/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="PaneBase"/> object from which to copy</param>
public PaneBase(PaneBase rhs)
{
// copy over all the value types
_isFontsScaled = rhs._isFontsScaled;
_isPenWidthScaled = rhs._isPenWidthScaled;
_titleGap = rhs._titleGap;
_baseDimension = rhs._baseDimension;
_margin = rhs._margin.Clone();
_rect = rhs._rect;
// Copy the reference types by cloning
_fill = rhs._fill.Clone();
_border = rhs._border.Clone();
_title = rhs._title.Clone();
_legend = rhs.Legend.Clone();
_title = rhs._title.Clone();
_graphObjList = rhs._graphObjList.Clone();
if (rhs._tag is ICloneable)
{
_tag = ((ICloneable)rhs._tag).Clone();
}
else
{
_tag = rhs._tag;
}
}
/// <summary>
/// Default constructor for the <see cref="PaneBase"/> class. Specifies the <see cref="Title"/> of
/// the <see cref="PaneBase"/>, and the size of the <see cref="Rect"/>.
/// </summary>
public PaneBase(string title, RectangleF paneRect)
{
_rect = paneRect;
_legend = new Legend();
_baseDimension = Default.BaseDimension;
_margin = new Margin();
_titleGap = Default.TitleGap;
_isFontsScaled = Default.IsFontsScaled;
_isPenWidthScaled = Default.IsPenWidthScaled;
_fill = new Fill(Default.FillColor);
_border = new Border(Default.IsBorderVisible, Default.BorderColor,
Default.BorderPenWidth);
_title = new GapLabel(title, Default.FontFamily,
Default.FontSize, Default.FontColor, Default.FontBold,
Default.FontItalic, Default.FontUnderline);
_title._fontSpec.Fill.IsVisible = false;
_title._fontSpec.Border.IsVisible = false;
_graphObjList = new GraphObjList();
_tag = null;
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphObjList"/> object from which to copy</param>
public GraphObjList(GraphObjList rhs)
{
foreach (GraphObj item in rhs)
{
this.Add((GraphObj)((ICloneable)item).Clone());
}
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphObjList"/> object from which to copy</param>
public GraphObjList(GraphObjList rhs)
{
for (var i = 0; i < rhs.list.Count; i++)
{
var item = rhs.list[i];
list.Add((GraphObj)((ICloneable)item).Clone());
}
}
public MSGraphPane(MSGraphPane other)
: base(other)
{
_currentItemType = other._currentItemType;
_pointAnnotations = new GraphObjList();
_manualLabels = new Dictionary<TextObj, RectangleF>();
_labelBoundsCache = other._labelBoundsCache;
}
/// <summary>
/// Find the pane and the object within that pane that lies closest to the specified
/// mouse (screen) point.
/// </summary>
/// <remarks>
/// This method first finds the <see cref="GraphPane"/> within the list that contains
/// the specified mouse point. It then calls the <see cref="GraphPane.FindNearestObject"/>
/// method to determine which object, if any, was clicked. With the exception of the
/// <see paramref="pane"/>, all the parameters in this method are identical to those
/// in the <see cref="GraphPane.FindNearestObject"/> method.
/// If the mouse point lies within the <see cref="PaneBase.Rect"/> of any
/// <see cref="GraphPane"/> item, then that pane will be returned (otherwise it will be
/// null). Further, within the selected pane, if the mouse point is within the
/// bounding box of any of the items (or in the case
/// of <see cref="ArrowObj"/> and <see cref="CurveItem"/>, within
/// <see cref="GraphPane.Default.NearestTol"/> pixels), then the object will be returned.
/// You must check the type of the object to determine what object was
/// selected (for example, "if ( object is Legend ) ..."). The
/// <see paramref="index"/> parameter returns the index number of the item
/// within the selected object (such as the point number within a
/// <see cref="CurveItem"/> object.
/// </remarks>
/// <param name="mousePt">The screen point, in pixel coordinates.</param>
/// <param name="g">
/// A graphic device object to be drawn into. This is normally e.Graphics from the
/// PaintEventArgs argument to the Paint() method.
/// </param>
/// <param name="pane">A reference to the <see cref="GraphPane"/> object that was clicked.</param>
/// <param name="nearestObj">A reference to the nearest object to the
/// specified screen point. This can be any of <see cref="Axis"/>,
/// <see cref="Legend"/>, <see cref="PaneBase.Title"/>,
/// <see cref="TextObj"/>, <see cref="ArrowObj"/>, or <see cref="CurveItem"/>.
/// Note: If the pane title is selected, then the <see cref="GraphPane"/> object
/// will be returned.
/// </param>
/// <param name="index">The index number of the item within the selected object
/// (where applicable). For example, for a <see cref="CurveItem"/> object,
/// <see paramref="index"/> will be the index number of the nearest data point,
/// accessible via <see cref="CurveItem.Points">CurveItem.Points[index]</see>.
/// index will be -1 if no data points are available.</param>
/// <returns>true if a <see cref="GraphPane"/> was found, false otherwise.</returns>
/// <seealso cref="GraphPane.FindNearestObject"/>
public bool FindNearestPaneObject(PointF mousePt, Graphics g, out GraphPane pane,
out object nearestObj, out int index)
{
pane = null;
nearestObj = null;
index = -1;
GraphObj saveGraphItem = null;
int saveIndex = -1;
float scaleFactor = CalcScaleFactor();
// See if the point is in a GraphObj
// If so, just save the object and index so we can see if other overlying objects were
// intersected as well.
if (GraphObjList.FindPoint(mousePt, this, g, scaleFactor, out index))
{
saveGraphItem = GraphObjList[index];
saveIndex = index;
// If it's an "In-Front" item, then just return it
if (saveGraphItem.ZOrder == ZOrder.A_InFront)
{
nearestObj = saveGraphItem;
index = saveIndex;
return(true);
}
}
foreach (GraphPane tPane in _paneList)
{
if (tPane.Rect.Contains(mousePt))
{
pane = tPane;
return(tPane.FindNearestObject(mousePt, g, out nearestObj, out index));
}
}
// If no items were found in the GraphPanes, then return the item found on the MasterPane (if any)
if (saveGraphItem != null)
{
nearestObj = saveGraphItem;
index = saveIndex;
return(true);
}
return(false);
}
public MSGraphPane(LabelBoundsCache labelBoundsCache = null)
{
Title.IsVisible = false;
Chart.Border.IsVisible = false;
Y2Axis.IsVisible = false;
X2Axis.IsVisible = false;
XAxis.MajorTic.IsOpposite = false;
YAxis.MajorTic.IsOpposite = false;
XAxis.MinorTic.IsOpposite = false;
YAxis.MinorTic.IsOpposite = false;
IsFontsScaled = false;
YAxis.Scale.MaxGrace = 0.1;
YAxis.MajorGrid.IsZeroLine = false; // Hide the y=0 line
LockYAxisAtZero = true;
_currentItemType = MSGraphItemType.unknown;
_pointAnnotations = new GraphObjList();
_manualLabels = new Dictionary<TextObj, RectangleF>();
_labelBoundsCache = labelBoundsCache ?? new LabelBoundsCache();
}
/// <summary>
/// Constructor for deserializing objects
/// </summary>
/// <param name="info">A <see cref="SerializationInfo"/> instance that defines the serialized data
/// </param>
/// <param name="context">A <see cref="StreamingContext"/> instance that contains the serialized data
/// </param>
protected PaneBase(SerializationInfo info, StreamingContext context)
{
// The schema value is just a file version parameter. You can use it to make future versions
// backwards compatible as new member variables are added to classes
int sch = info.GetInt32("schema");
_rect = (RectangleF)info.GetValue("rect", typeof(RectangleF));
_legend = (Legend)info.GetValue("legend", typeof(Legend));
_title = (GapLabel)info.GetValue("title", typeof(GapLabel));
//this.isShowTitle = info.GetBoolean( "isShowTitle" );
_isFontsScaled = info.GetBoolean("isFontsScaled");
_isPenWidthScaled = info.GetBoolean("isPenWidthScaled");
//this.fontSpec = (FontSpec) info.GetValue( "fontSpec" , typeof(FontSpec) );
_titleGap = info.GetSingle("titleGap");
_fill = (Fill)info.GetValue("fill", typeof(Fill));
_border = (Border)info.GetValue("border", typeof(Border));
_baseDimension = info.GetSingle("baseDimension");
_margin = (Margin)info.GetValue("margin", typeof(Margin));
_graphObjList = (GraphObjList)info.GetValue("graphObjList", typeof(GraphObjList));
_tag = info.GetValue("tag", typeof(object));
}
public virtual void Update (GraphItem item, pwiz.MSGraph.MSPointList pointList, GraphObjList annotations)
{
throw new NotImplementedException();
}
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)
{
///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
}
public override void Update( GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations )
{
double basePeakIntensity = 0;
double cutoff = 0;
foreach (var pointlist in points)
{
if (basePeakIntensity < pointlist.Y)
basePeakIntensity = pointlist.Y;
}
cutoff = basePeakIntensity * basePeakPercentage * 0.01;
if( !Enabled )
return;
if( !( item is MassSpectrum ) )
return; // throw exception?
