private PaneKey(int? precusorCharge, IsotopeLabelType isotopeLabelType, bool? isProducts)
: this()
{
PrecursorCharge = precusorCharge;
IsotopeLabelType = isotopeLabelType;
IsProducts = isProducts;
}
public void MultiLabelExplicitSerialTest()
{
// Create a simple document and add two peptides
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
var reader = new StringReader(string.Join("\n", new[] {">peptides1", pepSequence1, pepSequence2}));
IdentityPath path;
document = document.ImportFasta(reader, true, IdentityPath.ROOT, out path);
Assert.AreEqual(2, document.PeptideCount);
// Add some modifications in two new label types
var modCarb = new StaticMod("Carbamidomethyl Cysteine", "C", null, "C2H3ON");
var modOther = new StaticMod("Another Cysteine", "C", null, "CO8N2");
var staticMods = new[] {modCarb, modOther};
var mod15N = new StaticMod("All 15N", null, null, null, LabelAtoms.N15, null, null);
var modK13C = new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modR13C = new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modV13C = new StaticMod("Heavy V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var heavyMods = new[] { mod15N, modK13C, modR13C, modV13C };
var labelTypeAA = new IsotopeLabelType("heavy AA", IsotopeLabelType.FirstHeavy);
var labelTypeAll = new IsotopeLabelType("heavy All", IsotopeLabelType.FirstHeavy + 1);
var settings = document.Settings;
settings = settings.ChangePeptideModifications(mods =>
new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(labelTypeAA, new[] {modK13C, modR13C}),
new TypedModifications(labelTypeAll, new[] {mod15N})
}));
document = document.ChangeSettings(settings);
Assert.AreEqual(6, document.PeptideTransitionGroupCount);
// Add modifications to light and heavy AA in the first peptide
path = document.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var nodePepMod = (PeptideDocNode) document.FindNode(path);
var explicitMod = new ExplicitMods(nodePepMod.Peptide,
new[] {new ExplicitMod(pepSequence1.IndexOf('C'), modOther)},
new[] {new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAA, new ExplicitMod[0])});
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
// Add a modification to heavy All in the second peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
nodePepMod = (PeptideDocNode)document.FindNode(path);
explicitMod = new ExplicitMods(nodePepMod.Peptide, null,
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAll,
new[] {new ExplicitMod(pepSequence2.IndexOf('V'), modV13C)}) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
AssertEx.Serializable(document, 3, AssertEx.DocumentCloned);
}
public IEnumerable <TransitionGroup> GetTransitionGroups(SrmSettings settings, PeptideDocNode nodePep, ExplicitMods mods, bool useFilter)
{
if (IsCustomMolecule)
{
// TODO(bspratt) WHY NOT USING TRANSITION SETTINGS FILTER PRECURSOR ADDUCTS?
// We can't generate precursors as we do with peptides, so just filter what we do have on instrument mz range
//var precursorAdducts = settings.TransitionSettings.Filter.SmallMoleculePrecursorAdducts;
// TODO(bspratt) generate precursor transitions if doc has no fragments
// CONSIDER(bspratt) could we reasonably reuse fragments with proposed precursors of suitable charge and polarity (say, add an M+Na node that mimics an existing M+H node and children)
foreach (var group in nodePep.TransitionGroups.Where(tranGroup => tranGroup.TransitionGroup.IsCustomIon))
{
if (!useFilter || settings.TransitionSettings.IsMeasurablePrecursor(group.PrecursorMz))
{
yield return(group.TransitionGroup);
}
}
}
else
{
var precursorCharges = settings.TransitionSettings.Filter.PeptidePrecursorCharges;
if (!useFilter)
{
precursorCharges = new List <Adduct>();
for (int i = TransitionGroup.MIN_PRECURSOR_CHARGE; i < TransitionGroup.MAX_PRECURSOR_CHARGE; i++)
{
precursorCharges.Add(Adduct.FromChargeProtonated(i));
}
}
var modSettings = settings.PeptideSettings.Modifications;
var precursorMassLight = settings.GetPrecursorMass(IsotopeLabelType.light, Target, mods);
var listPrecursorMasses = new List <KeyValuePair <IsotopeLabelType, TypedMass> >
{
new KeyValuePair <IsotopeLabelType, TypedMass>(IsotopeLabelType.light, precursorMassLight)
};
foreach (var typeMods in modSettings.GetHeavyModifications())
{
IsotopeLabelType labelType = typeMods.LabelType;
var precursorMass = precursorMassLight;
if (settings.HasPrecursorCalc(labelType, mods))
{
precursorMass = settings.GetPrecursorMass(labelType, Target, mods);
}
listPrecursorMasses.Add(new KeyValuePair <IsotopeLabelType, TypedMass>(labelType, precursorMass));
}
foreach (var adduct in precursorCharges)
{
if (useFilter && !settings.Accept(settings, this, mods, adduct))
{
continue;
}
for (int i = 0; i < listPrecursorMasses.Count; i++)
{
var pair = listPrecursorMasses[i];
IsotopeLabelType labelType = pair.Key;
var precursorMass = pair.Value;
// Only return a heavy group, if the precursor masses differ
// between the light and heavy calculators
if (i == 0 || precursorMass != precursorMassLight)
{
if (settings.TransitionSettings.IsMeasurablePrecursor(SequenceMassCalc.GetMZ(precursorMass, adduct)))
{
yield return(new TransitionGroup(this, adduct, labelType));
}
}
}
}
}
}
/// <summary>
/// Creates a text sequence with the fully modified peptide sequence text
/// and font information for a given label type.
