public void SpecialFragmentTest()
{
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath path;
var docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8)); // y8
// Switch to the legacy version of the proline fragment where min length is 1
var docLegacyProline = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { MeasuredIonList.NTERM_PROLINE_LEGACY })));
Assert.AreEqual(5, docLegacyProline.PeptideTransitionCount);
// Allow b-ions
var docLegacyProlineB = docLegacyProline.ChangeSettings(docLegacyProline.Settings.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.b, IonType.y })));
Assert.AreEqual(9, docLegacyProlineB.PeptideTransitionCount);
// Add C-terminal Glu and Asp to the original peptide document
var docGluAsp = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List <MeasuredIon>(filter.MeasuredIons)
{
MeasuredIonList.CTERM_GLU_ASP
})));
Assert.AreEqual(5, docGluAsp.PeptideTransitionCount);
Assert.IsTrue(docGluAsp.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 3)); // y3
// Use the legacy version instead
var docGluAspLegacy = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List <MeasuredIon>(filter.MeasuredIons)
{
MeasuredIonList.CTERM_GLU_ASP_LEGACY
})));
Assert.AreEqual(6, docGluAspLegacy.PeptideTransitionCount);
Assert.IsTrue(docGluAspLegacy.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 2)); // y2
// Add Proline to the C-terminal modification
var docGluAspPro = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", null, SequenceTerminus.C, 1) })));
Assert.AreEqual(8, docGluAspPro.PeptideTransitionCount);
Assert.IsTrue(docGluAspPro.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // y2
nodeTran.Transition.Ordinal == 8)); // y8
// Restrict
var docGluAspProRestrict = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", "P", SequenceTerminus.C, 1) })));
Assert.AreEqual(6, docGluAspProRestrict.PeptideTransitionCount);
Assert.IsFalse(docGluAspProRestrict.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // not y2
nodeTran.Transition.Ordinal == 8)); // not y8
}
public void MultiLabelTypeListTest()
{
int startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
// Add some FASTA
IdentityPath pathRoot = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out _);
const int initProt = 2, initPep = 26, initTran = 89;
AssertEx.IsDocumentState(docFasta, ++startRev, initProt, initPep, initTran);
// Add multiple heavy types
var settings = docFasta.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(LABEL_TYPE13_C, HEAVY_MODS_13_C),
new TypedModifications(LABEL_TYPE15_N, HEAVY_MODS_15_N)
}));
var docMulti = docFasta.ChangeSettings(settings);
// CONSIDER: make explicit S-Lens, cone voltage, CE etc roundtrip?
// docMulti.MoleculeTransitionGroups.FirstOrDefault().ChangeExplicitValues(ExplicitTransitionGroupValues.TEST)
// Make sure transition lists export to various formats and roundtrip
VerifyExportRoundTrip(new ThermoMassListExporter(docMulti), docFasta);
// Add Oxidation (M) as a static modification to challenge new mass list importing flexibility
VerifyExportRoundTrip(new AbiMassListExporter(AddOxidationM(docMulti)), AddOxidationM(docFasta));
VerifyExportRoundTrip(new AgilentMassListExporter(docMulti), docFasta);
VerifyExportRoundTrip(new WatersMassListExporter(docMulti), docFasta);
}
public void NeutralLossListTest()
{
TestSmallMolecules = false; // No concept of neutral loss for small molecules
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List <StaticMod>(mods.StaticModifications)
{
phosphoLossMod
})));
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(TEXT_FASTA_YEAST_7), false, path, out path);
Assert.AreEqual(0, GetLossCount(docFasta, 1));
// Insert losses into the first transition group
var pathPeptide = docFasta.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodePep = (PeptideDocNode)docFasta.FindNode(pathPeptide);
var nodeGroup = (TransitionGroupDocNode)nodePep.Children[0];
var listChildren = new List <DocNode>(nodeGroup.Children);
foreach (var nodeTran in nodeGroup.GetTransitions(docFasta.Settings,
nodePep.ExplicitMods, nodeGroup.PrecursorMz, null, null, null, false))
{
if (!nodeTran.HasLoss)
{
continue;
}
var tran = nodeTran.Transition;
int matchIndex = listChildren.IndexOf(node =>
Equals(tran, ((TransitionDocNode)node).Transition));
if (matchIndex == -1)
{
continue;
}
while (matchIndex < listChildren.Count &&
Equals(tran, ((TransitionDocNode)listChildren[matchIndex]).Transition))
{
matchIndex++;
}
listChildren.Insert(matchIndex, nodeTran);
}
var docLosses = (SrmDocument)docFasta.ReplaceChild(pathPeptide,
nodeGroup.ChangeChildren(listChildren));
int lossCount = GetLossCount(docLosses, 1);
Assert.IsTrue(lossCount > 0);
var docRoundTripped = AssertEx.RoundTripTransitionList(new ThermoMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
docRoundTripped = AssertEx.RoundTripTransitionList(new AgilentMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
}
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 void DynamicMinMzTest()
{
var revisionIndex = 1;
var settings = SrmSettingsList.GetDefault().ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeFragmentRangeFirstName("ion 1")
.ChangeFragmentRangeLastName("last ion"));
var docOriginal = new SrmDocument(settings);
IdentityPath path;
var docPeptides = docOriginal.ImportFasta(new StringReader(">peptides\nESTIGNSAFELLLEVAK\nTVYHAGTK"),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides, revisionIndex++, 1, 2, 2, 40);
// Both precursors should contain 1 and 2 ions
foreach (var nodeGroup in docPeptides.PeptideTransitionGroups)
{
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
}
// Switch to using dynamic minimum for product ions
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(true));
var docDynamicMin = docPeptides.ChangeSettings(settings);
AssertEx.IsDocumentState(docDynamicMin, revisionIndex++, 1, 2, 35);
var arrayNodeGroups = docDynamicMin.PeptideTransitionGroups.ToArray();
// The larger precursor should no longer have 1 or 2 ions
Assert.IsFalse(arrayNodeGroups[0].Children.Contains(node =>
((TransitionDocNode)node).Transition.Ordinal == 1 ||
((TransitionDocNode)node).Transition.Ordinal == 2));
// But the smaller precursor should retain at least one of both
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
// Use a minimum that is high enough to exclude the smaller precursor
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(500));
var docHighMinDynamicMz = docDynamicMin.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinDynamicMz, revisionIndex++, 1, 2, 1, 22);
// Because of the dynamic minimum for product ions, the remaining precursor should not have changed
var nodeGroupHigh = docHighMinDynamicMz.PeptideTransitionGroups.ToArray()[0];
Assert.AreSame(arrayNodeGroups[0], nodeGroupHigh);
// Remove dynamic minimum, and verify that product ions are removed
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(false));
var docHighMinMz = docHighMinDynamicMz.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinMz, revisionIndex, 1, 2, 1, 17);
// No library test, because it is hard to test. Many of the library
// spectra are likely gathered with LTQs which apply the same dynamic
// minimum to the ms/ms peaks they measure.
