private double fragmentMass(pwiz.CLI.proteome.Fragmentation f, IonSeries series, int length, int charge)
{
switch (series)
{
case IonSeries.a: return(f.a(length, charge));
case IonSeries.b: return(f.b(length, charge));
case IonSeries.c: return(f.c(length, charge));
case IonSeries.cMinus1: return(f.c(length, charge) - Proton.Mass / charge);
case IonSeries.x: return(f.x(length, charge));
case IonSeries.y: return(f.y(length, charge));
case IonSeries.z: return(f.z(length, charge));
case IonSeries.zPlus1: return(f.zRadical(length, charge));
case IonSeries.zPlus2: return(f.zRadical(length, charge) + Proton.Mass / charge);
default: throw new ArgumentException();
}
}
public PredictedIon(int charge, double mz, int number, string finalAA, IonSeries series)
{
Charge = charge;
MZ = mz;
Number = number;
FinalAA = finalAA;
Series = series;
}
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();
}
bool ionSeriesIsEnabled (IonSeries series) { return (ionSeries & series) == series; }
void checkBox_CheckedChanged (object sender, EventArgs e)
{
if (panel.Tag != this)
return;
min = (int) annotationPanels.minChargeUpDown.Value;
max = (int) annotationPanels.maxChargeUpDown.Value;
precursorMassType = annotationPanels.precursorMassTypeComboBox.SelectedIndex;
fragmentMassType = annotationPanels.fragmentMassTypeComboBox.SelectedIndex;
showLadders = annotationPanels.showFragmentationLaddersCheckBox.Checked;
showFragmentationSummary = annotationPanels.showFragmentationSummaryCheckBox.Checked;
// any control which affects the columns displayed for fragments clears the column list;
// it gets repopulated on the next call to Update()
if (!ReferenceEquals(sender, annotationPanels.showMissesCheckBox))
annotationPanels.fragmentInfoGridView.Columns.Clear();
// when showLadders is checked, the ion series checkboxes act like radio buttons:
// series from the same terminus are grouped together
if ((showLadders || showFragmentationSummary) && sender is CheckBox)
{
panel.Tag = null;
if (ReferenceEquals(sender, annotationPanels.showFragmentationLaddersCheckBox) ||
ReferenceEquals(sender, annotationPanels.showFragmentationSummaryCheckBox))
{
// uncheck all but the first checked checkbox
annotationPanels.bCheckBox.Checked = !annotationPanels.aCheckBox.Checked;
annotationPanels.cCheckBox.Checked = !annotationPanels.aCheckBox.Checked && !annotationPanels.bCheckBox.Checked;
annotationPanels.yCheckBox.Checked = !annotationPanels.xCheckBox.Checked;
annotationPanels.zCheckBox.Checked = !annotationPanels.xCheckBox.Checked && !annotationPanels.yCheckBox.Checked;
annotationPanels.zRadicalCheckBox.Checked = !annotationPanels.xCheckBox.Checked && !annotationPanels.yCheckBox.Checked && !annotationPanels.zCheckBox.Checked;
}
else if (ReferenceEquals(sender, annotationPanels.aCheckBox))
annotationPanels.bCheckBox.Checked = annotationPanels.cCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.bCheckBox))
annotationPanels.aCheckBox.Checked = annotationPanels.cCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.cCheckBox))
annotationPanels.aCheckBox.Checked = annotationPanels.bCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.xCheckBox))
annotationPanels.yCheckBox.Checked = annotationPanels.zCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.yCheckBox))
annotationPanels.xCheckBox.Checked = annotationPanels.zCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.zCheckBox))
annotationPanels.xCheckBox.Checked = annotationPanels.yCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
else if (ReferenceEquals(sender, annotationPanels.zRadicalCheckBox))
annotationPanels.xCheckBox.Checked = annotationPanels.yCheckBox.Checked = annotationPanels.zCheckBox.Checked = false;
panel.Tag = this;
}
ionSeries = IonSeries.Off;
ionSeries |= annotationPanels.aCheckBox.Checked ? IonSeries.a : IonSeries.Off;
ionSeries |= annotationPanels.bCheckBox.Checked ? IonSeries.b : IonSeries.Off;
ionSeries |= annotationPanels.cCheckBox.Checked ? IonSeries.c : IonSeries.Off;
ionSeries |= annotationPanels.xCheckBox.Checked ? IonSeries.x : IonSeries.Off;
ionSeries |= annotationPanels.yCheckBox.Checked ? IonSeries.y : IonSeries.Off;
ionSeries |= annotationPanels.zCheckBox.Checked ? IonSeries.z : IonSeries.Off;