/// </summary>
private static TextSequence CreateTypeTextSequence(PeptideDocNode nodePep, SrmSettings settings,
IsotopeLabelType labelType, ModFontHolder fonts)
{
var calc = settings.TryGetPrecursorCalc(labelType, nodePep.ExplicitMods);
if (calc == null)
return null;
return new TextSequence
{
Text = nodePep.IsProteomic
? calc.GetModifiedSequence(nodePep.Peptide.Sequence, true)
: nodePep.CustomIon.DisplayName,
Font = fonts.GetModFont(labelType),
Color = ModFontHolder.GetModColor(labelType)
};
}
public static DocNodeCustomIon ConvertToSmallMolecule(ConvertToSmallMoleculesMode mode,
SrmDocument document, PeptideDocNode nodePep, int precursorCharge = 0, IsotopeLabelType isotopeLabelType = null)
{
// We're just using this masscalc to get the ion formula, so mono vs average doesn't matter
isotopeLabelType = isotopeLabelType ?? IsotopeLabelType.light;
var peptideSequence = nodePep.Peptide.Sequence;
var masscalc = document.Settings.TryGetPrecursorCalc(isotopeLabelType, nodePep.ExplicitMods) ?? new SequenceMassCalc(MassType.Monoisotopic);
// Determine the molecular formula of the charged/labeled peptide
var moleculeFormula = masscalc.GetIonFormula(peptideSequence, precursorCharge);
var moleculeCustomIon = new DocNodeCustomIon(moleculeFormula,
SmallMoleculeNameFromPeptide(peptideSequence, precursorCharge));
if (mode == ConvertToSmallMoleculesMode.masses_only)
{
// No formulas or names, just masses - see how we handle that
moleculeCustomIon = new DocNodeCustomIon(moleculeCustomIon.MonoisotopicMass,
moleculeCustomIon.AverageMass);
}
else if (mode == ConvertToSmallMoleculesMode.masses_and_names)
{
// Just masses and names - see how we handle that
moleculeCustomIon = new DocNodeCustomIon(moleculeCustomIon.MonoisotopicMass,
moleculeCustomIon.AverageMass, moleculeCustomIon.Name);
}
return moleculeCustomIon;
}
public TransitionGroup(Peptide peptide, DocNodeCustomIon customIon, int precursorCharge, IsotopeLabelType labelType, bool unlimitedCharge, int?decoyMassShift)
{
_peptide = peptide;
CustomIon = customIon ?? Peptide.CustomIon; // If parent molecule is a custom ion, and none specified, use that
PrecursorCharge = precursorCharge;
LabelType = labelType;
DecoyMassShift = decoyMassShift;
Validate(unlimitedCharge ? 0 : precursorCharge);
}
public TransitionGroup(Peptide peptide, DocNodeCustomIon customIon, int precursorCharge, IsotopeLabelType labelType)
: this(peptide, customIon, precursorCharge, labelType, false, null)
{
}
private ComboBox InitModificationCombo(ComboBox combo, int indexAA, IsotopeLabelType type)
{
var modsDoc = DocSettings.PeptideSettings.Modifications;
var modsExp = NodePeptide.ExplicitMods;
return type.IsLight
? InitModificationCombo(combo, modsDoc.StaticModifications,
modsExp != null ? modsExp.StaticModifications : null, StaticList, indexAA,
modsExp != null && modsExp.IsVariableStaticMods)
: InitModificationCombo(combo, modsDoc.GetModifications(type),
modsExp != null ? modsExp.GetModifications(type) : null, HeavyList, indexAA,
false);
}
private RatioValue CalcTransitionGroupGlobalRatio(int precursorCharge, IsotopeLabelType labelType)
{
if (GlobalStandardArea == 0)
return null;
double num = 0;
foreach (var pair in GetAreaPairs(labelType))
{
var key = pair.Key;
if (precursorCharge != -1 && key.PrecursorCharge != precursorCharge)
continue;
num += pair.Value;
}
return new RatioValue(num / GlobalStandardArea);
}
public float? CalcTransitionRatio(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, IsotopeLabelType labelTypeNum, IsotopeLabelType labelTypeDenom)
{
// Avoid 1.0 ratios for self-to-self
if (ReferenceEquals(labelTypeNum, labelTypeDenom))
return null;
float areaNum, areaDenom;
var key = nodeTran.Key(nodeGroup);
var keyNum = new TransitionKey(nodeGroup, key, labelTypeNum);
var keyDenom = new TransitionKey(nodeGroup, key, labelTypeDenom);
if (!TranAreas.TryGetValue(keyNum, out areaNum) ||
!TranAreas.TryGetValue(keyDenom, out areaDenom))
return null;
return areaNum/areaDenom;
}
public RatioValue CalcTransitionGroupRatio(TransitionGroupDocNode nodeGroup,
IsotopeLabelType labelTypeNum,
IsotopeLabelType labelTypeDenom)
{
return CalcTransitionGroupRatio(nodeGroup.TransitionGroup.PrecursorCharge,
labelTypeNum, labelTypeDenom);
}
public float? CalcTransitionGlobalRatio(TransitionGroupDocNode nodeGroup, TransitionDocNode nodeTran, IsotopeLabelType labelType)
{
if (GlobalStandardArea == 0)
return null;
float areaNum;
