/// <summary>
/// Creates a ComplexFragmentIon representing something which has no amino acids from the parent peptide.
/// </summary>
public static ComplexFragmentIon NewOrphanFragmentIon(TransitionGroup transitionGroup, ExplicitMods explicitMods, Adduct adduct)
{
var transition = new Transition(transitionGroup, IonType.precursor,
transitionGroup.Peptide.Sequence.Length - 1, 0, adduct);
return(new ComplexFragmentIon(transition, null, explicitMods?.Crosslinks, true));
}
private static void VerifyAdd(int numStaticMods, int numHeavyMods)
{
var calc = SkylineWindow.Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt;
Assert.IsNotNull(calc);
var standards = calc.GetStandardPeptides().Select(SequenceMassCalc.NormalizeModifiedSequence).ToArray();
var peptides = SkylineWindow.Document.PeptideGroups.First().Peptides.ToArray();
Assert.AreEqual(standards.Length, peptides.Length);
foreach (var peptide in peptides)
{
Assert.IsTrue(standards.Contains(peptide.ModifiedTarget));
foreach (var transitionGroup in peptide.TransitionGroups)
{
var transitions = transitionGroup.Transitions.ToList();
for (var i = 1; i < transitions.Count; i++)
{
Assert.IsTrue(TransitionGroup.CompareTransitions(transitions[i - 1], transitions[i]) < 0);
}
}
}
var mods = SkylineWindow.Document.Settings.PeptideSettings.Modifications;
Assert.AreEqual(numStaticMods, mods.StaticModifications.Count);
Assert.AreEqual(numHeavyMods, mods.AllHeavyModifications.Count());
}
public void TestCrosslinkModSerialization()
{
var settings = SrmSettingsList.GetDefault();
var crosslinkerDef = new StaticMod("disulfide", null, null, "-H2")
.ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
settings = settings.ChangePeptideSettings(settings.PeptideSettings.ChangeModifications(
settings.PeptideSettings.Modifications.ChangeStaticModifications(new[] { crosslinkerDef })));
settings = settings.ChangeTransitionSettings(settings.TransitionSettings.ChangeFilter(
settings.TransitionSettings.Filter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b })
)); var mainPeptide = new Peptide("MERCURY");
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, true);
var peptideDocNode = new PeptideDocNode(mainPeptide, settings, explicitModsWithCrosslink, null, ExplicitRetentionTimeInfo.EMPTY, new [] { transitionGroupDocNode }, false);
peptideDocNode = peptideDocNode.ChangeSettings(settings, SrmSettingsDiff.ALL);
Assert.AreNotEqual(0, peptideDocNode.TransitionCount);
var peptideGroupDocNode = new PeptideGroupDocNode(new PeptideGroup(), Annotations.EMPTY, "Peptides", null, new [] { peptideDocNode });
var srmDocument = (SrmDocument) new SrmDocument(settings).ChangeChildren(new[] { peptideGroupDocNode });
AssertEx.Serializable(srmDocument);
string docXML = null;
AssertEx.RoundTrip(srmDocument, ref docXML);
Assert.IsNotNull(docXML);
}
public void TestCrosslinkGetNeutralFormula()
{
var mainPeptide = new Peptide("MERCURY");
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(srmSettings.PeptideSettings.Modifications
.ChangeStaticModifications(new StaticMod[0])));
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var unlinkedFormula = mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C37H61N13O11S2Se", unlinkedFormula.ToString());
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var linkedPeptideFormula = linkedPeptide.GetNeutralFormula(srmSettings, IsotopeLabelType.light);
Assert.AreEqual("C30H53N11O12S", linkedPeptideFormula.ToString());
var crosslinkMod = new StaticMod("disulfide", null, null, "-H2");
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(3, crosslinkMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
var crosslinkedFormula =
mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, explicitModsWithCrosslink);
Assert.AreEqual("C67H112N24O23S3Se", crosslinkedFormula.Molecule.ToString());
}
public void TestPermuteComplexIons()
{
var mainPeptide = new Peptide("MERCURY");
var srmSettings = SrmSettingsList.GetDefault();
var transitionFilter = srmSettings.TransitionSettings.Filter;
transitionFilter = transitionFilter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b });
srmSettings = srmSettings.ChangeTransitionSettings(
srmSettings.TransitionSettings.ChangeFilter(transitionFilter));
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("disulfide", "C", null, "-H2");
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 6, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
Assert.AreNotEqual(0, complexFragmentIons.Length);
}
public static string GetLabel(TransitionGroup tranGroup, double precursorMz,
string resultsText)
{
return(string.Format(@"{0}{1}{2}{3}", GetMzLabel(tranGroup, precursorMz),
Transition.GetChargeIndicator(tranGroup.PrecursorAdduct),
tranGroup.LabelTypeText, resultsText));
}
public void TestSingleAminoAcidLinkedPeptide()
{
var srmSettings = SrmSettingsList.GetDefault();
var mainPeptide = new Peptide("A");
var staticMod = new StaticMod("crosslinker", null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("D"), 0, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null,
ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
var modsWithoutLinkedPeptide = new ExplicitMods(mainPeptide, new[] { new ExplicitMod(0, staticMod), }, new TypedExplicitModifications[0]);
Assert.AreEqual("C3H7NO2", AminoAcidFormulas.Default.GetFormula("A").ToString());
Assert.AreEqual("C3H7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null).Molecule.ToString());
Assert.AreEqual("CH7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithoutLinkedPeptide).Molecule.ToString());
Assert.AreEqual("C4H7NO4", AminoAcidFormulas.Default.GetFormula("D").ToString());
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual("C5H14N2O6", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithLinkedPeptide).Molecule.ToString());
var mainComplexFragmentIon = new ComplexFragmentIon(new Transition(mainTransitionGroup, IonType.precursor, mainPeptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, modsWithLinkedPeptide.Crosslinks);
var linkedComplexFragmentIon = new ComplexFragmentIon(
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
var complexFragmentIon =
mainComplexFragmentIon.AddChild(new ModificationSite(0, staticMod.Name), linkedComplexFragmentIon);
var transition = complexFragmentIon.MakeTransitionDocNode(srmSettings, modsWithLinkedPeptide, null);
