public static void SetComponentEnabledStateForModeUI(Component component, bool isDesired)
{
if (component is ToolStripMenuItem item)
{
item.Visible = isDesired;
return;
}
if (component is TabPage tabPage)
{
var parent = tabPage.Parent as TabControl;
if (parent != null)
{
if (!isDesired)
{
parent.TabPages.Remove(tabPage);
}
return;
}
}
if (component is Control ctrl)
{
ctrl.Visible = isDesired;
return;
}
Assume.Fail();
}
public static SpectrumPeakAnnotation Create(SmallMoleculeLibraryAttributes mol, Adduct adduct, string comment, double?mzTheoretical)
{
double?massTheoretical = mzTheoretical.HasValue ? adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic).Value : (double?)null;
var ion = new CustomIon(mol, adduct, massTheoretical);
if ((mzTheoretical ?? 0.0) > 0)
{
if (Equals(ion.MonoisotopicMassMz, 0.0))
{
// We didn't have enough info to calculate mz, use the provided theoretical value
var massMono = adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic);
var massAverage = adduct.MassFromMz(mzTheoretical.Value, MassType.Average);
ion = new CustomIon(ion.GetSmallMoleculeLibraryAttributes(), ion.Adduct, massMono, massAverage);
}
else
{
// Check our calculated value against provided theoretical value, allowing quite a lot of wiggle (not everybody is using the same precision out there)
var delta = .5; // Generous error for sanity check
if (Math.Abs(ion.MonoisotopicMassMz - mzTheoretical.Value) > delta)
{
Assume.Fail(string.Format(@"SpectrumPeakAnnotation: mzTheoretical {0} and mzActual {1} disagree by more than {2} in {3} {4}",
mzTheoretical, ion.MonoisotopicMassMz, delta, ion, comment ?? string.Empty));
}
}
}
return(ion.IsEmpty && string.IsNullOrEmpty(comment) ?
EMPTY :
new SpectrumPeakAnnotation(ion, comment));
}
private void WriteData(Block block, FileStream fileStream)
{
// Create back link to previous spilled block.
var lastFilePosition = new[] { _filePosition };
_filePosition = (int)fileStream.Position;
FastWrite.WriteInts(fileStream.SafeFileHandle, lastFilePosition, 0, 1);
// Write one data block.
if (typeof(TData) == typeof(short))
{
FastWrite.WriteShorts(fileStream.SafeFileHandle, (short[])(object)block._data, 0, _blockSize);
}
else if (typeof(TData) == typeof(int))
{
FastWrite.WriteInts(fileStream.SafeFileHandle, (int[])(object)block._data, 0, _blockSize);
}
else if (typeof(TData) == typeof(float))
{
FastWrite.WriteFloats(fileStream.SafeFileHandle, (float[])(object)block._data, 0, _blockSize);
}
else
{
Assume.Fail();
}
}
public IProgressStatus Complete()
{
var notFinal = ProgressList.Where(s => !s.IsFinal).ToArray();
if (notFinal.Any())
{
Assume.Fail(TextUtil.LineSeparate("Completing with non-final status:", // Not L10N
TextUtil.LineSeparate(notFinal.Select(s => string.Format("{0} {1}% - {2}", s.State, s.PercentComplete, s.FilePath))))); // Not L10N
}
return(ChangeProp(ImClone(this), s => s._complete = true));
}
// For all items in a menu, attempt to take a string like "{0} peptides" and return one like "{0} molecules" if menu item is not purely proteomic
// Update keyboard accelerators as needed
public static void TranslateMenuItems(ToolStripItemCollection items, SrmDocument.DOCUMENT_TYPE modeUI, ModeUIExtender extender)
{
var mapper = new PeptideToMoleculeTextMapper(modeUI, extender);
if (items != null)
{
mapper.FindInUseKeyboardAccelerators(items);
var activeItems = new List <ToolStripItem>();
for (int i = 0; i < items.Count; i++)
{
var item = items[i];
ModeUIExtender.MODE_UI_HANDLING_TYPE handlingType;
if (!mapper.HandledComponents.TryGetValue(item, out handlingType))
{
handlingType = ModeUIExtender.MODE_UI_HANDLING_TYPE.auto;
}
bool isActive;
switch (modeUI)
{
case SrmDocument.DOCUMENT_TYPE.proteomic:
isActive = handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.small_mol &&
handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.small_mol_only &&
handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.mixed_only;
break;
case SrmDocument.DOCUMENT_TYPE.small_molecules:
isActive = handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.proteomic &&
handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.mixed_only;