GraphObjList list = annotations;
Peptide peptide;
try
{
peptide = new Peptide( sequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets );
} catch( Exception )
{
return;
}
//if (annotationPanels.peptideInfoGridView.InvokeRequired)
//{
// annotationPanels.peptideInfoGridView.BeginInvoke(new MethodInvoker(() => Update(item, points, annotations)));
// //return;
//}
var spectrum = ( item as MassSpectrum ).Element;
if (spectrum.precursors.Count > 0 && ionSeriesIsEnabled(IonSeries.Auto))
{
bool cid = (item as MassSpectrum).Element.precursors[0].activation.hasCVParam(CVID.MS_CID);
bool etd = (item as MassSpectrum).Element.precursors[0].activation.hasCVParam(CVID.MS_ETD);
ionSeries |= cid ? IonSeries.b | IonSeries.y : IonSeries.Off;
ionSeries |= etd ? IonSeries.c | IonSeries.zRadical : IonSeries.Off;
}
string unmodifiedSequence = peptide.sequence;
int sequenceLength = unmodifiedSequence.Length;
Fragmentation fragmentation = peptide.fragmentation( fragmentMassType == 0 ? true : false, true );
//test neutral
ModificationMap modifications = peptide.modifications();
///
#region adding labels for series a/b/c/x/y/z:::::::::naive fragmentation modeling
if (!showBasophileModel)
{
for (int i = 1; i < sequenceLength; ++i)
{
//test neutral loss
//note here the Cseq is slightly different than those in addFragmentSummary
string Nseq = peptide.sequence.Substring(0, i);
string Cseq = peptide.sequence.Substring(sequenceLength - i, i);
string NTempSeq = peptide.sequence.Substring(0, sequenceLength - i);
char[] Nseqchars = Nseq.ToCharArray();
char[] NTempSeqchars = NTempSeq.ToCharArray();
char[] seqchars = peptide.sequence.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 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[k] == 'Y'))
{
Nphosmodi++;
}
}
for (int k = 0; k < sequenceLength - i; k++)
{
if (Math.Round(modifications[k].monoisotopicDeltaMass()) == 80 && (seqchars[k] == 'S' || seqchars[k] == 'T' || seqchars[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 charge = min; charge <= max; ++charge)
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a", i, charge, fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b", i, charge, fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y", i, charge, fragmentation.y(i, charge));
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z", i, charge, fragmentation.z(i, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*", i, charge, fragmentation.zRadical(i, charge));
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c", i, charge, fragmentation.c(i, charge));
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x", i, charge, fragmentation.x(i, charge));
}
//test neutral loss
#region water loss
if (waterLoss == true)
{
if (Nseq.Contains("S") || Nseq.Contains("T") || Nseq.Contains("E") || Nseq.Contains("D"))
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a-water", i, charge, fragmentation.a(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b-water", i, charge, fragmentation.b(i, charge) - WATERMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c-water", i, charge, fragmentation.c(i, charge) - WATERMONOMASS / charge);
}
}
if (Cseq.Contains("S") || Cseq.Contains("T") || Cseq.Contains("E") || Cseq.Contains("D"))
{
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y-water", i, charge, fragmentation.y(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z-water", i, charge, fragmentation.z(i, charge) - WATERMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*-water", i, charge, fragmentation.zRadical(i, charge) - WATERMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x-water", i, charge, fragmentation.x(i, charge) - WATERMONOMASS / charge);
}
}
}
#endregion
//test neutral loss
#region ammonium loss
if (ammoniumLoss == true)
{
if (Nseq.Contains("R") || Nseq.Contains("K") || Nseq.Contains("Q") || Nseq.Contains("N"))
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a-ammonium", i, charge, fragmentation.a(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b-ammonium", i, charge, fragmentation.b(i, charge) - AMMONIUMMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c-ammonium", i, charge, fragmentation.c(i, charge) - AMMONIUMMONOMASS / charge);
}
}
if (Cseq.Contains("R") || Cseq.Contains("K") || Cseq.Contains("Q") || Cseq.Contains("N"))
{
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y-ammonium", i, charge, fragmentation.y(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z-ammonium", i, charge, fragmentation.z(i, charge) - AMMONIUMMONOMASS / charge);
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*-ammonium", i, charge, fragmentation.zRadical(i, charge) - AMMONIUMMONOMASS / charge);
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x-ammonium", i, charge, fragmentation.x(i, charge) - AMMONIUMMONOMASS / charge);
}
}
}
#endregion
//test neutral loss
#region phosphate loss
if (phosphateLoss == true)
{
int minNPhosphate = Math.Min(Nphosmodi, numPhosphate);
if (minNPhosphate > 0)
{
if (ionSeriesIsEnabled(IonSeries.a))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "a-" + k + "phos", i, charge, fragmentation.a(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (ionSeriesIsEnabled(IonSeries.b))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "b-" + k + "phos", i, charge, fragmentation.b(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c))
{
for (int k = 1; k <= minNPhosphate; k++)
{
addFragment(list, points, "c-" + k + "phos", i, charge, fragmentation.c(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
}
}
int minCPhosphate = Math.Min(Cphosmodi, numPhosphate);
if (minCPhosphate > 0)
{
if (ionSeriesIsEnabled(IonSeries.y))
{
for (int k = 1; k <= minCPhosphate; k++)
{
addFragment(list, points, "y-" + k + "phos", i, charge, fragmentation.y(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
if (ionSeriesIsEnabled(IonSeries.z))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "z-" + k + "phos", i, charge, fragmentation.z(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "z*-" + k + "phos", i, charge, fragmentation.zRadical(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.x))
{
for (int k = 1; k <= minCPhosphate; k++)
addFragment(list, points, "x-" + k + "phos", i, charge, fragmentation.x(i, charge) - k * PHOSPHATEMONOMASS / charge);
}
}
}
}
#endregion
}
}
}
//for basophile fragmentation modeling
else if (showBasophileModel)
{
//clear the panel
//annotationPanels.bCheckBox.Checked = false;
//annotationPanels.yCheckBox.Checked = false;
String peptideSeq = peptide.sequence;
int seqLength = peptideSeq.Length;
char[] seq = peptideSeq.ToCharArray();
int totalR = 0, totalK = 0, totalH = 0;
for (int i = 0; i < seqLength; ++i)
{
if (seq[i] == 'R')
++totalR;
else if (seq[i] == 'K')
++totalK;
else if (seq[i] == 'H')
++totalH;
}
for (int c = 1; c < seqLength; c++)
{
int totalNR = 0, totalNK = 0, totalNH = 0, totalNL = 0;
int totalCR = 0, totalCK = 0, totalCH = 0, totalCL = 0;
for (int i = 0; i < c; ++i)
{
if (seq[i] == 'R') { ++totalNR; }
else if (seq[i] == 'K') { ++totalNK; }
else if (seq[i] == 'H') { ++totalNH; }
}
totalNL = c;
totalCR = totalR - totalNR;
totalCK = totalK - totalNK;
totalCH = totalH - totalNH;
totalCL = seqLength - totalNL;
double y1_logit = 0.1098112 * totalNR + 0.2085831 * totalNK + 0.1512109 * totalNH + 0.0460839 * totalNL
- 0.3872417 * totalCR - 0.3684911 * totalCK - 0.1634741 * totalCH - 0.1693931 * totalCL + 1.2632997;
double y2_logit = -0.6345364 * totalNR - 0.3365917 * totalNK - 0.4577882 * totalNH - 0.1492703 * totalNL
+ 0.7738133 * totalCR + 0.6036758 * totalCK + 0.5942542 * totalCH + 0.0701467 * totalCL + 0.0806280;
double b1_logit = 0.0801432 * totalNR - 0.1088081 * totalNK - 0.1338220 * totalNH - 0.1413059 * totalNL
- 0.3157957 * totalCR - 0.2708274 * totalCK - 0.3703136 * totalCH + 0.0157418 * totalCL + 1.2124699;
double b2_logit = 0.8606449 * totalNR + 0.2763119 * totalNK + 0.4969152 * totalNH + 0.0685712 * totalNL
- 1.3346995 * totalCR - 1.0977316 * totalCK - 1.0973677 * totalCH - 0.2028884 * totalCL + 1.9355980;
if (ionSeriesIsEnabled(IonSeries.b))
{
if (b1_logit > -0.5) addFragment(list, points, "b", c, 1, fragmentation.b(c, 1));
if (b2_logit > 0) addFragment(list, points, "b", c, 2, fragmentation.b(c, 2));
}
if (ionSeriesIsEnabled(IonSeries.y))
{
if (y1_logit > -0.5) addFragment(list, points, "y", seqLength - c, 1, fragmentation.y(seqLength - c, 1));
if (y2_logit > -0.5) addFragment(list, points, "y", seqLength - c, 2, fragmentation.y(seqLength - c, 2));
}
//if (b1_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.b))
// addFragment(list, points, "b", c, 1, fragmentation.b(c, 1));
//if (b2_logit > 0)
// if (ionSeriesIsEnabled(IonSeries.b))
// addFragment(list, points, "b", c, 2, fragmentation.b(c, 2));
//if (y1_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.y))
// addFragment(list, points, "y", seqLength - c, 1, fragmentation.y(seqLength - c, 1));
//if (y2_logit > -0.5)
// if (ionSeriesIsEnabled(IonSeries.y))
// addFragment(list, points, "y", seqLength - c, 2, fragmentation.y(seqLength - c, 2));
}
}
#endregion
if ( showLadders || showFragmentationSummary)
{
//test neutral loss
//string topSeries = ionSeriesIsEnabled(IonSeries.a) ? "a" : ionSeriesIsEnabled(IonSeries.b) ? "b" : ionSeriesIsEnabled(IonSeries.c) ? "c" : "";
//string bottomSeries = ionSeriesIsEnabled(IonSeries.x) ? "x" : ionSeriesIsEnabled(IonSeries.y) ? "y" : ionSeriesIsEnabled(IonSeries.z) ? "z" : ionSeriesIsEnabled(IonSeries.zRadical) ? "z*" : "";
//if (showLadders)
// addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
//if (showFragmentationSummary)
// addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
string topSeries = "";
string bottomSeries = "";
if (ionSeriesIsEnabled(IonSeries.a))
{
topSeries = "a";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.b))
{
topSeries = "b";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.c))
{
topSeries = "c";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.x))
{
bottomSeries = "x";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.y))
{
bottomSeries = "y";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.z))
{
bottomSeries = "z";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
{
bottomSeries = "z*";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
}
annotationPanels.peptideInfoGridView.Rows.Clear();
if( spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam( CVID.MS_selected_ion_m_z ) &&
spectrum.precursors[0].selectedIons[0].hasCVParam( CVID.MS_charge_state ) )
{
double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam( CVID.MS_selected_ion_m_z ).value;
int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam( CVID.MS_charge_state ).value;
double calculatedMass = ( precursorMassType == 0 ? peptide.monoisotopicMass( chargeState ) : peptide.molecularWeight( chargeState ) ) * chargeState;
double observedMass = selectedMz * chargeState;
annotationPanels.peptideInfoGridView.Rows.Add( "Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass );
annotationPanels.peptideInfoGridView.Rows.Add( "Observed mass:", observedMass, "Mass error (ppm):", ( ( observedMass - calculatedMass ) / calculatedMass ) * 1e6 );
} else
annotationPanels.peptideInfoGridView.Rows.Add( "Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight() );
annotationPanels.peptideInfoGridView.Columns[1].DefaultCellStyle.Format = "F4";
foreach( DataGridViewRow row in annotationPanels.peptideInfoGridView.Rows )
row.Height = row.InheritedStyle.Font.Height + 2;
// TODO: fragmentInfoGridView is slow: make it faster, optional, or both!
