PointDataMap <SeemsPointAnnotation> matchedAnnotations = new PointDataMap <SeemsPointAnnotation>();
// add automatic labels
foreach (ZedGraph.CurveItem curve in pane.CurveList)
{
SeemsPointList pointList = (SeemsPointList)curve.Points;
for (int i = 0; i < pointList.MaxCount; i++)
{
ZedGraph.PointPair pt = pointList.GetPointAtIndex(pointList.ScaledMaxIndexList[i]);
if (pt.X < xAxis.Scale.Min || pt.Y > yAxis.Scale.Max || pt.Y < yAxis.Scale.Min)
{
continue;
}
if (pt.X > xAxis.Scale.Max)
{
break;
}
StringBuilder pointLabel = new StringBuilder();
Color pointColor = curve.Color;
// Add annotation
double annotationX = 0.0;
SeemsPointAnnotation annotation = null;
if (CurrentScan.IsMassSpectrum)
{
PointDataMap <SeemsPointAnnotation> .MapPair annotationPair = AnnotationSettings.ScanPointAnnotations.FindNear(pt.X, AnnotationSettings.ScanMatchTolerance);
if (annotationPair != null)
{
annotationX = annotationPair.Key;
annotation = annotationPair.Value;
matchedAnnotations.Add(annotationPair);
}
}
else
{
PointDataMap <SeemsPointAnnotation> .MapPair annotationPair = AnnotationSettings.ChromatogramPointAnnotations.FindNear(pt.X, AnnotationSettings.ChromatogramMatchTolerance);
if (annotationPair != null)
{
annotationX = annotationPair.Key;
annotation = annotationPair.Value;
matchedAnnotations.Add(annotationPair);
}
}
if (AnnotationSettings.ShowMatchedAnnotations && annotation != null)
{
pointLabel.AppendLine(annotation.Label);
pointColor = annotation.Color;
//if( curve is ZedGraph.StickItem )
{
ZedGraph.LineObj stickOverlay = new ZedGraph.LineObj(annotationX, 0, annotationX, pt.Y);
//stickOverlay.IsClippedToChartRect = true;
stickOverlay.Location.CoordinateFrame = ZedGraph.CoordType.AxisXYScale;
stickOverlay.Line.Width = annotation.Width;
stickOverlay.Line.Color = pointColor;
zedGraphControl1.GraphPane.GraphObjList.Add(stickOverlay);
dataLabels.Add(stickOverlay);
//( (ZedGraph.StickItem) curve ).Color = pointColor;
//( (ZedGraph.StickItem) curve ).Line.Width = annotation.Width;
}
}
if (CurrentScan.IsMassSpectrum)
{
if (AnnotationSettings.ShowScanPointMZs)
{
pointLabel.AppendLine(pt.X.ToString("f2"));
}
if (AnnotationSettings.ShowScanPointIntensities)
{
pointLabel.AppendLine(pt.Y.ToString("f2"));
}
}
else
{
if (AnnotationSettings.ShowChromatogramPointTimes)
{
pointLabel.AppendLine(pt.X.ToString("f2"));
}
if (AnnotationSettings.ShowChromatogramPointIntensities)
{
pointLabel.AppendLine(pt.Y.ToString("f2"));
}
}
string pointLabelString = pointLabel.ToString();
if (pointLabelString.Length == 0)
{
continue;
}
// Create a text label from the X data value
ZedGraph.TextObj text = new ZedGraph.TextObj(pointLabelString, pt.X, yAxis.Scale.ReverseTransform(yAxis.Scale.Transform(pt.Y) - 5),
ZedGraph.CoordType.AxisXYScale, ZedGraph.AlignH.Center, ZedGraph.AlignV.Bottom);
text.ZOrder = ZedGraph.ZOrder.A_InFront;
//text.IsClippedToChartRect = true;
text.FontSpec.FontColor = pointColor;
// Hide the border and the fill
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
//text.FontSpec.Fill = new Fill( Color.FromArgb( 100, Color.White ) );
// Rotate the text to 90 degrees
text.FontSpec.Angle = 0;
string shape, coords;
