public void FindPeaks(double[] retentionTimes, TimeIntervals timeIntervals, ExplicitRetentionTimeInfo explicitRT)
{
Finder = Crawdads.NewCrawdadPeakFinder();
Finder.SetChromatogram(Times, Intensities);
if (timeIntervals == null)
{
RawPeaks = Finder.CalcPeaks(MAX_PEAKS, TimesToIndices(retentionTimes));
}
else
{
var identifiedIndices = TimesToIndices(retentionTimes);
var allPeaks = timeIntervals.Intervals.SelectMany(interval =>
FindIntervalPeaks(interval.Key, interval.Value, identifiedIndices));
RawPeaks = allPeaks.OrderByDescending(peak => Tuple.Create(peak.Identified, peak.Area))
.Take(MAX_PEAKS).ToArray();
}
// Calculate smoothing for later use in extending the Crawdad peaks
IntensitiesSmooth = ChromatogramInfo.SavitzkyGolaySmooth(Intensities.ToArray());
// Accept only peaks within the user-provided RT window, if any
if (explicitRT != null)
{
var winLow = (float)(explicitRT.RetentionTime - 0.5 * (explicitRT.RetentionTimeWindow ?? 0));
var winHigh = winLow + (float)(explicitRT.RetentionTimeWindow ?? 0);
RawPeaks = RawPeaks.Where(rp =>
{
var t = Times[rp.TimeIndex];
return(winLow <= t && t <= winHigh);
});
}
}
public ExplicitValues(ExplicitRetentionTimeInfo resultRetentionTimeInfo,
ExplicitTransitionGroupValues resultExplicitTransitionGroupValues,
ExplicitTransitionValues resultExplicitTransitionValues)
{
ResultRetentionTimeInfo = resultRetentionTimeInfo;
ResultExplicitTransitionGroupValues = resultExplicitTransitionGroupValues;
ResultExplicitTransitionValues = resultExplicitTransitionValues;
}
/// <summary>
/// For creating at the Molecule level (create molecule and first transition group) or modifying at the transition level
/// Null values imply "don't ask user for this"
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, string title, Identity initialId, IEnumerable <Identity> existingIds, int minCharge, int maxCharge,
SrmSettings settings, string defaultName, string defaultFormula, int?defaultCharge, ExplicitTransitionGroupValues explicitAttributes,
ExplicitRetentionTimeInfo explicitRetentionTime,
IsotopeLabelType defaultIsotopeLabelType, bool enableFormulaEditing = true)
{
Text = title;
_parent = parent;
_initialId = initialId;
_existingIds = existingIds;
_minCharge = minCharge;
_maxCharge = maxCharge;
_transitionSettings = settings != null ? settings.TransitionSettings : null;
_peptideSettings = settings != null ? settings.PeptideSettings : null;
InitializeComponent();
NameText = defaultName;
var needOptionalValuesBox = explicitRetentionTime != null || explicitAttributes != null;
var heightDelta = 0;
if (explicitAttributes == null)
{
ResultExplicitTransitionGroupValues = null;
labelCollisionEnergy.Visible = false;
textCollisionEnergy.Visible = false;
labelSLens.Visible = false;
textSLens.Visible = false;
labelCompensationVoltage.Visible = false;
textCompensationVoltage.Visible = false;
labelConeVoltage.Visible = false;
textConeVoltage.Visible = false;
labelDriftTimeHighEnergyOffsetMsec.Visible = false;
textDriftTimeHighEnergyOffsetMsec.Visible = false;
labelDriftTimeMsec.Visible = false;
textDriftTimeMsec.Visible = false;
if (needOptionalValuesBox)
{
// We blanked out everything but the retention time
var vmargin = labelRetentionTime.Location.Y;
var newHeight = textRetentionTime.Location.Y + textRetentionTime.Height + vmargin;
heightDelta = groupBoxOptionalValues.Height - newHeight;
groupBoxOptionalValues.Height = newHeight;
}
}
else
{
ResultExplicitTransitionGroupValues = new ExplicitTransitionGroupValues(explicitAttributes);
}
string labelAverage = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_mass_;
string labelMono = defaultCharge.HasValue
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_mass_;
_formulaBox =
new FormulaBox(Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_Ion__chemical_formula_,