annotationPanels.fragmentInfoGridView.SuspendLayout();
if( ionSeries > IonSeries.Auto )
{
if( annotationPanels.fragmentInfoGridView.Columns.Count == 0 )
{
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
annotationPanels.fragmentInfoGridView.Columns.Add("N", "#");
annotationPanels.fragmentInfoGridView.Columns.Add("Sequence", "seq");
annotationPanels.fragmentInfoGridView.Columns.Add("C", "#");
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
foreach( DataGridViewColumn column in annotationPanels.fragmentInfoGridView.Columns )
{
column.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
if( column.Name != "N" && column.Name != "C" && column.Name != "Sequence" )
column.DefaultCellStyle.Format = "F3";
}
}
while( annotationPanels.fragmentInfoGridView.Rows.Count > sequenceLength )
annotationPanels.fragmentInfoGridView.Rows.RemoveAt( annotationPanels.fragmentInfoGridView.Rows.Count - 1 );
if( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count > 0 )
annotationPanels.fragmentInfoGridView.Rows.Add( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count );
for( int i = 1; i <= sequenceLength; ++i )
{
int cTerminalLength = sequenceLength - i + 1;
var row = annotationPanels.fragmentInfoGridView.Rows[i - 1];
var values = new List<object>(10);
//var row = annotationPanels.fragmentInfoGridView.Rows.Add()];
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
if (i < sequenceLength)
values.Add(fragmentation.c(i, charge));
else
values.Add("");
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
if (i > 1)
values.Add(fragmentation.x(cTerminalLength, charge));
else
values.Add("");
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.y(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.z(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.zRadical(cTerminalLength, charge));
row.SetValues(values.ToArray());
}
//add my code in between
//the purpose is to switch the fragmentInfoGridView table into a html
//to solve the bug that the table can be copied, but the bold font information can not be copied
//basically, a stringbuilder object is created and going to copy values, formats from gridview, and then output
//currently the html output is only stored in local, and I am trying to adapt it into a applet-like viewer.
//first a stringbuilder is created
StringBuilder sb_original = new StringBuilder();
//Setting HTML and table tags
sb_original.Append("<html>");
sb_original.Append("<head>");
sb_original.Append("<title>fragmentGridView2HTML</title>");
sb_original.Append("</head>");
sb_original.Append("<body>");
sb_original.Append("<br>");
sb_original.AppendLine("<" + "table border='2' cellpadding='1' cellspacing='1'>");
sb_original.AppendLine("<tr>");
//setting table headers
//make them bold
for (int i = 0; i < annotationPanels.fragmentInfoGridView.Columns.Count; i++)
{
sb_original.AppendLine("<th>" + annotationPanels.fragmentInfoGridView.Columns[i].HeaderText + "</th>");
}
sb_original.AppendLine("</tr>");
//starting copying cells to html
foreach( DataGridViewRow row in annotationPanels.fragmentInfoGridView.Rows )
{
sb_original.AppendLine("<tr>");
row.Height = row.InheritedStyle.Font.Height + 2;
foreach( DataGridViewCell cell in row.Cells )
{
if (!(cell.Value is double))
{
//note: added two line here
sb_original.AppendLine("<td>" + cell.FormattedValue + "</td>");
continue;
}
double mz = (double) cell.Value;
int index = -1;
if( points != null )
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
//note: added two line here
//first is to pass value to sb;
//second is to change the cell fontstyle back to regular, if previouly bold
sb_original.AppendLine("<td>" + cell.FormattedValue + "</td>");
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Regular);
continue;
}
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
//note: added one line here
sb_original.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
}
}
sb_original.AppendLine("</tr>");
sb_original.AppendLine("</body>");
sb_original.AppendLine("</head>");
sb_original.AppendLine("</html>");
//for storation of stringbuilder into local file
//test only
string file_original = "C:\\Temp\\originalTable.html";
Directory.CreateDirectory(Path.GetDirectoryName(file_original));
TextWriter tw_original = new StreamWriter(file_original);
tw_original.WriteLine(sb_original.ToString());
tw_original.Flush();
tw_original.Close();
/////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////
//test neutral loss
#region Neutral Loss
StringBuilder sb_neutral = new StringBuilder();
if (waterLoss == false && ammoniumLoss == false && phosphateLoss == false)
{
sb_neutral = sb_original;
}
else //if any of the neutral loss is clicked
{
#region if any of the neutral loss is clicked
DataGridView neutralLossDataGridView = new DataGridView();
///
#region add first columns part
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "waterLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "ammoniumLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "phosphateLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"a" + charge.ToString() + "phosphateLoss",
"a" + (charge > 1 ? "(+" + charge.ToString() + ")-"+k+"PHO" : "-"+k+"PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "waterLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "ammoniumLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "phosphateLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"b" + charge.ToString() + "phosphateLoss",
"b" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "waterLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "ammoniumLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "phosphateLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"c" + charge.ToString() + "phosphateLoss",
"c" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
#endregion
neutralLossDataGridView.Columns.Add("N", "#");
neutralLossDataGridView.Columns.Add("Sequence", "seq");
neutralLossDataGridView.Columns.Add("C", "#");
///
#region add second columns part
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "waterLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "ammoniumLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "phosphateLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"x" + charge.ToString() + "phosphateLoss",
"x" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "waterLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "ammoniumLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "phosphateLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"y" + charge.ToString() + "phosphateLoss",
"y" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "waterLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "ammoniumLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "phosphateLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"z" + charge.ToString() + "phosphateLoss",
"z" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (waterLoss == true)
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "waterLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-H2O" : "-H2O"));
if (ammoniumLoss == true)
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "ammoniumLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-NH3" : "-NH3"));
if (phosphateLoss == true)
{
for (int k = 1; k<= numPhosphate; k++)
{
if (k == 1)
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "phosphateLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-PHO" : "-PHO"));
}
else
{
neutralLossDataGridView.Columns.Add(
"z*" + charge.ToString() + "phosphateLoss",
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")-" + k + "PHO" : "-" + k + "PHO"));
}
}
}
}
#endregion
while (neutralLossDataGridView.Rows.Count > sequenceLength)
neutralLossDataGridView.Rows.RemoveAt(neutralLossDataGridView.Rows.Count - 1);
if (sequenceLength - neutralLossDataGridView.Rows.Count > 0)
neutralLossDataGridView.Rows.Add(sequenceLength - neutralLossDataGridView.Rows.Count);
char[] aminoAcids = peptide.sequence.ToCharArray();
for (int i = 1; i <= sequenceLength; ++i)
{
int Nphosmodi = 0;
int Cphosmodi = 0;
int cTerminalLength = sequenceLength - i + 1;
var row = neutralLossDataGridView.Rows[i - 1];
var values = new List<object>();
//define the amino acides that are capable of losing water
//AA = S,T,E,D
bool nSTED = false;
bool cSTED = false;
bool nRKQN = false;
bool cRKQN = false;
for (int index = 0; index < i; index++)
{
if (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'E' || aminoAcids[index] == 'D')
nSTED = true;
if (aminoAcids[index] == 'R' || aminoAcids[index] == 'K' || aminoAcids[index] == 'Q' || aminoAcids[index] == 'N')
nRKQN = true;
if (Math.Round(modifications[index].monoisotopicDeltaMass()) == 80 && (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'Y'))
Nphosmodi++;
}
//here is more tricky. since the display is
//b1 ----- y(seq-1+1)
//b2 ----- y(seq-2+1)
for (int index = sequenceLength - 1; index >= i - 1; index--)
{
if (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'E' || aminoAcids[index] == 'D')
cSTED = true;
if (aminoAcids[index] == 'R' || aminoAcids[index] == 'K' || aminoAcids[index] == 'Q' || aminoAcids[index] == 'N')