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var expectedMz = sequenceMassCalc.GetPrecursorMass("A") + sequenceMassCalc.GetPrecursorMass("D") - 24 - BioMassCalc.MassProton;
Assert.AreEqual(expectedMz, transition.Mz, .00001);
}
public void TransitionGroupAddTransition()
{
tlog.Debug(tag, $"TransitionGroupAddTransition START");
var testingTarget = new TransitionGroup();
Assert.IsNotNull(testingTarget, "Return a null object of FontClient");
Assert.IsInstanceOf <TransitionGroup>(testingTarget, "Should be an instance of TransitionGroup type.");
try
{
using (TransitionBase tb = new TransitionBase())
{
tb.TimePeriod = new TimePeriod(300);
tb.AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Bounce);
testingTarget.AddTransition(tb);
}
}
catch (Exception e)
{
tlog.Debug(tag, e.Message.ToString());
Assert.Fail("Caught Exception : Failed!");
}
testingTarget.Dispose();
tlog.Debug(tag, $"TransitionGroupAddTransition END (OK)");
}
public void TestGetFragmentFormula()
{
var pepseq = "PEPTIDE";
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var precursor = FragmentedMolecule.EMPTY.ChangeModifiedSequence(
new ModifiedSequence(pepseq, new ModifiedSequence.Modification[0], MassType.Monoisotopic));
var peptide = new Peptide(precursor.UnmodifiedSequence);
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var settings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
ExplicitMods.EMPTY, null, null, null, new TransitionDocNode[0], false);
foreach (var ionType in new[] { IonType.a, IonType.b, IonType.c, IonType.x, IonType.y, IonType.z })
{
for (int ordinal = 1; ordinal < pepseq.Length; ordinal++)
{
var transition = new Transition(transitionGroup, ionType, Transition.OrdinalToOffset(ionType, ordinal, pepseq.Length), 0, Adduct.SINGLY_PROTONATED);
var fragment = precursor.ChangeFragmentIon(ionType, ordinal);
var actualMassDistribution = FragmentedMolecule.Settings.DEFAULT.GetMassDistribution(
fragment.FragmentFormula, 0, 0);
var expectedMz = sequenceMassCalc.GetFragmentMass(transition, transitionGroupDocNode.IsotopeDist);
if (expectedMz.IsMassH())
{
expectedMz = new TypedMass(expectedMz.Value - BioMassCalc.MassProton, expectedMz.MassType & ~MassType.bMassH);
}
var actualMz = actualMassDistribution.MostAbundanceMass;
if (Math.Abs(expectedMz - actualMz) > .001)
{
Assert.AreEqual(expectedMz, actualMz, .001, "Ion type {0} Ordinal {1}", ionType, ordinal);
}
}
}
}
public void TestComplexIonMz()
{
var srmSettings = SrmSettingsList.GetDefault();
var peptide = new Peptide("DLGEEHFKGLVLIAFSQYLQQCPFDEHVK");
var linkedPeptide = new LinkedPeptide(new Peptide("LVNELTEFAKTCVADESHAGCEK"), 9, null);
var transitionGroup = new TransitionGroup(peptide, Adduct.QUADRUPLY_PROTONATED, IsotopeLabelType.light);
var crosslinkMod = new StaticMod("linker", "K", null, "C8H10O2");
var explicitMod = new ExplicitMod(7, crosslinkMod).ChangeLinkedPeptide(linkedPeptide);
var explicitMods = new ExplicitMods(peptide, new[] { explicitMod }, new List <TypedExplicitModifications>());
var linkedTransition =
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED);
var expectedMzs = new[]
{
Tuple.Create(IonType.b, 2, 1, 229.1183),
Tuple.Create(IonType.b, 10, 3, 1291.2766)
};
foreach (var tuple in expectedMzs)
{
int offset = Transition.OrdinalToOffset(tuple.Item1, tuple.Item2, peptide.Sequence.Length);
var transition = new Transition(transitionGroup, tuple.Item1, offset, 0, Adduct.FromChargeProtonated(tuple.Item3));
var complexFragmentIon = new ComplexFragmentIon(transition, null, explicitMods.Crosslinks);
if (complexFragmentIon.IncludesAaIndex(explicitMod.IndexAA))
{
complexFragmentIon = complexFragmentIon.AddChild(explicitMod.ModificationSite,
new ComplexFragmentIon(linkedTransition, null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE));
}
var complexTransitionDocNode = complexFragmentIon.MakeTransitionDocNode(srmSettings, explicitMods, null);
Assert.AreEqual(tuple.Item4, complexTransitionDocNode.Mz, .0001, "{0}{1}{2}", tuple.Item1, tuple.Item2,
Transition.GetChargeIndicator(Adduct.FromChargeProtonated(tuple.Item3)));
}
}
public static string GetTitle(PeptideDocNode peptideDocNode, TransitionGroupDocNode transitionGroupDocNode, IsotopeLabelType labelType)
{
string libraryNamePrefix = string.Empty;
//if (!string.IsNullOrEmpty(libraryNamePrefix))
// libraryNamePrefix += @" - ";
TransitionGroup transitionGroup = transitionGroupDocNode.TransitionGroup;
string sequence;
if (transitionGroup.Peptide.IsCustomMolecule)
{
sequence = transitionGroupDocNode.CustomMolecule.DisplayName;
}
else if (peptideDocNode?.ExplicitMods != null && peptideDocNode.ExplicitMods.Crosslinks.Count != 0)
{
sequence = peptideDocNode.GetCrosslinkedSequence();
}
else
{
sequence = transitionGroup.Peptide.Target.Sequence;
}
var charge = transitionGroup.PrecursorAdduct.ToString(); // Something like "2" or "-3" for protonation, or "[M+Na]" for small molecules
if (transitionGroup.Peptide.IsCustomMolecule)
{
return(labelType.IsLight
? string.Format(@"{0}{1}{2}", libraryNamePrefix, transitionGroup.Peptide.CustomMolecule.DisplayName, charge)
: string.Format(@"{0}{1}{2} ({3})", libraryNamePrefix, sequence, charge, labelType));
}
return(labelType.IsLight
? string.Format(Resources.SpectrumGraphItem_Title__0__1__Charge__2__, libraryNamePrefix, sequence, charge)
: string.Format(Resources.SpectrumGraphItem_Title__0__1__Charge__2__3__, libraryNamePrefix, sequence, charge, labelType));
}
private static string GetMzLabel(TransitionGroup tranGroup, double precursorMz)
{
int? massShift = tranGroup.DecoyMassShift;
double shift = SequenceMassCalc.GetPeptideInterval(massShift);
return(string.Format(@"{0:F04}{1}", precursorMz - shift,
Transition.GetDecoyText(massShift)));
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info,
IsotopeLabelType labelType, TransitionGroup group,
SrmSettings settings, string lookupSequence, ExplicitMods lookupMods,
IEnumerable <int> charges, IEnumerable <IonType> types,
IEnumerable <int> rankCharges, IEnumerable <IonType> rankTypes)
: this(info, labelType, group, settings, lookupSequence, lookupMods,
charges, types, rankCharges, rankTypes, false, true, -1)
{
}
protected override TransitionDocNode CreateEmptyNode()
{
var transitionGroup = new TransitionGroup(new Model.Peptide(null, @"X", null, null, 0),
Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var transition = new Model.Transition(transitionGroup, 0, Adduct.SINGLY_PROTONATED);
return(new TransitionDocNode(transition, Annotations.EMPTY, null, TypedMass.ZERO_MONO_MASSH,