}
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 void RemoveDuplicatePeptidesTest()
{
// First try removals with no impact
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
SrmDocument docFasta = document.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 1)),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 1, 11, 36);
var refinementSettings = new RefinementSettings {
RemoveDuplicatePeptides = true
};
SrmDocument docFasta2 = refinementSettings.Refine(docFasta);
Assert.AreSame(docFasta, docFasta2);
docFasta2 = docFasta.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 2)),
false, IdentityPath.ROOT, out path);
// Adding same sequence twice, even with different custom names is ignored
Assert.AreSame(docFasta, docFasta2);
// Try a successful removal of duplicates that leaves no peptides
SrmDocument docPeptides = document.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides2, 2, 2, 26, 82);
SrmDocument docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 0, 0);
// Try again leaving a single peptide
docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1 + "\n" + TEXT_BOVINE_SINGLE_PEPTIDE),
true, IdentityPath.ROOT, out path);
docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 1, 3);
}
public void NeutralLossListTest()
{
TestSmallMolecules = false; // No concept of neutral loss for small molecules
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List<StaticMod>(mods.StaticModifications) { phosphoLossMod })));
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(TEXT_FASTA_YEAST_7), false, path, out path);
Assert.AreEqual(0, GetLossCount(docFasta, 1));
// Insert losses into the first transition group
var pathPeptide = docFasta.GetPathTo((int) SrmDocument.Level.Molecules, 0);
var nodePep = (PeptideDocNode) docFasta.FindNode(pathPeptide);
var nodeGroup = (TransitionGroupDocNode) nodePep.Children[0];
var listChildren = new List<DocNode>(nodeGroup.Children);
foreach (var nodeTran in nodeGroup.GetTransitions(docFasta.Settings,
nodePep.ExplicitMods, nodeGroup.PrecursorMz, null, null, null, false))
{
if (!nodeTran.HasLoss)
continue;
var tran = nodeTran.Transition;
int matchIndex = listChildren.IndexOf(node =>
Equals(tran, ((TransitionDocNode)node).Transition));
if (matchIndex == -1)
continue;
while (matchIndex < listChildren.Count &&
Equals(tran, ((TransitionDocNode)listChildren[matchIndex]).Transition))
{
matchIndex++;
}
listChildren.Insert(matchIndex, nodeTran);
}
var docLosses = (SrmDocument) docFasta.ReplaceChild(pathPeptide,
nodeGroup.ChangeChildren(listChildren));
int lossCount = GetLossCount(docLosses, 1);
Assert.IsTrue(lossCount > 0);
var docRoundTripped = AssertEx.RoundTripTransitionList(new ThermoMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
docRoundTripped = AssertEx.RoundTripTransitionList(new AgilentMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
}
private static SrmDocument CreateLibraryDocument(SrmSettings settings, string textFasta, bool peptideList,
TestDocumentContainer docContainer, BackgroundLoader libraryManager, out int startRev)
{
startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
Assert.IsTrue(docContainer.SetDocument(document, null));
// Register after first set document
libraryManager.Register(docContainer);
// Add libraries
SrmDocument docLibraries = document.ChangeSettings(settings);
++startRev;
// Add some FASTA
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = docLibraries.ImportFasta(new StringReader(textFasta), peptideList, path, out path);
++startRev;
// Until libraries are loaded, only the sequences should appear
if (!peptideList)
{
AssertEx.IsDocumentState(docFasta, startRev, textFasta.Count(c => c == '>'), 0, 0);
}
// Run the library load
Assert.IsTrue(docContainer.SetDocument(docFasta, document, true));
++startRev;
// After library load completes peptides and transitions should have expected library info
SrmDocument docLoaded = docContainer.Document;
// Check expected library inforamation
foreach (var nodePeptide in docLoaded.Peptides)
{
Assert.IsNull(nodePeptide.Rank);
}
foreach (var nodeTran in docLoaded.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasLibInfo);
Assert.IsTrue(nodeTran.LibInfo.Rank <= 3);
}
return(docLoaded);
}
private static SrmDocument CreateMixedDoc()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
// Add fasta sequences
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
// Insert peptide list at beginnning
SrmDocument docMixed = docFasta.ImportFasta(new StringReader(SrmDocEditTest.TEXT_BOVINE_PEPTIDES1),
true, docFasta.GetPathTo(0), out path);
AssertEx.IsDocumentState(docMixed, 2, 3, 111, 352);
return(docMixed);
}
public void MoveNodeTest()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
// 1. From peptide group to root
SrmDocument docMoved = docFasta.MoveNode(docFasta.GetPathTo(0), IdentityPath.ROOT, out path);
Assert.AreEqual(1, docMoved.FindNodeIndex(path));
Assert.AreSame(docFasta.Children[0], docMoved.Children[1]);
Assert.AreSame(docFasta.Children[1], docMoved.Children[0]);
// 2. From peptide group to before other peptide group
docMoved = docFasta.MoveNode(docFasta.GetPathTo(1), docFasta.GetPathTo(0), out path);
Assert.AreEqual(0, docMoved.FindNodeIndex(path));
Assert.AreSame(docFasta.Children[0], docMoved.Children[1]);
Assert.AreSame(docFasta.Children[1], docMoved.Children[0]);
// Some peptide lists
IdentityPath pathPeptides;
SrmDocument docPeptides = docFasta.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true,
docFasta.GetPathTo(1), out pathPeptides);
docPeptides = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true,
IdentityPath.ROOT, out path);
docPeptides = docPeptides.MoveNode(path, pathPeptides, out pathPeptides);
Assert.AreEqual(1, docPeptides.FindNodeIndex(pathPeptides));
// 3. Peptide from one group to another
IdentityPath fromParent = docPeptides.GetPathTo(2);
IdentityPath from = new IdentityPath(fromParent, ((DocNodeParent)docPeptides.FindNode(fromParent)).Children[0].Id);
SrmDocument docPeptides2 = docPeptides.MoveNode(from, pathPeptides, out path);
Assert.AreEqual(pathPeptides, path.Parent);
Assert.AreEqual(((DocNodeParent)docPeptides.Children[1]).Children.Count,
((DocNodeParent)docPeptides2.Children[1]).Children.Count - 1);
Assert.AreEqual(((DocNodeParent)docPeptides.Children[2]).Children.Count,
((DocNodeParent)docPeptides2.Children[2]).Children.Count + 1);
// Though moved to a different group, this should not have changed the overall
// peptide order, since it was moved from the beginning of one group to the end
// of the group before it.
Assert.AreEqual(docPeptides.FindNodeIndex(from), docPeptides2.FindNodeIndex(path));
// 4. To before another peptide
from = new IdentityPath(fromParent, ((DocNodeParent)docPeptides2.FindNode(fromParent)).Children[0].Id);
IdentityPath path2;
SrmDocument docPeptides3 = docPeptides2.MoveNode(from, path, out path2);
Assert.AreEqual(pathPeptides, path.Parent);
Assert.AreEqual(((DocNodeParent)docPeptides2.Children[1]).Children.Count,
((DocNodeParent)docPeptides3.Children[1]).Children.Count - 1);
Assert.AreEqual(((DocNodeParent)docPeptides2.Children[2]).Children.Count,
((DocNodeParent)docPeptides3.Children[2]).Children.Count + 1);
// Relative to all peptides, index should be 1 less than before
Assert.AreEqual(docPeptides2.FindNodeIndex(from), docPeptides3.FindNodeIndex(path2) + 1);
// 5. To within another peptide
IdentityPath to = new IdentityPath(path, ((DocNodeParent)docPeptides3.FindNode(path)).Children[0].Id);
SrmDocument docPeptides4 = docPeptides3.MoveNode(path2, to, out path);
// Should not have changed to count in the group
Assert.AreEqual(((DocNodeParent)docPeptides3.Children[1]).Children.Count,
((DocNodeParent)docPeptides4.Children[1]).Children.Count);
// Relative to all peptides, should have been returned to original order
Assert.AreEqual(docPeptides2.FindNodeIndex(from), docPeptides4.FindNodeIndex(path));
// Make sure expected exceptions are thrown
Assert.IsNull(docPeptides4.FindNode(from));
AssertEx.ThrowsException <IdentityNotFoundException>(() =>
docPeptides4.MoveNode(from, to, out path));
AssertEx.ThrowsException <InvalidOperationException>(() =>
