public override string ToString()
{
if (MZToleranceIsPPM)
{
return("m/z: " + MZ.ToString("0.0") + ", MZTolerance: " + MZTolerance.ToString("0.0") + " ppm");
}
return("m/z: " + MZ.ToString("0.0") + ", MZTolerance: " + MZTolerance.ToString("0.000") + " Da");
}
public FragmentationStatisticsForm(IDPickerForm owner)
{
InitializeComponent();
this.owner = owner;
FormClosing += delegate(object sender, FormClosingEventArgs e)
{
e.Cancel = true;
DockState = DockState.DockBottomAutoHide;
};
Text = TabText = "Fragmentation Statistics";
Icon = Properties.Resources.BlankIcon;
refreshButton.Image = new Icon(Properties.Resources.Refresh, refreshButton.Width / 2, refreshButton.Height / 2).ToBitmap();
refreshDataLabel.LinkClicked += (sender, e) => refreshButton_Click(sender, e);
percentTicGraphForm = new DockableForm {
Text = "%TIC"
};
percentPeakCountGraphForm = new DockableForm {
Text = "%PeakCount"
};
meanMzErrorGraphForm = new DockableForm {
Text = "Mean m/z error"
};
percentTicGraphControl = new ZedGraphControl {
Dock = DockStyle.Fill, Text = percentTicGraphForm.Text
};
percentPeakCountGraphControl = new ZedGraphControl {
Dock = DockStyle.Fill, Text = percentPeakCountGraphForm.Text
};
meanMzErrorGraphControl = new ZedGraphControl {
Dock = DockStyle.Fill, Text = meanMzErrorGraphForm.Text
};
percentTicGraphForm.Controls.Add(percentTicGraphControl);
percentPeakCountGraphForm.Controls.Add(percentPeakCountGraphControl);
meanMzErrorGraphForm.Controls.Add(meanMzErrorGraphControl);
initializeGraphControl(percentTicGraphControl);
initializeGraphControl(percentPeakCountGraphControl);
initializeGraphControl(meanMzErrorGraphControl);
lastActiveGraphForm = meanMzErrorGraphForm;
graphControls = new List <ZedGraphControl>
{
percentTicGraphControl,
percentPeakCountGraphControl,
meanMzErrorGraphControl
};
percentTicGraphForm.FormClosing += (sender, e) => e.Cancel = true;
percentPeakCountGraphForm.FormClosing += (sender, e) => e.Cancel = true;
meanMzErrorGraphForm.FormClosing += (sender, e) => e.Cancel = true;
fragmentTolerance = new MZTolerance(0.5, MZTolerance.Units.MZ);
fragmentToleranceUnitsComboBox.Text = fragmentTolerance.value.ToString();
fragmentToleranceUnitsComboBox.SelectedIndex = (int)fragmentTolerance.units;
}
public override void Update (GraphItem item, pwiz.MSGraph.MSPointList points, GraphObjList annotations)
{
if (!Enabled)
return;
if (!(item is MassSpectrum))
return; // throw exception?