var keyNum = new TransitionKey(nodeGroup, nodeTran.Key(nodeGroup), labelType);
if (!TranAreas.TryGetValue(keyNum, out areaNum))
return null;
return (float) (areaNum / GlobalStandardArea);
}
public TransitionKey(TransitionKey key, IsotopeLabelType labelType)
{
_ionType = key._ionType;
_customIonEquivalenceTestValue = key._customIonEquivalenceTestValue;
_ionOrdinal = key._ionOrdinal;
_massIndex = key._massIndex;
_decoyMassShift = key._decoyMassShift;
_charge = key._charge;
_precursorCharge = key._precursorCharge;
_losses = key._losses;
_labelType = labelType;
}
public TransitionKey(TransitionGroupDocNode nodeGroup, TransitionLossKey tranLossKey, IsotopeLabelType labelType)
{
var transition = tranLossKey.Transition;
_ionType = transition.IonType;
_customIonEquivalenceTestValue = tranLossKey.CustomIonEquivalenceTestValue;
_ionOrdinal = transition.Ordinal;
_massIndex = transition.MassIndex;
_decoyMassShift = transition.DecoyMassShift;
_charge = transition.Charge;
_precursorCharge = nodeGroup.TransitionGroup.PrecursorCharge;
_losses = tranLossKey.Losses;
_labelType = labelType;
}
public bool HasChildType(IsotopeLabelType labelType)
{
return Children.Contains(nodeGroup => ReferenceEquals(labelType,
((TransitionGroupDocNode)nodeGroup).TransitionGroup.LabelType));
}
public void AddNewModification(int indexAA, IsotopeLabelType type)
{
ComboBox combo;
if (type.IsLight)
combo = _listComboStatic[indexAA];
else
{
int indexHeavyList = _listLabelTypeHeavy.IndexOf(type);
combo = _listListComboHeavy[indexHeavyList][indexAA];
}
combo.SelectedItem = Resources.SettingsListComboDriver_Add;
}
public void SetModification(int indexAA, IsotopeLabelType type, string modification)
{
ComboBox combo;
if (type.IsLight)
combo = _listComboStatic[indexAA];
else
{
int indexHeavyList = _listLabelTypeHeavy.IndexOf(type);
combo = _listListComboHeavy[indexHeavyList][indexAA];
}
combo.SelectedItem = modification;
}
private RatioValue CalcTransitionGroupRatio(int precursorCharge,
IsotopeLabelType labelTypeNum,
IsotopeLabelType labelTypeDenom)
{
// Avoid 1.0 ratios for self-to-self
if (ReferenceEquals(labelTypeNum, labelTypeDenom))
{
return null;
}
// Delay allocation, which can be costly in DIA data with no ratios
List<double> numerators = null;
List<double> denominators = null;
foreach (var pair in GetAreaPairs(labelTypeNum))
{
var key = pair.Key;
if (precursorCharge != -1 && key.PrecursorCharge != precursorCharge)
continue;
float areaNum = pair.Value;
float areaDenom;
if (!TranAreas.TryGetValue(new TransitionKey(key, labelTypeDenom), out areaDenom))
continue;
if (numerators == null)
{
numerators = new List<double>();
denominators = new List<double>();
}
numerators.Add(areaNum);
denominators.Add(areaDenom);
}
if (numerators == null)
return null;
return RatioValue.Calculate(numerators, denominators);
}
public void RemoveModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToArray();
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
MatchesUpdated = true;
}
private IEnumerable<KeyValuePair<TransitionKey, float>> GetAreaPairs(IsotopeLabelType labelType)
{
return from pair in TranAreas
where ReferenceEquals(labelType, pair.Key.LabelType)
select pair;
}
public ExplicitSequenceMassCalc(ExplicitMods mods, SequenceMassCalc massCalcBase, IsotopeLabelType labelType)
{
_massCalcBase = massCalcBase;
_mods = new ExplicitSequenceMods
{
Mods = mods.GetModifications(labelType),
StaticBaseMods = mods.GetStaticBaseMods(labelType),
ModMasses = mods.GetModMasses(_massCalcBase.MassType, labelType),
RequiresAllCalcMods = mods.IsVariableStaticMods
};
}
public bool CanHaveImplicitHeavyMods(IsotopeLabelType labelType)
{
return !HasExplicitMods || !ExplicitMods.IsModified(labelType);
}
public TransitionGroup(Peptide peptide, int precursorCharge, IsotopeLabelType labelType, bool unlimitedCharge, int?decoyMassShift)
: this(peptide, null, precursorCharge, labelType, unlimitedCharge, decoyMassShift)
{
}
public IsotopeModificationPermuter(StaticMod isotopeModification, bool simplePermutation, IsotopeLabelType fullHeavyLabelType, List <StaticMod> globalStaticMods, List <StaticMod> globalIsotopeMods)
{
IsotopeModification = isotopeModification;
SimplePermutation = simplePermutation;
FullyHeavyLabelType = fullHeavyLabelType;
GlobalStaticMods = globalStaticMods;
GlobalIsotopeMods = globalIsotopeMods;
}
/// <summary>
/// Constructs a ModifiedSequence from SrmSettings and PeptideDocNode.
