public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out List <PeptideGroupDocNode> peptideGroupsNew)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
peptideGroupsNew = importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)).ToList();
document = document.AddPeptideGroups(peptideGroupsNew, false, to, out firstAdded, out nextAdd);
}
return(document);
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out int emptyProteinCount)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
document = document.AddPeptideGroups(importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)),
false, null, out firstAdded, out nextAdd);
}
emptyProteinCount = importer.EmptyPeptideGroupCount;
return(document);
}
public void ThermoMixedPeptidesTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument docMixed = InitMixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
SrmDocument docUnmixed = InitUnmixedDocument(testFilesDir, out docPath);
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
string extRaw = ExtensionTestContext.ExtThermoRaw;
var listChromatograms = new List <ChromatogramSet>
{
new ChromatogramSet("rep03", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_03" + extRaw))
}),
new ChromatogramSet("rep05", new[]
{
MsDataFileUri.Parse(testFilesDir.GetTestPath(
"Site20_STUDY9P_PHASEII_QC_05" + extRaw))
})
};
var docResults = docMixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerMixed = new ResultsTestDocumentContainer(docMixed, docPath);
Assert.IsTrue(docContainerMixed.SetDocument(docResults, docMixed, true));
docContainerMixed.AssertComplete();
docMixed = docContainerMixed.Document;
SrmDocument docMixedUnmixed = (SrmDocument)docMixed.ChangeChildren(new DocNode[0]);
IdentityPath tempPath;
docMixedUnmixed = docMixedUnmixed.AddPeptideGroups(docUnmixed.PeptideGroups, true, IdentityPath.ROOT,
out tempPath, out tempPath);
docResults = docUnmixed.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
var docContainerUnmixed = new ResultsTestDocumentContainer(docUnmixed, docPath);
Assert.IsTrue(docContainerUnmixed.SetDocument(docResults, docUnmixed, true));
docContainerUnmixed.AssertComplete();
docUnmixed = docContainerUnmixed.Document;
AssertEx.DocumentCloned(docMixedUnmixed, docUnmixed);
docContainerMixed.Release();
docContainerUnmixed.Release();
}
public SrmDocument AddFasta(SrmDocument document, ref IdentityPath selectedPath, out int emptyPeptideGroups)
{
emptyPeptideGroups = 0;
var text = TbxFasta.Text;
if (text.Length == 0)
{
return document;
}
if (!text.StartsWith(">")) // Not L10N
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_This_must_start_with____,
Column = 0,
Length = 1,
Line = 0,
});
return null;
}
string[] lines = text.Split('\n');
int lastNameLine = -1;
int aa = 0;
for (int i = 0; i < lines.Length; i++)
{
string line = lines[i];
if (line.StartsWith(">")) // Not L10N
{
if (line.Trim().Length == 1)
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_There_is_no_name_for_this_protein,
Column = 0,
Line = i,
Length = 1
});
return null;
}
if (!CheckSequence(aa, lastNameLine, lines))
return null;
lastNameLine = i;
aa = 0;
continue;
}
for (int column = 0; column < line.Length; column++)
{
char c = line[column];
if (AminoAcid.IsExAA(c))
aa++;
else if (!Char.IsWhiteSpace(c) && c != '*')
{
ShowFastaError(new PasteError
{
Message =
String.Format(Resources.ImportFastaHelper_AddFasta___0___is_not_a_capital_letter_that_corresponds_to_an_amino_acid_, c),
Column = column,
Line = i,
Length = 1,
});
return null;
}
}
}
if (!CheckSequence(aa, lastNameLine, lines))
return null;
var importer = new FastaImporter(document, false);
try
{
var reader = new StringReader(TbxFasta.Text);
IdentityPath to = selectedPath;
IdentityPath firstAdded, nextAdd;
// TODO: support long-wait broker
document = document.AddPeptideGroups(importer.Import(reader, null, -1), false,
to, out firstAdded, out nextAdd);
emptyPeptideGroups = importer.EmptyPeptideGroupCount;
selectedPath = firstAdded;
}
catch (Exception exception)
{
ShowFastaError(new PasteError
{
Message = Resources.ImportFastaHelper_AddFasta_An_unexpected_error_occurred__ + exception.Message + " (" + exception.GetType() + ")" // Not L10N
});
return null;
}
return document;
}
private SrmDocument AddTransitionList(SrmDocument document, ref IdentityPath selectedPath)
{
if (tabControl1.SelectedTab != tabPageTransitionList)