cRKQN = true;
if (Math.Round(modifications[index].monoisotopicDeltaMass()) == 80 && (aminoAcids[index] == 'S' || aminoAcids[index] == 'T' || aminoAcids[index] == 'Y'))
Cphosmodi++;
}
int minNPhosphate = Math.Min(numPhosphate, Nphosmodi);
int minCPhosphate = Math.Min(numPhosphate, Cphosmodi);
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.a(i, charge), 3));
if (waterLoss == true)
{
if (nSTED) values.Add(Math.Round(fragmentation.a(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN) values.Add(Math.Round(fragmentation.a(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.a(i, charge) - k*PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.b(i, charge), 3));
if (waterLoss == true)
{
if (nSTED) values.Add(Math.Round(fragmentation.b(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN) values.Add(Math.Round(fragmentation.b(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.b(i, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
{
if (i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge), 3));
else
values.Add("-");
if (waterLoss == true)
{
if (nSTED && i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (nRKQN && i < sequenceLength)
values.Add(Math.Round(fragmentation.c(i, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
if (i < sequenceLength)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minNPhosphate)
{
values.Add(Math.Round(fragmentation.c(i, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
else values.Add("-");
}
}
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
{
if (i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge), 3));
else
values.Add("-");
if (waterLoss == true)
{
if (cSTED && i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN && i > 1)
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
if (i > 1)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.x(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
else values.Add("-");
}
}
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.y(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.z(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
{
values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge), 3));
if (waterLoss == true)
{
if (cSTED) values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - WATERMONOMASS / charge, 3));
else values.Add("-");
}
if (ammoniumLoss == true)
{
if (cRKQN) values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - AMMONIUMMONOMASS / charge, 3));
else values.Add("-");
}
if (phosphateLoss == true)
{
for (int k = 1; k <= numPhosphate; k++)
{
if (k <= minCPhosphate)
{
values.Add(Math.Round(fragmentation.zRadical(sequenceLength - i + 1, charge) - k * PHOSPHATEMONOMASS / charge, 3));
}
else
{
values.Add("-");
}
}
}
}
row.SetValues(values.ToArray());
}//end for
//add sb_neutral loss table
#region add sb_neutral loss table
sb_neutral.Append("<html>");
sb_neutral.Append("<head>");
sb_neutral.Append("<title>neutralLossFragmentGridView2HTML</title>");
sb_neutral.Append("</head>");
sb_neutral.Append("<body>");
sb_neutral.Append("<br>");
sb_neutral.AppendLine("<" + "table border='2' cellpadding='1' cellspacing='1'>");
sb_neutral.AppendLine("<tr>");
for (int i = 0; i < neutralLossDataGridView.Columns.Count; i++)
{
sb_neutral.AppendLine("<th>" + neutralLossDataGridView.Columns[i].HeaderText + "</th>");
}
foreach (DataGridViewRow row in neutralLossDataGridView.Rows)
{
sb_neutral.AppendLine("<tr>");
#region basepeakthresholding is false
if (basePeakThresholding == false)
{
foreach (DataGridViewCell cell in row.Cells)
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
//cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Regular);
continue;
}
//cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
}
}
#endregion
else//basepeakthresholding is true
{
int columnIndex = 0;
foreach (DataGridViewCell cell in row.Cells)
{
if (neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("H2O") || neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("NH3") || neutralLossDataGridView.Columns[columnIndex].HeaderText.Contains("PHO"))
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5) || points.FullList[index].Y < cutoff)
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
columnIndex++;
}
else
{
if (!(cell.Value is double))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
double mz = (double)cell.Value;
int index = -1;
if (points != null)
index = points.FullLowerBound(mz - 0.5);
if (index == -1 || points.FullList[index].X > (mz + 0.5))
{
sb_neutral.AppendLine("<td>" + cell.FormattedValue + "</td>");
columnIndex++;
continue;
}
sb_neutral.AppendLine("<td><b>" + cell.FormattedValue + "</b></td>");
columnIndex++;
}
}
}
}
sb_neutral.AppendLine("</tr>");
sb_neutral.AppendLine("</body>");
sb_neutral.AppendLine("</head>");
sb_neutral.AppendLine("</html>");
#endregion
#endregion
} //end of else
string file_neutral = "C:\\Temp\\neutralLossTable.html";
Directory.CreateDirectory(Path.GetDirectoryName(file_neutral));
TextWriter tw_neutral = new StreamWriter(file_neutral);
tw_neutral.WriteLine(sb_neutral.ToString());
tw_neutral.Flush();
tw_neutral.Close();
#endregion
}
else
annotationPanels.fragmentInfoGridView.Rows.Clear();
annotationPanels.fragmentInfoGridView.ResumeLayout();
}
private void AddRetentionTimeAnnotation(MSGraphPane graphPane, Graphics g, GraphObjList annotations,
PointF ptTop, string title, GraphObjType graphObjType, Color color, ScaledRetentionTime retentionTime)
{
string label = string.Format("{0}\n{1:F01}", title, retentionTime.DisplayTime); // Not L10N
FontSpec fontLabel = CreateFontSpec(color, _fontSpec.Size);
SizeF sizeLabel = fontLabel.MeasureString(g, label, graphPane.CalcScaleFactor());
PointF realTopPoint = ptTop;
ptTop = new PointF(0, ptTop.Y + sizeLabel.Height + 15);
float chartHeightWithLabel = graphPane.Chart.Rect.Height + sizeLabel.Height + 15;
double intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
LineObj stick = new LineObj(color, retentionTime.DisplayTime, intensityChartFraction, retentionTime.DisplayTime, 1)
{
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction },
ZOrder = ZOrder.E_BehindCurves,
Line = { Width = 1 },
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(stick);
ptTop = new PointF(0, ptTop.Y - 5);
intensityChartFraction = (ptTop.Y - realTopPoint.Y) / chartHeightWithLabel;
TextObj text = new TextObj(label, retentionTime.DisplayTime, intensityChartFraction,
CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Bottom)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = CreateFontSpec(color, _fontSpec.Size),
Tag = new GraphObjTag(this, graphObjType, retentionTime),
};
annotations.Add(text);
}
private void 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>
/// Get all annotation label text, for testing purposes
/// </summary>
public IEnumerable<string> GetAnnotationLabelStrings()
{
foreach (CurveItem item in CurveList)
{
var info = item.Tag as IMSGraphItemExtended;
if (info == null || string.IsNullOrEmpty(info.ToString()))
continue;
var points = item.Points as MSPointList;
if (points == null)
continue;
var listAnnotations = new GraphObjList();
info.AddPreCurveAnnotations(this, null, points, listAnnotations);
foreach (var annotation in listAnnotations)
{
var textObj = annotation as TextObj;
if (textObj != null)
yield return textObj.Text;
}
foreach (var pt in points.FullList)
{
var annotation = info.AnnotatePoint(pt);
if (annotation != null)
yield return annotation.Label;
}
}
}
public override void UpdateGraph(bool checkData)
{
_dotpLabels = new GraphObjList();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
EmptyGraph(document);
return;
}
BarSettings.Type = BarType;
Title.Text = null;
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
bool optimizationPresent = results.Chromatograms.Contains(
chrom => chrom.OptimizationFunction != null);
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType == DisplayTypeChrom.single)
{
BarSettings.Type = BarType.Cluster;
}
else
{
SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent;
parentNode = parentTreeNode.Model;
identityPath = parentTreeNode.Path;
}
}
// If the selected node is a peptide with one child, then show the children,
// unless chromatogram display type is total
else if (selectedTreeNode is PeptideTreeNode)
{
var children = ((PeptideDocNode) selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
else
{
BarSettings.Type = BarType.Cluster;
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_peak_area_graph;
CanShowPeakAreaLegend = false;
CanShowDotProduct = false;
return;
}
var parentGroupNode = parentNode as TransitionGroupDocNode;
// If a precursor is going to be displayed with display type single
if (parentGroupNode != null && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!optimizationPresent)
displayType = DisplayTypeChrom.all;
// Otherwise, do not stack the bars
else
BarSettings.Type = BarType.Cluster;
}
int ratioIndex = AreaGraphData.RATIO_INDEX_NONE;
var standardType = IsotopeLabelType.light;
var areaView = AreaGraphController.AreaView;
if (areaView == AreaNormalizeToView.area_ratio_view)
{
ratioIndex = GraphSummary.RatioIndex;