GraphObjList list = annotations;
Peptide peptide;
try
{
peptide = new Peptide(sequence,
pwiz.CLI.proteome.ModificationParsing.ModificationParsing_Auto,
pwiz.CLI.proteome.ModificationDelimiter.ModificationDelimiter_Brackets);
}
catch (Exception)
{
return;
}
var spectrum = (item as MassSpectrum).Element;
if (ReferenceEquals(manualTolerance, null))
{
MZTolerance maxTolerance = new MZTolerance(0.5);
foreach (var scan in spectrum.scanList.scans.Where(o => o.instrumentConfiguration != null))
{
// assume the last analyzer of the instrument configuration is responsible for the resolution
if (scan.instrumentConfiguration.componentList.Count == 0)
continue;
var analyzer = scan.instrumentConfiguration.componentList.Where(o => o.type == ComponentType.ComponentType_Analyzer).Last().cvParamChild(CVID.MS_mass_analyzer_type);
if (analyzer.cvid == CVID.CVID_Unknown)
continue;
MZTolerance analyzerTolerance = null;
foreach (var kvp in mzToleranceByAnalyzer)
if (CV.cvIsA(analyzer.cvid, kvp.Key))
{
analyzerTolerance = kvp.Value;
break;
}
if (analyzerTolerance == null)
continue;
if (maxTolerance.units == analyzerTolerance.units)
{
if (maxTolerance.value < analyzerTolerance.value)
maxTolerance = analyzerTolerance;
}
else if (analyzerTolerance.units == MZTolerance.Units.PPM)
maxTolerance = analyzerTolerance;
}
tolerance = maxTolerance;
}
else
tolerance = manualTolerance;
if (ionSeriesIsEnabled(IonSeries.Auto))
foreach (var precursor in spectrum.precursors)
foreach (var method in precursor.activation.cvParamChildren(CVID.MS_dissociation_method))
{
if (!ionSeriesByDissociationMethod.Contains(method.cvid))
ionSeries = IonSeries.All;
else
ionSeries |= ionSeriesByDissociationMethod[method.cvid];
}
int nSeries = (ionSeriesIsEnabled(IonSeries.a) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.b) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.c) ? 1 : 0);
int cSeries = (ionSeriesIsEnabled(IonSeries.x) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.y) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.z) ? 1 : 0) +
(ionSeriesIsEnabled(IonSeries.zRadical) ? 1 : 0);
showLadders = showLadders && nSeries < 2 && cSeries < 2;
string unmodifiedSequence = peptide.sequence;
int sequenceLength = unmodifiedSequence.Length;
Fragmentation fragmentation = peptide.fragmentation(fragmentMassType == 0 ? true : false, true);
for (int i = 1; i <= sequenceLength; ++i)
{
if (ionSeriesIsEnabled(IonSeries.Immonium))
addFragment(list, points, "immonium-" + unmodifiedSequence[i - 1], 0, 1, immoniumIonByResidue[unmodifiedSequence[i - 1]]);
for (int charge = min; charge <= max; ++charge)
{
if (ionSeriesIsEnabled(IonSeries.a)) addFragment(list, points, "a", i, charge, fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b)) addFragment(list, points, "b", i, charge, fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.y)) addFragment(list, points, "y", i, charge, fragmentation.y(i, charge));
if (ionSeriesIsEnabled(IonSeries.z)) addFragment(list, points, "z", i, charge, fragmentation.z(i, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical)) addFragment(list, points, "z*", i, charge, fragmentation.zRadical(i, charge));
if (i < sequenceLength)
{
if (ionSeriesIsEnabled(IonSeries.c)) addFragment(list, points, "c", i, charge, fragmentation.c(i, charge));
if (ionSeriesIsEnabled(IonSeries.x)) addFragment(list, points, "x", i, charge, fragmentation.x(i, charge));
}
}
}
if (showLadders || showFragmentationSummary)
{
string topSeries = ionSeriesIsEnabled(IonSeries.a) ? "a" : ionSeriesIsEnabled(IonSeries.b) ? "b" : ionSeriesIsEnabled(IonSeries.c) ? "c" : "";
string bottomSeries = ionSeriesIsEnabled(IonSeries.x) ? "x" : ionSeriesIsEnabled(IonSeries.y) ? "y" : ionSeriesIsEnabled(IonSeries.z) ? "z" : ionSeriesIsEnabled(IonSeries.zRadical) ? "z*" : "";
if (showLadders)
addIonSeries(list, points, peptide, fragmentation, topSeries, bottomSeries);
if (showFragmentationSummary)
addFragmentationSummary(list, points, peptide, fragmentation, topSeries, bottomSeries);