return document;
if (IsMolecule)
{
// Save the current column order to settings
var active = new List<string>();
for (int order = 0; order < gridViewTransitionList.Columns.Count; order++)
{
for (int gridcol = 0; gridcol < gridViewTransitionList.Columns.Count; gridcol++)
{
var dataGridViewColumn = gridViewTransitionList.Columns[gridcol];
if (dataGridViewColumn.DisplayIndex == order)
{
if (dataGridViewColumn.Visible)
active.Add(dataGridViewColumn.Name);
break;
}
}
}
Settings.Default.CustomMoleculeTransitionInsertColumnsList = active;
// We will accept a completely empty product list as meaning
// "these are all precursor transitions"
var requireProductInfo = false;
for (var i = 0; i < gridViewTransitionList.RowCount - 1; i++)
{
var row = gridViewTransitionList.Rows[i];
var productMz = row.Cells[INDEX_PRODUCT_MZ].Value;
var productFormula = row.Cells[INDEX_PRODUCT_FORMULA].Value;
var productCharge = row.Cells[INDEX_PRODUCT_CHARGE].Value;
if ((productMz != null && productMz.ToString().Length > 0) ||
(productFormula != null && productFormula.ToString().Length > 0) ||
(productCharge != null && productCharge.ToString().Length > 0))
{
requireProductInfo = true; // Product list is not completely empty
break;
}
}
// For each row in the grid, add to or begin MoleculeGroup|Molecule|TransitionList tree
for(int i = 0; i < gridViewTransitionList.RowCount - 1; i ++)
{
DataGridViewRow row = gridViewTransitionList.Rows[i];
var precursor = ReadPrecursorOrProductColumns(document, row, true); // Get molecule values
if (precursor == null)
return null;
if (requireProductInfo && ReadPrecursorOrProductColumns(document, row, false) == null)
{
return null;
}
var charge = precursor.Charge;
var precursorMonoMz = BioMassCalc.CalculateIonMz(precursor.MonoMass, charge);
var precursorAverageMz = BioMassCalc.CalculateIonMz(precursor.AverageMass, charge);
// Preexisting molecule group?
bool pepGroupFound = false;
foreach (var pepGroup in document.MoleculeGroups)
{
var pathPepGroup = new IdentityPath(pepGroup.Id);
if (Equals(pepGroup.Name, Convert.ToString(row.Cells[INDEX_MOLECULE_GROUP].Value)))
{
// Found a molecule group with the same name - can we find an existing transition group to which we can add a transition?
pepGroupFound = true;
bool pepFound = false;
foreach (var pep in pepGroup.SmallMolecules)
{
var pepPath = new IdentityPath(pathPepGroup, pep.Id);
var ionMonoMz = BioMassCalc.CalculateIonMz(pep.CustomIon.MonoisotopicMass, charge);
var ionAverageMz = BioMassCalc.CalculateIonMz(pep.CustomIon.AverageMass, charge);
// Match existing molecule if same name (if any) and same formula (if any) and similar m/z at the precursor charge
// (we don't just check mass since we don't have a tolerance value for that)
// Or same name If any) and identical formula when stripped of labels
// Or same name, no formula, and different isotope labels
if (Equals(pep.CustomIon.Name, precursor.Name) &&
((Equals(pep.CustomIon.Formula, precursor.Formula) &&
Math.Abs(ionMonoMz - precursorMonoMz) <= document.Settings.TransitionSettings.Instrument.MzMatchTolerance &&
Math.Abs(ionAverageMz - precursorAverageMz) <= document.Settings.TransitionSettings.Instrument.MzMatchTolerance) ||
(!Equals(pep.CustomIon.Formula, precursor.Formula) &&
Equals(pep.CustomIon.UnlabeledFormula, BioMassCalc.MONOISOTOPIC.StripLabelsFromFormula(precursor.Formula))) ||
(string.IsNullOrEmpty(pep.CustomIon.Formula) && string.IsNullOrEmpty(precursor.Formula) &&
!pep.TransitionGroups.Any(t => Equals(t.TransitionGroup.LabelType, precursor.IsotopeLabelType??IsotopeLabelType.light))) ))
{
pepFound = true;
bool tranGroupFound = false;
foreach (var tranGroup in pep.TransitionGroups)
{
var pathGroup = new IdentityPath(pepPath, tranGroup.Id);
if (Math.Abs(tranGroup.PrecursorMz - precursor.Mz) <= document.Settings.TransitionSettings.Instrument.MzMatchTolerance)
{
tranGroupFound = true;
var tranFound = false;
try
{
var tranNode = GetMoleculeTransition(document, row, pep.Peptide, tranGroup.TransitionGroup, requireProductInfo);
if (tranNode == null)
return null;
foreach (var tran in tranGroup.Transitions)
{
if (Equals(tranNode.Transition.CustomIon,tran.Transition.CustomIon))
{
tranFound = true;
break;
}
}
if (!tranFound)
{
document = (SrmDocument) document.Add(pathGroup, tranNode);
}
}
catch (InvalidDataException e)
{
// Some error we didn't catch in the basic checks