standardType = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[ratioIndex];
}
else if (areaView == AreaNormalizeToView.area_global_standard_view)
{
if (document.Settings.HasGlobalStandardArea)
ratioIndex = ChromInfo.RATIO_INDEX_GLOBAL_STANDARDS;
else
areaView = AreaNormalizeToView.none;
}
// Sets normalizeData to optimization, maximum_stack, maximum, total, or none
AreaNormalizeToData normalizeData;
if (optimizationPresent && displayType == DisplayTypeChrom.single &&
areaView == AreaNormalizeToView.area_percent_view)
{
normalizeData = AreaNormalizeToData.optimization;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
normalizeData = BarSettings.Type == BarType.Stack
? AreaNormalizeToData.maximum_stack
: AreaNormalizeToData.maximum;
}
else if (BarSettings.Type == BarType.PercentStack)
{
normalizeData = AreaNormalizeToData.total;
}
else
{
normalizeData = AreaNormalizeToData.none;
}
// Calculate graph data points
// IsExpectedVisible depends on ExpectedVisible
ExpectedVisible = AreaExpectedValue.none;
if (parentGroupNode != null &&
displayType != DisplayTypeChrom.total &&
areaView != AreaNormalizeToView.area_ratio_view &&
!(optimizationPresent && displayType == DisplayTypeChrom.single))
{
var displayTrans = GraphChromatogram.GetDisplayTransitions(parentGroupNode, displayType).ToArray();
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = document.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if (isFullScanMs)
{
if (!isShowingMsMs && parentGroupNode.HasIsotopeDist)
ExpectedVisible = AreaExpectedValue.isotope_dist;
}
else
{
if (parentGroupNode.HasLibInfo)
ExpectedVisible = AreaExpectedValue.library;
}
}
var expectedValue = IsExpectedVisible ? ExpectedVisible : AreaExpectedValue.none;
var replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
var graphData = new AreaGraphData(document,
parentNode,
displayType,
replicateGroupOp,
ratioIndex,
normalizeData,
expectedValue,
PaneKey);
var aggregateOp = replicateGroupOp.AggregateOp;
// Avoid stacking CVs
if (aggregateOp.Cv || aggregateOp.CvDecimal)
BarSettings.Type = BarType.Cluster;
int countNodes = graphData.DocNodes.Count;
if (countNodes == 0)
ExpectedVisible = AreaExpectedValue.none;
CanShowDotProduct = ExpectedVisible != AreaExpectedValue.none &&
areaView != AreaNormalizeToView.area_percent_view;
CanShowPeakAreaLegend = countNodes != 0;
InitFromData(graphData);
// Add data to the graph
int selectedReplicateIndex = SelectedIndex;
if (IsExpectedVisible)
{
if (GraphSummary.ActiveLibrary)
selectedReplicateIndex = 0;
}
double maxArea = -double.MaxValue;
double sumArea = 0;
// An array to keep track of height of all bars to determine
// where each dot product annotation (if showing) should be placed
var sumAreas = new double[graphData.ReplicateGroups.Count];
// If only one bar to show, then use cluster instead of stack bar type, since nothing to stack
// Important for mean error bar checking below
if (BarSettings.Type == BarType.Stack && countNodes == 1 && graphData.PointPairLists[0].Count == 1)
BarSettings.Type = BarType.Cluster;
int colorOffset = 0;
if(parentGroupNode != null)
{
// We want the product ion colors to stay the same whether they are displayed:
// 1. In a single pane with the precursor ions (Transitions -> All)
// 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph)
// 3. In a single pane by themselves (Transition -> Products)
// We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors.
var nodeDisplayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
if (displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && !optimizationPresent)))
{
colorOffset =
GraphChromatogram.GetDisplayTransitions(parentGroupNode, DisplayTypeChrom.precursors).Count();
}
}
int iColor = 0, iCharge = -1;
int? charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
for (int i = 0; i < countNodes; i++)
{
var docNode = graphData.DocNodes[i];
var pointPairLists = graphData.PointPairLists[i];
int numSteps = pointPairLists.Count/2;
for (int iStep = 0; iStep < pointPairLists.Count; iStep++)
{
int step = iStep - numSteps;
var pointPairList = pointPairLists[iStep];
Color color;
var nodeGroup = docNode as TransitionGroupDocNode;
if (parentNode is PeptideDocNode)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Length];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor%COLORS_GROUPS.Length];
}
else if (docNode.Equals(selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Length];
}
iColor++;
// If showing ratios, do not add the standard type to the graph,
// since it will always be empty, but make sure the colors still
// correspond with the other graphs.
if (nodeGroup != null && ratioIndex >= 0)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (ReferenceEquals(labelType, standardType))
continue;
}
string label = graphData.DocNodeLabels[i];
if (step != 0)
label = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Step__0_, step);
BarItem curveItem;
// Only use a MeanErrorBarItem if bars are not going to be stacked.
// TODO(nicksh): AreaGraphData.NormalizeTo does not know about MeanErrorBarItem
if (BarSettings.Type != BarType.Stack && BarSettings.Type != BarType.PercentStack && normalizeData == AreaNormalizeToData.none)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new BarItem(label, pointPairList, color);
}
if (0 <= selectedReplicateIndex && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
sumArea += pointPair.Y;
maxArea = Math.Max(maxArea, pointPair.Y);
}
}
// Add area for this transition to each area entry
AddAreasToSums(pointPairList, sumAreas);
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
ParentGroupNode = parentGroupNode;
SumAreas = sumAreas;
// Draw a box around the currently selected replicate
if (ShowSelection && maxArea > -double.MaxValue)
{
double yValue;
switch (BarSettings.Type)
{
case BarType.Stack:
// The Math.Min(sumArea, .999) makes sure that if graph is in normalized view
// height of the selection rectangle does not exceed 1, so that top of the rectangle
// can be viewed when y-axis scale maximum is at 1
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(sumArea, .999) : sumArea);
break;
case BarType.PercentStack:
yValue = 99.99;
break;
default:
// Scale the selection box to fit exactly the bar height
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(maxArea, .999) : maxArea);
break;
}
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, yValue, 0.99,
yValue, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
bool resetAxes = (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id));
_parentNode = parentNode;
UpdateAxes(resetAxes, aggregateOp, normalizeData, areaView, standardType);
}
/// <summary>
/// Default constructor for the <see cref="PaneBase"/> class. Specifies the <see cref="Title"/> of
/// the <see cref="PaneBase"/>, and the size of the <see cref="Rect"/>.
/// </summary>
public PaneBase( string title, RectangleF paneRect )
{
_rect = paneRect;
_legend = new Legend();
_baseDimension = Default.BaseDimension;
_margin = new Margin();
_titleGap = Default.TitleGap;
_isFontsScaled = Default.IsFontsScaled;
_isPenWidthScaled = Default.IsPenWidthScaled;
_fill = new Fill( Default.FillColor );
_border = new Border( Default.IsBorderVisible, Default.BorderColor,
Default.BorderPenWidth );
_title = new GapLabel( title, Default.FontFamily,
Default.FontSize, Default.FontColor, Default.FontBold,
Default.FontItalic, Default.FontUnderline );
_title._fontSpec.Fill.IsVisible = false;
_title._fontSpec.Border.IsVisible = false;
_graphObjList = new GraphObjList();
_tag = null;
}
/// <summary>
/// Constructor for deserializing objects
/// </summary>
/// <param name="info">A <see cref="SerializationInfo"/> instance that defines the serialized data
/// </param>
/// <param name="context">A <see cref="StreamingContext"/> instance that contains the serialized data
/// </param>
protected PaneBase( SerializationInfo info, StreamingContext context )
{
// The schema value is just a file version parameter. You can use it to make future versions
// backwards compatible as new member variables are added to classes
int sch = info.GetInt32( "schema" );
_rect = (RectangleF) info.GetValue( "rect", typeof(RectangleF) );
_legend = (Legend) info.GetValue( "legend", typeof(Legend) );
_title = (GapLabel) info.GetValue( "title", typeof(GapLabel) );
//this.isShowTitle = info.GetBoolean( "isShowTitle" );
_isFontsScaled = info.GetBoolean( "isFontsScaled" );
_isPenWidthScaled = info.GetBoolean( "isPenWidthScaled" );
//this.fontSpec = (FontSpec) info.GetValue( "fontSpec" , typeof(FontSpec) );
_titleGap = info.GetSingle( "titleGap" );
_fill = (Fill) info.GetValue( "fill", typeof(Fill) );
_border = (Border) info.GetValue( "border", typeof(Border) );
_baseDimension = info.GetSingle( "baseDimension" );
_margin = (Margin)info.GetValue( "margin", typeof( Margin ) );
_graphObjList = (GraphObjList) info.GetValue( "graphObjList", typeof(GraphObjList) );
_tag = info.GetValue( "tag", typeof(object) );
}
public override void Update (GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations)
{
if (!Enabled)
return;
if (!(item is MassSpectrum))
return; // throw exception?