docPeptides2.MoveNode(from, docPeptides2.GetPathTo(0), out path));
AssertEx.ThrowsException <InvalidOperationException>(() =>
docPeptides3.MoveNode(docPeptides2.GetPathTo((int)SrmDocument.Level.Molecules, 0), to, out path));
AssertEx.ThrowsException <InvalidOperationException>(() =>
docPeptides3.MoveNode(docPeptides2.GetPathTo((int)SrmDocument.Level.Transitions, 0), to, out path));
}
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 void VariableModBasicTest()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
// Make sure default document produces no variable modifications
IdentityPath path = IdentityPath.ROOT;
var docYeast = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
Assert.AreEqual(0, GetVariableModCount(docYeast));
// Add a single variable modification
var settings = document.Settings;
var modsDefault = settings.PeptideSettings.Modifications;
var listStaticMods = new List<StaticMod>(modsDefault.StaticModifications) {VAR_MET_OXIDIZED};
var docMetOxidized = document.ChangeSettings(settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listStaticMods.ToArray())));
// Make sure variable modifications are added as expected to imported FASTA
path = IdentityPath.ROOT;
var docMoYeast = docMetOxidized.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
Assert.AreEqual(21, GetVariableModCount(docMoYeast));
AssertEx.IsDocumentState(docMoYeast, 2, 2, 119, 374);
// Exclude unmodified peptides
var docNoMoExclude = docMoYeast.ChangeSettings(docMoYeast.Settings.ChangePeptideFilter(f =>
f.ChangeExclusions(new[] { new PeptideExcludeRegex("Non-Oxidized Meth", "M\\[", true, true) })));
Assert.AreEqual(GetVariableModCount(docMoYeast), GetVariableModCount(docNoMoExclude));
Assert.AreEqual(docNoMoExclude.PeptideCount, GetVariableModCount(docNoMoExclude));
AssertEx.IsDocumentState(docNoMoExclude, 3, 2, 21, 63);
// Exclude multiply modified peptides
var docMultMoExclude = docNoMoExclude.ChangeSettings(docNoMoExclude.Settings.ChangePeptideFilter(f =>
f.ChangeExclusions(new List<PeptideExcludeRegex>(f.Exclusions) { new PeptideExcludeRegex("Multi-Oxidized Meth", "M\\[.*M\\[", false, true) })));
Assert.AreEqual(docMultMoExclude.PeptideCount, GetVariableModCount(docMultMoExclude));
AssertEx.IsDocumentState(docMultMoExclude, 4, 2, 18, 56);
// And that removing the variable modification removes the variably modifide peptides
var docYeast2 = docMoYeast.ChangeSettings(docMoYeast.Settings.ChangePeptideModifications(mods => modsDefault));
Assert.AreEqual(0, GetVariableModCount(docYeast2));
Assert.AreEqual(docYeast, docYeast2);
Assert.AreNotSame(docYeast, docYeast2);
// Even when automanage children is turned off
var docNoAuto = (SrmDocument)docMoYeast.ChangeChildren((from node in docYeast2.MoleculeGroups
select node.ChangeAutoManageChildren(false)).ToArray());
var docYeastNoAuto = docNoAuto.ChangeSettings(docYeast.Settings);
Assert.AreEqual(0, GetVariableModCount(docYeastNoAuto));
// Shouldn't come back, if the mods are restored
var docMoNoAuto = docYeastNoAuto.ChangeSettings(docMetOxidized.Settings);
Assert.AreEqual(0, GetVariableModCount(docMoNoAuto));
Assert.AreSame(docYeastNoAuto.Children, docMoNoAuto.Children);
// Make sure loss modification result in smaller m/z values
var listModsLoss = new List<StaticMod>(modsDefault.StaticModifications) { VAR_ASP_WATER_LOSS };
var docAspLoss = docYeast2.ChangeSettings(docYeast2.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listModsLoss.ToArray())));
Assert.AreEqual(145, GetVariableModCount(docAspLoss));
VerifyModificationOrder(docAspLoss, false);
// Add multiple variable modifications
listStaticMods.Add(VAR_ASP_WATER_ADD);
var docVarMulti = docYeast2.ChangeSettings(docYeast2.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listStaticMods.ToArray())));
Assert.AreEqual(220, GetVariableModCount(docVarMulti));
int maxModifiableMulti = GetMaxModifiableCount(docVarMulti);
Assert.IsTrue(maxModifiableMulti > GetMaxModifiedCount(docVarMulti));
VerifyModificationOrder(docVarMulti, true);
// Repeat with a single variable modification on multiple amino acids
// and verify that this creates the same number of variably modified peptides
var listModsMultiAA = new List<StaticMod>(modsDefault.StaticModifications) { VAR_MET_ASP_OXIDIZED };
var docVarMultiAA = docYeast2.ChangeSettings(docYeast2.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listModsMultiAA.ToArray())));
Assert.AreEqual(220, GetVariableModCount(docVarMultiAA));
VerifyModificationOrder(docVarMultiAA, true);
// And also multiple modifications on the same amino acid residue
listStaticMods.Add(VAR_MET_AMONIA_ADD);
var docVarAaMulti = docVarMulti.ChangeSettings(docVarMulti.Settings.ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(listStaticMods.ToArray())));
Assert.AreEqual(315, GetVariableModCount(docVarAaMulti));
int maxModifiableAaMulti = GetMaxModifiableCount(docVarAaMulti);
Assert.AreEqual(maxModifiableMulti, maxModifiableAaMulti,
"Unexptected change in the maximum number of modifiable amino acids");
Assert.IsTrue(maxModifiableAaMulti > GetMaxModifiedCount(docVarAaMulti));
VerifyModificationOrder(docVarAaMulti, true);
// Reduce the maximum number of variable modifications allowed
var docVar2AaMulti = docVarAaMulti.ChangeSettings(docVarAaMulti.Settings.ChangePeptideModifications(mods =>
mods.ChangeMaxVariableMods(2)));
Assert.AreEqual(242, GetVariableModCount(docVar2AaMulti));
Assert.AreEqual(2, GetMaxModifiedCount(docVar2AaMulti));
VerifyModificationOrder(docVar2AaMulti, true);
var docVar1AaMulti = docVar2AaMulti.ChangeSettings(docVar2AaMulti.Settings.ChangePeptideModifications(mods =>
mods.ChangeMaxVariableMods(1)));
Assert.AreEqual(128, GetVariableModCount(docVar1AaMulti));
Assert.AreEqual(1, GetMaxModifiedCount(docVar1AaMulti));
VerifyModificationOrder(docVar1AaMulti, true);
var docVarAaMultiReset = docVar1AaMulti.ChangeSettings(docVarAaMulti.Settings);
Assert.AreEqual(315, GetVariableModCount(docVarAaMultiReset));
// Repeat with auto-manage turned off to make sure it also removes
// variable modifications which are made invalide by changing the limit
var docMultiNoAuto = (SrmDocument)docVarAaMulti.ChangeChildren((from node in docVarAaMulti.MoleculeGroups
select node.ChangeAutoManageChildren(false)).ToArray());
var docMulti2NoAuto = docMultiNoAuto.ChangeSettings(docVar2AaMulti.Settings);
Assert.IsTrue(ArrayUtil.ReferencesEqual(docVar2AaMulti.Molecules.ToArray(),
docMulti2NoAuto.Molecules.ToArray()));
var docMulti1NoAuto = docMulti2NoAuto.ChangeSettings(docVar1AaMulti.Settings);
Assert.IsTrue(ArrayUtil.ReferencesEqual(docVar1AaMulti.Molecules.ToArray(),
docMulti1NoAuto.Molecules.ToArray()));
var docMultiNoAutoReset = docMulti1NoAuto.ChangeSettings(docVarAaMulti.Settings);
Assert.AreSame(docMulti1NoAuto.Children, docMultiNoAutoReset.Children);
// Add heavy modifications to an earlier document to verify
// that heavy precursors all get greater precursor m/z values than
// their light versions
var docVarHeavy = docVarMulti.ChangeSettings(docVarMulti.Settings.ChangePeptideModifications(
mods => mods.ChangeHeavyModifications(HEAVY_MODS)));
foreach (var nodePep in docVarHeavy.Peptides)
{
if (nodePep.Peptide.NextAA == '-')
continue;
Assert.AreEqual(2, nodePep.Children.Count);
Assert.AreEqual(GetPrecursorMz(nodePep, 0), GetPrecursorMz(nodePep, 1)-3, 0.02);
}
// Repeat with a modification specifying multiple amino acids
// and make sure the resulting m/z values are the same
var docVarHeavyMulti = docVarMulti.ChangeSettings(docVarMulti.Settings.ChangePeptideModifications(
mods => mods.ChangeHeavyModifications(HEAVY_MODS_MULTI)));
var varHeavyGroups = docVarHeavy.PeptideTransitionGroups.ToArray();
var varHeavyMultiPeptides = docVarHeavyMulti.PeptideTransitionGroups.ToArray();
Assert.AreEqual(varHeavyGroups.Length, varHeavyMultiPeptides.Length);
for (int i = 0; i < varHeavyGroups.Length; i++)
Assert.AreEqual(varHeavyGroups[i].PrecursorMz, varHeavyMultiPeptides[i].PrecursorMz);
}
public void ReporterIonTest()
{
// Test the code that updates old-style formulas
Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2"));
Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2"));
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy!