/// </summary>
public static ModifiedSequence GetModifiedSequence(SrmSettings settings, PeptideDocNode docNode, IsotopeLabelType labelType)
{
if (docNode.Peptide.IsCustomMolecule)
{
return(null);
}
var unmodifiedSequence = docNode.Peptide.Sequence;
bool includeStaticMods = true;
bool includeStaticHeavyMods = false;
List <Modification> explicitMods = new List <Modification>();
if (null != docNode.ExplicitMods)
{
var staticBaseMods = docNode.ExplicitMods.GetStaticBaseMods(labelType);
var labelMods = docNode.ExplicitMods.GetModifications(labelType);
if (labelMods == null && !labelType.IsLight)
{
labelMods = docNode.ExplicitMods.GetModifications(IsotopeLabelType.light);
includeStaticHeavyMods = true;
}
if (labelMods != null || staticBaseMods != null)
{
IEnumerable <ExplicitMod> modsToAdd = (labelMods ?? Enumerable.Empty <ExplicitMod>())
.Concat(staticBaseMods ?? Enumerable.Empty <ExplicitMod>());
foreach (var mod in modsToAdd)
{
explicitMods.Add(MakeModification(unmodifiedSequence, mod));
}
includeStaticMods = docNode.ExplicitMods.IsVariableStaticMods && staticBaseMods == null;
}
}
if (includeStaticMods || includeStaticHeavyMods)
{
var peptideModifications = settings.PeptideSettings.Modifications;
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
IEnumerable <StaticMod> staticMods = peptideModifications.GetModifications(labelType);
if (!labelType.IsLight && includeStaticMods)
{
staticMods = peptideModifications.GetModifications(IsotopeLabelType.light).Concat(staticMods);
}
foreach (var staticMod in staticMods)
{
if (staticMod.IsExplicit || staticMod.IsVariable)
{
continue;
}
if (staticMod.Terminus.HasValue)
{
if (staticMod.Terminus == ModTerminus.N && i != 0)
{
continue;
}
if (staticMod.Terminus == ModTerminus.C && i != unmodifiedSequence.Length - 1)
{
continue;
}
}
if (!string.IsNullOrEmpty(staticMod.AAs) && !staticMod.AAs.Contains(unmodifiedSequence[i]))
{
continue;
}
explicitMods.Add(MakeModification(unmodifiedSequence, new ExplicitMod(i, staticMod)));
}
}
}
return(new ModifiedSequence(unmodifiedSequence, explicitMods, settings.TransitionSettings.Prediction.PrecursorMassType));
}
public const string UnimodPrefix = "unimod:"; // Not L10N
/// <summary>
/// Constructs a ModifiedSequence from SrmSettings and PeptideDocNode.
/// </summary>
public static ModifiedSequence GetModifiedSequence(SrmSettings settings, PeptideDocNode docNode, IsotopeLabelType labelType)
{
if (docNode.Peptide.IsCustomMolecule)
{
return(null);
}
var unmodifiedSequence = docNode.Peptide.Sequence;
bool includeStaticMods = true;
bool includeStaticHeavyMods = false;
List <Modification> explicitMods = new List <Modification>();
if (null != docNode.ExplicitMods)
{
var staticBaseMods = docNode.ExplicitMods.GetStaticBaseMods(labelType);
var labelMods = docNode.ExplicitMods.GetModifications(labelType);
var explicitLabelType = labelType;
if (labelMods == null && !labelType.IsLight)
{
labelMods = docNode.ExplicitMods.GetModifications(IsotopeLabelType.light);
explicitLabelType = IsotopeLabelType.light;
includeStaticHeavyMods = true;
}
if (labelMods != null || staticBaseMods != null)
{
IEnumerable <ExplicitMod> modsToAdd = (labelMods ?? Enumerable.Empty <ExplicitMod>())
.Concat(staticBaseMods ?? Enumerable.Empty <ExplicitMod>());
var monoMasses = docNode.ExplicitMods.GetModMasses(MassType.Monoisotopic, explicitLabelType);
var avgMasses = docNode.ExplicitMods.GetModMasses(MassType.Average, explicitLabelType);
foreach (var mod in modsToAdd)
{
explicitMods.Add(new Modification(mod, monoMasses[mod.IndexAA], avgMasses[mod.IndexAA]));
}
includeStaticMods = docNode.ExplicitMods.IsVariableStaticMods && staticBaseMods == null;
}
}
if (includeStaticMods || includeStaticHeavyMods)
{
var peptideModifications = settings.PeptideSettings.Modifications;
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
IEnumerable <StaticMod> staticMods = peptideModifications.GetModifications(labelType);
if (!labelType.IsLight && includeStaticMods)
{
staticMods = peptideModifications.GetModifications(IsotopeLabelType.light).Concat(staticMods);
}
foreach (var staticMod in staticMods)
{
if (staticMod.IsExplicit || staticMod.IsVariable)
{
continue;
}
if (staticMod.Terminus.HasValue)
{
if (staticMod.Terminus == ModTerminus.N && i != 0)
{
continue;
}
if (staticMod.Terminus == ModTerminus.C && i != unmodifiedSequence.Length - 1)
{
continue;
}
}
if (!string.IsNullOrEmpty(staticMod.AAs) && !staticMod.AAs.Contains(unmodifiedSequence[i]))
{
continue;
}
var monoMass = staticMod.MonoisotopicMass ??
