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 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)); }