IdentityPath path;
SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8));
const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1
const string hydrogenPeroxide = "Hydrogen Perxoide";
var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, 1), new MeasuredIon(hydrogenPeroxide, formula, null, null, 2), new MeasuredIon(hydrogenPeroxide, formula, null, null, 3), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
double mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i ++)
{
TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron/100);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Check with Average
TransitionPrediction predSettings =
docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average);
TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings);
SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings);
SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings);
mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].CustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateIonMz(formula, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, i + 1), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Make sure the rest of the transitions aren't reporter ions
for (int i = 3; i < 7; i ++)
{
Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition;
Assert.AreNotEqual(tran.CustomIon, reporterIons);
}
var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null,1, true);
SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] {optionalIon})));
Assert.AreEqual(3, optionalDoc.PeptideTransitionCount);
optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] {optionalIon.ChangeIsOptional(false)})));
AssertEx.IsDocumentTransitionCount(optionalDoc, 4);
Assert.AreEqual(optionalIon.ChangeIsOptional(false).CustomIon,
optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
optionalDoc =
optionalDoc.ChangeSettings(
optionalDoc.Settings.ChangeTransitionFilter(
filter => filter.ChangeMeasuredIons(new[] {optionalIon.ChangeIsOptional(true)})));
TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0);
var filteredNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon));
var unfilteredNodes =
TransitionGroupTreeNode.GetChoices(nodeGroup, optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast<TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.CustomIon));
Assert.AreEqual(0,filteredNodes.Count());
Assert.AreEqual(1,unfilteredNodes.Count());
}
public void MultiLabelTypeTest()
{
int startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
// Add some FASTA
IdentityPath pathRoot = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out _);
const int initProt = 2, initPep = 26, initTran = 89;
AssertEx.IsDocumentState(docFasta, ++startRev, initProt, initPep, initTran);
// Add multiple heavy types
var settings = docFasta.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(LABEL_TYPE13_C, HEAVY_MODS_13_C),
new TypedModifications(LABEL_TYPE15_N, HEAVY_MODS_15_N)
}));
var docMulti = docFasta.ChangeSettings(settings);
// Make sure the contents of the resulting document are as expected.
int countProteinTermTran, countProteinTerm;
VerifyMultiLabelContent(docFasta, docMulti, out countProteinTerm, out countProteinTermTran);
int multiGroupCount = initPep * 3 - countProteinTerm;
int multiTranCount = initTran * 3 - countProteinTermTran;
AssertEx.IsDocumentState(docMulti, ++startRev, initProt, initPep,
multiGroupCount, multiTranCount);
// Turn off auto-manage children on all peptides
var listPepGroups = new List <DocNode>();
foreach (PeptideGroupDocNode nodePepGroup in docMulti.MoleculeGroups)
{
var listPeptides = new List <DocNode>();
foreach (PeptideDocNode nodePep in nodePepGroup.Children)
{
listPeptides.Add(nodePep.ChangeAutoManageChildren(false));
}
listPepGroups.Add(nodePepGroup.ChangeChildren(listPeptides));
}
var docNoAuto = (SrmDocument)docMulti.ChangeChildren(listPepGroups);
startRev++;
// Switch back to settings without isotope labels
var docNoAutoLight = docNoAuto.ChangeSettings(docFasta.Settings);
// The document should return to its initial state
AssertEx.IsDocumentState(docNoAutoLight, ++startRev, initProt, initPep, initTran);
// Switch back to Settings with isotope labels
var docNoAutoLabeled = docNoAutoLight.ChangeSettings(docMulti.Settings);
// The number of nodes should not change
AssertEx.IsDocumentState(docNoAutoLabeled, ++startRev, initProt, initPep, initTran);
// Remove all document nodes
var docEmpty = (SrmDocument)docNoAutoLabeled.ChangeChildren(new PeptideGroupDocNode[0]);
// Paste FASTA back in
var docRePaste = docEmpty.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out _);
// This should produce the same document as the original settings change
Assert.AreEqual(docMulti, docRePaste);
}
public void ImportFastaTest()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
Assert.AreEqual("YAL001C", ((PeptideGroupDocNode)docFasta.Children[0]).Name);
Assert.AreEqual("YAL002W", ((PeptideGroupDocNode)docFasta.Children[1]).Name);
Assert.AreEqual(1, path.Length);
Assert.IsInstanceOfType(path.GetIdentity(0), typeof(FastaSequence));
Assert.AreEqual("YAL001C", ((FastaSequence) path.GetIdentity(0)).Name);
int maxMz = docFasta.Settings.TransitionSettings.Instrument.MaxMz - 120;
foreach (PeptideGroupDocNode nodeGroup in docFasta.Children)
{
if (SrmDocument.IsSpecialNonProteomicTestDocNode(nodeGroup))
continue;
Assert.IsInstanceOfType(nodeGroup.Id, typeof(FastaSequence));
int lastEnd = docFasta.Settings.PeptideSettings.Filter.ExcludeNTermAAs - 1;
foreach (PeptideDocNode nodePeptide in nodeGroup.Children)
{
Peptide peptide = nodePeptide.Peptide;
char prev = peptide.PrevAA;
if (prev != 'K' && prev != 'R')
Assert.Fail("Unexpected preceding cleavage at {0}", prev);
string seq = peptide.Sequence;
char last = seq[seq.Length - 1];
if (last != 'K' && last != 'R' && peptide.NextAA != '-')
Assert.Fail("Unexpected cleavage at {0}", last);
Assert.IsNotNull(peptide.Begin);
Assert.IsNotNull(peptide.End);
// Make sure peptides are ordered, and not overlapping
if (peptide.Begin.Value < lastEnd)
Assert.Fail("Begin {0} less than last end {1}.", peptide.Begin.Value, lastEnd);
lastEnd = peptide.End.Value;
IList<DocNode> nodesTrans = ((DocNodeParent) nodePeptide.Children[0]).Children;
int trans = nodesTrans.Count;
if (trans < 3)
{
// Might have been cut off by the instrument limit.
if ((trans == 0 && ((TransitionGroupDocNode)nodePeptide.Children[0]).PrecursorMz < maxMz) ||
(trans > 0 && ((TransitionDocNode)nodesTrans[0]).Mz < maxMz))
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
// Might have extra proline transitions
else if (trans > 3 && peptide.Sequence.IndexOf('P') == -1)
Assert.Fail("Found {0} transitions, expecting 3.", trans);
// Make sure transitions are ordered correctly
IonType lastType = IonType.a;
int lastOffset = -1;
foreach (TransitionDocNode nodeTran in nodesTrans)
{
Transition transition = nodeTran.Transition;
if (lastType == transition.IonType)
Assert.IsTrue(transition.CleavageOffset > lastOffset);
else
Assert.IsTrue(((int)transition.IonType) > ((int) lastType));
lastType = transition.IonType;
lastOffset = transition.CleavageOffset;
}
}
}
// Make sure old document is unmodified.
Assert.AreEqual(0, document.RevisionIndex);
Assert.AreEqual(0, document.PeptideTransitionCount);
// Re-paste of fasta should have no impact.