SrmSettings.MonoisotopicMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
var avgMass = staticMod.AverageMass ??
SrmSettings.AverageMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
if (monoMass == 0 && avgMass == 0)
{
char aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
string heavyFormula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, heavyFormula,
SequenceMassCalc.MassPrecision);
avgMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, heavyFormula,
SequenceMassCalc.MassPrecision);
}
}
explicitMods.Add(new Modification(new ExplicitMod(i, staticMod), monoMass, avgMass));
}
}
}
return(new ModifiedSequence(unmodifiedSequence, explicitMods, settings.TransitionSettings.Prediction.PrecursorMassType));
}
public void TestPaste()
{
ClearDefaultModifications();
_yeastDoc = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMaxMz(1600)));
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new MeasuredIon[0])));
IdentityPath path;
_yeastDocReadOnly = _yeastDoc = _yeastDoc.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB),
false, IdentityPath.ROOT, out path);
_study7DocReadOnly = _study7Doc = CreateStudy7Doc();
IdentityPath pathRoot = IdentityPath.ROOT;
// Test pasting into document with same implicit modifications does not create any extra explicit modifications.
var study7EmptyDoc = (SrmDocument) _study7Doc.ChangeChildren(new DocNode[0]);
var study7PasteDoc = CopyPaste(_study7Doc, null, study7EmptyDoc, pathRoot);
var arrayPeptides = _study7Doc.Peptides.ToArray();
var arrayPastePeptides = study7PasteDoc.Peptides.ToArray();
Assert.AreEqual(arrayPeptides.Length, arrayPastePeptides.Length);
AssertEx.DocsEqual(_study7Doc, study7PasteDoc); // DocsEqual gives a more verbose failure message using XML output
// Test implicit mods in source document become explicit mods in target document.
ResetDocuments();
_yeastDoc = (SrmDocument) _yeastDoc.ChangeChildren(new DocNode[0]);
var settings = _yeastDoc.Settings;
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new StaticMod[0])));
_yeastDoc = CopyPaste(_study7Doc, null, _yeastDoc, pathRoot);
var pepMods = _yeastDoc.Settings.PeptideSettings.Modifications;
Assert.IsTrue(pepMods.StaticModifications != null);
Assert.IsTrue(pepMods.HasHeavyModifications);
Assert.IsFalse(pepMods.StaticModifications.Contains(mod => !mod.IsExplicit));
Assert.IsFalse(pepMods.HeavyModifications.Contains(mod => !mod.IsExplicit));
// Test explicit mods are dropped if the target document has matching implicit modifications.
study7PasteDoc = CopyPaste(_yeastDoc, null, study7EmptyDoc, pathRoot);
Assert.AreEqual(_study7Doc, study7PasteDoc);
// Add new label type to source document.
ResetDocuments();
const string labelTypeName13C = "heavy 13C";
var labelType13C = new IsotopeLabelType(labelTypeName13C, IsotopeLabelType.light.SortOrder + 1);
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] {new TypedModifications(labelType13C, HEAVY_MODS_13_C)});
Assert.IsTrue(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
Equals(nodeGroup.TransitionGroup.LabelType, labelType13C)));
// Test pasting into the same document with new label type.
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
// Check all transition have correct label type references.
Assert.IsFalse(_yeastDoc.PeptideTransitionGroups.Contains(nodeGroup =>
{
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
return !ReferenceEquals(labelType,
_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelType.Name).LabelType);
}));
// Check new document still serializes correctly.
AssertEx.Serializable(_yeastDoc, AssertEx.DocumentCloned);
// Test pasting into new document drops label types from source document that are not found in the target document.
_yeastDoc = CopyPaste(_yeastDoc, null, new SrmDocument(SrmSettingsList.GetDefault()), pathRoot);
Assert.IsNull(_yeastDoc.Settings.PeptideSettings.Modifications.GetModificationsByName(labelTypeName13C));
// If only specific children are selected, test that only these children get copied.
ResetDocuments();
var arrayTrans = _study7Doc.PeptideTransitions.ToArray();
IList<DocNode> selNodes = new List<DocNode>();
for (int i = 0; i < arrayTrans.Length; i += 2)
{
selNodes.Add(arrayTrans[i]);
}
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
Assert.AreEqual(arrayTrans.Length + selNodes.Count, _study7Doc.PeptideTransitionCount);
// Test after pasting to a peptide list, all children have been updated to point to the correct parent.
ResetDocuments();
_study7Doc = CopyPaste(_yeastDoc, new[] { _yeastDoc.Peptides.ToArray()[0] }, _study7Doc,
_study7Doc.GetPathTo((int) SrmDocument.Level.MoleculeGroups, 0));
Assert.AreEqual(_yeastDoc.Peptides.ToArray()[0].Peptide, _study7Doc.Peptides.ToArray()[0].Peptide);
Assert.AreEqual(_study7Doc.Peptides.ToArray()[0].Peptide,
_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup.Peptide);
Assert.AreEqual(_study7Doc.PeptideTransitionGroups.ToArray()[0].TransitionGroup,
_study7Doc.PeptideTransitions.ToArray()[0].Transition.Group);
// If only specific transition are selected for a peptide, but all transition groups are included, test AutoManageChildren is true.
