/// <summary>
/// Render text to the specified <see cref="Graphics"/> device
/// by calling the Draw method of each <see cref="GraphItem"/> object in
/// the collection.
/// </summary>
/// <remarks>This method is normally only called by the Draw method
/// of the parent <see cref="GraphPane"/> object.
/// </remarks>
/// <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="PaneBase"/> object that is the parent or
/// owner of this object.
/// </param>
/// <param name="scaleFactor">
/// The scaling factor to be used for rendering objects. This is calculated and
/// passed down by the parent <see cref="GraphPane"/> object using the
/// <see cref="PaneBase.CalcScaleFactor"/> method, and is used to proportionally adjust
/// font sizes, etc. according to the actual size of the graph.
/// </param>
/// <param name="zOrder">A <see cref="ZOrder"/> enumeration that controls
/// the placement of this <see cref="GraphItem"/> relative to other
/// graphic objects. The order of <see cref="GraphItem"/>'s with the
/// same <see cref="ZOrder"/> value is control by their order in
/// this <see cref="GraphItemList"/>.</param>
public void Draw(Graphics g, PaneBase pane, float scaleFactor,
ZOrder zOrder)
{
// Draw the items in reverse order, so the last items in the
// list appear behind the first items (consistent with
// CurveList)
for (int i = this.Count - 1; i >= 0; i--)
{
GraphItem item = this[i];
if (item.ZOrder == zOrder && item.IsVisible)
{
Region region = null;
if (item.IsClippedToAxisRect && pane is GraphPane)
{
region = g.Clip.Clone();
g.SetClip(((GraphPane)pane).AxisRect);
}
item.Draw(g, pane, scaleFactor);
if (item.IsClippedToAxisRect && pane is GraphPane)
{
g.Clip = region;
}
}
}
}
public DataPointTableForm(GraphItem graphItem)
{
InitializeComponent();
item = graphItem;
pointList = item.Points;
dataGridView.Rows.Insert( 0, pointList.Count );
}
/// <summary>
/// Render text to the specified <see cref="Graphics"/> device
/// by calling the Draw method of each <see cref="GraphItem"/> object in
/// the collection.
/// </summary>
/// <remarks>This method is normally only called by the Draw method
/// of the parent <see cref="GraphPane"/> object.
/// </remarks>
/// <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 is the parent or
/// owner of this object.
/// </param>
/// <param name="scaleFactor">
/// The scaling factor to be used for rendering objects. This is calculated and
/// passed down by the parent <see cref="GraphPane"/> object using the
/// <see cref="GraphPane.CalcScaleFactor"/> method, and is used to proportionally adjust
/// font sizes, etc. according to the actual size of the graph.
/// </param>
/// <param name="zOrder">A <see cref="ZOrder"/> enumeration that controls
/// the placement of this <see cref="GraphItem"/> relative to other
/// graphic objects. The order of <see cref="GraphItem"/>'s with the
/// same <see cref="ZOrder"/> value is control by their order in
/// this <see cref="GraphItemList"/>.</param>
public void Draw(Graphics g, GraphPane pane, double scaleFactor,
ZOrder zOrder)
{
// Draw the items in reverse order, so the last items in the
// list appear behind the first items (consistent with
// CurveList)
for (int i = this.Count - 1; i >= 0; i--)
{
GraphItem item = this[i];
if (item.ZOrder == zOrder)
{
item.Draw(g, pane, scaleFactor);
}
}
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphItem"/> object from which to copy</param>
public GraphItem(GraphItem rhs)
{
this.isVisible = rhs.IsVisible;
if (rhs.Tag is ICloneable)
{
this.Tag = ((ICloneable)rhs.Tag).Clone();
}
else
{
this.Tag = rhs.Tag;
}
this.zOrder = rhs.ZOrder;
this.location = (Location)rhs.Location.Clone();
}
/// <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.PaneRect"/> 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="ArrowItem"/> 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="TextItem"/>, <see cref="ArrowItem"/>, 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;
GraphItem saveGraphItem = null;
int saveIndex = -1;
float scaleFactor = CalcScaleFactor();
// See if the point is in a GraphItem
// If so, just save the object and index so we can see if other overlying objects were
// intersected as well.
if (this.GraphItemList.FindPoint(mousePt, this, g, scaleFactor, out index))
{
saveGraphItem = this.GraphItemList[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 this.paneList)
{
if (tPane.PaneRect.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);
}
private void showDataStacked(GraphForm hostGraph, GraphItem item )
{
Pane pane = new Pane();
pane.Add( item );
hostGraph.PaneList.Add( pane );
hostGraph.Refresh();
}
private void showDataOverlay(GraphForm hostGraph, GraphItem item )
{
hostGraph.PaneList[0].Add( item );
hostGraph.Refresh();
}
private void showData( GraphForm hostGraph, GraphItem item )
{
Pane pane;
if( hostGraph.PaneList.Count == 0 || hostGraph.PaneList.Count > 1 )
{
hostGraph.PaneList.Clear();
pane = new Pane();
hostGraph.PaneList.Add( pane );
} else
{
pane = hostGraph.PaneList[0];
pane.Clear();
}
pane.Add( item );
hostGraph.Refresh();
}
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();
}
public virtual void Update (GraphItem item, pwiz.MSGraph.MSPointList pointList, GraphObjList annotations)
{
throw new NotImplementedException();
}
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();
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphItem"/> object from which to copy</param>
public GraphItem( GraphItem rhs )
{
this.Tag = rhs.Tag;
this.zOrder = rhs.ZOrder;
this.location = rhs.Location;
}
/// <summary>
/// The Copy Constructor
/// </summary>
/// <param name="rhs">The <see cref="GraphItem"/> object from which to copy</param>
public GraphItem(GraphItem rhs)
{
this.Tag = rhs.Tag;
this.zOrder = rhs.ZOrder;
this.location = rhs.Location;
}
/// <summary>
/// Insert a <see cref="GraphItem"/> object into the collection
/// at the specified zero-based index location.
/// </summary>
/// <param name="index">The zero-based index location for insertion.</param>
/// <param name="item">The <see cref="GraphItem"/> object that is to be
/// inserted.</param>
/// <seealso cref="IList.Insert"/>
public void Insert(int index, GraphItem item)
{
List.Insert(index, item);
}
/// <summary>
/// Add a <see cref="GraphItem"/> object to the <see cref="GraphItemList"/>
/// collection at the end of the list.
/// </summary>
/// <param name="item">A reference to the <see cref="GraphItem"/> object to
/// be added</param>
/// <seealso cref="IList.Add"/>
public GraphItem Add(GraphItem item)
{
List.Add(item);
return(item);
}
/// <summary>
/// Add a <see cref="GraphItem"/> object to the <see cref="GraphItemList"/>
/// collection at the end of the list.
/// </summary>
/// <param name="item">A reference to the <see cref="GraphItem"/> object to
/// be added</param>
/// <seealso cref="IList.Add"/>
public GraphItem Add( GraphItem item )
{
List.Add( item );
return item;
}
/// <summary>
/// Insert a <see cref="GraphItem"/> object into the collection
/// at the specified zero-based index location.
/// </summary>
/// <param name="index">The zero-based index location for insertion.</param>
/// <param name="item">The <see cref="GraphItem"/> object that is to be
/// inserted.</param>
/// <seealso cref="IList.Insert"/>
public void Insert( int index, GraphItem item )
{
List.Insert( index, item );
}
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();
}