// path = IdentityPath.ROOT; use null as substitute for Root
SrmDocument docFasta2 = docFasta.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, null, out path);
// Returns the original document to avoid adding undo record in running app
Assert.AreSame(docFasta, docFasta2);
Assert.IsNull(path);
// Discard double-insert document, and add peptides list into previous document
path = IdentityPath.ROOT;
SrmDocument docPeptides = docFasta.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides, 2, 3, 111, 352);
Assert.AreEqual(1, path.Length);
Assert.IsNotInstanceOfType(path.GetIdentity(0), typeof(FastaSequence));
Assert.AreEqual("Peptides1", ((PeptideGroupDocNode)docPeptides.FindNode(path)).Name);
PeptideGroupDocNode nodePepList = (PeptideGroupDocNode) docPeptides.Children[2];
Assert.IsNotInstanceOfType(nodePepList.Id, typeof(FastaSequence));
// Make sure other two nodes are unchanged
Assert.AreSame(docFasta.Children[0], docPeptides.Children[0]);
Assert.AreSame(docFasta.Children[1], docPeptides.Children[1]);
foreach (PeptideDocNode nodePeptide in nodePepList.Children)
{
if (SrmDocument.IsSpecialNonProteomicTestDocNode(nodePeptide))
continue;
char prev = nodePeptide.Peptide.PrevAA;
char next = nodePeptide.Peptide.NextAA;
if (prev != 'X' || next != 'X')
Assert.Fail("Expected amino acids X, but found {0} or {1}", prev, next);
string seq = nodePeptide.Peptide.Sequence;
char last = seq[seq.Length - 1];
// Just because they are tryptic peptides in the list
if (last != 'K' && last != 'R' && nodePeptide.Peptide.NextAA != '-')
Assert.Fail("Unexpected cleavage at {0}", last);
Assert.IsNull(nodePeptide.Peptide.Begin);
Assert.IsNull(nodePeptide.Peptide.End);
IList<DocNode> nodesTrans = ((DocNodeParent)nodePeptide.Children[0]).Children;
int trans = nodesTrans.Count;
if (trans < 3)
{
// Might have been cut off by the instrument limit.
if ((trans == 0 && ((TransitionGroupDocNode)nodePeptide.Children[0]).PrecursorMz < maxMz) ||
(trans > 0 && ((TransitionDocNode)nodesTrans[0]).Mz < maxMz))
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
// Might have extra proline transitions
else if (trans > 3 && nodePeptide.Peptide.Sequence.IndexOf('P') == -1)
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
// Make sure old documents are unmodified.
AssertEx.IsDocumentState(document, 0, 0, 0, 0);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
AssertEx.IsDocumentState(docPeptides, 2, 3, 111, 352);
// Add peptides in all possible locations.
// 1. Root (already done)
// 1. Before another group
path = docPeptides.GetPathTo(0);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides2, 3, 4, 124, 393);
Assert.IsNotInstanceOfType(docPeptides2.Children[0].Id, typeof(FastaSequence));
Assert.AreEqual(docPeptides2.Children[0].Id, path.GetIdentity(0));
Assert.IsInstanceOfType(docPeptides2.Children[1].Id, typeof(FastaSequence));
// Make sure previously existing groups are unchanged
Assert.AreSame(docPeptides.Children[0], docPeptides2.Children[1]);
Assert.AreSame(docPeptides.Children[1], docPeptides2.Children[2]);
Assert.AreSame(docPeptides.Children[2], docPeptides2.Children[3]);
// 2. Inside a FASTA group
path = docPeptides2.GetPathTo((int) SrmDocument.Level.Transitions, 100);
SrmDocument docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 5, 137, 434);
Assert.AreEqual(2, docPeptides3.FindNodeIndex(path));
// Make sure previously existing groups are unchanged
Assert.AreSame(docPeptides2.Children[1], docPeptides3.Children[1]);
Assert.AreSame(docPeptides2.Children[2], docPeptides3.Children[3]);
// 3. To a peptide list
// a. Same peptides
path = docPeptides2.GetPathTo(0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
// No longer filter repeated peptides, because they are useful for explicit modifictations.
Assert.AreNotSame(docPeptides2, docPeptides3);
Assert.IsNotNull(path);
// b. Different paptides
path = docPeptides2.GetPathTo(0);
IdentityPath pathFirstPep = docPeptides3.GetPathTo((int) SrmDocument.Level.Molecules, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual("LVTDLTK", ((PeptideDocNode) docPeptides3.FindNode(path)).Peptide.Sequence);
int index = docPeptides3.FindNodeIndex(path);
IdentityPath pathPreceding = docPeptides3.GetPathTo(path.Depth, index - 1);
Assert.AreEqual("IVGYLDEEGVLDQNR", ((PeptideDocNode)docPeptides3.FindNode(pathPreceding)).Peptide.Sequence);
Assert.AreEqual(0, docPeptides3.FindNodeIndex(pathFirstPep));
// 4. At a peptide in a peptide list
path = docPeptides2.GetPathTo((int) SrmDocument.Level.Molecules, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual(0, docPeptides3.FindNodeIndex(path));
Assert.AreEqual(16, docPeptides3.FindNodeIndex(pathFirstPep));
// 5. Inside a peptide in a peptide list
path = docPeptides2.GetPathTo((int)SrmDocument.Level.Transitions, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual(1, docPeptides3.FindNodeIndex(path));
Assert.AreEqual(0, docPeptides3.FindNodeIndex(pathFirstPep));
}
public void ReporterIonTest()
{
// Test the code that updates old-style formulas
Assert.AreEqual("C5C'H13N2", BioMassCalc.AddH("C5C'H12N2"));
Assert.AreEqual("CO2H", BioMassCalc.AddH("CO2"));
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(10))); // H2O2 is not very heavy!