TransitionDocNode.TransitionQuantInfo.DEFAULT, ExplicitTransitionValues.EMPTY, null));
}
private TransitionGroupDocNode MakeTransitionGroupWithAllPossibleChildren(SrmSettings settings, IsotopeLabelType labelType)
{
var peptide = new Peptide(TargetInfoObj.LookupSequence);
var transitionGroup = new TransitionGroup(peptide, TargetInfoObj.TransitionGroupDocNode.PrecursorAdduct, labelType);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings, TargetInfoObj.LookupMods, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var children = transitionGroupDocNode.GetTransitions(settings, TargetInfoObj.LookupMods,
transitionGroupDocNode.PrecursorMz, null, null, null, FragmentFilterObj.UseFilter).Cast <DocNode>().ToList();
return((TransitionGroupDocNode)transitionGroupDocNode.ChangeChildren(children));
}
public void TestTransitionGroupDocNodeGetNeutralFormula()
{
var peptide = new Peptide("PEPTIDE");
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var srmSettings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var moleculeOffset = transitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C34H53N7O15", moleculeOffset.Molecule.ToString());
}
private TransitionGroupDocNode CreateChoice(Identity childId, ExplicitMods mods)
{
TransitionGroup tranGroup = (TransitionGroup)childId;
TransitionDocNode[] transitions = DocNode.GetMatchingTransitions(
tranGroup, DocSettings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
return(nodeGroup.ChangeSettings(DocSettings, DocNode, mods, SrmSettingsDiff.ALL));
}
public LibraryRankedSpectrumInfo(SpectrumPeaksInfo info, IsotopeLabelType labelType,
TransitionGroup group, SrmSettings settings, ExplicitMods lookupMods,
bool useFilter, int minPeaks)
: this(info, labelType, group, settings, group.Peptide.Sequence, lookupMods,
null, // charges
null, // types
// ReadOnlyCollection enumerators are too slow, and show under a profiler
settings.TransitionSettings.Filter.ProductCharges.ToArray(),
settings.TransitionSettings.Filter.IonTypes.ToArray(),
useFilter, false, minPeaks)
{
}
private Page CreatePage(Color color, string colorTag, string greyTag)
{
View pageRoot = new View()
{
WidthResizePolicy = ResizePolicyType.FillToParent,
HeightResizePolicy = ResizePolicyType.FillToParent
};
View pageBackground = CreatePageScene(color, colorTag, greyTag);
pageBackground.TouchEvent += (object sender, View.TouchEventArgs e) =>
{
if (e.Touch.GetState(0) == PointStateType.Down)
{
navigator?.PopWithTransition();
}
return(true);
};
pageRoot.Add(pageBackground);
TransitionGroup transitionGroup = new TransitionGroup();
FadeTransition slide = new FadeTransition()
{
TimePeriod = new TimePeriod(500),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
};
transitionGroup.AddTransition(slide);
Page page = new ContentPage()
{
AppBar = new AppBar()
{
Title = "Second Page",
},
BackgroundColor = new Color(0.7f, 0.9f, 0.8f, 1.0f),
Content = pageRoot,
AppearingTransition = transitionGroup,
DisappearingTransition = new SlideTransition()
{
TimePeriod = new TimePeriod(500),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
Direction = SlideTransitionDirection.Left
},
};
return(page);
}
public int CompareTo(ComplexFragmentIon other)
{
if (IsIonTypePrecursor)
{
if (!other.IsIonTypePrecursor)
{
return(-1);
}
}
else if (other.IsIonTypePrecursor)
{
return(1);
}
int result = IsOrphan.CompareTo(other.IsOrphan);
if (result == 0)
{
result = TransitionGroup.CompareTransitionIds(Transition, other.Transition);
}
if (result == 0)
{
result = Comparer <double?> .Default.Compare(TransitionLosses?.Mass, other.TransitionLosses?.Mass);
}
if (result != 0)
{
return(result);
}
for (int i = 0; i < Children.Count && i < other.Children.Count; i++)
{
result = Children[i].Key.CompareTo(other.Children[i].Key);
if (result == 0)
{
result = Children[i].Value.CompareTo(other.Children[i].Value);
}
if (result != 0)
{
return(result);
}
}
return(Children.Count.CompareTo(other.Children.Count));
}
public void TestTwoAminoAcidLinkedPeptide()
{
const string modName = "crosslinker";
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangeTransitionSettings(srmSettings.TransitionSettings.ChangeFilter(
srmSettings.TransitionSettings.Filter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b })
));
var mainPeptide = new Peptide("AD");
var staticMod = new StaticMod(modName, null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("EF"), 1, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY, null,
new TransitionDocNode[0], false);
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual(1, srmSettings.PeptideSettings.Modifications.MaxNeutralLosses);
var oneNeutralLossChoices = mainTransitionGroupDocNode.GetTransitions(
srmSettings,
modsWithLinkedPeptide,
mainTransitionGroupDocNode.PrecursorMz,
mainTransitionGroupDocNode.IsotopeDist,
null,
null,
true).Select(transition => transition.ComplexFragmentIon.GetName()).ToList();
var modSite = new ModificationSite(0, modName);
var expectedFragmentIons = new[]
{
ComplexFragmentIonName.PRECURSOR.AddChild(modSite, ComplexFragmentIonName.PRECURSOR),
ComplexFragmentIonName.PRECURSOR.AddChild(modSite, new ComplexFragmentIonName(IonType.y, 1)),
new ComplexFragmentIonName(IonType.y, 1),
new ComplexFragmentIonName(IonType.b, 1).AddChild(modSite, new ComplexFragmentIonName(IonType.precursor, 0)),
ComplexFragmentIonName.ORPHAN.AddChild(modSite, new ComplexFragmentIonName(IonType.b, 1)),
};
CollectionAssert.AreEquivalent(expectedFragmentIons, oneNeutralLossChoices);
}
public IEnumerable <TransitionDocNode> GetComplexTransitions(TransitionGroup transitionGroup,
double precursorMz,
IsotopeDistInfo isotopeDist,
Dictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
IEnumerable <TransitionDocNode> simpleTransitions,
bool useFilter)
{
var allTransitions =
RemoveUnmeasurable(precursorMz,
RemoveDuplicates(
GetAllComplexTransitions(transitionGroup, isotopeDist, simpleTransitions, useFilter)))
.OrderBy(tran => tran.ComplexFragmentIon)
.ToList();
IList <TransitionDocNode> ms2transitions;
IList <TransitionDocNode> ms1transitions;
if (Settings.TransitionSettings.FullScan.IsEnabledMs)
{
ms2transitions = allTransitions.Where(tran => !tran.IsMs1).ToList();
ms1transitions = allTransitions.Where(tran => tran.IsMs1).ToList();
if (Settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
ms1transitions = ms1transitions.SelectMany(tran =>