ResetDocuments();
selNodes = new List<DocNode>();
foreach (TransitionGroupDocNode transGroup in _study7Doc.PeptideTransitionGroups)
{
selNodes.Add(transGroup.Children[0]);
}
// TODO: Fix this and make it pass
// var emptyDoc = (SrmDocument)_study7Doc.ChangeChildren(new List<DocNode>());
// _study7Doc = CopyPaste(_study7Doc, selNodes, emptyDoc, pathRoot);
_study7Doc = (SrmDocument)_study7Doc.ChangeChildren(new List<DocNode>());
_study7Doc = CopyPaste(_study7Doc, selNodes, _study7Doc, pathRoot);
foreach (PeptideDocNode peptide in _study7Doc.Peptides)
Assert.IsTrue(peptide.AutoManageChildren);
// Test pasting in modifications with the same name as but different definition from existing modifications not allowed.
ResetDocuments();
_yeastDoc = ChangePeptideModifications(_yeastDoc,
new[] { new TypedModifications(IsotopeLabelType.heavy, HEAVY_C_K_DIFDEF) });
SetDefaultModifications(_study7Doc);
AssertEx.ThrowsException<Exception>(() => _yeastDoc.Settings.UpdateDefaultModifications(false));
// Test variable modifications kept if target document has matching variable modifications turned on.
ResetDocuments();
settings = _yeastDoc.Settings;
var modsDefault = settings.PeptideSettings.Modifications;
var listVariableMods = new List<StaticMod>(modsDefault.StaticModifications) { VAR_MET_OXIDIZED };
_yeastDoc = _yeastDoc.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listVariableMods.ToArray())));
// Make sure there is an implicitly modified peptide in the yeast document
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.Peptide.Sequence.Contains("C")));
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
_yeastDoc = CopyPaste(_yeastDoc, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods && !nodePep.HasVariableMods));
// Otherwise the variable modifications become only explicit modifications.
var yeastDocVar = _yeastDoc;
_yeastDoc = _yeastDoc.ChangeSettings(_yeastDoc.Settings.ChangePeptideModifications(mods => modsDefault));
_yeastDoc = CopyPaste(yeastDocVar, null, _yeastDoc, pathRoot);
Assert.IsFalse(_yeastDoc.Settings.PeptideSettings.Modifications.HasVariableModifications);
Assert.IsTrue(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasExplicitMods));
Assert.IsFalse(_yeastDoc.Peptides.Contains(nodePep => nodePep.HasVariableMods));
}
public TransitionGroup(Peptide peptide, Adduct precursorAdduct, IsotopeLabelType labelType)
: this(peptide, precursorAdduct, labelType, false, null)
{
}
/// <summary>
/// Constructs a ModifiedSequence from SrmSettings and PeptideDocNode.
/// </summary>
public static ModifiedSequence GetModifiedSequence(SrmSettings settings, ISequenceContainer peptide, IsotopeLabelType labelType)
{
if (!peptide.Target.IsProteomic)
{
return(null);
}
var unmodifiedSequence = peptide.Target.Sequence;
List <IsotopeLabelType> implicitLabelTypes = new List <IsotopeLabelType>();
implicitLabelTypes.Add(IsotopeLabelType.light);
if (!labelType.IsLight)
{
implicitLabelTypes.Add(labelType);
}
List <Modification> explicitMods = new List <Modification>();
if (null != peptide.ExplicitMods)
{
var staticBaseMods = peptide.ExplicitMods.GetStaticBaseMods(labelType);
if (staticBaseMods != null)
{
implicitLabelTypes.Clear();
}
var labelMods = peptide.ExplicitMods.GetModifications(labelType);
if (labelMods != null)
{
if (!peptide.ExplicitMods.IsVariableStaticMods)
{
implicitLabelTypes.Remove(labelType);
}
}
else if (!labelType.IsLight)
{
labelMods = peptide.ExplicitMods.GetModifications(IsotopeLabelType.light);
if (labelMods != null && !peptide.ExplicitMods.IsVariableStaticMods)
{
implicitLabelTypes.Remove(IsotopeLabelType.light);
}
}
if (labelMods != null || staticBaseMods != null)
{
IEnumerable <ExplicitMod> modsToAdd = (labelMods ?? Enumerable.Empty <ExplicitMod>())
.Concat(staticBaseMods ?? Enumerable.Empty <ExplicitMod>());
foreach (var mod in modsToAdd)
{
explicitMods.Add(MakeModification(unmodifiedSequence, mod));
}
}
}
List <StaticMod> implicitMods = new List <StaticMod>();
var peptideModifications = settings.PeptideSettings.Modifications;
foreach (var implicitLabelType in implicitLabelTypes)
{
implicitMods.AddRange(peptideModifications.GetModifications(implicitLabelType));
}
for (int i = 0; i < unmodifiedSequence.Length; i++)
{
