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 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 static SrmDocument CreateNISTLibraryDocument(string textFasta, bool peptideList, string textLib,
out LibraryManager libraryManager, out TestDocumentContainer docContainer, out int startRev)
{
var streamManager = new MemoryStreamManager();
streamManager.TextFiles.Add(LibraryLoadTest.PATH_NIST_LIB, textLib);
var librarySpec = new NistLibSpec("Yeast (NIST)", LibraryLoadTest.PATH_NIST_LIB);
// For serialization, add the library spec to the settings
TestLibraryList = new SpectralLibraryList {
librarySpec
};
libraryManager = new LibraryManager {
StreamManager = streamManager
};
docContainer = new TestDocumentContainer();
SrmSettings settings = SrmSettingsList.GetDefault0_6();
settings = settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(new[] { librarySpec }));
return(CreateLibraryDocument(settings, textFasta, peptideList, docContainer, libraryManager, out startRev));
}
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));
}