ExpandPrecursorIsotopes(tran, isotopeDist, useFilter)).ToList();
}
}
else
{
ms2transitions = allTransitions;
ms1transitions = new TransitionDocNode[0];
}
if (useFilter)
{
if (!Settings.TransitionSettings.Filter.PeptideIonTypes.Contains(IonType.precursor))
{
ms1transitions = new TransitionDocNode[0];
}
ms2transitions = FilterTransitions(transitionRanks, ms2transitions).ToList();
}
return(ms1transitions.Concat(ms2transitions));
}
public static IList <DocNode> GetChoices(TransitionGroupDocNode nodeGroup, SrmSettings settings, ExplicitMods mods, bool useFilter)
{
TransitionGroup group = nodeGroup.TransitionGroup;
SpectrumHeaderInfo libInfo = null;
var transitionRanks = new Dictionary <double, LibraryRankedSpectrumInfo.RankedMI>();
group.GetLibraryInfo(settings, mods, useFilter, ref libInfo, transitionRanks);
var listChoices = new List <DocNode>();
foreach (TransitionDocNode nodeTran in nodeGroup.GetTransitions(settings, mods,
nodeGroup.PrecursorMz, nodeGroup.IsotopeDist, libInfo, transitionRanks, useFilter))
{
listChoices.Add(nodeTran);
}
return(listChoices);
}
public void TestIncludesAaIndex()
{
var peptide = new Peptide("AD");
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var precursor =
new ComplexFragmentIon(new Transition(transitionGroup, IonType.precursor, peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.IsTrue(precursor.IncludesAaIndex(0));
Assert.IsTrue(precursor.IncludesAaIndex(1));
var y1 = new ComplexFragmentIon(new Transition(transitionGroup, IonType.y, Transition.OrdinalToOffset(IonType.y, 1, peptide.Length), 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.AreEqual(1, y1.Transition.Ordinal);
Assert.IsFalse(y1.IncludesAaIndex(0));
Assert.IsTrue(y1.IncludesAaIndex(1));
var b1 = new ComplexFragmentIon(new Transition(transitionGroup, IonType.b, Transition.OrdinalToOffset(IonType.b, 1, peptide.Length), 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.AreEqual(1, b1.Transition.Ordinal);
Assert.IsTrue(b1.IncludesAaIndex(0));
Assert.IsFalse(b1.IncludesAaIndex(1));
}
public void TestCrosslinkPrecursorMz()
{
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(
srmSettings.PeptideSettings.Modifications.ChangeStaticModifications(new StaticMod[0])));
var mainPeptide = new Peptide("WQEGNVFSCSVMHEALHNHYTQK");
var otherPeptide = new Peptide("NQVSLTCLVK");
var linkedPeptide = new LinkedPeptide(otherPeptide, 6, ExplicitMods.EMPTY);
var crosslinkMod = new StaticMod("disulfide", "C", null, "-H2").ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var explicitMod = new ExplicitMod(8, crosslinkMod).ChangeLinkedPeptide(linkedPeptide);
var explicitMods = new ExplicitMods(mainPeptide, new[] { explicitMod }, new List <TypedExplicitModifications>());
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings, explicitMods, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
Assert.AreEqual(1923.9111, transitionGroupDocNode.PrecursorMz, .001);
}
public MockTranPeakData(double[] data,
IonType ionType = IonType.a,
IsotopeLabelType labelType = null,
int charge = 2,
double?massError = null,
double libIntensity = 0,
double?isotopeProportion = null)
{
if (labelType == null)
{
labelType = IsotopeLabelType.light;
}
PeakData = new MockPeakData(data, massError) as TPeak;
var peptide = new Peptide(null, "AVVAVVA", null, null, 0);
var tranGroup = new TransitionGroup(peptide, null, charge, labelType);
int offset = ionType == IonType.precursor ? 6 : 0;
var isotopeInfo = isotopeProportion == null ? null : new TransitionIsotopeDistInfo(1, (float)isotopeProportion);
NodeTran = new TransitionDocNode(new Transition(tranGroup, ionType, offset, 0, charge, null),
null, 0, isotopeInfo, new TransitionLibInfo(1, (float)libIntensity));
}
public void TransitionGroupConstructor()
{
tlog.Debug(tag, $"TransitionGroupConstructor START");
var testingTarget = new TransitionGroup();
Assert.IsNotNull(testingTarget, "Return a null object of FontClient");
Assert.IsInstanceOf <TransitionGroup>(testingTarget, "Should be an instance of TransitionGroup type.");
testingTarget.UseGroupTimePeriod = true;
tlog.Debug(tag, "UseGroupTimePeriod : " + testingTarget.UseGroupTimePeriod);
testingTarget.StepTransition = true;
tlog.Debug(tag, "StepTransition : " + testingTarget.StepTransition);
testingTarget.UseGroupAlphaFunction = true;
tlog.Debug(tag, "UseGroupAlphaFunction : " + testingTarget.UseGroupAlphaFunction);
testingTarget.Dispose();
tlog.Debug(tag, $"TransitionGroupConstructor END (OK)");
}
public void TestLooplink()
{
var peptide = new Peptide("PEPTIDE");
var srmSettings = SrmSettingsList.GetDefault();
var transitionFilter = srmSettings.TransitionSettings.Filter;
transitionFilter = transitionFilter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b });
srmSettings = srmSettings.ChangeTransitionSettings(
srmSettings.TransitionSettings.ChangeFilter(transitionFilter));
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("dss", null, null, "C8H10O2");
var linkedPeptide = new LinkedPeptide(null, 5, null);
var crosslinkMod = new ExplicitMod(2, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(peptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var modifiedSequence = ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence,
explicitModsWithCrosslink, IsotopeLabelType.light);
Assert.AreEqual("PEPTIDE-[dss@3-6]", modifiedSequence.FullNames);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
// Make sure none of the transitions involve a cleavage in between the two ends of the looplink
// PEpTIdE
var yOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.y).Select(ion => ion.Ordinal)
.Distinct().ToList();
var bOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.b).Select(ion => ion.Ordinal)
.Distinct().ToList();
CollectionAssert.AreEquivalent(new[] { 6, 5, 1 }, yOrdinals);
CollectionAssert.AreEquivalent(new[] { 1, 2, 6 }, bOrdinals);
}
public MockTranPeakData(double[] data,
IonType ionType = IonType.a,
IsotopeLabelType labelType = null,
int?charge = null,
double?massError = null,
double libIntensity = 0,
double?isotopeProportion = null)
{
if (labelType == null)
{
labelType = IsotopeLabelType.light;
}
PeakData = new MockPeakData(data, massError) as TPeak;
var peptide = new Peptide(null, "AVVAVVA", null, null, 0);
charge = charge ?? 2;
var tranGroup = new TransitionGroup(peptide, Adduct.FromChargeProtonated(charge), labelType);
int offset = ionType == IonType.precursor ? 6 : 0;