foreach (var staticMod in implicitMods)
{
if (staticMod.IsExplicit || staticMod.IsVariable)
{
continue;
}
if (staticMod.Terminus.HasValue)
{
if (staticMod.Terminus == ModTerminus.N && i != 0)
{
continue;
}
if (staticMod.Terminus == ModTerminus.C && i != unmodifiedSequence.Length - 1)
{
continue;
}
}
if (!string.IsNullOrEmpty(staticMod.AAs) && !staticMod.AAs.Contains(unmodifiedSequence[i]))
{
continue;
}
explicitMods.Add(MakeModification(unmodifiedSequence, new ExplicitMod(i, staticMod)));
}
}
return(new ModifiedSequence(unmodifiedSequence, explicitMods, settings.TransitionSettings.Prediction.PrecursorMassType));
}
public bool Equals(IsotopeLabelType other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other.Name, Name) && other.SortOrder == SortOrder;
}
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;
}
private void UpdateAxes(bool resetAxes, GraphValues.AggregateOp aggregateOp, AreaNormalizeToData normalizeData,
AreaNormalizeToView areaView, IsotopeLabelType standardType)
{
if (resetAxes)
{
XAxis.Scale.MaxAuto = XAxis.Scale.MinAuto = true;
YAxis.Scale.MaxAuto = true;
}
if (BarSettings.Type == BarType.PercentStack)
{
YAxis.Scale.Max = 100;
YAxis.Scale.MaxAuto = false;
YAxis.Title.Text = aggregateOp.AnnotateTitle(Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area_Percentage);
YAxis.Type = AxisType.Linear;
YAxis.Scale.MinAuto = false;
FixedYMin = YAxis.Scale.Min = 0;
}
else
{
if (normalizeData == AreaNormalizeToData.optimization)
{
// If currently log scale or normalized to max, reset the y-axis max
if (YAxis.Type == AxisType.Log || YAxis.Scale.Max == 1)
YAxis.Scale.MaxAuto = true;
YAxis.Title.Text = aggregateOp.AnnotateTitle(Resources.AreaReplicateGraphPane_UpdateGraph_Percent_of_Regression_Peak_Area);
YAxis.Type = AxisType.Linear;
YAxis.Scale.MinAuto = false;
FixedYMin = YAxis.Scale.Min = 0;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
YAxis.Scale.Max = 1;
if (IsDotProductVisible)
// Make YAxis Scale Max a little higher to accommodate for the dot products
YAxis.Scale.Max = 1.1;
YAxis.Scale.MaxAuto = false;
YAxis.Title.Text = aggregateOp.AnnotateTitle(Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area_Normalized);
YAxis.Type = AxisType.Linear;
YAxis.Scale.MinAuto = false;
FixedYMin = YAxis.Scale.Min = 0;
}
else if (Settings.Default.AreaLogScale)
{
// If currently not log scale, reset the y-axis max
if (YAxis.Type != AxisType.Log)
YAxis.Scale.MaxAuto = true;
if (Settings.Default.PeakAreaMaxArea != 0)
{
YAxis.Scale.MaxAuto = false;
YAxis.Scale.Max = Settings.Default.PeakAreaMaxArea;
}
YAxis.Type = AxisType.Log;
YAxis.Title.Text = GraphValues.AnnotateLogAxisTitle(aggregateOp.AnnotateTitle(
Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area));
YAxis.Scale.MinAuto = false;
FixedYMin = YAxis.Scale.Min = 1;
}
else
{
// If currently log scale, reset the y-axis max
if (YAxis.Type == AxisType.Log)
YAxis.Scale.MaxAuto = true;
if (Settings.Default.PeakAreaMaxArea != 0)
{
YAxis.Scale.MaxAuto = false;
YAxis.Scale.Max = Settings.Default.PeakAreaMaxArea;
}
else if (!YAxis.Scale.MaxAuto)
{
YAxis.Scale.MaxAuto = true;
}
string yTitle = Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area;
switch (areaView)
{
case AreaNormalizeToView.area_ratio_view:
yTitle = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area_Ratio_To__0_,
standardType.Title);
break;
case AreaNormalizeToView.area_global_standard_view:
yTitle = Resources.AreaReplicateGraphPane_UpdateGraph_Peak_Area_Ratio_To_Global_Standards;
break;
}
YAxis.Title.Text = aggregateOp.AnnotateTitle(yTitle);
YAxis.Type = AxisType.Linear;
YAxis.Scale.MinAuto = false;
FixedYMin = YAxis.Scale.Min = 0;
}
// Handle a switch from percent stack
if (!YAxis.Scale.MaxAuto && YAxis.Scale.Max == 100)
YAxis.Scale.MaxAuto = true;
}
Legend.IsVisible = Settings.Default.ShowPeakAreaLegend;
AxisChange();
// Reformat Y-Axis for labels and whiskers
var maxY = GraphHelper.GetMaxY(CurveList,this);
if (IsDotProductVisible)
{
var extraSpace = _lableHeight*(maxY/(Chart.Rect.Height - _lableHeight*2))*2;
maxY += extraSpace;
}
GraphHelper.ReformatYAxis(this, maxY);
}
public void SelectModification(IsotopeLabelType labelType, int indexAA, string modName)
{
int row = indexAA + 1;
string comboName = (labelType.IsLight ?