ShowTransitionError(new PasteError
{
Column = 0,
Line = row.Index,
Message = e.Message
});
return null;
}
break;
}
}
if (!tranGroupFound)
{
var node = GetMoleculeTransitionGroup(document, row, pep.Peptide, requireProductInfo);
if (node == null)
return null;
document =
(SrmDocument)
document.Add(pepPath, node);
}
break;
}
}
if (!pepFound)
{
var node = GetMoleculePeptide(document, row, pepGroup.PeptideGroup, requireProductInfo);
if (node == null)
return null;
document =
(SrmDocument)
document.Add(pathPepGroup,node);
}
break;
}
}
if (!pepGroupFound)
{
var node = GetMoleculePeptideGroup(document, row, requireProductInfo);
if (node == null)
return null;
IdentityPath first;
IdentityPath next;
document =
document.AddPeptideGroups(new[] {node}, false,null
, out first,out next);
}
}
}
else
{
var backgroundProteome = GetBackgroundProteome(document);
var sbTransitionList = new StringBuilder();
var dictNameSeq = new Dictionary<string, FastaSequence>();
// Add all existing FASTA sequences in the document to the name to seq dictionary
// Including named peptide lists would cause the import code to give matching names
// in this list new names (e.g. with 1, 2, 3 appended). In this code, the names
// are intended to be merged.
foreach (var nodePepGroup in document.Children.Cast<PeptideGroupDocNode>().Where(n => !n.IsPeptideList))
{
if (!dictNameSeq.ContainsKey(nodePepGroup.Name))
dictNameSeq.Add(nodePepGroup.Name, (FastaSequence) nodePepGroup.PeptideGroup);
}
// Check for simple errors and build strings for import
for (int i = 0; i < gridViewTransitionList.Rows.Count; i++)
{
var row = gridViewTransitionList.Rows[i];
var peptideSequence = Convert.ToString(row.Cells[colTransitionPeptide.Index].Value);
var proteinName = Convert.ToString(row.Cells[colTransitionProteinName.Index].Value);
var precursorMzText = Convert.ToString(row.Cells[colTransitionPrecursorMz.Index].Value);
var productMzText = Convert.ToString(row.Cells[colTransitionProductMz.Index].Value);
if (string.IsNullOrEmpty(peptideSequence) && string.IsNullOrEmpty(proteinName))
{
continue;
}
if (string.IsNullOrEmpty(peptideSequence))
{
ShowTransitionError(new PasteError
{
Column = colTransitionPeptide.Index,
Line = i,
Message = Resources.PasteDlg_ListPeptideSequences_The_peptide_sequence_cannot_be_blank
});
return null;
}
if (!FastaSequence.IsExSequence(peptideSequence))
{
ShowTransitionError(new PasteError
{
Column = colTransitionPeptide.Index,
Line = i,
Message = Resources.PasteDlg_ListPeptideSequences_This_peptide_sequence_contains_invalid_characters
});
return null;
}
double mz;
if (!double.TryParse(precursorMzText, out mz))
{
ShowTransitionError(new PasteError
{
Column = colTransitionPrecursorMz.Index,
Line = i,
Message = Resources.PasteDlg_AddTransitionList_The_precursor_m_z_must_be_a_number_
});
return null;
}
if (!double.TryParse(productMzText, out mz))
{
ShowTransitionError(new PasteError
{
Column = colTransitionProductMz.Index,
Line = i,
Message = Resources.PasteDlg_AddTransitionList_The_product_m_z_must_be_a_number_
});
return null;
}
const char sep = TRANSITION_LIST_SEPARATOR;
// Add columns in order specified by TRANSITION_LIST_COL_INDICES
sbTransitionList
.Append(proteinName).Append(sep)
.Append(peptideSequence).Append(sep)
.Append(precursorMzText).Append(sep)
.Append(productMzText).AppendLine();
// Build FASTA sequence text in cases where it is known
if (!dictNameSeq.ContainsKey(proteinName))
{
var fastaSeq = backgroundProteome.GetFastaSequence(proteinName);
if (fastaSeq != null)
dictNameSeq.Add(proteinName, fastaSeq);
}
}
if (sbTransitionList.Length == 0)
return document;
// Do the actual import into PeptideGroupDocNodes
IEnumerable<PeptideGroupDocNode> peptideGroupDocNodes;
try
{
List<TransitionImportErrorInfo> errorList;
List<MeasuredRetentionTime> irtPeptides;
List<SpectrumMzInfo> librarySpectra;
var inputs = new MassListInputs(sbTransitionList.ToString(), LocalizationHelper.CurrentCulture, TRANSITION_LIST_SEPARATOR);
var importer = new MassListImporter(document, inputs);
// TODO: support long-wait broker
peptideGroupDocNodes = importer.Import(null,
TRANSITION_LIST_COL_INDICES,
dictNameSeq,
out irtPeptides,
out librarySpectra,
out errorList);
if (errorList.Any())
{
var firstError = errorList[0];
if (firstError.Row.HasValue)
{
throw new LineColNumberedIoException(firstError.ErrorMessage, firstError.Row.Value, firstError.Column ?? -1);