var isotopeInfo = isotopeProportion == null ? null : new TransitionIsotopeDistInfo(1, (float)isotopeProportion);
NodeTran = new TransitionDocNode(new Transition(tranGroup, ionType, offset, 0, Adduct.FromChargeProtonated(charge), null),
null, TypedMass.ZERO_MONO_MASSH, new TransitionDocNode.TransitionQuantInfo(isotopeInfo, new TransitionLibInfo(1, (float)libIntensity), true));
}
private static string GetMzLabel(TransitionGroup tranGroup, double precursorMz)
{
int? massShift = tranGroup.DecoyMassShift;
double shift = SequenceMassCalc.GetPeptideInterval(massShift);
return string.Format("{0:F04}{1}", precursorMz - shift, // Not L10N
Transition.GetDecoyText(massShift));
}
private TransitionGroupDocNode GetMoleculeTransitionGroup(SrmDocument document, DataGridViewRow row, Peptide pep, bool requireProductInfo)
{
var moleculeInfo = ReadPrecursorOrProductColumns(document, row, true); // Re-read the precursor columns
if (!document.Settings.TransitionSettings.IsMeasurablePrecursor(moleculeInfo.Mz))
{
ShowTransitionError(new PasteError
{
Column = INDEX_MOLECULE_MZ,
Line = row.Index,
Message = string.Format(Resources.PasteDlg_GetMoleculeTransitionGroup_The_precursor_m_z__0__is_not_measureable_with_your_current_instrument_settings_, moleculeInfo.Mz)
});
return null;
}
var customIon = moleculeInfo.ToCustomIon();
var isotopeLabelType = moleculeInfo.IsotopeLabelType ?? IsotopeLabelType.light;
var group = new TransitionGroup(pep, customIon, moleculeInfo.Charge, isotopeLabelType);
try
{
var tran = GetMoleculeTransition(document, row, pep, group, requireProductInfo);
if (tran == null)
return null;
return new TransitionGroupDocNode(group, document.Annotations, document.Settings, null,
null, moleculeInfo.ExplicitTransitionGroupValues, null, new[] {tran}, true);
}
catch (InvalidDataException e)
{
ShowTransitionError(new PasteError
{
Column = INDEX_PRODUCT_MZ, // Don't actually know that mz was the issue, but at least it's the right row, and in the product columns
Line = row.Index,
Message = e.Message
});
return null;
}
}
private TransitionDocNode GetMoleculeTransition(SrmDocument document, DataGridViewRow row, Peptide pep, TransitionGroup group, bool requireProductInfo)
{
var massType =
document.Settings.TransitionSettings.Prediction.FragmentMassType;
var molecule = ReadPrecursorOrProductColumns(document, row, !requireProductInfo); // Re-read the product columns, or copy precursor
if (requireProductInfo && molecule == null)
{
return null;
}
var ion = molecule.ToCustomIon();
var ionType = (!requireProductInfo || // We inspected the input list and found only precursor info
((ion.MonoisotopicMass.Equals(pep.CustomIon.MonoisotopicMass) &&
ion.AverageMass.Equals(pep.CustomIon.AverageMass)))) // Same mass, must be a precursor transition
? IonType.precursor
: IonType.custom;
double mass = ion.GetMass(massType);
var transition = new Transition(group, molecule.Charge, null, ion, ionType);
var annotations = document.Annotations;
if (!string.IsNullOrEmpty(molecule.Note))
{
var note = document.Annotations.Note;
note = string.IsNullOrEmpty(note) ? molecule.Note : (note + "\r\n" + molecule.Note); // Not L10N
annotations = new Annotations(note, document.Annotations.ListAnnotations(), 0);
}
return new TransitionDocNode(transition, annotations, null, mass, null, null, null);
}
public TransitionDocNode[] GetMatchingTransitions(TransitionGroup tranGroup, SrmSettings settings, ExplicitMods explicitMods)
{
int iMatch = Children.IndexOf(nodeGroup =>
((TransitionGroupDocNode)nodeGroup).TransitionGroup.PrecursorCharge == tranGroup.PrecursorCharge);
if (iMatch == -1)
return null;
TransitionGroupDocNode nodeGroupMatching = (TransitionGroupDocNode) Children[iMatch];
// If the matching node is auto-managed, and auto-select is on in the settings,
// then returning no transitions should allow transitions to be chosen correctly
// automatically.
if (nodeGroupMatching.AutoManageChildren && settings.TransitionSettings.Filter.AutoSelect &&
// Having disconnected libraries can mess up automatic picking
settings.PeptideSettings.Libraries.DisconnectedLibraries == null)
return null;
return tranGroup.GetMatchingTransitions(settings, nodeGroupMatching, explicitMods);
}
public static bool IsCustom(IonType type, TransitionGroup parent)
{
return type == IonType.custom || (type == IonType.precursor && parent.IsCustomIon);
}
private static TransitionDocNode[] GetDecoyTransitions(TransitionGroupDocNode nodeGroup, TransitionGroup decoyGroup, bool shiftMass)
{
var decoyNodeTranList = new List<TransitionDocNode>();
foreach (var nodeTran in nodeGroup.Transitions)
{
var transition = nodeTran.Transition;
int productMassShift = 0;
if (shiftMass)
productMassShift = GetProductMassShift();
else if (transition.IsPrecursor() && decoyGroup.DecoyMassShift.HasValue)
productMassShift = decoyGroup.DecoyMassShift.Value;
var decoyTransition = new Transition(decoyGroup, transition.IonType, transition.CleavageOffset,
transition.MassIndex, transition.Charge, productMassShift, transition.CustomIon);
decoyNodeTranList.Add(new TransitionDocNode(decoyTransition, nodeTran.Losses, 0,
nodeTran.IsotopeDistInfo, nodeTran.LibInfo));
}
return decoyNodeTranList.ToArray();
}
private static List<TransitionGroupDocNode> GetDecoyGroups(PeptideDocNode nodePep, Peptide decoyPeptide,
ExplicitMods mods, IEnumerable<TransitionGroupDocNode> comparableGroups, SrmDocument document, bool shiftMass)
{
var decoyNodeTranGroupList = new List<TransitionGroupDocNode>();
var chargeToPrecursor = new Tuple<int, TransitionGroupDocNode>[TransitionGroup.MAX_PRECURSOR_CHARGE+1];
foreach (TransitionGroupDocNode nodeGroup in comparableGroups)
{
var transGroup = nodeGroup.TransitionGroup;
int precursorMassShift;
TransitionGroupDocNode nodeGroupPrimary = null;
var primaryPrecursor = chargeToPrecursor[nodeGroup.TransitionGroup.PrecursorCharge];
if (primaryPrecursor != null)
{
precursorMassShift = primaryPrecursor.Item1;
nodeGroupPrimary = primaryPrecursor.Item2;
}
else if (shiftMass)
{
precursorMassShift = GetPrecursorMassShift();
}
else
{
precursorMassShift = TransitionGroup.ALTERED_SEQUENCE_DECOY_MZ_SHIFT;
}
var decoyGroup = new TransitionGroup(decoyPeptide, transGroup.PrecursorCharge,
transGroup.LabelType, false, precursorMassShift);
var decoyNodeTranList = nodeGroupPrimary != null
? decoyGroup.GetMatchingTransitions(document.Settings, nodeGroupPrimary, mods)
: GetDecoyTransitions(nodeGroup, decoyGroup, shiftMass);