GetStaticName(row) :
GetHeavyName(row, labelType.SortOrder));
foreach (var comboBox in _listComboStatic)
{
if (Equals(comboName, comboBox.Name))
{
comboBox.SelectedItem = modName;
return;
}
}
foreach (var listComboHeavy in _listListComboHeavy)
{
foreach (var comboBox in listComboHeavy)
{
if (Equals(comboName, comboBox.Name))
{
comboBox.SelectedItem = modName;
return;
}
}
}
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] {MATCHER.GetModifiedNode(STR_MOD_BY_NAME)})}, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList<string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList<string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.HeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List<string> { STR_MOD_BY_NAME }, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException<FormatException>(() => UpdateMatcher(new[] {OXIDATION_M_C_TERM}, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] {LABEL15_N}, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] {carbC}, null, new[] {MET_OX_ROUNDED}, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List<StaticMod> { LABEL15_N });
var peptideMods = new PeptideModifications(new List<StaticMod>(), new List<TypedModifications> { typedMod });
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList<string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList<string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add( LABEL15_N );
MATCHER.CreateMatches(settingsMultiLabel, new List<string> { STR_HEAVY_15_F }, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] {MATCHER.GetModifiedNode(STR_HEAVY_15_F)})}, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications, settingsNew);
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F});
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
{
var modMatchDocContainer = InitMatchDocContainer(testDir);
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17
&& match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx)
&& match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
private static string GetIsotopeLabelText(IsotopeLabelType labelType)
{
return string.Format(Resources.EditPepModsDlg_GetIsotopeLabelText_Isotope__0__, labelType);
}
/// <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 void AddModification(StaticMod mod, IsotopeLabelType labelType)
{
if (MatcherPepMods.GetModificationTypes().Contains(labelType))
{
var newMods = MatcherPepMods.GetModifications(labelType)
.Where(existingMod => !existingMod.Equivalent(mod)).ToList();
newMods.Add(mod);
MatcherPepMods = MatcherPepMods.ChangeModifications(labelType, newMods);
}
else if (labelType.IsLight)
{
MatcherPepMods =
new PeptideModifications(new List<StaticMod> { mod }, MatcherPepMods.GetHeavyModifications().ToArray());
}
else
{
var typedHeavyMods =
new List<TypedModifications>(MatcherPepMods.GetHeavyModifications())
{ new TypedModifications(labelType, new List<StaticMod> { mod }) };
MatcherPepMods = new PeptideModifications(MatcherPepMods.StaticModifications, typedHeavyMods);
}
MatchesUpdated = true;
}
public TypedMassCalc(IsotopeLabelType labelType, SequenceMassCalc massCalc)
{
LabelType = labelType;
MassCalc = massCalc;
}
public IEnumerable <TransitionGroup> GetTransitionGroups(SrmSettings settings, PeptideDocNode nodePep, ExplicitMods mods, bool useFilter)
{
if (IsCustomIon)
{
// We can't generate nodes as we do with peptides, so just filter what we do have on instrument mz range
foreach (var group in nodePep.TransitionGroups.Where(tranGroup => tranGroup.TransitionGroup.IsCustomIon))
{
if (!useFilter || settings.TransitionSettings.IsMeasurablePrecursor(group.PrecursorMz))
{
yield return(group.TransitionGroup);
}
}
}
else
{
IList <int> precursorCharges = settings.TransitionSettings.Filter.PrecursorCharges;
if (!useFilter)
{
precursorCharges = new List <int>();
for (int i = TransitionGroup.MIN_PRECURSOR_CHARGE; i < TransitionGroup.MAX_PRECURSOR_CHARGE; i++)
{
precursorCharges.Add(i);
}
}
var modSettings = settings.PeptideSettings.Modifications;
double precursorMassLight = settings.GetPrecursorMass(IsotopeLabelType.light, Sequence, mods);
var listPrecursorMasses = new List <KeyValuePair <IsotopeLabelType, double> >
{
new KeyValuePair <IsotopeLabelType, double>(IsotopeLabelType.light, precursorMassLight)
};
foreach (var typeMods in modSettings.GetHeavyModifications())
{
IsotopeLabelType labelType = typeMods.LabelType;
double precursorMass = precursorMassLight;
if (settings.HasPrecursorCalc(labelType, mods))
{
precursorMass = settings.GetPrecursorMass(labelType, Sequence, mods);
}
listPrecursorMasses.Add(new KeyValuePair <IsotopeLabelType, double>(labelType, precursorMass));
}
foreach (int charge in precursorCharges)
{
if (useFilter && !settings.Accept(settings, this, mods, charge))
{
continue;
}
for (int i = 0; i < listPrecursorMasses.Count; i++)
{
var pair = listPrecursorMasses[i];
IsotopeLabelType labelType = pair.Key;
double precursorMass = pair.Value;
// Only return a heavy group, if the precursor masses differ
// between the light and heavy calculators
if (i == 0 || precursorMass != precursorMassLight)
{
if (settings.TransitionSettings.IsMeasurablePrecursor(SequenceMassCalc.GetMZ(precursorMass, charge)))
{
yield return(new TransitionGroup(this, null, charge, labelType));
}
}
}
}
}
}
public PaneKey(IsotopeLabelType isotopeLabelType)
: this(null, isotopeLabelType, false)
{
}