ionSeries |= annotationPanels.zRadicalCheckBox.Checked ? IonSeries.zRadical : IonSeries.Off;
ionSeries |= annotationPanels.immoniumCheckBox.Checked ? IonSeries.Immonium : IonSeries.Off;
showMisses = annotationPanels.showMissesCheckBox.Checked;
OnOptionsChanged(this, EventArgs.Empty);
}
public PeptideFragmentationAnnotation (string sequence,
int minCharge, int maxCharge,
MZTolerance tolerance,
IonSeries ionSeries,
bool showFragmentationLadders,
bool showMissedFragments,
bool showLabels,
bool showFragmentationSummary)
{
this.sequence = sequence;
this.min = minCharge;
this.max = maxCharge;
this.manualTolerance = tolerance;
this.tolerance = new MZTolerance(0.5);
this.ionSeries = ionSeries;
this.showLadders = showFragmentationLadders;
this.showMisses = showMissedFragments;
this.showLabels = showLabels;
this.showFragmentationSummary = showFragmentationSummary;
annotationPanels.precursorMassTypeComboBox.SelectedIndex = 0;
annotationPanels.fragmentMassTypeComboBox.SelectedIndex = 0;
if (!ReferenceEquals(tolerance, null))
annotationPanels.fragmentToleranceUnitsComboBox.SelectedIndex = (int) tolerance.units;
else
annotationPanels.fragmentToleranceUnitsComboBox.SelectedIndex = 0;
annotationPanels.sequenceTextBox.TextChanged += sequenceTextBox_TextChanged;
annotationPanels.minChargeUpDown.ValueChanged += checkBox_CheckedChanged;
annotationPanels.maxChargeUpDown.ValueChanged += checkBox_CheckedChanged;
annotationPanels.fragmentToleranceTextBox.TextChanged += toleranceChanged;
annotationPanels.fragmentToleranceUnitsComboBox.SelectedIndexChanged += toleranceChanged;
annotationPanels.precursorMassTypeComboBox.SelectedIndexChanged += checkBox_CheckedChanged;
annotationPanels.fragmentMassTypeComboBox.SelectedIndexChanged += checkBox_CheckedChanged;
annotationPanels.aCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.bCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.cCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.xCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.yCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.zCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.zRadicalCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.immoniumCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.showFragmentationLaddersCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.showMissesCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.showFragmentationSummaryCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.showFragmentationTableCheckBox.CheckedChanged += checkBox_CheckedChanged;
annotationPanels.fragmentInfoGridView.Columns.Clear();
}
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();
}
void checkBox_CheckedChanged( object sender, EventArgs e )
{
if( panel.Tag == this )
{
min = (int) annotationPanels.minChargeUpDown.Value;
max = (int) annotationPanels.maxChargeUpDown.Value;
precursorMassType = annotationPanels.precursorMassTypeComboBox.SelectedIndex;
fragmentMassType = annotationPanels.fragmentMassTypeComboBox.SelectedIndex;
showLadders = annotationPanels.showFragmentationLaddersCheckBox.Checked;
showFragmentationSummary = annotationPanels.showFragmentationSummaryCheckBox.Checked;
showBasophileModel = annotationPanels.showBasophileCheckBox.Checked;
//test neutral loss
waterLoss = annotationPanels.waterLossCheckBox.Checked;
ammoniumLoss = annotationPanels.ammoniumLossCheckBox.Checked;
phosphateLoss = annotationPanels.phosphateLossCheckBox.Checked;
basePeakThresholding = annotationPanels.thresholdCheckBox.Checked;
numPhosphate = (int)annotationPanels.phosphateUpDown.Value;
basePeakPercentage = (double)annotationPanels.basePeakIntenPercentageUpDown.Value;
// any control which affects the columns displayed for fragments clears the column list;
// it gets repopulated on the next call to Update()
if(!ReferenceEquals(sender, annotationPanels.showMissesCheckBox))
annotationPanels.fragmentInfoGridView.Columns.Clear();
//test neutral loss
//I think the waterLoss checkbox will affect the fragments, so I guess this should be related to clear()
//not sure about this
if (!ReferenceEquals(sender, annotationPanels.waterLossCheckBox))
annotationPanels.fragmentInfoGridView.Columns.Clear();
if (!ReferenceEquals(sender, annotationPanels.ammoniumLossCheckBox))