var nodeGroupDecoy = new TransitionGroupDocNode(decoyGroup,
Annotations.EMPTY,
document.Settings,
mods,
nodeGroup.LibInfo,
nodeGroup.ExplicitValues,
nodeGroup.Results,
decoyNodeTranList,
false);
decoyNodeTranGroupList.Add(nodeGroupDecoy);
if (primaryPrecursor == null)
{
chargeToPrecursor[transGroup.PrecursorCharge] =
new Tuple<int, TransitionGroupDocNode>(precursorMassShift, nodeGroupDecoy);
}
}
return decoyNodeTranGroupList;
}
/// <summary>
/// Creates a precursor transition
/// </summary>
/// <param name="group">The <see cref="TransitionGroup"/> which the transition represents</param>
/// <param name="massIndex">Isotope mass shift</param>
/// <param name="customIon">Non-null if this is a custom transition</param>
public Transition(TransitionGroup group, int massIndex, CustomIon customIon = null)
: this(group, IonType.precursor, group.Peptide.Length - 1, massIndex, group.PrecursorCharge, null, customIon)
{
}
private void CompleteTransitionGroup()
{
var precursorExp = GetBestPrecursorExp();
var transitionGroup = new TransitionGroup(_activePeptide,
precursorExp.PrecursorCharge,
precursorExp.LabelType,
false,
precursorExp.MassShift);
var transitions = _activeTransitionInfos.ConvertAll(info =>
{
var productExp = info.TransitionExps.Single(exp => Equals(precursorExp, exp.Precursor)).Product;
var ionType = productExp.IonType;
var ordinal = productExp.FragmentOrdinal;
int offset = Transition.OrdinalToOffset(ionType, ordinal, _activePeptide.Sequence.Length);
int? massShift = productExp.MassShift;
if (massShift == null && precursorExp.MassShift.HasValue)
massShift = 0;
var tran = new Transition(transitionGroup, ionType, offset, 0, productExp.Charge, massShift);
// m/z and library info calculated later
return new TransitionDocNode(tran, productExp.Losses, 0, null, null);
});
// m/z calculated later
var newTransitionGroup = new TransitionGroupDocNode(transitionGroup, CompleteTransitions(transitions));
var currentLibrarySpectrum = !_activeLibraryIntensities.Any() ? null :
new SpectrumMzInfo
{
Key = new LibKey(_activePeptide.Sequence, precursorExp.PrecursorCharge),
PrecursorMz = _activePrecursorMz,
Label = precursorExp.LabelType,
SpectrumPeaks = new SpectrumPeaksInfo(_activeLibraryIntensities.ToArray())
};
_groupLibTriples.Add(new TransitionGroupLibraryIrtTriple(currentLibrarySpectrum, newTransitionGroup, _irtValue, _activePrecursorMz));
_activePrecursorMz = 0;
_activePrecursorExps.Clear();
_activeTransitionInfos.Clear();
_activeLibraryIntensities.Clear();
_irtValue = null;
}
public static string GetLabel(TransitionGroup tranGroup, double precursorMz,
string resultsText)
{
return string.Format("{0}{1}{2}{3}", GetMzLabel(tranGroup, precursorMz), // Not L10N
Transition.GetChargeIndicator(tranGroup.PrecursorCharge),
tranGroup.LabelTypeText, resultsText);
}
private PeptideDocNode Refine(PeptideDocNode nodePep,
SrmDocument document,
int bestResultIndex,
List<int> acceptedCharges)
{
int minTrans = MinTransitionsPepPrecursor ?? 0;
bool addedGroups = false;
var listGroups = new List<TransitionGroupDocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (acceptedCharges != null && !acceptedCharges.Contains(nodeGroup.TransitionGroup.PrecursorCharge))
continue;
if (!AddLabelType && RefineLabelType != null && Equals(RefineLabelType, nodeGroup.TransitionGroup.LabelType))
continue;
double? peakFoundRatio = nodeGroup.GetPeakCountRatio(bestResultIndex);
if (!peakFoundRatio.HasValue)
{
if (RemoveMissingResults)
continue;
}
else
{
if (MinPeakFoundRatio.HasValue)
{
if (peakFoundRatio < MinPeakFoundRatio.Value)
continue;
}
if (MaxPeakFoundRatio.HasValue)
{
if (peakFoundRatio > MaxPeakFoundRatio.Value)
continue;
}
}
TransitionGroupDocNode nodeGroupRefined = nodeGroup;
if (AutoPickTransitionsAll && nodeGroup.AutoManageChildren == AutoPickChildrenOff)
{
nodeGroupRefined = (TransitionGroupDocNode) nodeGroupRefined.ChangeAutoManageChildren(!AutoPickChildrenOff);
var settings = document.Settings;
if (!settings.TransitionSettings.Filter.AutoSelect && !AutoPickChildrenOff)
settings = settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(!AutoPickChildrenOff));
nodeGroupRefined = nodeGroupRefined.ChangeSettings(settings, nodePep, nodePep.ExplicitMods,
new SrmSettingsDiff(false, false, false, false, true, false));
}
nodeGroupRefined = Refine(nodeGroupRefined, bestResultIndex);
if (nodeGroupRefined.Children.Count < minTrans)
continue;
if (peakFoundRatio.HasValue)
{
if (DotProductThreshold.HasValue)
{
float? dotProduct = nodeGroupRefined.GetLibraryDotProduct(bestResultIndex);
if (dotProduct.HasValue && dotProduct.Value < DotProductThreshold.Value)
continue;
}
if (IdotProductThreshold.HasValue)
{
float? idotProduct = nodeGroupRefined.GetIsotopeDotProduct(bestResultIndex);
if (idotProduct.HasValue && idotProduct.Value < IdotProductThreshold.Value)
continue;
}
}
// If this precursor node is going to be added, check to see if it
// should be added with another matching isotope label type.
var explicitMods = nodePep.ExplicitMods;
if (IsLabelTypeRequired(nodePep, nodeGroup, listGroups) &&
document.Settings.TryGetPrecursorCalc(RefineLabelType, explicitMods) != null)
{
// CONSIDER: This is a lot like some code in PeptideDocNode.ChangeSettings
Debug.Assert(RefineLabelType != null); // Keep ReSharper from warning
var tranGroup = new TransitionGroup(nodePep.Peptide,
nodeGroup.TransitionGroup.PrecursorCharge,
RefineLabelType,
false,
nodeGroup.TransitionGroup.DecoyMassShift);
var settings = document.Settings;
// string sequence = nodePep.Peptide.Sequence;
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(
tranGroup, settings, explicitMods);
var nodeGroupMatch = new TransitionGroupDocNode(tranGroup,
Annotations.EMPTY,
settings,
explicitMods,
nodeGroup.LibInfo,
nodeGroup.ExplicitValues,
null, // results
transitions,
transitions == null);
nodeGroupMatch = nodeGroupMatch.ChangeSettings(settings, nodePep, explicitMods, SrmSettingsDiff.ALL);
// Make sure it is measurable before adding it
if (settings.TransitionSettings.IsMeasurablePrecursor(nodeGroupMatch.PrecursorMz))
{
listGroups.Add(nodeGroupMatch);
addedGroups = true;
}
}
listGroups.Add(nodeGroupRefined);
}
// If groups were added, make sure everything is in the right order.
if (addedGroups)
listGroups.Sort(Peptide.CompareGroups);
// Change the children, but only change auto-management, if the child
// identities have changed, not if their contents changed.