IdentityPath path;
SrmDocument docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8));
const string formula = "H2O2"; // This was H2O, but that falls below mz=10 at z > 1
const string hydrogenPeroxide = "Hydrogen Perxoide";
var reporterIons = new[] { new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.DOUBLY_PROTONATED), new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.TRIPLY_PROTONATED), MeasuredIonList.NTERM_PROLINE };
SrmDocument docReporterIon = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(reporterIons)));
AssertEx.IsDocumentTransitionCount(docReporterIon, 7);
//Check With Monoisotopic
var mass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = docReporterIon.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Check with Average
TransitionPrediction predSettings =
docReporterIon.Settings.TransitionSettings.Prediction.ChangeFragmentMassType(MassType.Average);
TransitionSettings tranSettings = docReporterIon.Settings.TransitionSettings.ChangePrediction(predSettings);
SrmSettings srmSettings = docReporterIon.Settings.ChangeTransitionSettings(tranSettings);
SrmDocument averageDocument = docReporterIon.ChangeSettings(srmSettings);
mass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
for (int i = 0; i < 3; i++)
{
TransitionDocNode tranNode = averageDocument.MoleculeTransitions.ElementAt(i);
Transition tran = tranNode.Transition;
Assert.AreEqual(reporterIons[i].SettingsCustomIon, tran.CustomIon);
Assert.AreEqual(tran.Charge, i + 1);
Assert.AreEqual(BioMassCalc.CalculateIonMz(mass, tran.Adduct), tranNode.Mz, BioMassCalc.MassElectron / 100);
}
//Make sure the rest of the transitions aren't reporter ions
for (int i = 3; i < 7; i++)
{
Transition tran = docReporterIon.MoleculeTransitions.ElementAt(i).Transition;
Assert.AreNotEqual(tran.CustomIon, reporterIons);
}
var optionalIon = new MeasuredIon(hydrogenPeroxide, formula, null, null, Adduct.SINGLY_PROTONATED, true);
SrmDocument optionalDoc = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon })));
Assert.AreEqual(3, optionalDoc.PeptideTransitionCount);
optionalDoc = optionalDoc.ChangeSettings(optionalDoc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(false) })));
AssertEx.IsDocumentTransitionCount(optionalDoc, 4);
Assert.AreEqual(optionalIon.ChangeIsOptional(false).SettingsCustomIon,
optionalDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
optionalDoc =
optionalDoc.ChangeSettings(
optionalDoc.Settings.ChangeTransitionFilter(
filter => filter.ChangeMeasuredIons(new[] { optionalIon.ChangeIsOptional(true) })));
TransitionGroupDocNode nodeGroup = optionalDoc.MoleculeTransitionGroups.ElementAt(0);
var filteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, true)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
var unfilteredNodes =
nodeGroup.GetPrecursorChoices(optionalDoc.Settings,
optionalDoc.Molecules.ElementAt(0).ExplicitMods, false)
.Cast <TransitionDocNode>()
.Where(node => Equals(node.Transition.CustomIon, optionalIon.SettingsCustomIon));
Assert.AreEqual(0, filteredNodes.Count());
Assert.AreEqual(1, unfilteredNodes.Count());
}
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 void SpecialFragmentTest()
{
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath path;
var docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8)); // y8
// Switch to the legacy version of the proline fragment where min length is 1
var docLegacyProline = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { MeasuredIonList.NTERM_PROLINE_LEGACY })));
Assert.AreEqual(5, docLegacyProline.PeptideTransitionCount);
// Allow b-ions
var docLegacyProlineB = docLegacyProline.ChangeSettings(docLegacyProline.Settings.ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.b, IonType.y })));
Assert.AreEqual(9, docLegacyProlineB.PeptideTransitionCount);
// Add C-terminal Glu and Asp to the original peptide document
var docGluAsp = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List<MeasuredIon>(filter.MeasuredIons) { MeasuredIonList.CTERM_GLU_ASP })));
Assert.AreEqual(5, docGluAsp.PeptideTransitionCount);
Assert.IsTrue(docGluAsp.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 3)); // y3
// Use the legacy version instead
var docGluAspLegacy = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List<MeasuredIon>(filter.MeasuredIons) { MeasuredIonList.CTERM_GLU_ASP_LEGACY })));
Assert.AreEqual(6, docGluAspLegacy.PeptideTransitionCount);
Assert.IsTrue(docGluAspLegacy.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 2)); // y2
// Add Proline to the C-terminal modification
var docGluAspPro = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", null, SequenceTerminus.C, 1) })));
Assert.AreEqual(8, docGluAspPro.PeptideTransitionCount);
Assert.IsTrue(docGluAspPro.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // y2
nodeTran.Transition.Ordinal == 8)); // y8
// Restrict
var docGluAspProRestrict = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", "P", SequenceTerminus.C, 1) })));
Assert.AreEqual(6, docGluAspProRestrict.PeptideTransitionCount);
Assert.IsFalse(docGluAspProRestrict.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // not y2
nodeTran.Transition.Ordinal == 8)); // not y8
}
public void RemoveDuplicatePeptidesTest()
{
// First try removals with no impact
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
SrmDocument docFasta = document.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 1)),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 1, 11, 36);
var refinementSettings = new RefinementSettings {RemoveDuplicatePeptides = true};
SrmDocument docFasta2 = refinementSettings.Refine(docFasta);
Assert.AreSame(docFasta, docFasta2);
docFasta2 = docFasta.ImportFasta(new StringReader(string.Format(TEXT_FASTA_YEAST_FRAGMENT, 2)),
false, IdentityPath.ROOT, out path);
// Adding same sequence twice, even with different custom names is ignored
Assert.AreSame(docFasta, docFasta2);
// Try a successful removal of duplicates that leaves no peptides
SrmDocument docPeptides = document.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides2, 2, 2, 26, 82);
SrmDocument docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 0, 0);
// Try again leaving a single peptide
docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1 + "\n" + TEXT_BOVINE_SINGLE_PEPTIDE),
true, IdentityPath.ROOT, out path);
docPeptides3 = refinementSettings.Refine(docPeptides2);
Assert.AreNotSame(docPeptides2, docPeptides3);
AssertEx.IsDocumentState(docPeptides3, 3, 2, 1, 3);
}
public void ImportFastaTest()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
Assert.AreEqual("YAL001C", ((PeptideGroupDocNode)docFasta.Children[0]).Name);
Assert.AreEqual("YAL002W", ((PeptideGroupDocNode)docFasta.Children[1]).Name);
Assert.AreEqual(1, path.Length);
Assert.IsInstanceOfType(path.GetIdentity(0), typeof(FastaSequence));
Assert.AreEqual("YAL001C", ((FastaSequence)path.GetIdentity(0)).Name);
int maxMz = docFasta.Settings.TransitionSettings.Instrument.MaxMz - 120;
foreach (PeptideGroupDocNode nodeGroup in docFasta.Children)
{
Assert.IsInstanceOfType(nodeGroup.Id, typeof(FastaSequence));
int lastEnd = docFasta.Settings.PeptideSettings.Filter.ExcludeNTermAAs - 1;
foreach (PeptideDocNode nodePeptide in nodeGroup.Children)
{
Peptide peptide = nodePeptide.Peptide;
char prev = peptide.PrevAA;
if (prev != 'K' && prev != 'R')
{
Assert.Fail("Unexpected preceding cleavage at {0}", prev);
}
string seq = peptide.Sequence;
char last = seq[seq.Length - 1];
if (last != 'K' && last != 'R' && peptide.NextAA != '-')
{
Assert.Fail("Unexpected cleavage at {0}", last);
}
Assert.IsNotNull(peptide.Begin);
Assert.IsNotNull(peptide.End);
// Make sure peptides are ordered, and not overlapping
if (peptide.Begin.Value < lastEnd)
{
Assert.Fail("Begin {0} less than last end {1}.", peptide.Begin.Value, lastEnd);
}
lastEnd = peptide.End.Value;
IList <DocNode> nodesTrans = ((DocNodeParent)nodePeptide.Children[0]).Children;
int trans = nodesTrans.Count;
if (trans < 3)
{
// Might have been cut off by the instrument limit.
if ((trans == 0 && ((TransitionGroupDocNode)nodePeptide.Children[0]).PrecursorMz < maxMz) ||
(trans > 0 && ((TransitionDocNode)nodesTrans[0]).Mz < maxMz))
{
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
}
// Might have extra proline transitions
else if (trans > 3 && peptide.Sequence.IndexOf('P') == -1)
{
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
// Make sure transitions are ordered correctly
IonType lastType = IonType.a;
int lastOffset = -1;
foreach (TransitionDocNode nodeTran in nodesTrans)
{
Transition transition = nodeTran.Transition;
if (lastType == transition.IonType)
{
Assert.IsTrue(transition.CleavageOffset > lastOffset);
}
else
{
Assert.IsTrue(((int)transition.IonType) > ((int)lastType));
}
lastType = transition.IonType;
lastOffset = transition.CleavageOffset;
}
}
}
// Make sure old document is unmodified.
Assert.AreEqual(0, document.RevisionIndex);
Assert.AreEqual(0, document.PeptideTransitionCount);
// Re-paste of fasta should have no impact.