annotationPanels.fragmentInfoGridView.Columns.Clear();
if (!ReferenceEquals(sender, annotationPanels.phosphateLossCheckBox))
annotationPanels.fragmentInfoGridView.Columns.Clear();
// when showLadders is checked, the ion series checkboxes act like radio buttons:
// series from the same terminus are grouped together
if ((showLadders || showFragmentationSummary) && sender is CheckBox)
{
panel.Tag = null;
if (ReferenceEquals(sender, annotationPanels.showFragmentationLaddersCheckBox) ||
ReferenceEquals(sender, annotationPanels.showFragmentationSummaryCheckBox))
{
// uncheck all but the first checked checkbox
annotationPanels.bCheckBox.Checked = !annotationPanels.aCheckBox.Checked;
annotationPanels.cCheckBox.Checked = !annotationPanels.aCheckBox.Checked && !annotationPanels.bCheckBox.Checked;
annotationPanels.yCheckBox.Checked = !annotationPanels.xCheckBox.Checked;
annotationPanels.zCheckBox.Checked = !annotationPanels.xCheckBox.Checked && !annotationPanels.yCheckBox.Checked;
annotationPanels.zRadicalCheckBox.Checked = !annotationPanels.xCheckBox.Checked && !annotationPanels.yCheckBox.Checked && !annotationPanels.zCheckBox.Checked;
}
//else if (ReferenceEquals(sender, annotationPanels.aCheckBox))
// annotationPanels.bCheckBox.Checked = annotationPanels.cCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.bCheckBox))
// annotationPanels.aCheckBox.Checked = annotationPanels.cCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.cCheckBox))
// annotationPanels.aCheckBox.Checked = annotationPanels.bCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.xCheckBox))
// annotationPanels.yCheckBox.Checked = annotationPanels.zCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.yCheckBox))
// annotationPanels.xCheckBox.Checked = annotationPanels.zCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.zCheckBox))
// annotationPanels.xCheckBox.Checked = annotationPanels.yCheckBox.Checked = annotationPanels.zRadicalCheckBox.Checked = false;
//else if (ReferenceEquals(sender, annotationPanels.zRadicalCheckBox))
// annotationPanels.xCheckBox.Checked = annotationPanels.yCheckBox.Checked = annotationPanels.zCheckBox.Checked = false;
panel.Tag = this;
}
ionSeries = IonSeries.Off;
ionSeries |= annotationPanels.aCheckBox.Checked ? IonSeries.a : IonSeries.Off;
ionSeries |= annotationPanels.bCheckBox.Checked ? IonSeries.b : IonSeries.Off;
ionSeries |= annotationPanels.cCheckBox.Checked ? IonSeries.c : IonSeries.Off;
ionSeries |= annotationPanels.xCheckBox.Checked ? IonSeries.x : IonSeries.Off;
ionSeries |= annotationPanels.yCheckBox.Checked ? IonSeries.y : IonSeries.Off;
ionSeries |= annotationPanels.zCheckBox.Checked ? IonSeries.z : IonSeries.Off;
ionSeries |= annotationPanels.zRadicalCheckBox.Checked ? IonSeries.zRadical : IonSeries.Off;
showMisses = annotationPanels.showMissesCheckBox.Checked;
OnOptionsChanged( this, EventArgs.Empty );
}
}
public PeptideFragmentationAnnotation(string sequence,
int minCharge, int maxCharge,
IonSeries ionSeries,
bool showFragmentationLadders,
bool showMissedFragments,
bool showLabels,
bool showFragmentationSummary)
{
this.sequence = sequence;
this.min = minCharge;
this.max = maxCharge;
this.ionSeries = ionSeries;
this.showLadders = showFragmentationLadders;
this.showMisses = showMissedFragments;
this.showLabels = showLabels;
this.showFragmentationSummary = showFragmentationSummary;
//this.showBasophileModel = showBasophileModel;
//test neutral loss
this.numPhosphate = 1;
basePeakThresholding = false;
this.basePeakPercentage = 0;
annotationPanels.precursorMassTypeComboBox.SelectedIndex = 0;
annotationPanels.fragmentMassTypeComboBox.SelectedIndex = 0;
annotationPanels.sequenceTextBox.TextChanged += new EventHandler( sequenceTextBox_TextChanged );