labelAverage,
labelMono,
defaultCharge)
{
Formula = defaultFormula,
Location = new Point(textName.Left, textName.Bottom + 12)
};
Controls.Add(_formulaBox);
_formulaBox.TabIndex = 2;
_formulaBox.Enabled = enableFormulaEditing;
bool needCharge = defaultCharge.HasValue;
textCharge.Visible = labelCharge.Visible = needCharge;
Charge = defaultCharge ?? 0;
if (needOptionalValuesBox && !needCharge)
{
heightDelta += groupBoxOptionalValues.Location.Y - labelCharge.Location.Y;
groupBoxOptionalValues.Location = new Point(groupBoxOptionalValues.Location.X, labelCharge.Location.Y);
}
if (explicitRetentionTime == null)
{
// Don't ask user for retetention times
RetentionTime = null;
RetentionTimeWindow = null;
labelRetentionTime.Visible = false;
labelRetentionTimeWindow.Visible = false;
textRetentionTime.Visible = false;
textRetentionTimeWindow.Visible = false;
if (needOptionalValuesBox)
{
var rtHeight = labelCollisionEnergy.Location.Y - labelRetentionTimeWindow.Location.Y;
groupBoxOptionalValues.Height -= rtHeight;
heightDelta += rtHeight;
}
}
else
{
RetentionTime = explicitRetentionTime.RetentionTime;
RetentionTimeWindow = explicitRetentionTime.RetentionTimeWindow;
}
if (!needOptionalValuesBox)
{
groupBoxOptionalValues.Visible = false;
heightDelta = groupBoxOptionalValues.Height;
}
// Initialize label
if (settings != null && defaultIsotopeLabelType != null)
{
_driverLabelType = new PeptideSettingsUI.LabelTypeComboDriver(comboIsotopeLabelType,
settings.PeptideSettings.Modifications, null, null, null, null)
{
SelectedName = defaultIsotopeLabelType.Name
};
}
else
{
comboIsotopeLabelType.Visible = false;
labelIsotopeLabelType.Visible = false;
}
Height -= heightDelta;
}
/// <summary>
/// For modifying at the Molecule level
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, string title,
SrmSettings settings, string defaultName, string defaultFormula, ExplicitRetentionTimeInfo explicitRetentionTime) :
this(parent, title, null, null, 0, 0, null, defaultName, defaultFormula, null, null, explicitRetentionTime, null, false)
{
}
/// <summary>
/// For creating at the Molecule level (create molecule and first transition group) or modifying at the transition level
/// Null values imply "don't ask user for this"
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, UsageMode usageMode, string title, Identity initialId,
IEnumerable <Identity> existingIds, int minCharge, int maxCharge,
SrmSettings settings, CustomMolecule molecule, Adduct defaultCharge,
ExplicitTransitionGroupValues explicitTransitionGroupAttributes,
ExplicitTransitionValues explicitTransitionAttributes,
ExplicitRetentionTimeInfo explicitRetentionTime,
IsotopeLabelType defaultIsotopeLabelType)
{
Text = title;
_parent = parent;
_initialId = initialId;
_existingIds = existingIds;
_minCharge = minCharge;
_maxCharge = maxCharge;
_transitionSettings = settings != null ? settings.TransitionSettings : null;
_peptideSettings = settings != null ? settings.PeptideSettings : null;
_resultAdduct = Adduct.EMPTY;
_resultCustomMolecule = molecule;
_usageMode = usageMode;
var enableFormulaEditing = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.moleculeEdit ||
usageMode == UsageMode.fragment;
var enableAdductEditing = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.precursor ||
usageMode == UsageMode.fragment;
var suggestOnlyAdductsWithMass = usageMode != UsageMode.fragment;
var needExplicitTransitionValues = usageMode == UsageMode.fragment;
var needExplicitTransitionGroupValues = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.precursor;
InitializeComponent();
NameText = molecule == null ? String.Empty : molecule.Name;
textName.Enabled = usageMode == UsageMode.moleculeNew || usageMode == UsageMode.moleculeEdit ||
usageMode == UsageMode.fragment; // Can user edit name?