// path = IdentityPath.ROOT; use null as substitute for Root
SrmDocument docFasta2 = docFasta.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, null, out path);
// Returns the original document to avoid adding undo record in running app
Assert.AreSame(docFasta, docFasta2);
Assert.IsNull(path);
// Discard double-insert document, and add peptides list into previous document
path = IdentityPath.ROOT;
SrmDocument docPeptides = docFasta.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides, 2, 3, 111, 352);
Assert.AreEqual(1, path.Length);
Assert.IsNotInstanceOfType(path.GetIdentity(0), typeof(FastaSequence));
Assert.AreEqual("Peptides1", ((PeptideGroupDocNode)docPeptides.FindNode(path)).Name);
PeptideGroupDocNode nodePepList = (PeptideGroupDocNode)docPeptides.Children[2];
Assert.IsNotInstanceOfType(nodePepList.Id, typeof(FastaSequence));
// Make sure other two nodes are unchanged
Assert.AreSame(docFasta.Children[0], docPeptides.Children[0]);
Assert.AreSame(docFasta.Children[1], docPeptides.Children[1]);
foreach (PeptideDocNode nodePeptide in nodePepList.Children)
{
char prev = nodePeptide.Peptide.PrevAA;
char next = nodePeptide.Peptide.NextAA;
if (prev != 'X' || next != 'X')
{
Assert.Fail("Expected amino acids X, but found {0} or {1}", prev, next);
}
string seq = nodePeptide.Peptide.Sequence;
char last = seq[seq.Length - 1];
// Just because they are tryptic peptides in the list
if (last != 'K' && last != 'R' && nodePeptide.Peptide.NextAA != '-')
{
Assert.Fail("Unexpected cleavage at {0}", last);
}
Assert.IsNull(nodePeptide.Peptide.Begin);
Assert.IsNull(nodePeptide.Peptide.End);
IList <DocNode> nodesTrans = ((DocNodeParent)nodePeptide.Children[0]).Children;
int trans = nodesTrans.Count;
if (trans < 3)
{
// Might have been cut off by the instrument limit.
if ((trans == 0 && ((TransitionGroupDocNode)nodePeptide.Children[0]).PrecursorMz < maxMz) ||
(trans > 0 && ((TransitionDocNode)nodesTrans[0]).Mz < maxMz))
{
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
}
// Might have extra proline transitions
else if (trans > 3 && nodePeptide.Peptide.Sequence.IndexOf('P') == -1)
{
Assert.Fail("Found {0} transitions, expecting 3.", trans);
}
}
// Make sure old documents are unmodified.
AssertEx.IsDocumentState(document, 0, 0, 0, 0);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
AssertEx.IsDocumentState(docPeptides, 2, 3, 111, 352);
// Add peptides in all possible locations.
// 1. Root (already done)
// 1. Before another group
path = docPeptides.GetPathTo(0);
SrmDocument docPeptides2 = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides2, 3, 4, 124, 393);
Assert.IsNotInstanceOfType(docPeptides2.Children[0].Id, typeof(FastaSequence));
Assert.AreEqual(docPeptides2.Children[0].Id, path.GetIdentity(0));
Assert.IsInstanceOfType(docPeptides2.Children[1].Id, typeof(FastaSequence));
// Make sure previously existing groups are unchanged
Assert.AreSame(docPeptides.Children[0], docPeptides2.Children[1]);
Assert.AreSame(docPeptides.Children[1], docPeptides2.Children[2]);
Assert.AreSame(docPeptides.Children[2], docPeptides2.Children[3]);
// 2. Inside a FASTA group
path = docPeptides2.GetPathTo((int)SrmDocument.Level.Transitions, 100);
SrmDocument docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 5, 137, 434);
Assert.AreEqual(2, docPeptides3.FindNodeIndex(path));
// Make sure previously existing groups are unchanged
Assert.AreSame(docPeptides2.Children[1], docPeptides3.Children[1]);
Assert.AreSame(docPeptides2.Children[2], docPeptides3.Children[3]);
// 3. To a peptide list
// a. Same peptides
path = docPeptides2.GetPathTo(0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true, path, out path);
// No longer filter repeated peptides, because they are useful for explicit modifictations.
Assert.AreNotSame(docPeptides2, docPeptides3);
Assert.IsNotNull(path);
// b. Different paptides
path = docPeptides2.GetPathTo(0);
IdentityPath pathFirstPep = docPeptides3.GetPathTo((int)SrmDocument.Level.Molecules, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual("LVTDLTK", ((PeptideDocNode)docPeptides3.FindNode(path)).Peptide.Sequence);
int index = docPeptides3.FindNodeIndex(path);
IdentityPath pathPreceding = docPeptides3.GetPathTo(path.Depth, index - 1);
Assert.AreEqual("IVGYLDEEGVLDQNR", ((PeptideDocNode)docPeptides3.FindNode(pathPreceding)).Peptide.Sequence);
Assert.AreEqual(0, docPeptides3.FindNodeIndex(pathFirstPep));
// 4. At a peptide in a peptide list
path = docPeptides2.GetPathTo((int)SrmDocument.Level.Molecules, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual(0, docPeptides3.FindNodeIndex(path));
Assert.AreEqual(16, docPeptides3.FindNodeIndex(pathFirstPep));
// 5. Inside a peptide in a peptide list
path = docPeptides2.GetPathTo((int)SrmDocument.Level.Transitions, 0);
docPeptides3 = docPeptides2.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true, path, out path);
AssertEx.IsDocumentState(docPeptides3, 4, 4, 140, 448);
Assert.AreSame(docPeptides2.Children[0].Id, docPeptides3.Children[0].Id);
Assert.AreNotSame(docPeptides2.Children[0], docPeptides3.Children[0]);
Assert.AreEqual(1, docPeptides3.FindNodeIndex(path));
Assert.AreEqual(0, docPeptides3.FindNodeIndex(pathFirstPep));
}
public void DynamicMinMzTest()
{
var revisionIndex = 1;
var settings = SrmSettingsList.GetDefault().ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.y, IonType.b })
.ChangeFragmentRangeFirstName("ion 1")
.ChangeFragmentRangeLastName("last ion"));
var docOriginal = new SrmDocument(settings);
IdentityPath path;
var docPeptides = docOriginal.ImportFasta(new StringReader(">peptides\nESTIGNSAFELLLEVAK\nTVYHAGTK"),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides, revisionIndex++, 1, 2, 2, 40);
// Both precursors should contain 1 and 2 ions
foreach (var nodeGroup in docPeptides.PeptideTransitionGroups)
{
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
}
// Switch to using dynamic minimum for product ions
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(true));
var docDynamicMin = docPeptides.ChangeSettings(settings);
AssertEx.IsDocumentState(docDynamicMin, revisionIndex++, 1, 2, 35);
var arrayNodeGroups = docDynamicMin.PeptideTransitionGroups.ToArray();
// The larger precursor should no longer have 1 or 2 ions
Assert.IsFalse(arrayNodeGroups[0].Children.Contains(node =>
((TransitionDocNode)node).Transition.Ordinal == 1 ||
((TransitionDocNode)node).Transition.Ordinal == 2));
// But the smaller precursor should retain at least one of both
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
// Use a minimum that is high enough to exclude the smaller precursor
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(500));
var docHighMinDynamicMz = docDynamicMin.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinDynamicMz, revisionIndex++, 1, 2, 1, 22);
// Because of the dynamic minimum for product ions, the remaining precursor should not have changed
var nodeGroupHigh = docHighMinDynamicMz.PeptideTransitionGroups.ToArray()[0];
Assert.AreSame(arrayNodeGroups[0], nodeGroupHigh);
// Remove dynamic minimum, and verify that product ions are removed
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(false));
var docHighMinMz = docHighMinDynamicMz.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinMz, revisionIndex, 1, 2, 1, 17);
// No library test, because it is hard to test. Many of the library
// spectra are likely gathered with LTQs which apply the same dynamic
// minimum to the ms/ms peaks they measure.
}
public void MultiLabelTypeListTest()
{
TestSmallMolecules = false; // we don't expect to roundtrip export/import of transition lists for non-proteomic molecules
int startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
// Add some FASTA
IdentityPath path, pathRoot = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out path);
const int initProt = 2, initPep = 26, initTran = 89;
AssertEx.IsDocumentState(docFasta, ++startRev, initProt, initPep, initTran);
// Add multiple heavy types
var settings = docFasta.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(LABEL_TYPE13_C, HEAVY_MODS_13_C),
new TypedModifications(LABEL_TYPE15_N, HEAVY_MODS_15_N)
}));
var docMulti = docFasta.ChangeSettings(settings);
// CONSIDER: make explicit S-Lens, cone voltage, CE etc roundtrip?