}
// fill peptide info table
annotationPanels.peptideInfoGridView.Rows.Clear();
if (spectrum.precursors.Count > 0 &&
spectrum.precursors[0].selectedIons.Count > 0 &&
spectrum.precursors[0].selectedIons[0].hasCVParam(CVID.MS_selected_ion_m_z) &&
spectrum.precursors[0].selectedIons[0].hasCVParam(CVID.MS_charge_state))
{
double selectedMz = (double) spectrum.precursors[0].selectedIons[0].cvParam(CVID.MS_selected_ion_m_z).value;
int chargeState = (int) spectrum.precursors[0].selectedIons[0].cvParam(CVID.MS_charge_state).value;
double calculatedMass = (precursorMassType == 0 ? peptide.monoisotopicMass(chargeState) : peptide.molecularWeight(chargeState)) * chargeState;
double observedMass = selectedMz * chargeState;
annotationPanels.peptideInfoGridView.Rows.Add("Calculated mass:", calculatedMass, "Mass error (daltons):", observedMass - calculatedMass);
annotationPanels.peptideInfoGridView.Rows.Add("Observed mass:", observedMass, "Mass error (ppm):", ((observedMass - calculatedMass) / calculatedMass) * 1e6);
}
else
annotationPanels.peptideInfoGridView.Rows.Add("Calculated neutral mass:", precursorMassType == 0 ? peptide.monoisotopicMass() : peptide.molecularWeight());
annotationPanels.peptideInfoGridView.Columns[1].DefaultCellStyle.Format = "F4";
foreach (DataGridViewRow row in annotationPanels.peptideInfoGridView.Rows)
row.Height = row.InheritedStyle.Font.Height + 2;
// show/hide/update fragment table
if (!annotationPanels.showFragmentationTableCheckBox.Checked || ionSeries <= IonSeries.Auto)
{
annotationPanels.fragmentInfoGridView.Visible = false;
annotationPanels.fragmentInfoGridView.Rows.Clear();
return;
}
annotationPanels.fragmentInfoGridView.Visible = true;
annotationPanels.fragmentInfoGridView.SuspendLayout();
if (annotationPanels.fragmentInfoGridView.Columns.Count == 0)
{
#region Add columns for fragment types
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"a" + charge.ToString(),
"a" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"b" + charge.ToString(),
"b" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"c" + charge.ToString(),
"c" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
annotationPanels.fragmentInfoGridView.Columns.Add("N", "");
annotationPanels.fragmentInfoGridView.Columns.Add("Sequence", "");
annotationPanels.fragmentInfoGridView.Columns.Add("C", "");
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"x" + charge.ToString(),
"x" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"y" + charge.ToString(),
"y" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z" + charge.ToString(),
"z" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
annotationPanels.fragmentInfoGridView.Columns.Add(
"z*" + charge.ToString(),
"z*" + (charge > 1 ? "(+" + charge.ToString() + ")" : ""));
#endregion
foreach (DataGridViewColumn column in annotationPanels.fragmentInfoGridView.Columns)
{
column.DefaultCellStyle.Alignment = DataGridViewContentAlignment.MiddleCenter;
if (column.Name != "N" && column.Name != "C" && column.Name != "Sequence")
column.DefaultCellStyle.Format = "F3";
}
}
while (annotationPanels.fragmentInfoGridView.Rows.Count > sequenceLength)
annotationPanels.fragmentInfoGridView.Rows.RemoveAt(annotationPanels.fragmentInfoGridView.Rows.Count - 1);
if (sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count > 0)
annotationPanels.fragmentInfoGridView.Rows.Add(sequenceLength - annotationPanels.fragmentInfoGridView.Rows.Count);
for (int i = 1; i <= sequenceLength; ++i)
{
int cTerminalLength = sequenceLength - i + 1;
var row = annotationPanels.fragmentInfoGridView.Rows[i - 1];
var values = new List<object>(10);
//var row = annotationPanels.fragmentInfoGridView.Rows.Add()];
if (ionSeriesIsEnabled(IonSeries.a))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.a(i, charge));
if (ionSeriesIsEnabled(IonSeries.b))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.b(i, charge));
if (ionSeriesIsEnabled(IonSeries.c))
for (int charge = min; charge <= max; ++charge)