break;
case SrmDocument.DOCUMENT_TYPE.mixed:
isActive = handlingType != ModeUIExtender.MODE_UI_HANDLING_TYPE.small_mol_only;
break;
default:
isActive = false;
Assume.Fail(@"unknown UI mode");
break;
}
if (isActive)
{
activeItems.Add(item);
}
item.Visible = isActive;
}
mapper.Translate(activeItems); // Update the menu items that aren't inherently wrong for current UI mode
}
}
private XmlReader HandleMassOnlyDeclarations(ref Peptide peptide)
{
for (var retry = 0; retry < 4; retry++) // Looking for a common mass and set of adducts that all agree
{
var adjustParentMass = retry < 2; // Do/don't try adjusting the neutral mass as if it had proton gain or loss built in
var assumeProtonated = retry % 2 == 0; // Do/don't try [M+H] vs [M+]
foreach (var detail in _precursorRawDetails.OrderBy(d => d._declaredHeavy ? 1 : 0, SortOrder.Ascending)) // Look at lights first
{
var parentMassAdjustment = adjustParentMass
? Adduct.NonProteomicProtonatedFromCharge(detail._declaredCharge).ApplyToMass(TypedMass.ZERO_MONO_MASSH)
: TypedMass.ZERO_MONO_MASSH;
var parentMonoisotopicMass = ProposedMolecule.MonoisotopicMass - parentMassAdjustment;
if (_precursorRawDetails.TrueForAll(d =>
{
var adduct = assumeProtonated
? Adduct.NonProteomicProtonatedFromCharge(d._declaredCharge)
: Adduct.FromChargeNoMass(d._declaredCharge);
if (d._declaredHeavy)
{
var unexplainedMass = adduct.MassFromMz(d._declaredMz, MassType.Monoisotopic) - parentMonoisotopicMass;
adduct = adduct.ChangeIsotopeLabels(unexplainedMass, _mzDecimalPlaces);
}
d._proposedAdduct = adduct;
return(Math.Abs(d._declaredMz - d._proposedAdduct.MzFromNeutralMass(parentMonoisotopicMass)) <= MzToler);
}))
{
var parentAverageMass = ProposedMolecule.AverageMass - parentMassAdjustment;
ProposedMolecule = new CustomMolecule(parentMonoisotopicMass, parentAverageMass,
peptide.CustomMolecule.Name);
return(UpdatePeptideAndInsertAdductsInXML(ref peptide, _precursorRawDetails.Select(d => d._proposedAdduct)));
}
}
}
// Unexplained masses can be expressed as mass labels
if (_precursorRawDetails.TrueForAll(d =>
{
var adduct = Adduct.FromChargeNoMass(d._declaredCharge);
var unexplainedMass = adduct.MassFromMz(d._declaredMz, MassType.Monoisotopic) - ProposedMolecule.MonoisotopicMass;
d._proposedAdduct = adduct.ChangeIsotopeLabels(unexplainedMass, _mzDecimalPlaces);
return(Math.Abs(d._declaredMz - d._proposedAdduct.MzFromNeutralMass(ProposedMolecule.MonoisotopicMass)) <= MzToler);
}))
{
return(UpdatePeptideAndInsertAdductsInXML(ref peptide, _precursorRawDetails.Select(d => d._proposedAdduct)));
}
// Should never arrive here
Assume.Fail("Unable to to deduce adducts and common molecule for " + peptide); // Not L10N
return(UpdatePeptideAndInsertAdductsInXML(ref peptide, _precursorRawDetails.Select(d => d._nominalAdduct)));
}
public TypedMass GetIonMass(IonType ionType, int ionIndex)
{
switch (ionType)
{
case IonType.precursor:
return(PrecursorMass);
case IonType.custom:
Assume.Fail();
break;
}
return(FragmentMasses[ionType, ionIndex]);
}
private void CheckRefSpectra(IList <DbRefSpectra> spectra, string name, string formula, string precursorAdduct,
double precursorMz, ushort numPeaks, string[] fragmentNames = null,
double?ionMobility = null, double?ionMobilityHighEnergyOffset = null)
{
if (_convertedFromPeptides)
{
name = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + name;
}
for (var i = 0; i < spectra.Count; i++)
{
var spectrum = spectra[i];
if (spectrum.MoleculeName.Equals(name) &&
spectrum.ChemicalFormula.Equals(formula) &&
spectrum.PrecursorCharge.Equals(Adduct.FromStringAssumeProtonated(precursorAdduct).AdductCharge) &&
spectrum.PrecursorAdduct.Equals(precursorAdduct) &&
Math.Abs(spectrum.PrecursorMZ - precursorMz) < 0.001 &&
spectrum.NumPeaks.Equals(numPeaks))
{
// Found the item - check its fragment info if provided
// This demonstrates fix for "Issue 689: File > Export > Spectral Library losing information from small molecule documents",
// point 3 "Ion annotations do not preserve the ion names from the document but instead always use 'ion[mass]' for the annotations
// when the document gave them names."