annotationPanels.minChargeUpDown.ValueChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.maxChargeUpDown.ValueChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.precursorMassTypeComboBox.SelectedIndexChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.fragmentMassTypeComboBox.SelectedIndexChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.aCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.bCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.cCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.xCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.yCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.zCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.zRadicalCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.showFragmentationLaddersCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.showMissesCheckBox.CheckedChanged += new EventHandler( checkBox_CheckedChanged );
annotationPanels.showFragmentationSummaryCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.showBasophileCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
//test neutral loss
annotationPanels.waterLossCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.ammoniumLossCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.phosphateLossCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.thresholdCheckBox.CheckedChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.basePeakIntenPercentageUpDown.ValueChanged += new EventHandler(checkBox_CheckedChanged);
annotationPanels.fragmentInfoGridView.Columns.Clear();
}
private double fragmentMass(pwiz.CLI.proteome.Fragmentation f, IonSeries series, int length, int charge)
{
switch (series)
{
case IonSeries.a: return f.a(length, charge);
case IonSeries.b: return f.b(length, charge);
case IonSeries.c: return f.c(length, charge);
case IonSeries.x: return f.x(length, charge);
case IonSeries.y: return f.y(length, charge);
case IonSeries.z: return f.z(length, charge);
default: throw new ArgumentException();
}
}
private void PlotSequence(List <PredictedIon> peaks, IonSeries ionType, double yHeight, SolidColorBrush theBrush)
{
if (IonsInDisplay.Count == 0)
{
IonsInDisplay = myMS;
if (myMS.Count == 0)
{
return;
}
}
double lowestMass = IonsInDisplay.Min(a => a.MZ);
double largestMass = IonsInDisplay.Max(a => a.MZ);
List <PredictedIon> peaksOfInterest = peaks.FindAll(a => a.Number >= 0 && a.Series.Equals(ionType));
peaksOfInterest.Sort((a, b) => a.MZ.CompareTo(b.MZ));
string upperLabel = "";
string lowerLabel = "";
int matchCounter = 0;
double lastX = ConvertMZToPixelX(lowestMass, lowestMass, largestMass);
for (int i = 0; i < peaksOfInterest.Count; i++)
{
if (peaksOfInterest[i].Matched || i == peaksOfInterest.Count - 1)
{
matchCounter++;
upperLabel += peaksOfInterest[i].FinalAA;
lowerLabel += peaksOfInterest[i].Number;
//Plot
double startX = lastX;
double endX = ConvertMZToPixelX(peaksOfInterest[i].MZ, lowestMass, largestMass);
ArrowHeads.ArrowEnds thisArrowEnds = ArrowHeads.ArrowEnds.Both;
if (matchCounter == 1 && peaksOfInterest[i].Number > i)
{
thisArrowEnds = ArrowHeads.ArrowEnds.End;
}
if (i == peaksOfInterest.Count - 1)
{
endX = ConvertMZToPixelX(largestMass, lowestMass, largestMass);
if (peaksOfInterest[i].MZ > largestMass)
{
thisArrowEnds = ArrowHeads.ArrowEnds.Start;
}
}
PatternTools.ArrowHeads.ArrowDeNovo.ArrowDeNovoDraw(upperLabel, lowerLabel, theBrush, canvasDenovo, startX, endX, yHeight, thisArrowEnds);
//And now clear for the next labels
upperLabel = "";
lowerLabel = "";
lastX = endX;
}
else
{
upperLabel += peaksOfInterest[i].FinalAA + " ";
lowerLabel += peaksOfInterest[i].Number + ", ";
}
}
}
private static List <PredictedIon> SequentialScore(List <PredictedIon> theoretical, IonSeries ionSerie)
{
int greatestSequence = 0;
int sequenceCounter = 0;
List <PredictedIon> theIons = theoretical.FindAll(a => a.Series.Equals(ionSerie));
List <PredictedIon> theResult = new List <PredictedIon>(10);
List <PredictedIon> partialResult = new List <PredictedIon>(10);
if (theIons[0].Matched)
{
sequenceCounter++;
partialResult.Add(theIons[0]);
greatestSequence = sequenceCounter;
theResult.Clear();
theResult.AddRange(partialResult);
}
for (int i = 1; i < theIons.Count - 1; i++)
{
if (theIons[i].Matched && theIons[i + 1].Matched)
{
sequenceCounter++;
partialResult.Add(theIons[i + 1]);
}
else
{
if (sequenceCounter > greatestSequence)
{
greatestSequence = sequenceCounter;
theResult.Clear();
theResult.AddRange(partialResult);
}
}
}
if (theIons[theIons.Count - 2].Matched)
{
sequenceCounter++;
partialResult.Add(theIons[theIons.Count - 1]);
greatestSequence = sequenceCounter;
theResult.Clear();
theResult.AddRange(partialResult);
}
return(theResult);
}