}
else
{
throw new InvalidDataException(firstError.ErrorMessage);
}
}
}
catch (LineColNumberedIoException x)
{
var columns = new[]
{
colTransitionProteinName,
colPeptideSequence,
colTransitionPrecursorMz,
colTransitionProductMz
};
ShowTransitionError(new PasteError
{
Column = x.ColumnIndex >= 0 ? columns[x.ColumnIndex].Index : 0,
Line = (int) x.LineNumber - 1,
Message = x.PlainMessage
});
return null;
}
catch (InvalidDataException x)
{
ShowTransitionError(new PasteError
{
Message = x.Message
});
return null;
}
// Insert the resulting nodes into the document tree, merging when possible
bool after = false;
foreach (var nodePepGroup in peptideGroupDocNodes)
{
PeptideGroupDocNode nodePepGroupExist = FindPeptideGroupDocNode(document, nodePepGroup);
if (nodePepGroupExist != null)
{
var nodePepGroupNew = nodePepGroupExist.Merge(nodePepGroup);
if (!ReferenceEquals(nodePepGroupExist, nodePepGroupNew))
document = (SrmDocument) document.ReplaceChild(nodePepGroupNew);
}
else
{
// Add to the end, if no insert node
var to = selectedPath;
if (to == null || to.Depth < (int) SrmDocument.Level.MoleculeGroups)
document = (SrmDocument) document.Add(nodePepGroup);
else
{
Identity toId = selectedPath.GetIdentity((int) SrmDocument.Level.MoleculeGroups);
document = (SrmDocument) document.Insert(toId, nodePepGroup, after);
}
selectedPath = new IdentityPath(nodePepGroup.Id);
// All future insertions should be after, to avoid reversing the list
after = true;
}
}
}
return document;
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] { MATCHER.GetModifiedNode(STR_MOD_BY_NAME) }) }, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList <string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList <string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.AllHeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List <string> {
STR_MOD_BY_NAME
}, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException <FormatException>(() => UpdateMatcher(new[] { OXIDATION_M_C_TERM }, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] { LABEL15_N }, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { MET_OX_ROUNDED }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List <StaticMod> {
LABEL15_N
});
var peptideMods = new PeptideModifications(new List <StaticMod>(), new List <TypedModifications> {
typedMod
});
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList <string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList <string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add(LABEL15_N);
MATCHER.CreateMatches(settingsMultiLabel, new List <string> {
STR_HEAVY_15_F
}, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] { MATCHER.GetModifiedNode(STR_HEAVY_15_F) }) }, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications.ChangeHasHeavyModifications(false),
settingsNew.ChangeHasHeavyModifications(false));
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
using (var modMatchDocContainer = InitMatchDocContainer(testDir))
{
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17 &&
match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx) &&
match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection <PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
var listPeptides = new List <PeptideDocNode>();
var hasSmallMolecules = false;
foreach (var match in listMatches)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return(document);
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
hasSmallMolecules |= !match.NodePep.IsProteomic;
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
var nodeName = hasSmallMolecules
? Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Molecules
: Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides;
var nodePepGroupNew = FindPeptideGroupDocNode(document, nodeName);
if (nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode)nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
return((SrmDocument)document.ReplaceChild(nodePepGroupNew));
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
nodeName,
string.Empty, listPeptides.ToArray());
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
return(document);
}
}
/// <summary>
/// Adds all peptides which can be matched to a background proteome to the
/// proteins in the background proteins, and returns a new document with those
/// proteins and peptides added.