if (fragmentNames != null)
{
Assume.AreEqual(fragmentNames.Length, spectrum.PeakAnnotations.Count);
foreach (var annotation in spectrum.PeakAnnotations)
{
Assume.IsTrue(fragmentNames.Contains(annotation.Name));
}
}
if (ionMobility.HasValue)
{
AssertEx.AreEqualNullable(spectrum.IonMobility, ionMobility, .00001);
if (ionMobilityHighEnergyOffset.HasValue)
{
AssertEx.AreEqualNullable(spectrum.IonMobilityHighEnergyOffset, ionMobilityHighEnergyOffset, .00001);
}
}
// Item is OK, remove from further searches
spectra.RemoveAt(i);
return;
}
}
Assume.Fail(string.Format("{0}, {1}, precursor charge {2}, precursor m/z {3}, with {4} peaks not found", name, formula, precursorAdduct, precursorMz, numPeaks));
}
public bool IsReadyForUniquenessFilter(PeptideFilter.PeptideUniquenessConstraint constraint)
{
switch (constraint)
{
case PeptideFilter.PeptideUniquenessConstraint.none:
case PeptideFilter.PeptideUniquenessConstraint.protein:
return(true);
case PeptideFilter.PeptideUniquenessConstraint.gene:
case PeptideFilter.PeptideUniquenessConstraint.species:
return(!NeedsProteinMetadataSearch);
default:
Assume.Fail();
return(false); // Should never be here
}
}
public static CustomMolecule FromTSV(string val)
{
var vals = val.FromEscapedTSV();
var name = vals.Length > 0 ? vals[0] : null;
var formula = vals.Length > 1 ? vals[1] : null;
// ReSharper disable PossibleNullReferenceException
var keysTSV = vals.Length > 2 ? val.Substring(name.Length + formula.Length + 2) : null;
// ReSharper restore PossibleNullReferenceException
if (formula == null && name != null && name.StartsWith(INVARIANT_NAME_DETAIL))
{
// Looks like a mass-only description
Regex r = new Regex(massFormatRegex, RegexOptions.IgnoreCase | RegexOptions.Singleline | RegexOptions.CultureInvariant);
Match m = r.Match(val);
if (m.Success)
{
try
{
var massMono = new TypedMass(double.Parse(m.Groups[1].Value, CultureInfo.InvariantCulture), MassType.Monoisotopic);
var massAvg = new TypedMass(double.Parse(m.Groups[2].Value, CultureInfo.InvariantCulture), MassType.Average);
return(new CustomMolecule(massMono, massAvg));
}
catch
{
Assume.Fail("unable to read custom molecule information"); // Not L10N
}
}
}
else if (formula != null && formula.Contains("/")) // Not L10N
{
// "formula" is actually mono and average masses
try
{
var values = formula.Split('/');
var massMono = new TypedMass(double.Parse(values[0], CultureInfo.InvariantCulture), MassType.Monoisotopic);
var massAvg = new TypedMass(double.Parse(values[1], CultureInfo.InvariantCulture), MassType.Average);
return(new CustomMolecule(massMono, massAvg, name, new MoleculeAccessionNumbers(keysTSV)));
}
catch
{
Assume.Fail("unable to read custom molecule information"); // Not L10N
}
}
return(new CustomMolecule(formula, null, null, name, new MoleculeAccessionNumbers(keysTSV)));
}
private static void CheckRefSpectra(IList <DbRefSpectra> spectra, string name, string formula, string precursorAdduct, double precursorMz, ushort numPeaks)
{
name = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + name;
for (var i = 0; i < spectra.Count; i++)
{
var spectrum = spectra[i];
if (spectrum.MoleculeName.Equals(name) &&
spectrum.ChemicalFormula.Equals(formula) &&
spectrum.PrecursorCharge.Equals(Adduct.FromStringAssumeProtonated(precursorAdduct).AdductCharge) &&
spectrum.PrecursorAdduct.Equals(precursorAdduct) &&
Math.Abs(spectrum.PrecursorMZ - precursorMz) < 0.001 &&
spectrum.NumPeaks.Equals(numPeaks))
{
spectra.RemoveAt(i);
return;
}
}
Assume.Fail(string.Format("{0}, {1}, precursor charge {2}, precursor m/z {3}, with {4} peaks not found", name, formula, precursorAdduct, precursorMz, numPeaks));
}
/// <summary>
/// Reconstitute data from memory and disk.