var childrenNew = listGroups.ToArray();
bool updateAutoManage = !PeptideDocNode.AreEquivalentChildren(nodePep.Children, childrenNew);
return (PeptideDocNode) nodePep.ChangeChildrenChecked(childrenNew, updateAutoManage);
}
public Transition(TransitionGroup group, IonType type, int? offset, int? massIndex, int charge, int? decoyMassShift, CustomIon customIon = null)
{
_group = group;
IonType = type;
CleavageOffset = offset ?? 0;
MassIndex = massIndex ?? 0;
Charge = charge;
DecoyMassShift = decoyMassShift;
// Small molecule precursor transition should have same custom ion as parent
if (IsPrecursor(type) && group.IsCustomIon)
CustomIon = group.CustomIon;
else
CustomIon = customIon;
// Derived values
if (!IsCustom(type, group))
{
Peptide peptide = group.Peptide;
Ordinal = OffsetToOrdinal(type, (int)offset, peptide.Length);
AA = (IsNTerminal()
? peptide.Sequence[(int)offset]
: peptide.Sequence[(int)offset + 1]);
}
else
{
// caller may have passed in offset = group.Peptide.Length - 1, which for custom ions gives -1
CleavageOffset = 0;
}
Validate();
}
public void Activate()
{
Window window = NUIApplication.GetDefaultWindow();
Vector2 windowSize = new Vector2((float)(window.Size.Width), (float)(window.Size.Height));
magnification = Math.Min(windowSize.X / baseSize.X, windowSize.Y / baseSize.Y);
contentSize = baseSize * magnification;
navigator = new Navigator()
{
WidthResizePolicy = ResizePolicyType.FillToParent,
HeightResizePolicy = ResizePolicyType.FillToParent,
Transition = new Transition()
{
TimePeriod = new TimePeriod(400),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.EaseInOutSine),
},
};
window.Add(navigator);
View mainRoot = new View()
{
WidthResizePolicy = ResizePolicyType.FillToParent,
HeightResizePolicy = ResizePolicyType.FillToParent
};
View layoutView = new View()
{
PositionUsesPivotPoint = true,
PivotPoint = PivotPoint.BottomCenter,
ParentOrigin = ParentOrigin.BottomCenter,
Layout = new LinearLayout()
{
LinearAlignment = LinearLayout.Alignment.Center,
LinearOrientation = LinearLayout.Orientation.Horizontal,
CellPadding = new Size(convertSize(60), convertSize(60)),
},
Position = new Position(0, -convertSize(30))
};
mainRoot.Add(layoutView);
View redButton = CreateButton(TileColor[0], Keywords[0, 0], Keywords[0, 1], redPage);
View greenButton = CreateButton(TileColor[1], Keywords[1, 0], Keywords[1, 1], greenPage);
View blueButton = CreateButton(TileColor[2], Keywords[2, 0], Keywords[2, 1], bluePage);
layoutView.Add(redButton);
layoutView.Add(greenButton);
layoutView.Add(blueButton);
TransitionGroup transitionGroup = new TransitionGroup()
{
UseGroupAlphaFunction = true,
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.EaseInOut),
};
SlideTransition slide = new SlideTransition()
{
TimePeriod = new TimePeriod(400),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
Direction = SlideTransitionDirection.Top
};
transitionGroup.AddTransition(slide);
FadeTransition fade = new FadeTransition()
{
Opacity = 0.3f,
TimePeriod = new TimePeriod(400),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default)
};
transitionGroup.AddTransition(fade);
ScaleTransition scale = new ScaleTransition()
{
ScaleFactor = new Vector2(0.3f, 0.3f),
TimePeriod = new TimePeriod(400),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default)
};
transitionGroup.AddTransition(scale);
mainPage = new ContentPage()
{
BackgroundColor = Color.Transparent,
Content = mainRoot,
DisappearingTransition = new ScaleTransition()
{
TimePeriod = new TimePeriod(500),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
ScaleFactor = new Vector2(0.5f, 1.5f)
},
AppearingTransition = transitionGroup,
};
navigator.Push(mainPage);
View totalGreyView = new View()
{
Size = new Size(convertSize(50), convertSize(50)),
CornerRadius = convertSize(25),
BackgroundColor = ColorGrey,
TransitionOptions = new TransitionOptions()
{
TransitionTag = totalGreyTag,
}
};
totalGreyView.TouchEvent += (object sender, View.TouchEventArgs e) =>
{
if (e.Touch.GetState(0) == PointStateType.Down)
{
navigator.PushWithTransition(totalPage);
}
return(true);
};
layoutView.Add(totalGreyView);
// ------------------------------------------------------
View totalPageRoot = new View()
{
WidthResizePolicy = ResizePolicyType.FillToParent,
SizeHeight = contentSize.Height,
};
View totalLayoutView = new View()
{
Layout = new GridLayout()
{
Rows = 2,
GridOrientation = GridLayout.Orientation.Vertical,
},
PositionUsesPivotPoint = true,
PivotPoint = PivotPoint.Center,
ParentOrigin = ParentOrigin.Center,
};
totalPageRoot.Add(totalLayoutView);
for (int i = 0; i < 3; ++i)
{
View sizeView = new View()
{
Size = new Size(contentSize.Width / 2.0f, contentSize.Height / 2.0f),
};
View smallView = CreatePageScene(TileColor[i], Keywords[i, 0], Keywords[i, 1]);
smallView.Scale = new Vector3(0.45f, 0.45f, 1.0f);
smallView.PositionUsesPivotPoint = true;
smallView.PivotPoint = PivotPoint.Center;
smallView.ParentOrigin = ParentOrigin.Center;
sizeView.Add(smallView);
totalLayoutView.Add(sizeView);
}
View sizeGreyView = new View()
{
Size = new Size(contentSize.Width / 2.0f, contentSize.Height / 2.0f),
};
View totalGreyReturnView = new View()
{
PositionUsesPivotPoint = true,
PivotPoint = PivotPoint.Center,
ParentOrigin = ParentOrigin.Center,
Size = new Size(convertSize(70), convertSize(70)),
CornerRadius = convertSize(20),
BackgroundColor = ColorGrey,
TransitionOptions = new TransitionOptions()
{
TransitionTag = totalGreyTag,
}
};
sizeGreyView.Add(totalGreyReturnView);
totalLayoutView.Add(sizeGreyView);
totalGreyReturnView.TouchEvent += (object sender, View.TouchEventArgs e) =>
{
if (e.Touch.GetState(0) == PointStateType.Down)
{
navigator.PopWithTransition();
}
return(true);
};
totalPage = new ContentPage()
{
BackgroundColor = Color.Transparent,
Content = totalPageRoot,
AppearingTransition = new FadeTransition()
{
TimePeriod = new TimePeriod(500),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
},
DisappearingTransition = new FadeTransition()
{
TimePeriod = new TimePeriod(500),
AlphaFunction = new AlphaFunction(AlphaFunction.BuiltinFunctions.Default),
},
};
}
public SrmDocument ConvertToSmallMolecules(SrmDocument document,
ConvertToSmallMoleculesMode mode = ConvertToSmallMoleculesMode.formulas,
bool invertCharges = false,
bool ignoreDecoys=false)
{
if (mode == ConvertToSmallMoleculesMode.none)
return document;
var newdoc = new SrmDocument(document.Settings);
var note = new Annotations(TestingConvertedFromProteomic, null, 1); // Mark this as a testing node so we don't sort it
newdoc = (SrmDocument)newdoc.ChangeIgnoreChangingChildren(true); // Retain copied results
foreach (var peptideGroupDocNode in document.MoleculeGroups)