/// </summary>
/// <param name="document">The starting document</param>
/// <param name="dictCopy">A dictionary of peptides to peptide matches. All added
/// peptides are removed</param>
/// <param name="broker">For reporting long wait status</param>
/// <param name="toPath">Path to the location in the document to add new items</param>
/// <param name="selectedPath">Path to item in the document that should be selected
/// after this operation is complete</param>
/// <returns>A new document with matching peptides and their proteins addded</returns>
private SrmDocument AddProteomePeptides(SrmDocument document,
Dictionary <PeptideSequenceModKey, PeptideMatch> dictCopy,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Build a list of new PeptideGroupDocNodes to add to the document.
var dictPeptideGroupsNew = new Dictionary <string, PeptideGroupDocNode>();
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = dictCopy.Count;
// Just to make sure this is set
selectedPath = toPath;
foreach (PeptideMatch pepMatch in dictCopy.Values)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = toPath;
return(document);
}
// All peptides with protein get processed in this loop. Peptides
// without proteins get added later.
if (pepMatch.Proteins != null)
{
processedCount++;
}
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
// Peptide should be added to the document,
// unless the NoDuplicates radio was selected and the peptide has more than 1 protein associated with it.
if (pepMatch.Proteins == null ||
(FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.NoDuplicates && pepMatch.Proteins.Count > 1))
{
continue;
}
foreach (ProteinInfo protein in pepMatch.Proteins)
{
// Look for the protein in the document.
string name = protein.ProteinMetadata.Name;
var peptideGroupDocNode = FindPeptideGroupDocNode(document, name);
bool foundInDoc = peptideGroupDocNode != null;
bool foundInList = false;
if (!foundInDoc)
{
// If the protein is not already in the document,
// check to see if we have already created a PeptideGroupDocNode for it.
if (name != null && dictPeptideGroupsNew.TryGetValue(name, out peptideGroupDocNode))
{
foundInList = true;
}
// If not, create a new PeptideGroupDocNode.
else
{
List <ProteinMetadata> alternativeProteins = new List <ProteinMetadata>(protein.Alternatives);
peptideGroupDocNode = new PeptideGroupDocNode(
new FastaSequence(name, protein.ProteinMetadata.Description, alternativeProteins, protein.Sequence),
null, null, new PeptideDocNode[0]);
}
}
// Create a new peptide that matches this protein.
var fastaSequence = peptideGroupDocNode.PeptideGroup as FastaSequence;
var peptideSequence = pepMatch.NodePep.Peptide.Target.Sequence;
// ReSharper disable PossibleNullReferenceException
var begin = fastaSequence.Sequence.IndexOf(peptideSequence, StringComparison.Ordinal);
// ReSharper restore PossibleNullReferenceException
// Create a new PeptideDocNode using this peptide.
var newPeptide = new Peptide(fastaSequence, peptideSequence, begin, begin + peptideSequence.Length,
Settings.PeptideSettings.Enzyme.CountCleavagePoints(peptideSequence));
// Make sure we keep the same children.
