public MoleculeInfo(string name, string formula, int charge, double mz, double monoMass, double averageMass,
IsotopeLabelType isotopeLabelType,
ExplicitRetentionTimeInfo explicitRetentionTime,
ExplicitTransitionGroupValues explicitTransitionGroupValues,
string note)
{
Name = name;
Formula = formula;
Charge = charge;
Mz = mz;
MonoMass = monoMass;
AverageMass = averageMass;
IsotopeLabelType = isotopeLabelType;
ExplicitRetentionTime = explicitRetentionTime;
ExplicitTransitionGroupValues = explicitTransitionGroupValues;
Note = note;
}
/// <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;
}
public SrmDocument ConvertToExplicitRetentionTimes(SrmDocument document, double timeOffset, double winOffset)
{
for (bool changing = true; changing;)
{
changing = false;
foreach (var peptideGroupDocNode in document.MoleculeGroups)
{
var pepGroupPath = new IdentityPath(IdentityPath.ROOT, peptideGroupDocNode.Id);
foreach (var nodePep in peptideGroupDocNode.Molecules)
{
var pepPath = new IdentityPath(pepGroupPath, nodePep.Id);
var rt = nodePep.AverageMeasuredRetentionTime;
if (rt.HasValue)
{
double? rtWin = document.Settings.PeptideSettings.Prediction.MeasuredRTWindow;
var explicitRetentionTimeInfo = new ExplicitRetentionTimeInfo(rt.Value+timeOffset, rtWin+winOffset);
if (!explicitRetentionTimeInfo.Equals(nodePep.ExplicitRetentionTime))
{
document = (SrmDocument)document.ReplaceChild(pepPath.Parent, nodePep.ChangeExplicitRetentionTime(explicitRetentionTimeInfo));
changing = true;
break;
}
}
}
if (changing)
break;
}
}
return document;
}
public PeptideDocNode ChangeExplicitRetentionTime(ExplicitRetentionTimeInfo prop)
{
return ChangeProp(ImClone(this), im => im.ExplicitRetentionTime = prop);
}
/// <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)
{
}
// Note: this potentially returns a node with a different ID, which has to be Inserted rather than Replaced
public PeptideDocNode ChangeCustomIonValues(SrmSettings settings, DocNodeCustomIon customIon, ExplicitRetentionTimeInfo explicitRetentionTime)
{
var newPeptide = new Peptide(customIon);
Helpers.AssignIfEquals(ref newPeptide, Peptide);
if (Equals(Peptide, newPeptide))
{
return Equals(ExplicitRetentionTime, explicitRetentionTime) ? this : ChangeExplicitRetentionTime(explicitRetentionTime);
}
else
{
// ID Changes impact all children, because IDs have back pointers to their parents
var children = new List<TransitionGroupDocNode>();
foreach (var nodeGroup in TransitionGroups)
{
children.Add(nodeGroup.UpdateSmallMoleculeTransitionGroup(newPeptide, null, settings));
}
return new PeptideDocNode(newPeptide, settings, ExplicitMods, SourceKey, explicitRetentionTime, children.ToArray(), AutoManageChildren);
}
}
public PeptideDocNode(Peptide id,
SrmSettings settings,
ExplicitMods mods,
ModifiedSequenceMods sourceKey,
string standardType,
int? rank,
ExplicitRetentionTimeInfo explicitRetentionTimeInfo,
Annotations annotations,
Results<PeptideChromInfo> results,
TransitionGroupDocNode[] children,
bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
ExplicitMods = mods;
SourceKey = sourceKey;
GlobalStandardType = standardType;
Rank = rank;
ExplicitRetentionTime = explicitRetentionTimeInfo;
Results = results;
BestResult = CalcBestResult();
if (settings != null)
{
var calcPre = settings.GetPrecursorCalc(IsotopeLabelType.light, ExplicitMods);
ModifiedSequence = calcPre.GetModifiedSequence(Peptide.Sequence, false);
ModifiedSequenceDisplay = calcPre.GetModifiedSequence(Peptide.Sequence, true);
}
}
public PeptideDocNode(Peptide id, SrmSettings settings, ExplicitMods mods, ModifiedSequenceMods sourceKey, ExplicitRetentionTimeInfo explicitRetentionTime,
TransitionGroupDocNode[] children, bool autoManageChildren)
: this(id, settings, mods, sourceKey, null, null, explicitRetentionTime, Annotations.EMPTY, null, children, autoManageChildren)
{
}
public PeptideDocNode(Peptide id, ExplicitMods mods = null, ExplicitRetentionTimeInfo explicitRetentionTime = null)
: this(id, null, mods, null, null, null, explicitRetentionTime, Annotations.EMPTY, null, new TransitionGroupDocNode[0], true)
{
}
public bool Equals(ExplicitRetentionTimeInfo other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other.RetentionTime, RetentionTime) &&
Equals(other.RetentionTimeWindow, RetentionTimeWindow);
}