var needOptionalValuesBox = explicitRetentionTime != null || explicitTransitionGroupAttributes != null || explicitTransitionAttributes != null;
if (!needExplicitTransitionValues)
{
labelCollisionEnergy.Visible = false;
textCollisionEnergy.Visible = false;
labelSLens.Visible = false;
textSLens.Visible = false;
labelConeVoltage.Visible = false;
textConeVoltage.Visible = false;
labelIonMobilityHighEnergyOffset.Visible = false;
textIonMobilityHighEnergyOffset.Visible = false;
labelDeclusteringPotential.Visible = false;
textDeclusteringPotential.Visible = false;
}
if (!needExplicitTransitionGroupValues)
{
labelCCS.Visible = false;
textBoxCCS.Visible = false;
labelIonMobility.Visible = false;
textIonMobility.Visible = false;
labelIonMobilityUnits.Visible = false;
comboBoxIonMobilityUnits.Visible = false;
}
var heightDelta = 0;
// Initialise the ion mobility units dropdown with L10N values
foreach (eIonMobilityUnits t in Enum.GetValues(typeof(eIonMobilityUnits)))
{
comboBoxIonMobilityUnits.Items.Add(IonMobilityFilter.IonMobilityUnitsL10NString(t));
}
if (needOptionalValuesBox)
{
var newHeight = groupBoxOptionalValues.Height;
var movers = new List <Control>();
int offset = 0;
if (!needExplicitTransitionGroupValues && !needExplicitTransitionValues)
{
// We blanked out everything but the retention time
newHeight = labelCollisionEnergy.Location.Y;
}
else if (!needExplicitTransitionGroupValues)
{
// We need to shift transition-level items up to where retention time was
movers.AddRange(new Control[] {
textCollisionEnergy, labelCollisionEnergy, textDeclusteringPotential, labelDeclusteringPotential, textSLens,
labelSLens, textConeVoltage, labelConeVoltage, textIonMobilityHighEnergyOffset, labelIonMobilityHighEnergyOffset
});
labelIonMobilityHighEnergyOffset.Location = labelIonMobility.Location;
textIonMobilityHighEnergyOffset.Location = textIonMobility.Location;
offset = labelCollisionEnergy.Location.Y - labelRetentionTime.Location.Y;
newHeight = textBoxCCS.Location.Y;
}
else if (!needExplicitTransitionValues)
{
// We need to shift precursor-level items up to where retention time was
movers.AddRange(new Control[] { textBoxCCS, labelCCS, textIonMobility,
labelIonMobility, comboBoxIonMobilityUnits, labelIonMobilityUnits });
offset = labelIonMobility.Location.Y - (explicitRetentionTime == null ? labelRetentionTime.Location.Y : labelCollisionEnergy.Location.Y);
newHeight = explicitRetentionTime == null ? textSLens.Location.Y : textIonMobility.Location.Y;
}
foreach (var mover in movers)
{
mover.Anchor = AnchorStyles.Left | AnchorStyles.Top;
mover.Location = new Point(mover.Location.X, mover.Location.Y - offset);
}
heightDelta = groupBoxOptionalValues.Height - newHeight;
groupBoxOptionalValues.Height = newHeight;
}
ResultExplicitTransitionGroupValues = new ExplicitTransitionGroupValues(explicitTransitionGroupAttributes);
ResultExplicitTransitionValues = new ExplicitTransitionValues(explicitTransitionAttributes);
string labelAverage = !defaultCharge.IsEmpty
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_A_verage_mass_;
string labelMono = !defaultCharge.IsEmpty
? Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_m_z_
: Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg__Monoisotopic_mass_;
var defaultFormula = molecule == null ? string.Empty : molecule.Formula;
var transition = initialId as Transition;
FormulaBox.EditMode editMode;
if (enableAdductEditing && !enableFormulaEditing)
{
editMode = FormulaBox.EditMode.adduct_only;
}
else if (!enableAdductEditing && enableFormulaEditing)
{
editMode = FormulaBox.EditMode.formula_only;