PeptideMatch match = pepMatch;
var newNodePep = ((PeptideDocNode) new PeptideDocNode(newPeptide, pepMatch.NodePep.ExplicitMods, pepMatch.NodePep.ExplicitRetentionTime)
.ChangeChildren(pepMatch.NodePep.Children.ToList().ConvertAll(nodeGroup =>
{
// Create copies of the children in order to prevent transition groups with the same
// global indices.
var nodeTranGroup = (TransitionGroupDocNode)nodeGroup;
if (match.Proteins != null && match.Proteins.Count > 1)
{
nodeTranGroup = (TransitionGroupDocNode)nodeTranGroup.CopyId();
nodeTranGroup = (TransitionGroupDocNode)nodeTranGroup.ChangeChildren(
nodeTranGroup.Children.ToList().ConvertAll(nodeTran => nodeTran.CopyId()));
}
return((DocNode)nodeTranGroup);
})).ChangeAutoManageChildren(false)).ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
// If this PeptideDocNode is already a child of the PeptideGroupDocNode,
// ignore it.
if (peptideGroupDocNode.Children.Contains(nodePep => Equals(((PeptideDocNode)nodePep).Key, newNodePep.Key)))
{
Console.WriteLine(Resources.ViewLibraryPepMatching_AddProteomePeptides_Skipping__0__already_present, newNodePep.Peptide.Target);
continue;
}
// Otherwise, add it to the list of children for the PeptideGroupNode.
var newChildren = peptideGroupDocNode.Children.Cast <PeptideDocNode>().ToList();
newChildren.Add(newNodePep);
newChildren.Sort(FastaSequence.ComparePeptides);
// Store modified proteins by global index in a HashSet for second pass.
var newPeptideGroupDocNode = peptideGroupDocNode.ChangeChildren(newChildren.Cast <DocNode>().ToArray())
.ChangeAutoManageChildren(false);
// If the protein was already in the document, replace with the new PeptideGroupDocNode.
if (foundInDoc)
{
document = (SrmDocument)document.ReplaceChild(newPeptideGroupDocNode);
}
// Otherwise, update the list of new PeptideGroupDocNodes to add.
else
{
if (foundInList)
{
dictPeptideGroupsNew.Remove(peptideGroupDocNode.Name);
}
dictPeptideGroupsNew.Add(peptideGroupDocNode.Name, (PeptideGroupDocNode)newPeptideGroupDocNode);
}
// If we are only adding a single node, select it.
if (PeptideMatches.Count == 1)
{
selectedPath = new IdentityPath(new[] { peptideGroupDocNode.Id, newNodePep.Peptide });
}
// If the user only wants to add the first protein found,
// we break the foreach loop after peptide has been added to its first protein.)
if (FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.FirstOccurence)
{
break;
}
}
}
if (dictPeptideGroupsNew.Count == 0)
{
return(document);
}
// Sort the peptides.
var nodePepGroupsSortedChildren = new List <PeptideGroupDocNode>();
foreach (PeptideGroupDocNode nodePepGroup in dictPeptideGroupsNew.Values)
{
var newChildren = nodePepGroup.Children.ToList();
// Have to cast all children to PeptideDocNodes in order to sort.
var newChildrenNodePeps = newChildren.Cast <PeptideDocNode>().ToList();
newChildrenNodePeps.Sort(FastaSequence.ComparePeptides);
nodePepGroupsSortedChildren.Add((PeptideGroupDocNode)
nodePepGroup.ChangeChildren(newChildrenNodePeps.Cast <DocNode>().ToArray()));
}
// Sort the proteins.
nodePepGroupsSortedChildren.Sort((node1, node2) => Comparer <string> .Default.Compare(node1.Name, node2.Name));
IdentityPath selPathTemp = selectedPath, nextAdd;
document = document.AddPeptideGroups(nodePepGroupsSortedChildren, false,
toPath, out selectedPath, out nextAdd);
selectedPath = PeptideMatches.Count == 1 ? selPathTemp : selectedPath;
return(document);
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] {MATCHER.GetModifiedNode(STR_MOD_BY_NAME)})}, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList<string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList<string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.HeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List<string> { STR_MOD_BY_NAME }, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException<FormatException>(() => UpdateMatcher(new[] {OXIDATION_M_C_TERM}, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] {LABEL15_N}, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] {carbC}, null, new[] {MET_OX_ROUNDED}, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List<StaticMod> { LABEL15_N });
var peptideMods = new PeptideModifications(new List<StaticMod>(), new List<TypedModifications> { typedMod });
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList<string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList<string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add( LABEL15_N );
MATCHER.CreateMatches(settingsMultiLabel, new List<string> { STR_HEAVY_15_F }, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] {MATCHER.GetModifiedNode(STR_HEAVY_15_F)})}, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications, settingsNew);
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F});
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
{
var modMatchDocContainer = InitMatchDocContainer(testDir);
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17
&& match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx)
&& match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
/// <summary>
/// Adds all peptides which can be matched to a background proteome to the
/// proteins in the background proteins, and returns a new document with those
/// proteins and peptides added.