GraphObjList list = annotations;
Peptide peptide;
try
{
peptide = new Peptide(sequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
}
catch (Exception)
{
return;
}
var spectrum = (item as MassSpectrum).Element;
if (ReferenceEquals(manualTolerance, null))
{
MZTolerance maxTolerance = new MZTolerance(0.5);
foreach (var scan in spectrum.scanList.scans.Where(o => o.instrumentConfiguration != null))
{
// assume the last analyzer of the instrument configuration is responsible for the resolution
if (scan.instrumentConfiguration.componentList.Count == 0)
continue;
var analyzer = scan.instrumentConfiguration.componentList.Where(o => o.type == ComponentType.ComponentType_Analyzer).Last().cvParamChild(CVID.MS_mass_analyzer_type);
if (analyzer.cvid == CVID.CVID_Unknown)
continue;
MZTolerance analyzerTolerance = null;
foreach (var kvp in mzToleranceByAnalyzer)
if (CV.cvIsA(analyzer.cvid, kvp.Key))
{
analyzerTolerance = kvp.Value;
break;
}
if (analyzerTolerance == null)
continue;
if (maxTolerance.units == analyzerTolerance.units)
{
if (maxTolerance.value < analyzerTolerance.value)
maxTolerance = analyzerTolerance;
}
else if (analyzerTolerance.units == MZTolerance.Units.PPM)
maxTolerance = analyzerTolerance;
}
tolerance = maxTolerance;
}
else
tolerance = manualTolerance;
if (ionSeriesIsEnabled(IonSeries.Auto))
foreach (var precursor in spectrum.precursors)
foreach (var method in precursor.activation.cvParamChildren(CVID.MS_dissociation_method))
{
if (!ionSeriesByDissociationMethod.Contains(method.cvid))
ionSeries = IonSeries.All;
else
ionSeries |= ionSeriesByDissociationMethod[method.cvid];
}
int nSeries = (ionSeriesIsEnabled(IonSeries.a) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.b) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.c) ? 1 : 0);
int cSeries = (ionSeriesIsEnabled(IonSeries.x) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.y) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.z) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.zRadical) ? 1 : 0);
showLadders = showLadders && nSeries < 2 && cSeries < 2;
string unmodifiedSequence = peptide.sequence;
int sequenceLength = unmodifiedSequence.Length;
Fragmentation fragmentation = peptide.fragmentation(fragmentMassType == 0 ? true : false, true);
for (int i = 1; i <= sequenceLength; ++i)
{
if (ionSeriesIsEnabled(IonSeries.Immonium))
addFragment(list, points, "immonium-" + unmodifiedSequence[i - 1], 0, 1, immoniumIonByResidue[unmodifiedSequence[i - 1]]);
for (int charge = min; charge <= max; ++charge)
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a", i, charge, fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b", i, charge, fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y", i, charge, fragmentation.y(i, charge));
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z", i, charge, fragmentation.z(i, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*", i, charge, fragmentation.zRadical(i, charge));
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c", i, charge, fragmentation.c(i, charge));
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x", i, charge, fragmentation.x(i, charge));
}
}
}
if (showLadders || showFragmentationSummary)
{
string topSeries = ionSeriesIsEnabled(IonSeries.a) ? "a" : ionSeriesIsEnabled(IonSeries.b) ? "b" : ionSeriesIsEnabled(IonSeries.c) ? "c" : "";
string bottomSeries = ionSeriesIsEnabled(IonSeries.x) ? "x" : ionSeriesIsEnabled(IonSeries.y) ? "y" : ionSeriesIsEnabled(IonSeries.z) ? "z" : ionSeriesIsEnabled(IonSeries.zRadical) ? "z*" : "";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
// fill peptide info table
annotationPanels.peptideInfoGridView.Rows.Clear();
if (spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam(CVID.MS_selected_ion_m_z) &&
spectrum.precursors[0].selectedIons[0].hasCVParam(CVID.MS_charge_state))
{
double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam(CVID.MS_selected_ion_m_z).value;
int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam(CVID.MS_charge_state).value;
double calculatedMass = (precursorMassType == 0 ? peptide.monoisotopicMass(chargeState) : peptide.molecularWeight(chargeState)) * chargeState;
double observedMass = selectedMz * chargeState;
annotationPanels.peptideInfoGridView.Rows.Add("Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass);
annotationPanels.peptideInfoGridView.Rows.Add("Observed mass:", observedMass, "Mass error (ppm):", ((observedMass - calculatedMass) / calculatedMass) * 1e6);
}
else
annotationPanels.peptideInfoGridView.Rows.Add("Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight());
annotationPanels.peptideInfoGridView.Columns[1].DefaultCellStyle.Format = "F4";
foreach (DataGridViewRow row in annotationPanels.peptideInfoGridView.Rows)
row.Height = row.InheritedStyle.Font.Height + 2;
// show/hide/update fragment table
if (!annotationPanels.showFragmentationTableCheckBox.Checked || ionSeries <= IonSeries.Auto)
{
annotationPanels.fragmentInfoGridView.Visible = false;
annotationPanels.fragmentInfoGridView.Rows.Clear();
return;
}
annotationPanels.fragmentInfoGridView.Visible = true;
annotationPanels.fragmentInfoGridView.SuspendLayout();
if (annotationPanels.fragmentInfoGridView.Columns.Count == 0)
{
#region Add columns for fragment types
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
annotationPanels.fragmentInfoGridView.Columns.Add("N", "");
annotationPanels.fragmentInfoGridView.Columns.Add("Sequence", "");
annotationPanels.fragmentInfoGridView.Columns.Add("C", "");
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
#endregion
foreach (DataGridViewColumn column in annotationPanels.fragmentInfoGridView.Columns)
{
column.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
if (column.Name != "N" && column.Name != "C" && column.Name != "Sequence")
column.DefaultCellStyle.Format = "F3";
}
}
while (annotationPanels.fragmentInfoGridView.Rows.Count > sequenceLength)
annotationPanels.fragmentInfoGridView.Rows.RemoveAt(annotationPanels.fragmentInfoGridView.Rows.Count - 1);
if (sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count > 0)
annotationPanels.fragmentInfoGridView.Rows.Add(sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count);
for (int i = 1; i <= sequenceLength; ++i)
{
int cTerminalLength = sequenceLength - i + 1;
var row = annotationPanels.fragmentInfoGridView.Rows[i - 1];
var values = new List<object>(10);
//var row = annotationPanels.fragmentInfoGridView.Rows.Add()];
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
if (i < sequenceLength)
values.Add(fragmentation.c(i, charge));
else
values.Add("");
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
if (i > 1)
values.Add(fragmentation.x(cTerminalLength, charge));
else
values.Add("");
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.y(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.z(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.zRadical(cTerminalLength, charge));
row.SetValues(values.ToArray());
}
foreach (DataGridViewRow row in annotationPanels.fragmentInfoGridView.Rows)
{
row.Height = row.InheritedStyle.Font.Height + 2;
foreach (DataGridViewCell cell in row.Cells)
{
if (!(cell.Value is double))
continue;
double mz = (double) cell.Value;
if (findPointWithTolerance(points, mz, tolerance) > -1)
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
else
cell.Style.Font = annotationPanels.fragmentInfoGridView.Font;
}
}
annotationPanels.fragmentInfoGridView.ResumeLayout();
}
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;
}
}
}
public override void Update( GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations )
{
if( !Enabled )
return;
if( !( item is MassSpectrum ) )
return; // throw exception?
GraphObjList list = annotations;
Peptide peptide;
try
{
peptide = new Peptide( currentSequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets );
} catch( Exception )
{
return;
}
string unmodifiedSequence = peptide.sequence;
int sequenceLength = unmodifiedSequence.Length;
Fragmentation fragmentation = peptide.fragmentation( fragmentMassType == 0 ? true : false, true );
// Keeps track of number of fragments predicted and matched in each ion series
numFragmentsMatched.Clear();
numFragmentsPredicted.Clear();
for( int charge = min; charge <= max; ++charge )
{
for( int i = 1; i <= sequenceLength; ++i )
{
if( a ) addFragment( list, points, "a", i, charge, fragmentation.a( i, charge ) );
if( b ) addFragment( list, points, "b", i, charge, fragmentation.b( i, charge ) );
if( y ) addFragment( list, points, "y", i, charge, fragmentation.y( i, charge ) );
if( z ) addFragment( list, points, "z", i, charge, fragmentation.z( i, charge ) );
if( zRadical ) addFragment( list, points, "z*", i, charge, fragmentation.zRadical( i, charge ) );
if( i < sequenceLength )
{
if( c ) addFragment( list, points, "c", i, charge, fragmentation.c( i, charge ) );
if( x ) addFragment( list, points, "x", i, charge, fragmentation.x( i, charge ) );