if (i < sequenceLength)
values.Add(fragmentation.c(i, charge));
else
values.Add("");
values.Add(i);
values.Add(unmodifiedSequence[i - 1]);
values.Add(cTerminalLength);
if (ionSeriesIsEnabled(IonSeries.x))
for (int charge = min; charge <= max; ++charge)
if (i > 1)
values.Add(fragmentation.x(cTerminalLength, charge));
else
values.Add("");
if (ionSeriesIsEnabled(IonSeries.y))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.y(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.z))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.z(cTerminalLength, charge));
if (ionSeriesIsEnabled(IonSeries.zRadical))
for (int charge = min; charge <= max; ++charge)
values.Add(fragmentation.zRadical(cTerminalLength, charge));
row.SetValues(values.ToArray());
}
foreach (DataGridViewRow row in annotationPanels.fragmentInfoGridView.Rows)
{
row.Height = row.InheritedStyle.Font.Height + 2;
foreach (DataGridViewCell cell in row.Cells)
{
if (!(cell.Value is double))
continue;
double mz = (double) cell.Value;
if (findPointWithTolerance(points, mz, tolerance) > -1)
cell.Style.Font = new Font(annotationPanels.fragmentInfoGridView.Font, FontStyle.Bold);
else
cell.Style.Font = annotationPanels.fragmentInfoGridView.Font;
}
}
annotationPanels.fragmentInfoGridView.ResumeLayout();
}
private int findPointWithTolerance(pwiz.MSGraph.MSPointList points, double mz, MZTolerance tolerance, bool scaled = false)
{
double lowestMatchMz = mz - tolerance;
double highestMatchMz = mz + tolerance;
var pointPairList = scaled ? points.ScaledList : points.FullList;
int index = scaled ? points.ScaledLowerBound(mz) : points.FullLowerBound(mz);
// if index is below the tolerance threshold, bump it to the next one or set to -1 if doing so would exceed the list size
if (index > -1 && pointPairList[index].X < lowestMatchMz)
index = index + 1 == pointPairList.Count ? -1 : index + 1;
if (index == -1 || pointPairList[index].X > highestMatchMz)
return -1;
return index;
}
void toleranceChanged (object sender, EventArgs e)
{
if (panel.Tag != this)
return;
if (String.IsNullOrEmpty(annotationPanels.fragmentToleranceTextBox.Text))
manualTolerance = null;
else
{
manualTolerance = new MZTolerance();
manualTolerance.value = Convert.ToDouble(annotationPanels.fragmentToleranceTextBox.Text);
manualTolerance.units = (MZTolerance.Units) annotationPanels.fragmentToleranceUnitsComboBox.SelectedIndex;
}
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 PeptideFragmentationAnnotation ()
{
sequence = "PEPTIDE";
min = 1;
max = 1;
tolerance = manualTolerance = new MZTolerance(0.5);
precursorMassType = 0;
fragmentMassType = 0;
showLadders = true;
showMisses = false;
showLabels = true;
showFragmentationSummary = false;
annotationPanels.precursorMassTypeComboBox.SelectedIndex = precursorMassType;
annotationPanels.fragmentMassTypeComboBox.SelectedIndex = fragmentMassType;
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;
}
public FragmentationStatisticsForm (IDPickerForm owner)
{
InitializeComponent();
this.owner = owner;
FormClosing += delegate(object sender, FormClosingEventArgs e)
{
e.Cancel = true;
DockState = DockState.DockBottomAutoHide;
};
Text = TabText = "Fragmentation Statistics";
Icon = Properties.Resources.BlankIcon;
refreshButton.Image = new Icon(Properties.Resources.Refresh, refreshButton.Width / 2, refreshButton.Height / 2).ToBitmap();
refreshDataLabel.LinkClicked += (sender, e) => refreshButton_Click(sender, e);
percentTicGraphForm = new DockableForm { Text = "%TIC" };
percentPeakCountGraphForm = new DockableForm { Text = "%PeakCount" };
meanMzErrorGraphForm = new DockableForm { Text = "Mean m/z error" };
percentTicGraphControl = new ZedGraphControl { Dock = DockStyle.Fill, Text = percentTicGraphForm.Text };
percentPeakCountGraphControl = new ZedGraphControl { Dock = DockStyle.Fill, Text = percentPeakCountGraphForm.Text };
meanMzErrorGraphControl = new ZedGraphControl { Dock = DockStyle.Fill, Text = meanMzErrorGraphForm.Text };