/// </summary>
/// <param name="document">The starting document</param>
/// <param name="dictCopy">A dictionary of peptides to peptide matches. All added
/// peptides are removed</param>
/// <param name="broker">For reporting long wait status</param>
/// <param name="toPath">Path to the location in the document to add new items</param>
/// <param name="selectedPath">Path to item in the document that should be selected
/// after this operation is complete</param>
/// <returns>A new document with matching peptides and their proteins addded</returns>
private SrmDocument AddProteomePeptides(SrmDocument document,
Dictionary<PeptideSequenceModKey, PeptideMatch> dictCopy,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Build a list of new PeptideGroupDocNodes to add to the document.
var dictPeptideGroupsNew = new Dictionary<string, PeptideGroupDocNode>();
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = dictCopy.Count;
// Just to make sure this is set
selectedPath = toPath;
foreach (PeptideMatch pepMatch in dictCopy.Values)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = toPath;
return document;
}
// All peptides with protein get processed in this loop. Peptides
// without proteins get added later.
if (pepMatch.Proteins != null)
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
// Peptide should be added to the document,
// unless the NoDuplicates radio was selected and the peptide has more than 1 protein associated with it.
if (pepMatch.Proteins == null ||
(FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.NoDuplicates && pepMatch.Proteins.Count > 1))
continue;
foreach (ProteinInfo protein in pepMatch.Proteins)
{
// Look for the protein in the document.
string name = protein.ProteinMetadata.Name;
var peptideGroupDocNode = FindPeptideGroupDocNode(document, name);
bool foundInDoc = peptideGroupDocNode != null;
bool foundInList = false;
if (!foundInDoc)
{
// If the protein is not already in the document,
// check to see if we have already created a PeptideGroupDocNode for it.
if (dictPeptideGroupsNew.TryGetValue(name, out peptideGroupDocNode))
foundInList = true;
// If not, create a new PeptideGroupDocNode.
else
{
List<ProteinMetadata> alternativeProteins = new List<ProteinMetadata>(protein.Alternatives);
peptideGroupDocNode = new PeptideGroupDocNode(
new FastaSequence(name, protein.ProteinMetadata.Description, alternativeProteins, protein.Sequence),
null, null, new PeptideDocNode[0]);
}
}
// Create a new peptide that matches this protein.
var fastaSequence = peptideGroupDocNode.PeptideGroup as FastaSequence;
var peptideSequence = pepMatch.NodePep.Peptide.Sequence;
// ReSharper disable PossibleNullReferenceException
var begin = fastaSequence.Sequence.IndexOf(peptideSequence, StringComparison.Ordinal);
// ReSharper restore PossibleNullReferenceException
// Create a new PeptideDocNode using this peptide.
var newPeptide = new Peptide(fastaSequence, peptideSequence, begin, begin + peptideSequence.Length,
Settings.PeptideSettings.Enzyme.CountCleavagePoints(peptideSequence));
// Make sure we keep the same children.
PeptideMatch match = pepMatch;
var newNodePep = ((PeptideDocNode) new PeptideDocNode(newPeptide, pepMatch.NodePep.ExplicitMods, pepMatch.NodePep.ExplicitRetentionTime)
.ChangeChildren(pepMatch.NodePep.Children.ToList().ConvertAll(nodeGroup =>
{
// Create copies of the children in order to prevent transition groups with the same
// global indices.