}
}
}
if( showLadders )
{
string topSeries = a ? "a" : b ? "b" : c ? "c" : "";
string bottomSeries = x ? "x" : y ? "y" : z ? "z" : zRadical ? "z*" : "";
addIonSeries( list, points, peptide, fragmentation, topSeries, bottomSeries );
}
// fill peptide info table
annotationPanels.peptideInfoGridView.Rows.Clear();
var spectrum = ( item as MassSpectrum ).Element;
//if( spectrum.precursors.Count > 0 &&
// spectrum.precursors[0].selectedIons.Count > 0 &&
// spectrum.precursors[0].selectedIons[0].hasCVParam( pwiz.CLI.cv.CVID.MS_selected_ion_m_z ) &&
// spectrum.precursors[0].selectedIons[0].hasCVParam( pwiz.CLI.cv.CVID.MS_charge_state ) )
//{
// double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam( pwiz.CLI.cv.CVID.MS_selected_ion_m_z ).value;
// int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam( pwiz.CLI.cv.CVID.MS_charge_state ).value;
// double calculatedMass = ( precursorMassType == 0 ? peptide.monoisotopicMass( chargeState ) : peptide.molecularWeight( chargeState ) ) * chargeState;
// double observedMass = selectedMz * chargeState;
// annotationPanels.peptideInfoGridView.Rows.Add( "Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass );
// annotationPanels.peptideInfoGridView.Rows.Add( "Observed mass:", observedMass, "Mass error (ppm):", ( ( observedMass - calculatedMass ) / calculatedMass ) * 1e6 );
//} else
// annotationPanels.peptideInfoGridView.Rows.Add( "Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight() );
if (spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam(pwiz.CLI.cv.CVID.MS_selected_ion_m_z))
{
double selectedMz = (double)spectrum.precursors[0].selectedIons[0].cvParam(pwiz.CLI.cv.CVID.MS_selected_ion_m_z).value;
// Add xcorr score
ZedGraph.IPointList peaks = (item as MassSpectrum).Points;
List<ScoringUtils.Peak> rawPeaks = new List<ScoringUtils.Peak>();
for (int i = 0; i < peaks.Count; ++i)
rawPeaks.Add(new ScoringUtils.Peak(peaks[i].X, peaks[i].Y));
// Remove the precursor and associated neutral loss peaks
ScoringUtils.erasePrecursorIons(selectedMz, ref rawPeaks); //selectedMz = precursorMz
if (spectrum.precursors[0].selectedIons[0].hasCVParam(pwiz.CLI.cv.CVID.MS_charge_state)) // known precursor charge state
{
int chargeState = (int)spectrum.precursors[0].selectedIons[0].cvParam(pwiz.CLI.cv.CVID.MS_charge_state).value;
double calculatedMass = (precursorMassType == 0 ? peptide.monoisotopicMass(chargeState) : peptide.molecularWeight(chargeState)) * chargeState;
double observedMass = selectedMz * chargeState;
// compute XCorr
double precursorMH = (selectedMz * chargeState) - ((chargeState - 1) * 1.007276);
double xcorr = ScoringUtils.computeXCorr(rawPeaks, peptide, precursorMH);
annotationPanels.peptideInfoGridView.Rows.Add("Observed precursor charge:", chargeState, "XCorr:", xcorr);
annotationPanels.peptideInfoGridView.Rows.Add("Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass);
annotationPanels.peptideInfoGridView.Rows.Add("Observed mass:", observedMass, "Mass error (ppm):", ((observedMass - calculatedMass) / calculatedMass) * 1e6);
}
else // unknown precursor charge state, assume +2 or +3
{
int[] assumedChargeStates = new int[2] { 2, 3 };
foreach (int chargeState in assumedChargeStates)
{
double calculatedMass = (precursorMassType == 0 ? peptide.monoisotopicMass(chargeState) : peptide.molecularWeight(chargeState)) * chargeState;
double observedMass = selectedMz * chargeState;
// compute XCorr
double precursorMH = (selectedMz * chargeState) - ((chargeState - 1) * 1.007276);
double xcorr = ScoringUtils.computeXCorr(rawPeaks, peptide, precursorMH);
annotationPanels.peptideInfoGridView.Rows.Add("Assumed precursor charge:", chargeState, "XCorr:", xcorr);
//annotationPanels.peptideInfoGridView.Rows.Add("Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass);
//annotationPanels.peptideInfoGridView.Rows.Add("Observed mass:", observedMass, "Mass error (ppm):", ((observedMass - calculatedMass) / calculatedMass) * 1e6);
}
}
}
else
annotationPanels.peptideInfoGridView.Rows.Add("Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight());
// Adds number of fragments matched/predicted in each ion series
foreach(var ionSeries in numFragmentsMatched.Keys)
annotationPanels.peptideInfoGridView.Rows.Add( ionSeries+" (matched/predicted):", numFragmentsMatched[ionSeries].Count +"/" + numFragmentsPredicted[ionSeries].Count);
annotationPanels.peptideInfoGridView.Columns[1].DefaultCellStyle.Format = "F4";
foreach( DataGridViewRow row in annotationPanels.peptideInfoGridView.Rows )
row.Height = row.InheritedStyle.Font.Height + 2;
annotationPanels.fragmentInfoGridView.SuspendLayout();
if( a || b || c || x || y || z || zRadical )
{
if( annotationPanels.fragmentInfoGridView.Columns.Count == 0 )
{
#region Add columns for fragment types
if( a )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"a" + charge.ToString(),
"a" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
if( b )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"b" + charge.ToString(),
"b" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
if( c )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"c" + charge.ToString(),
"c" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
annotationPanels.fragmentInfoGridView.Columns.Add( "N", "" );
annotationPanels.fragmentInfoGridView.Columns.Add( "Sequence", "" );
annotationPanels.fragmentInfoGridView.Columns.Add( "C", "" );
if( x )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"x" + charge.ToString(),
"x" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
if( y )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"y" + charge.ToString(),
"y" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
if( z )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"z" + charge.ToString(),
"z" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
if( zRadical )
for( int charge = min; charge <= max; ++charge )
annotationPanels.fragmentInfoGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + ( charge > 1 ? "(+" + charge.ToString() + ")" : "" ) );
#endregion
foreach( DataGridViewColumn column in annotationPanels.fragmentInfoGridView.Columns )
{
column.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
if( column.Name != "N" && column.Name != "C" && column.Name != "Sequence" )
column.DefaultCellStyle.Format = "F3";
}
}
while( annotationPanels.fragmentInfoGridView.Rows.Count > sequenceLength )
annotationPanels.fragmentInfoGridView.Rows.RemoveAt( annotationPanels.fragmentInfoGridView.Rows.Count - 1 );
if( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count > 0 )
annotationPanels.fragmentInfoGridView.Rows.Add( sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count );
for( int i = 1; i <= sequenceLength; ++i )
{
int cTerminalLength = sequenceLength - i + 1;
var row = annotationPanels.fragmentInfoGridView.Rows[i - 1];
var values = new List<object>( 10 );
//var row = annotationPanels.fragmentInfoGridView.Rows.Add()];
if( a )
for( int charge = min; charge <= max; ++charge )
values.Add( fragmentation.a( i, charge ) );
if( b )
for( int charge = min; charge <= max; ++charge )
values.Add( fragmentation.b( i, charge ) );
if( c )
for( int charge = min; charge <= max; ++charge )
if( i < sequenceLength )
values.Add( fragmentation.c( i, charge ) );
else
values.Add( "" );
values.Add( i );
values.Add( unmodifiedSequence[i - 1] );
values.Add( cTerminalLength );
if( x )
for( int charge = min; charge <= max; ++charge )
if( i > 1 )
values.Add( fragmentation.x( cTerminalLength, charge ) );
else
values.Add( "" );
if( y )
for( int charge = min; charge <= max; ++charge )
values.Add( fragmentation.y( cTerminalLength, charge ) );
if( z )
for( int charge = min; charge <= max; ++charge )
values.Add( fragmentation.z( cTerminalLength, charge ) );
if( zRadical )
for( int charge = min; charge <= max; ++charge )
values.Add( fragmentation.zRadical( cTerminalLength, charge ) );
row.SetValues( values.ToArray() );
}
foreach( DataGridViewRow row in annotationPanels.fragmentInfoGridView.Rows )
{
row.Height = row.InheritedStyle.Font.Height + 2;
foreach( DataGridViewCell cell in row.Cells )
{
if( !( cell.Value is double ) )
continue;
double mz = (double) cell.Value;
int index = -1;
if( points != null )
index = points.LowerBound( mz - 0.5 );
if( index == -1 || points.ScaledList[index].X > ( mz + 0.5 ) )
continue;
cell.Style.Font = new Font( annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold );
}
}
}
else
annotationPanels.fragmentInfoGridView.Rows.Clear();
annotationPanels.fragmentInfoGridView.ResumeLayout();
}
///<summary>Adds user requested ion series to the fragmentation summary.</summary>
private void addFragmentationSummary (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
{
int ionSeriesChargeState = min;
string sequence = peptide.sequence;
ModificationMap modifications = peptide.modifications();
// Select the color for the ion series.