percentTicGraphForm.Controls.Add(percentTicGraphControl);
percentPeakCountGraphForm.Controls.Add(percentPeakCountGraphControl);
meanMzErrorGraphForm.Controls.Add(meanMzErrorGraphControl);
initializeGraphControl(percentTicGraphControl);
initializeGraphControl(percentPeakCountGraphControl);
initializeGraphControl(meanMzErrorGraphControl);
lastActiveGraphForm = meanMzErrorGraphForm;
graphControls = new List<ZedGraphControl>
{
percentTicGraphControl,
percentPeakCountGraphControl,
meanMzErrorGraphControl
};
percentTicGraphForm.FormClosing += (sender, e) => e.Cancel = true;
percentPeakCountGraphForm.FormClosing += (sender, e) => e.Cancel = true;
meanMzErrorGraphForm.FormClosing += (sender, e) => e.Cancel = true;
fragmentTolerance = new MZTolerance(0.5, MZTolerance.Units.MZ);
fragmentToleranceUnitsComboBox.Text = fragmentTolerance.value.ToString();
fragmentToleranceUnitsComboBox.SelectedIndex = (int) fragmentTolerance.units;
}
void spectrumTableForm_SpectrumViewVisualize (object sender, SpectrumViewVisualizeEventArgs e)
{
var spectrum = e.Spectrum;
var source = e.SpectrumSource;
string sourcePath;
if (source.Metadata != null)
{
//BeginInvoke(new MethodInvoker(() => toolStripStatusLabel.Text = "Extracting embedded spectrum source: " + source.Name));
// accessing the Metadata property creates a temporary mz5 file
var mz5 = source.Metadata as TemporaryMSDataFile;
sourcePath = mz5.Filepath;
}
else
{
sourcePath = LocateSpectrumSource(source.Name, session.Connection.GetDataSource());
if (String.IsNullOrEmpty(sourcePath))
return; // file still not found, abort the visualization
}
var param = e.Analysis.Parameters.Where(o => o.Name == "SpectrumListFilters").SingleOrDefault();
string spectrumListFilters = param == null ? String.Empty : param.Value;
spectrumListFilters = spectrumListFilters.Replace("0 ", "false ");
var ionSeries = PeptideFragmentationAnnotation.IonSeries.Auto;
if (sourcePath.ToLower().EndsWith(".mgf"))
ionSeries = PeptideFragmentationAnnotation.IonSeries.b | PeptideFragmentationAnnotation.IonSeries.y;
bool showFragmentationLadders = true;
bool showMissedFragments = false;
bool showLabels = true;
bool showFragmentationSummary = false;
MZTolerance tolerance = null;
if (manager.CurrentGraphForm != null && annotationByGraphForm[manager.CurrentGraphForm] != null)
{
var panel = PeptideFragmentationAnnotation.annotationPanels;
showFragmentationLadders = panel.showFragmentationLaddersCheckBox.Checked;
showMissedFragments = panel.showMissesCheckBox.Checked;
showFragmentationSummary = panel.showFragmentationSummaryCheckBox.Checked;
if (panel.fragmentToleranceTextBox.Text.Length > 0)
{
tolerance = new MZTolerance();
tolerance.value = Convert.ToDouble(panel.fragmentToleranceTextBox.Text);
tolerance.units = (MZTolerance.Units) panel.fragmentToleranceUnitsComboBox.SelectedIndex;
}
else
tolerance = null;
}
var annotation = new PeptideFragmentationAnnotation(e.ModifiedSequence, 1, Math.Max(1, e.Charge - 1),
tolerance,
ionSeries,
showFragmentationLadders,
showMissedFragments,
showLabels,
showFragmentationSummary);
(manager.SpectrumAnnotationForm.Controls[0] as ToolStrip).Hide();
(manager.SpectrumAnnotationForm.Controls[1] as SplitContainer).Panel1Collapsed = true;
(manager.SpectrumAnnotationForm.Controls[1] as SplitContainer).Dock = DockStyle.Fill;
//BeginInvoke(new MethodInvoker(() => toolStripStatusLabel.Text = toolStripStatusLabel.Text = "Opening spectrum source: " + sourcePath));
manager.OpenFile(sourcePath, spectrum.NativeID, annotation, spectrumListFilters);
manager.CurrentGraphForm.Focus();
manager.CurrentGraphForm.Icon = Properties.Resources.SpectrumViewIcon;
//BeginInvoke(new MethodInvoker(() => toolStripStatusLabel.Text = toolStripStatusLabel.Text = "Ready"));
annotationByGraphForm[manager.CurrentGraphForm] = annotation;
if (!handlerIsAttached.ContainsKey(manager.CurrentGraphForm))
{
handlerIsAttached[manager.CurrentGraphForm] = true;
manager.CurrentGraphForm.ZedGraphControl.PreviewKeyDown += CurrentGraphForm_PreviewKeyDown;
}
}