/// </summary>
public TData[] ToArray(byte[] bytes)
{
// Return final cached array.
if (_blockIndex < 0)
{
return(_block._data);
}
// Allocate final array.
int dest = Count;
var array = new TData[dest];
if (dest == 0)
{
return(array);
}
int length = (_blockIndex > 0) ? _blockIndex : _blockSize;
// Copy data from memory blocks.
while (_block != null)
{
dest -= length;
Array.Copy(_block._data, 0, array, dest, length);
_block = _block._previousBlock;
length = _blockSize;
}
Assume.IsTrue(bytes != null || _blocksOnDisk == 0);
// Copy data that was spilled.
while (_blocksOnDisk > 0)
{
dest -= _blockSize;
int source = _filePosition;
// ReSharper disable once AssignNullToNotNullAttribute
_filePosition = BitConverter.ToInt32(bytes, source);
source += sizeof(int);
int dest2 = dest;
// Convert byte data.
if (typeof(TData) == typeof(short))
{
for (int j = 0; j < _blockSize; j++)
{
// ReSharper disable once AssignNullToNotNullAttribute
array[dest2++] = (TData)(object)BitConverter.ToInt16(bytes, source);
source += sizeof(short);
}
}
else if (typeof(TData) == typeof(int))
{
for (int j = 0; j < _blockSize; j++)
{
// ReSharper disable once AssignNullToNotNullAttribute
array[dest2++] = (TData)(object)BitConverter.ToInt32(bytes, source);
source += sizeof(int);
}
}
else if (typeof(TData) == typeof(float))
{
for (int j = 0; j < _blockSize; j++)
{
// ReSharper disable once AssignNullToNotNullAttribute
array[dest2++] = (TData)(object)BitConverter.ToSingle(bytes, source);
source += sizeof(float);
}
}
else
{
Assume.Fail();
}
_blocksOnDisk--;
}
// Cache the final array in case this collector is shared (i.e., shared times).
_block = new Block(array, null);
_blockIndex = -1;
return(array);
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible &&
!helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
{
return;
}
var adduct = Adduct.NonProteomicProtonatedFromCharge(charge);
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources
.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge)
{
Adduct =
adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
{
return;
}
if (!_formulaBox.ValidateMonoText(helper))
{
return;
}
}
var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic);
var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average);
if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomMolecule.MIN_MASS));
return;
}
if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__,
CustomMolecule.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(
adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) ||
!_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average))))
{
_formulaBox.ShowTextBoxErrorFormula(helper,
Resources
.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
// Ion mobility value must have ion mobility units
if (textIonMobility.Visible && IonMobility.HasValue)
{
if (IonMobilityUnits == eIonMobilityUnits.none)
{
helper.ShowTextBoxError(textIonMobility, Resources.EditCustomMoleculeDlg_OkDialog_Please_specify_the_ion_mobility_units_);
comboBoxIonMobilityUnits.Focus();
return;
}
if (IonMobility.Value == 0 ||
(IonMobility.Value < 0 && !IonMobilityFilter.AcceptNegativeMobilityValues(IonMobilityUnits)))
{
helper.ShowTextBoxError(textIonMobility,
string.Format(Resources.SmallMoleculeTransitionListReader_ReadPrecursorOrProductColumns_Invalid_ion_mobility_value__0_, IonMobility));
textIonMobility.Focus();
return;
}
}
if (_usageMode == UsageMode.precursor)
{
// Only the adduct should be changing
SetResult(_resultCustomMolecule, Adduct);
}
else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
try
{
var name = textName.Text;
if (string.IsNullOrEmpty(name))
{
name = _formulaBox.NeutralFormula; // Clip off any adduct description
}
SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
// This is the only thing the user may have altered
var newHeavyMods = _driverLabelType.GetHeavyModifications().ToArray();
if (!ArrayUtil.EqualsDeep(newHeavyMods, _peptideSettings.Modifications.HeavyModifications))
{
var labelTypes = _peptideSettings.Modifications.InternalStandardTypes.Where(t =>
newHeavyMods.Any(m => Equals(m.LabelType, t))).ToArray();
if (labelTypes.Length == 0)
{
labelTypes = new[] { newHeavyMods.First().LabelType }
}
;
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
newHeavyMods,
labelTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
// Not expected, since we checked for a change before calling
// Otherwise, this is very confusing. The form just refuses to go away
// We would prefer to get an unhandled exception and fix this
Assume.Fail();
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorAdduct.AsFormula(),
Adduct
.AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing
!ReferenceEquals(t, _initialId));
}))
{
helper.ShowTextBoxError(textName,
Resources
.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_,
textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) &&
Equals(transition.CustomIon, ResultCustomMolecule)) &&
!ReferenceEquals(t, _initialId));
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