text.GetCoords(pane, g, 1.0f, out shape, out coords);
if (shape != "poly")
{
throw new InvalidOperationException("shape must be 'poly'");
}
string[] textBoundsPointStrings = coords.Split(",".ToCharArray());
if (textBoundsPointStrings.Length != 9)
{
throw new InvalidOperationException("coords length must be 8");
}
Point[] textBoundsPoints = new Point[]
{
new Point(Convert.ToInt32(textBoundsPointStrings[0]), Convert.ToInt32(textBoundsPointStrings[1])),
new Point(Convert.ToInt32(textBoundsPointStrings[2]), Convert.ToInt32(textBoundsPointStrings[3])),
new Point(Convert.ToInt32(textBoundsPointStrings[4]), Convert.ToInt32(textBoundsPointStrings[5])),
new Point(Convert.ToInt32(textBoundsPointStrings[6]), Convert.ToInt32(textBoundsPointStrings[7]))
};
byte[] textBoundsPointTypes = new byte[]
{
(byte)PathPointType.Start,
(byte)PathPointType.Line,
(byte)PathPointType.Line,
(byte)PathPointType.Line
};
GraphicsPath textBoundsPath = new GraphicsPath(textBoundsPoints, textBoundsPointTypes);
textBoundsPath.CloseFigure();
Region textBoundsRegion = new Region(textBoundsPath);
textBoundsRegion.Intersect(pane.Chart.Rect);
RectangleF[] textBoundsRectangles = textBoundsRegion.GetRegionScans(g.Transform);
bool overlapDetected = false;
for (int j = 0; j < textBoundsRectangles.Length && !overlapDetected; ++j)
{
if (g.Clip.IsVisible(textBoundsRectangles[j]))
{
overlapDetected = true;
}
for (float y = textBoundsRectangles[j].Top; y <= textBoundsRectangles[j].Bottom && !overlapDetected; ++y)
{
for (float x = textBoundsRectangles[j].Left; x <= textBoundsRectangles[j].Right && !overlapDetected; ++x)
{
if (gmap.GetPixel(Convert.ToInt32(x), Convert.ToInt32(y)).ToArgb() != pane.Chart.Fill.Color.ToArgb())
{
overlapDetected = true;
}
}
}
}
if (!overlapDetected)
{
pane.GraphObjList.Add(text);
clipRegion.Union(textBoundsRegion);
//g.SetClip( chartRegion, CombineMode.Replace );
g.SetClip(clipRegion, CombineMode.Replace);
//clipG.Clear( Color.White );
//clipG.FillRegion( new SolidBrush( Color.Black ), g.Clip );
//clipBmp.Save( "C:\\clip.bmp" );
dataLabels.Add(text);
//text.Draw( g, pane, 1.0f );
//zedGraphControl1.DrawToBitmap( gmap, Rectangle.Round( pane.Rect ) );
}
}
}
if (AnnotationSettings.ShowUnmatchedAnnotations)
{
PointDataMap <SeemsPointAnnotation> annotations;
if (CurrentScan.IsMassSpectrum)
{
annotations = AnnotationSettings.ScanPointAnnotations;
}
else
{
annotations = AnnotationSettings.ChromatogramPointAnnotations;
}
foreach (PointDataMap <SeemsPointAnnotation> .MapPair annotationPair in annotations)
{
if (matchedAnnotations.Contains(annotationPair))
{
continue;
}
float stickLength = (yAxis.MajorTic.Size * 2) / pane.Chart.Rect.Height;
ZedGraph.LineObj stickOverlay = new ZedGraph.LineObj(annotationPair.Key, 1, annotationPair.Key, -stickLength);
//stickOverlay.IsClippedToChartRect = true;
stickOverlay.Location.CoordinateFrame = ZedGraph.CoordType.XScaleYChartFraction;
stickOverlay.Line.Width = annotationPair.Value.Width;
stickOverlay.Line.Color = annotationPair.Value.Color;
zedGraphControl1.GraphPane.GraphObjList.Add(stickOverlay);
dataLabels.Add(stickOverlay);
}
}
g.Dispose();
}
else
{
// remove labels
}
}
