private void VerifyFoldChanges(SrmDocument testDocument, GroupComparisonDef groupComparisonDef,
IDictionary <string, LinearFitResult> expectedResults)
{
var groupComparer = new GroupComparer(groupComparisonDef, testDocument, new QrFactorizationCache());
foreach (var protein in testDocument.MoleculeGroups)
{
var groupComparisonResult = groupComparer.CalculateFoldChanges(protein, null).FirstOrDefault();
LinearFitResult expectedResult;
if (expectedResults.TryGetValue(protein.Name, out expectedResult))
{
Assert.IsNotNull(groupComparisonResult);
var foldChange = groupComparisonResult.LinearFitResult;
Assert.AreEqual(expectedResult.EstimatedValue, foldChange.EstimatedValue, 1E-5);
Assert.AreEqual(expectedResult.DegreesOfFreedom, foldChange.DegreesOfFreedom);
Assert.AreEqual(expectedResult.StandardError, foldChange.StandardError, 1E-5);
Assert.AreEqual(expectedResult.TValue, foldChange.TValue, 1E-5);
Assert.AreEqual(expectedResult.PValue, foldChange.PValue, 1E-5);
}
else if (!SrmDocument.IsSpecialNonProteomicTestDocNode(protein)) // Avoid the special small molecule test nodes
{
Assert.IsNull(groupComparisonResult);
var standardPeptides = protein.Molecules.Where(mol => null != mol.GlobalStandardType).ToArray();
Assert.AreNotEqual(0, standardPeptides.Length);
}
}
}
protected override void DoTest()
{
// Formerly this little .sky file would not update its (unsearchable) protein metdata on load
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Mutant Peptides with Braf AG A00Y - Cut Down.sky")));
var doc = WaitForDocumentLoaded();
var nodeProt = doc.MoleculeGroups.First();
var metadata = nodeProt.ProteinMetadata;
Assert.IsFalse(metadata.NeedsSearch());
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("ProteinMetadataFunctionalTests.sky")));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First();
metadata = nodeProt.ProteinMetadata;
// Examine the various View | Targets | By* modes
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
ProteinMetadataManager.ProteinDisplayMode arg = mode;
RunUI(() => SkylineWindow.UpdateTargetsDisplayMode(arg)); // This should alter the text displayed by the node in the sequence tree view
WaitForConditionUI(() =>
{
var displayText = SkylineWindow.SequenceTree.GetSequenceNodes().First().Text;
if (arg != ProteinMetadataManager.ProteinDisplayMode.ByName &&
Equals(displayText, GetDisplayText(ProteinMetadataManager.ProteinDisplayMode.ByName, metadata)))
{
return(false);
}
return(Equals(displayText, GetDisplayText(arg, metadata)));
});
}
// Examine the various Edit | Refine | Sort Proteins | By* modes
Assert.AreEqual("YIL075C", nodeProt.Name); // unsorted
foreach (ProteinMetadataManager.ProteinDisplayMode mode in Enum.GetValues(typeof(ProteinMetadataManager.ProteinDisplayMode)))
{
string expectedTopName = null;
switch (mode)
{
case ProteinMetadataManager.ProteinDisplayMode.ByName:
expectedTopName = "YAL003W";
RunUI(() => SkylineWindow.sortProteinsByNameToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByAccession:
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YFL038C";
RunUI(() => SkylineWindow.sortProteinsByAccessionToolStripMenuItem_Click(null, null));
break;
case ProteinMetadataManager.ProteinDisplayMode.ByPreferredName:
RunUI(() => SkylineWindow.sortProteinsByPreferredNameToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YAL016W";
break;
case ProteinMetadataManager.ProteinDisplayMode.ByGene:
RunUI(() => SkylineWindow.sortProteinsByGeneToolStripMenuItem_Click(null, null));
expectedTopName = TestSmallMolecules ? "ZZZTESTINGNONPROTEOMICMOLECULEGROUP" : "YGL234W";
break;
}
var actualTopName = WaitForDocumentLoaded().MoleculeGroups.First().Name.ToUpperInvariant();
Assert.AreEqual(expectedTopName, actualTopName);
}
// Now paste in our fake fasta test data, and handle it with our fake webaccess handler
var protdbLoader = SkylineWindow.BackgroundProteomeManager;
protdbLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
var treeLoader = SkylineWindow.ProteinMetadataManager;
treeLoader.FastaImporter = new WebEnabledFastaImporter(new CommonTest.FastaImporterTest.PlaybackProvider());
const int maxEntries = 5;
var fastaText = CommonTest.FastaImporterTest.GetFastaTestText(maxEntries); // Just get the first few
SetClipboardTextUI(fastaText);
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteFastaDlg); // Show the paste dialog
RunDlg <EmptyProteinsDlg>(() => // Anticpate the EmptyProteinsDialog as a side effect
{
pasteDlg.PasteFasta(); // Doing this in pastDlg...
pasteDlg.OkDialog();
},
dlg =>
{
Assert.AreEqual(maxEntries, dlg.EmptyProteins);
dlg.KeepEmptyProteins();
dlg.OkDialog(); // ... will cause EmptyProteinsDlg to pop up, so OK it.