{
if (!peptideGroupDocNode.IsProteomic)
{
newdoc = (SrmDocument)newdoc.Add(peptideGroupDocNode); // Already a small molecule
}
else
{
var newPeptideGroup = new PeptideGroup();
var newPeptideGroupDocNode = new PeptideGroupDocNode(newPeptideGroup,
peptideGroupDocNode.Annotations.Merge(note), peptideGroupDocNode.Name,
peptideGroupDocNode.Description, new PeptideDocNode[0],
peptideGroupDocNode.AutoManageChildren);
foreach (var mol in peptideGroupDocNode.Molecules)
{
var peptideSequence = mol.Peptide.Sequence;
// Create a PeptideDocNode with the presumably baseline charge and label
var precursorCharge = (mol.TransitionGroups.Any() ? mol.TransitionGroups.First().TransitionGroup.PrecursorCharge : 0) * (invertCharges ? -1 : 1);
var isotopeLabelType = mol.TransitionGroups.Any() ? mol.TransitionGroups.First().TransitionGroup.LabelType : IsotopeLabelType.light;
var moleculeCustomIon = ConvertToSmallMolecule(mode, document, mol, precursorCharge, isotopeLabelType);
var precursorCustomIon = moleculeCustomIon;
var newPeptide = new Peptide(moleculeCustomIon);
var newPeptideDocNode = new PeptideDocNode(newPeptide, newdoc.Settings, null, null,
null, null, mol.ExplicitRetentionTime, note, mol.Results, new TransitionGroupDocNode[0],
mol.AutoManageChildren);
foreach (var transitionGroupDocNode in mol.TransitionGroups)
{
if (transitionGroupDocNode.IsDecoy)
{
if (ignoreDecoys)
continue;
throw new Exception("There is no translation from decoy to small molecules"); // Not L10N
}
if (transitionGroupDocNode.TransitionGroup.PrecursorCharge != Math.Abs(precursorCharge) ||
!Equals(isotopeLabelType, transitionGroupDocNode.TransitionGroup.LabelType))
{
// Different charges or labels mean different ion formulas
precursorCharge = transitionGroupDocNode.TransitionGroup.PrecursorCharge * (invertCharges ? -1 : 1);
isotopeLabelType = transitionGroupDocNode.TransitionGroup.LabelType;
precursorCustomIon = ConvertToSmallMolecule(mode, document, mol, precursorCharge, isotopeLabelType);
}
var newTransitionGroup = new TransitionGroup(newPeptide, precursorCustomIon, precursorCharge, isotopeLabelType);
// Remove any library info, since for the moment at least small molecules don't support this and it won't roundtrip
var resultsNew = RemoveTransitionGroupChromInfoLibraryInfo(transitionGroupDocNode);
var newTransitionGroupDocNode = new TransitionGroupDocNode(newTransitionGroup,
transitionGroupDocNode.Annotations.Merge(note), document.Settings,
null, null, transitionGroupDocNode.ExplicitValues, resultsNew, null,
transitionGroupDocNode.AutoManageChildren);
var mzShift = invertCharges ? 2.0 * BioMassCalc.MassProton : 0; // We removed hydrogen rather than added
Assume.IsTrue((Math.Abs(newTransitionGroupDocNode.PrecursorMz + mzShift - transitionGroupDocNode.PrecursorMz) - Math.Abs(transitionGroupDocNode.TransitionGroup.PrecursorCharge * BioMassCalc.MassElectron)) <= 1E-5);
foreach (var transition in transitionGroupDocNode.Transitions)
{
double mass = 0;
var transitionCharge = transition.Transition.Charge * (invertCharges ? -1 : 1);
var ionType = IonType.custom;
CustomIon transitionCustomIon;
double mzShiftTransition = 0;
if (transition.Transition.IonType == IonType.precursor)
{
ionType = IonType.precursor;
transitionCustomIon = new DocNodeCustomIon(precursorCustomIon.Formula,
string.IsNullOrEmpty(precursorCustomIon.Formula) ? precursorCustomIon.MonoisotopicMass : (double?) null,
string.IsNullOrEmpty(precursorCustomIon.Formula) ? precursorCustomIon.AverageMass : (double?) null,
SmallMoleculeNameFromPeptide(peptideSequence, transitionCharge));
mzShiftTransition = invertCharges ? 2.0 * BioMassCalc.MassProton : 0; // We removed hydrogen rather than added
}
else if (transition.Transition.IonType == IonType.custom)
{
transitionCustomIon = transition.Transition.CustomIon;
mass = transitionCustomIon.MonoisotopicMass;
}
else
{
// TODO - try to get fragment formula?
mass = BioMassCalc.CalculateIonMassFromMz(transition.Mz, transition.Transition.Charge);
transitionCustomIon = new DocNodeCustomIon(mass, mass,// We can't really get at mono vs average mass from m/z, but for test purposes this is fine
transition.Transition.FragmentIonName);
}
if (mode == ConvertToSmallMoleculesMode.masses_and_names)
{
// Discard the formula if we're testing the use of mass-with-names (for matching in ratio calcs) target specification
transitionCustomIon = new DocNodeCustomIon(transitionCustomIon.MonoisotopicMass, transitionCustomIon.AverageMass,
transition.Transition.FragmentIonName);
}
else if (mode == ConvertToSmallMoleculesMode.masses_only)
{
// Discard the formula and name if we're testing the use of mass-only target specification
transitionCustomIon = new DocNodeCustomIon(transitionCustomIon.MonoisotopicMass, transitionCustomIon.AverageMass);
}
var newTransition = new Transition(newTransitionGroup, ionType,
null, transition.Transition.MassIndex, transition.Transition.Charge * (invertCharges ? -1 : 1), null,
transitionCustomIon);
if (ionType == IonType.precursor)
{
mass = document.Settings.GetFragmentMass(transitionGroupDocNode.TransitionGroup.LabelType, null, newTransition, newTransitionGroupDocNode.IsotopeDist);
}
var newTransitionDocNode = new TransitionDocNode(newTransition, transition.Annotations.Merge(note),
null, mass, transition.IsotopeDistInfo, null,
transition.Results);
Assume.IsTrue((Math.Abs(newTransitionDocNode.Mz + mzShiftTransition - transition.Mz) - Math.Abs(transitionGroupDocNode.TransitionGroup.PrecursorCharge * BioMassCalc.MassElectron)) <= 1E-5, String.Format("unexpected mz difference {0}-{1}={2}", newTransitionDocNode.Mz , transition.Mz, newTransitionDocNode.Mz - transition.Mz)); // Not L10N
newTransitionGroupDocNode =
(TransitionGroupDocNode)newTransitionGroupDocNode.Add(newTransitionDocNode);
}
if (newPeptideDocNode != null)
newPeptideDocNode = (PeptideDocNode)newPeptideDocNode.Add(newTransitionGroupDocNode);
}
newPeptideGroupDocNode =
(PeptideGroupDocNode)newPeptideGroupDocNode.Add(newPeptideDocNode);
}
newdoc = (SrmDocument)newdoc.Add(newPeptideGroupDocNode);
}
}
// No retention time prediction for small molecules (yet?)
newdoc = newdoc.ChangeSettings(newdoc.Settings.ChangePeptideSettings(newdoc.Settings.PeptideSettings.ChangePrediction(
newdoc.Settings.PeptideSettings.Prediction.ChangeRetentionTime(null))));
return newdoc;
}
public Transition(TransitionGroup group, IonType type, int offset, int massIndex, int charge)
: this(group, type, offset, massIndex, charge, null)
{
}
public Transition(TransitionGroup group, int charge, int? massIndex, CustomIon customIon, IonType type=IonType.custom)
: this(group, type, null, massIndex, charge, null, customIon)
{
}