// docMulti.MoleculeTransitionGroups.FirstOrDefault().ChangeExplicitValues(ExplicitTransitionGroupValues.TEST)
// Make sure transition lists export to various formats and roundtrip
VerifyExportRoundTrip(new ThermoMassListExporter(docMulti), docFasta);
VerifyExportRoundTrip(new AbiMassListExporter(docMulti), docFasta);
VerifyExportRoundTrip(new AgilentMassListExporter(docMulti), docFasta);
VerifyExportRoundTrip(new WatersMassListExporter(docMulti), docFasta);
}
public void MultiLabelTypeTest()
{
int startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
// Add some FASTA
IdentityPath path, pathRoot = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out path);
const int initProt = 2, initPep = 26, initTran = 89;
AssertEx.IsDocumentState(docFasta, ++startRev, initProt, initPep, initTran);
// Add multiple heavy types
var settings = docFasta.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(LABEL_TYPE13_C, HEAVY_MODS_13_C),
new TypedModifications(LABEL_TYPE15_N, HEAVY_MODS_15_N)
}));
var docMulti = docFasta.ChangeSettings(settings);
// Make sure the contents of the resulting document are as expected.
int countProteinTermTran, countProteinTerm;
VerifyMultiLabelContent(docFasta, docMulti, out countProteinTerm, out countProteinTermTran);
int multiGroupCount = initPep*3 - countProteinTerm;
int multiTranCount = initTran*3 - countProteinTermTran;
AssertEx.IsDocumentState(docMulti, ++startRev, initProt, initPep,
multiGroupCount, multiTranCount);
// Turn off auto-manage children on all peptides
var listPepGroups = new List<DocNode>();
foreach (PeptideGroupDocNode nodePepGroup in docMulti.MoleculeGroups)
{
var listPeptides = new List<DocNode>();
foreach (PeptideDocNode nodePep in nodePepGroup.Children)
listPeptides.Add(nodePep.ChangeAutoManageChildren(false));
listPepGroups.Add(nodePepGroup.ChangeChildren(listPeptides));
}
var docNoAuto = (SrmDocument) docMulti.ChangeChildren(listPepGroups);
startRev++;
// Switch back to settings without isotope labels
var docNoAutoLight = docNoAuto.ChangeSettings(docFasta.Settings);
// The document should return to its initial state
AssertEx.IsDocumentState(docNoAutoLight, ++startRev, initProt, initPep, initTran);
// Switch back to Settings with isotope labels
var docNoAutoLabeled = docNoAutoLight.ChangeSettings(docMulti.Settings);
// The number of nodes should not change
AssertEx.IsDocumentState(docNoAutoLabeled, ++startRev, initProt, initPep, initTran);
// Remove all document nodes
var docEmpty = (SrmDocument) docNoAutoLabeled.ChangeChildren(new PeptideGroupDocNode[0]);
// Paste FASTA back in
var docRePaste = docEmpty.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out path);
// This should produce the same document as the original settings change
Assert.AreEqual(docMulti, docRePaste);
}
private static SrmDocument CreateMixedDoc()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
IdentityPath path;
// Add fasta sequences
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST),
false, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docFasta, 1, 2, 98, 311);
// Insert peptide list at beginnning
SrmDocument docMixed = docFasta.ImportFasta(new StringReader(SrmDocEditTest.TEXT_BOVINE_PEPTIDES1),
true, docFasta.GetPathTo(0), out path);
AssertEx.IsDocumentState(docMixed, 2, 3, 111, 352);
return docMixed;
}
public void MoveNodeTest()
{
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST), false, path, out path);
// 1. From peptide group to root
SrmDocument docMoved = docFasta.MoveNode(docFasta.GetPathTo(0), IdentityPath.ROOT, out path);
Assert.AreEqual(1, docMoved.FindNodeIndex(path));
Assert.AreSame(docFasta.Children[0], docMoved.Children[1]);
Assert.AreSame(docFasta.Children[1], docMoved.Children[0]);
// 2. From peptide group to before other peptide group
docMoved = docFasta.MoveNode(docFasta.GetPathTo(1), docFasta.GetPathTo(0), out path);
Assert.AreEqual(0, docMoved.FindNodeIndex(path));
Assert.AreSame(docFasta.Children[0], docMoved.Children[1]);
Assert.AreSame(docFasta.Children[1], docMoved.Children[0]);
// Some peptide lists
IdentityPath pathPeptides;
SrmDocument docPeptides = docFasta.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES2), true,
docFasta.GetPathTo(1), out pathPeptides);
docPeptides = docPeptides.ImportFasta(new StringReader(TEXT_BOVINE_PEPTIDES1), true,
IdentityPath.ROOT, out path);
docPeptides = docPeptides.MoveNode(path, pathPeptides, out pathPeptides);
Assert.AreEqual(1, docPeptides.FindNodeIndex(pathPeptides));
// 3. Peptide from one group to another
IdentityPath fromParent = docPeptides.GetPathTo(2);
IdentityPath from = new IdentityPath(fromParent, ((DocNodeParent)docPeptides.FindNode(fromParent)).Children[0].Id);
SrmDocument docPeptides2 = docPeptides.MoveNode(from, pathPeptides, out path);
Assert.AreEqual(pathPeptides, path.Parent);
Assert.AreEqual(((DocNodeParent)docPeptides.Children[1]).Children.Count,
((DocNodeParent)docPeptides2.Children[1]).Children.Count - 1);
Assert.AreEqual(((DocNodeParent)docPeptides.Children[2]).Children.Count,
((DocNodeParent)docPeptides2.Children[2]).Children.Count + 1);
// Though moved to a different group, this should not have changed the overall
// peptide order, since it was moved from the beginning of one group to the end
// of the group before it.
Assert.AreEqual(docPeptides.FindNodeIndex(from), docPeptides2.FindNodeIndex(path));
// 4. To before another peptide
from = new IdentityPath(fromParent, ((DocNodeParent)docPeptides2.FindNode(fromParent)).Children[0].Id);
IdentityPath path2;
SrmDocument docPeptides3 = docPeptides2.MoveNode(from, path, out path2);
Assert.AreEqual(pathPeptides, path.Parent);
Assert.AreEqual(((DocNodeParent)docPeptides2.Children[1]).Children.Count,
((DocNodeParent)docPeptides3.Children[1]).Children.Count - 1);
Assert.AreEqual(((DocNodeParent)docPeptides2.Children[2]).Children.Count,
((DocNodeParent)docPeptides3.Children[2]).Children.Count + 1);
// Relative to all peptides, index should be 1 less than before
Assert.AreEqual(docPeptides2.FindNodeIndex(from), docPeptides3.FindNodeIndex(path2) + 1);
// 5. To within another peptide
IdentityPath to = new IdentityPath(path, ((DocNodeParent)docPeptides3.FindNode(path)).Children[0].Id);
SrmDocument docPeptides4 = docPeptides3.MoveNode(path2, to, out path);
// Should not have changed to count in the group
Assert.AreEqual(((DocNodeParent)docPeptides3.Children[1]).Children.Count,
((DocNodeParent)docPeptides4.Children[1]).Children.Count);
// Relative to all peptides, should have been returned to original order
Assert.AreEqual(docPeptides2.FindNodeIndex(from), docPeptides4.FindNodeIndex(path));
// Make sure expected exceptions are thrown
Assert.IsNull(docPeptides4.FindNode(from));
AssertEx.ThrowsException<IdentityNotFoundException>(() =>
docPeptides4.MoveNode(from, to, out path));
AssertEx.ThrowsException<InvalidOperationException>(() =>
docPeptides2.MoveNode(from, docPeptides2.GetPathTo(0), out path));
AssertEx.ThrowsException<InvalidOperationException>(() =>
docPeptides3.MoveNode(docPeptides2.GetPathTo((int) SrmDocument.Level.Molecules, 0), to, out path));
AssertEx.ThrowsException<InvalidOperationException>(() =>
docPeptides3.MoveNode(docPeptides2.GetPathTo((int)SrmDocument.Level.Transitions, 0), to, out path));
}