});
// Check that IPI:IPI00197700.1 got an accession number P04638
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals("IPI:IPI00197700.1", pg.Name)));
doc = WaitForDocumentLoaded();
nodeProt = doc.MoleculeGroups.First(pg => Equals("IPI:IPI00197700.1", pg.Name));
Assert.AreEqual("P04638", nodeProt.ProteinMetadata.Accession);
// Now make our fake fasta into a protdb file, and check statement completion against that
const string basename = "fake.fasta";
var protdbPath = TestFilesDir.GetTestPath(basename + ProteomeDb.EXT_PROTDB);
var fastapath = TestFilesDir.GetTestPath(basename);
using (StreamWriter outfile = new StreamWriter(fastapath))
{
outfile.Write(CommonTest.FastaImporterTest.GetFastaTestText()); // write them all
}
BackgroundProteomeTest.CreateBackgroundProteome(protdbPath, basename, fastapath);
doc = WaitForDocumentChange(doc);
// Test for getting accession info from protdb
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "NP_313205";
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals("NP_313205", pg.Name));
Assert.AreEqual("P0A7T9", nodeProt.ProteinMetadata.Accession);
var snapshot = SkylineWindow.Document;
// Test for getting protein from protdb by preferredName
const string uniRef100A5Di11 = "UniRef100_A5DI11";
const string a5Di11 = "A5DI11";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
// ReSharper disable LocalizableElement
sequenceTree.StatementCompletionEditBox.TextBox.Text = "EF2_PICGU"; // PreferredName for UniRef100_A5DI11
// ReSharper restore LocalizableElement
sequenceTree.CommitEditBox(false);
});
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// Paste in some junk and make sure we handle the View Targets By* gracefully
const string badname = "badname";
RunUI(() =>
{
SequenceTree sequenceTree = SkylineWindow.SequenceTree;
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1]; // Select the creation node
sequenceTree.BeginEdit(false);
sequenceTree.StatementCompletionEditBox.TextBox.Text = badname;
sequenceTree.CommitEditBox(false);
});
doc = WaitForDocumentChange(doc);
var nodeText = SkylineWindow.SequenceTree.GetSequenceNodes().Last(n => !SrmDocument.IsSpecialNonProteomicTestDocNode(n.DocNode)).Text;
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, badname); // As in PeptideGroupTreeNode.cs
Assert.AreEqual(failsafe, nodeText);
// Revert those changes, so we can insert another way
Assert.IsTrue(SkylineWindow.SetDocument(snapshot, doc));
WaitForCondition(() => !SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = SkylineWindow.Document;
// Test for pasting accession number in protein paste dialog, and having it populate with correct name
SetClipboardTextUI(a5Di11);
PasteDlg pasteProteinsDlgA = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgA.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgA.PasteProteins();
});
OkDialog(pasteProteinsDlgA, pasteProteinsDlgA.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(uniRef100A5Di11, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(uniRef100A5Di11, pg.Name));
Assert.AreEqual(a5Di11, nodeProt.ProteinMetadata.Accession);
// See what happens when you paste in a gene name shared by a couple of proteins
const string dupeGene = "Apoa2";
const string ipi00197700 = "IPI:IPI00197700.1";
SetClipboardTextUI(dupeGene);
PasteDlg pasteProteinsDlgB = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlgB.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlgB.PasteProteins();
});
OkDialog(pasteProteinsDlgB, pasteProteinsDlgB.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(ipi00197700, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(ipi00197700, pg.Name));
Assert.AreEqual(dupeGene, nodeProt.ProteinMetadata.Gene);
// Test for pasting in protein PasteDlg with sequence and metadata - metadata values are same as DocumentGrid column names
const string pasteProteinName = "Protein";
const string pasteProteinDescription = "Description";
const string pasteProteinAccession = "Accession";
const string pasteProteinPreferredName = "PreferredName";
const string pasteProteinGene = "Gene";
const string pasteProteinSpecies = "Species";
var pasteProteinText = String.Join("\t", pasteProteinName, pasteProteinDescription,
"MFEQFDLDSELLASINK IGYTKPTSIQELVIPQAMV", pasteProteinAccession, pasteProteinPreferredName, // Note the whitespace embedded in the sequence - UI should deal with that
pasteProteinGene, pasteProteinSpecies);
SetClipboardTextUI(pasteProteinText);
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var selectedNode = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = selectedNode;
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
WaitForCondition(() => SkylineWindow.Document.MoleculeGroups.Any(pg => Equals(pasteProteinName, pg.Name)));
doc = WaitForDocumentChange(doc);
nodeProt = doc.MoleculeGroups.First(pg => Equals(pasteProteinName, pg.Name));
Assert.AreEqual(pasteProteinAccession, nodeProt.ProteinMetadata.Accession);
// Verify DocumentGrid's use of protein metadata - last line should agree with var pasteProteinText
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Proteins));
WaitForCondition(() => (documentGrid.RowCount > 0)); // Let it initialize
foreach (var colName in new[]
{
pasteProteinAccession,
pasteProteinPreferredName,
pasteProteinGene,
pasteProteinSpecies
})
{ // Column content should match column name, for pasteProteinText as input
string value = null;
string name = colName;
RunUI(() =>
{
var col = documentGrid.FindColumn(PropertyPath.Parse(name));
value =
documentGrid.DataGridView.Rows[documentGrid.RowCount - 1].Cells[col.Index].Value.ToString();
});
Assert.AreEqual(colName, value);
}
}
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));
}