Color topSeriesColor;
Color bottomSeriesColor;
switch (topSeries)
{
default: topSeriesColor = Color.Gray; break;
case "a": topSeriesColor = Color.YellowGreen; break;
case "b": topSeriesColor = Color.BlueViolet; break;
case "c": topSeriesColor = Color.Orange; break;
}
switch (bottomSeries)
{
default: bottomSeriesColor = Color.Gray; break;
case "x": bottomSeriesColor = Color.Green; break;
case "y": bottomSeriesColor = Color.Blue; break;
case "z": bottomSeriesColor = Color.OrangeRed; break;
case "z*": bottomSeriesColor = Color.Crimson; break;
}
// Ion series offsets. These offsets control where on the chart a particular ion series get displayed
double seriesTopLeftOffset = 0.2;
// Set the constants for starting the label paint
double topSeriesLeftPoint = 0.025;
double residueWidth = 0.5 / ((double) sequence.Length);
double topSeriesRightPoint = topSeriesLeftPoint + 0.5 - residueWidth;
double tickStart = residueWidth / 2.0;
// Process all the series except c and x
for (int i = 1; i <= sequence.Length; ++i)
{
double topSeriesFragmentMZ = 0.0;
double bottomSeriesFragmentMZ = 0.0;
switch (topSeries)
{
case "a": topSeriesFragmentMZ = fragmentation.a(i, ionSeriesChargeState); break;
case "b": topSeriesFragmentMZ = fragmentation.b(i, ionSeriesChargeState); break;
case "c": if (i < sequence.Length) topSeriesFragmentMZ = fragmentation.c(i, ionSeriesChargeState); break;
default: continue;
}
switch (bottomSeries)
{
case "x": if (i < sequence.Length) bottomSeriesFragmentMZ = fragmentation.x(i, ionSeriesChargeState); break;
case "y": bottomSeriesFragmentMZ = fragmentation.y(i, ionSeriesChargeState); break;
case "z": bottomSeriesFragmentMZ = fragmentation.z(i, ionSeriesChargeState); break;
case "z*": bottomSeriesFragmentMZ = fragmentation.zRadical(i, ionSeriesChargeState); break;
default: continue;
}
// Check if the top and bottom fragments have evidence
bool topSeriesHasMatch = false;
bool bottomSeriesHasMatch = false;
if (points != null)
{
topSeriesHasMatch = topSeriesFragmentMZ > 0 && findPointWithTolerance(points, topSeriesFragmentMZ, tolerance) > -1;
bottomSeriesHasMatch = bottomSeriesFragmentMZ > 0 && findPointWithTolerance(points, bottomSeriesFragmentMZ, tolerance) > -1;
}
// Build the label for the amino acid
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), topSeriesLeftPoint, seriesTopLeftOffset, CoordType.ChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = false;
list.Add(text);
if (topSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(topSeriesColor, topSeriesLeftPoint + tickStart, (seriesTopLeftOffset - 0.05), topSeriesLeftPoint + tickStart, seriesTopLeftOffset);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(topSeriesColor, topSeriesLeftPoint, (seriesTopLeftOffset - 0.08), topSeriesLeftPoint + tickStart, seriesTopLeftOffset - 0.05);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
if (bottomSeriesHasMatch)
{
// Paint the tick in the middle
LineObj tick = new LineObj(bottomSeriesColor, topSeriesRightPoint + tickStart, seriesTopLeftOffset, topSeriesRightPoint + tickStart, seriesTopLeftOffset + 0.05);
tick.Location.CoordinateFrame = CoordType.ChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Paint the hook
LineObj hook = new LineObj(bottomSeriesColor, topSeriesRightPoint + tickStart, seriesTopLeftOffset + 0.05, topSeriesRightPoint + 2.0 * tickStart, seriesTopLeftOffset + 0.08);
hook.Location.CoordinateFrame = CoordType.ChartFraction;
hook.Line.Width = 2;
hook.IsClippedToChartRect = true;
list.Add(hook);
}
// Update the next paint point
topSeriesLeftPoint += residueWidth;
topSeriesRightPoint -= residueWidth;
}
}
public abstract void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g,
MSPointList pointList, GraphObjList annotations);
///<summary>Adds user requested ion series on top of the chart.</summary>
private void addIonSeries (GraphObjList list, pwiz.MSGraph.MSPointList points, Peptide peptide, Fragmentation fragmentation, string topSeries, string bottomSeries)
{
int ionSeriesChargeState = min;
string sequence = peptide.sequence;
ModificationMap modifications = peptide.modifications();
// Select the color for the ion series.
Color topSeriesColor;
Color bottomSeriesColor;
switch (topSeries)
{
default: topSeriesColor = Color.Gray; break;
case "a": topSeriesColor = Color.YellowGreen; break;
case "b": topSeriesColor = Color.BlueViolet; break;
case "c": topSeriesColor = Color.Orange; break;
}
switch (bottomSeries)
{
default: bottomSeriesColor = Color.Gray; break;
case "x": bottomSeriesColor = Color.Green; break;
case "y": bottomSeriesColor = Color.Blue; break;
case "z": bottomSeriesColor = Color.OrangeRed; break;
case "z*": bottomSeriesColor = Color.Crimson; break;
}
// Ion series offsets. These offsets control where on the chart a particular ion series
// get displayed
double topSeriesOffset = 0.025;
double bottomSeriesOffset = 0.1;
if (topSeries.Length == 0)
bottomSeriesOffset = topSeriesOffset;
double topSeriesLeftPoint = 0.0;
double bottomSeriesLeftPoint = 0.0;
// Step through each fragmentation site
for (int i = 1; i <= sequence.Length; ++i)
{
// Paint the top series first
double rightPoint = 0.0;
// Figure out the right mz for this fragmentaion site
switch (topSeries)
{
case "a": rightPoint = fragmentation.a(i, ionSeriesChargeState); break;
case "b": rightPoint = fragmentation.b(i, ionSeriesChargeState); break;
case "c": if (i < sequence.Length) rightPoint = fragmentation.c(i, ionSeriesChargeState); break;
default: continue;
}
// If the left mz and right mz are different
if (rightPoint > 0 && topSeriesLeftPoint != rightPoint)
{
LineObj line;
// Use a dashed line format if there are fragment ions supporting this
// amino acid
if (!aminoAcidHasFragmentEvidence(points, topSeriesLeftPoint, rightPoint))
{
// Draw the line from previous mz to site to this mz in trasparent color.
line = new LineObj(Color.FromArgb(115, topSeriesColor), topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
}
else
{
// Draw the line from previous mz to site to this mz in solid color.
line = new LineObj(topSeriesColor, topSeriesLeftPoint, topSeriesOffset, rightPoint, topSeriesOffset);
}
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.Line.Width = 2;
line.ZOrder = ZOrder.F_BehindGrid;
line.IsClippedToChartRect = true;
list.Add(line);
// Add a tick demarking the fragmentation site.
LineObj tick = new LineObj(topSeriesColor, rightPoint, (topSeriesOffset - 0.015), rightPoint, (topSeriesOffset + 0.015));
tick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Add a text box in the middle of the left and right mz boundaries
StringBuilder label = new StringBuilder(sequence[i - 1].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[i - 1].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), (topSeriesLeftPoint + rightPoint) / 2.0,
topSeriesOffset, CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = true;
list.Add(text);
topSeriesLeftPoint = rightPoint;
}
// Time to paint the bottom series
// Get the right mz for this series
switch (bottomSeries)
{
case "x": if (i < sequence.Length) rightPoint = fragmentation.x(i, ionSeriesChargeState); break;
case "y": rightPoint = fragmentation.y(i, ionSeriesChargeState); break;
case "z": rightPoint = fragmentation.z(i, ionSeriesChargeState); break;
case "z*": rightPoint = fragmentation.zRadical(i, ionSeriesChargeState); break;
default: rightPoint = 0.0; break;
}
// If the left and right mz are different
if (rightPoint > 0 && bottomSeriesLeftPoint != rightPoint)
{
LineObj line;
// Use a dashed line format if there are fragment ions supporting this
// amino acid
if (!aminoAcidHasFragmentEvidence(points, bottomSeriesLeftPoint, rightPoint))
{
// Draw the line from previous mz to site to this mz in trasparent color.
line = new LineObj(Color.FromArgb(115, bottomSeriesColor), bottomSeriesLeftPoint, bottomSeriesOffset, rightPoint, bottomSeriesOffset);
line.Line.Style = System.Drawing.Drawing2D.DashStyle.Dash;
}
else
{
// Draw the line from previous mz to site to this mz in solid color.
line = new LineObj(bottomSeriesColor, bottomSeriesLeftPoint, bottomSeriesOffset, rightPoint, bottomSeriesOffset);
}
line.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
line.Line.Width = 2;
line.ZOrder = ZOrder.F_BehindGrid;
line.IsClippedToChartRect = true;
list.Add(line);
// Draw a tick mark demarking the fragmentation site
LineObj tick = new LineObj(bottomSeriesColor, rightPoint, (bottomSeriesOffset - 0.015), rightPoint, (bottomSeriesOffset + 0.015));
tick.Location.CoordinateFrame = CoordType.XScaleYChartFraction;
tick.Line.Width = 2;
tick.IsClippedToChartRect = true;
list.Add(tick);
// Add the text label containing the amino acid
StringBuilder label = new StringBuilder(sequence[sequence.Length - i].ToString());
// Figure out if any mods are there on this amino acid
double deltaMass = modifications[sequence.Length - i].monoisotopicDeltaMass();
// Round the mod mass and append it to the amino acid as a string
if (deltaMass > 0.0)
{
label.Append("+" + Math.Round(deltaMass));
}
else if (deltaMass < 0.0)
{
label.Append(Math.Round(deltaMass));
}
TextObj text = new TextObj(label.ToString(), (bottomSeriesLeftPoint + rightPoint) / 2.0,
bottomSeriesOffset, CoordType.XScaleYChartFraction, AlignH.Center, AlignV.Center);
text.ZOrder = ZOrder.A_InFront;
text.FontSpec = new FontSpec("Arial", 13, Color.Black, true, false, false);
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.Color = Color.White;
text.IsClippedToChartRect = true;
list.Add(text);
bottomSeriesLeftPoint = rightPoint;
}
}
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// 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
}
public override void AddPreCurveAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// Do nothing
}
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);
}
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="PaneBase"/> object from which to copy</param>
public PaneBase( PaneBase rhs )
{
// copy over all the value types
_isFontsScaled = rhs._isFontsScaled;
_isPenWidthScaled = rhs._isPenWidthScaled;
_titleGap = rhs._titleGap;
_baseDimension = rhs._baseDimension;
_margin = rhs._margin.Clone();
_rect = rhs._rect;
// Copy the reference types by cloning
_fill = rhs._fill.Clone();
_border = rhs._border.Clone();
_title = rhs._title.Clone();
_legend = rhs.Legend.Clone();
_title = rhs._title.Clone();
_graphObjList = rhs._graphObjList.Clone();
if ( rhs._tag is ICloneable )
_tag = ((ICloneable) rhs._tag).Clone();
else
_tag = rhs._tag;
}
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)
{
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphObjList"/> object from which to copy</param>
public GraphObjList( GraphObjList rhs )
{
foreach ( GraphObj item in rhs )
this.Add( (GraphObj) ((ICloneable)item).Clone() );
}