}
else
{
editMode = FormulaBox.EditMode.formula_and_adduct;
}
string formulaBoxLabel;
if (defaultCharge.IsEmpty)
{
formulaBoxLabel = Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_Chemi_cal_formula_;
}
else if (editMode == FormulaBox.EditMode.adduct_only)
{
var prompt = defaultFormula;
if (string.IsNullOrEmpty(defaultFormula) && molecule != null)
{
// Defined by mass only
prompt = molecule.ToString();
}
formulaBoxLabel = string.Format(Resources.EditCustomMoleculeDlg_EditCustomMoleculeDlg_Addu_ct_for__0__,
prompt);
}
else
{
formulaBoxLabel = Resources.EditMeasuredIonDlg_EditMeasuredIonDlg_Ion__chemical_formula_;
}
double?averageMass = null;
double?monoMass = null;
if (transition != null && string.IsNullOrEmpty(defaultFormula) && transition.IsCustom())
{
averageMass = transition.CustomIon.AverageMass;
monoMass = transition.CustomIon.MonoisotopicMass;
}
else if (molecule != null)
{
averageMass = molecule.AverageMass;
monoMass = molecule.MonoisotopicMass;
}
_formulaBox =
new FormulaBox(false, // Not proteomic, so offer Cl and Br in atoms popup
formulaBoxLabel,
labelAverage,
labelMono,
defaultCharge,
editMode,
suggestOnlyAdductsWithMass)
{
NeutralFormula = defaultFormula,
AverageMass = averageMass,
MonoMass = monoMass,
Location = new Point(textName.Left, textName.Bottom + 12)
};
_formulaBox.ChargeChange += (sender, args) =>
{
if (!_formulaBox.Adduct.IsEmpty)
{
Adduct = _formulaBox.Adduct;
var revisedFormula = _formulaBox.NeutralFormula + Adduct.AdductFormula;
if (!Equals(revisedFormula, _formulaBox.Formula))
{
_formulaBox.Formula = revisedFormula;
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula) && averageMass.HasValue)
{
_formulaBox.AverageMass = averageMass;
_formulaBox.MonoMass = monoMass;
}
}
};
Controls.Add(_formulaBox);
_formulaBox.TabIndex = 2;
_formulaBox.Enabled = enableFormulaEditing || enableAdductEditing;
Adduct = defaultCharge;
var needCharge = !Adduct.IsEmpty;
textCharge.Visible = labelCharge.Visible = needCharge;
if (needOptionalValuesBox && !needCharge)
{
heightDelta += groupBoxOptionalValues.Location.Y - labelCharge.Location.Y;
groupBoxOptionalValues.Location = new Point(groupBoxOptionalValues.Location.X, labelCharge.Location.Y);
}
if (explicitRetentionTime == null)
{
// Don't ask user for retetention times
RetentionTime = null;
RetentionTimeWindow = null;
labelRetentionTime.Visible = false;
labelRetentionTimeWindow.Visible = false;
textRetentionTime.Visible = false;
textRetentionTimeWindow.Visible = false;
}
else
{
RetentionTime = explicitRetentionTime.RetentionTime;
RetentionTimeWindow = explicitRetentionTime.RetentionTimeWindow;
}
if (!needOptionalValuesBox)
{
groupBoxOptionalValues.Visible = false;
heightDelta = groupBoxOptionalValues.Height;
}
// Initialize label
if (settings != null && defaultIsotopeLabelType != null)
{
_driverLabelType = new PeptideSettingsUI.LabelTypeComboDriver(PeptideSettingsUI.LabelTypeComboDriver.UsageType.InternalStandardPicker, comboIsotopeLabelType,
settings.PeptideSettings.Modifications, null, null, null, null)
{
SelectedName = defaultIsotopeLabelType.Name
};
}
else
{
comboIsotopeLabelType.Visible = false;
labelIsotopeLabelType.Visible = false;
}
Height -= heightDelta;
}
/// <summary>
/// For modifying at the Molecule level
/// </summary>
public EditCustomMoleculeDlg(SkylineWindow parent, string title,
SrmSettings settings, CustomMolecule molecule, ExplicitRetentionTimeInfo explicitRetentionTime) :
this(parent, UsageMode.moleculeEdit, title, null, null, 0, 0, null, molecule, Adduct.EMPTY, null, null,
explicitRetentionTime, null)
{
}