var nodeTranGroup = (TransitionGroupDocNode) nodeGroup;
if(match.Proteins != null && match.Proteins.Count() > 1)
{
nodeTranGroup = (TransitionGroupDocNode) nodeTranGroup.CopyId();
nodeTranGroup = (TransitionGroupDocNode) nodeTranGroup.ChangeChildren(
nodeTranGroup.Children.ToList().ConvertAll(nodeTran => nodeTran.CopyId()));
}
return (DocNode) nodeTranGroup;
})).ChangeAutoManageChildren(false)).ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
// If this PeptideDocNode is already a child of the PeptideGroupDocNode,
// ignore it.
if (peptideGroupDocNode.Children.Contains(nodePep => Equals(((PeptideDocNode) nodePep).Key, newNodePep.Key)))
{
Console.WriteLine(Resources.ViewLibraryPepMatching_AddProteomePeptides_Skipping__0__already_present, newNodePep.Peptide.Sequence);
continue;
}
// Otherwise, add it to the list of children for the PeptideGroupNode.
var newChildren = peptideGroupDocNode.Children.Cast<PeptideDocNode>().ToList();
newChildren.Add(newNodePep);
newChildren.Sort(FastaSequence.ComparePeptides);
// Store modified proteins by global index in a HashSet for second pass.
var newPeptideGroupDocNode = peptideGroupDocNode.ChangeChildren(newChildren.Cast<DocNode>().ToArray())
.ChangeAutoManageChildren(false);
// If the protein was already in the document, replace with the new PeptideGroupDocNode.
if (foundInDoc)
document = (SrmDocument)document.ReplaceChild(newPeptideGroupDocNode);
// Otherwise, update the list of new PeptideGroupDocNodes to add.
else
{
if (foundInList)
dictPeptideGroupsNew.Remove(peptideGroupDocNode.Name);
dictPeptideGroupsNew.Add(peptideGroupDocNode.Name, (PeptideGroupDocNode) newPeptideGroupDocNode);
}
// If we are only adding a single node, select it.
if (PeptideMatches.Count == 1)
selectedPath = new IdentityPath(new[] {peptideGroupDocNode.Id, newNodePep.Peptide});
// If the user only wants to add the first protein found,
// we break the foreach loop after peptide has been added to its first protein.)
if (FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.FirstOccurence)
break;
}
}
if (dictPeptideGroupsNew.Count == 0)
{
return document;
}
// Sort the peptides.
var nodePepGroupsSortedChildren = new List<PeptideGroupDocNode>();
foreach(PeptideGroupDocNode nodePepGroup in dictPeptideGroupsNew.Values)
{
var newChildren = nodePepGroup.Children.ToList();
// Have to cast all children to PeptideDocNodes in order to sort.
var newChildrenNodePeps = newChildren.Cast<PeptideDocNode>().ToList();
newChildrenNodePeps.Sort(FastaSequence.ComparePeptides);
nodePepGroupsSortedChildren.Add((PeptideGroupDocNode)
nodePepGroup.ChangeChildren(newChildrenNodePeps.Cast<DocNode>().ToArray()));
}
// Sort the proteins.
nodePepGroupsSortedChildren.Sort((node1, node2) => Comparer<string>.Default.Compare(node1.Name, node2.Name));
IdentityPath selPathTemp = selectedPath, nextAdd;
document = document.AddPeptideGroups(nodePepGroupsSortedChildren, false,
toPath, out selectedPath, out nextAdd);
selectedPath = PeptideMatches.Count == 1 ? selPathTemp : selectedPath;
return document;
}
private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection<PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
var listPeptides = new List<PeptideDocNode>();
foreach (var match in listMatches)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return document;
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
var nodePepGroupNew = FindPeptideGroupDocNode(document, Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides);
if(nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode) nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeAutoManageChildren(false);
return (SrmDocument) document.ReplaceChild(nodePepGroupNew);
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides,
string.Empty, listPeptides.ToArray());
if (hasVariable)
nodePepGroupNew = (PeptideGroupDocNode) nodePepGroupNew.ChangeAutoManageChildren(false);
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
return document;
}
}
public static SrmDocument ImportFasta(SrmDocument document, string fastaPath, IProgressMonitor monitor,
IdentityPath to, out IdentityPath firstAdded, out IdentityPath nextAdd, out int emptyProteinCount)
{
var importer = new FastaImporter(document, false);
using (TextReader reader = File.OpenText(fastaPath))
{
document = document.AddPeptideGroups(importer.Import(reader, monitor, Helpers.CountLinesInFile(fastaPath)),
false, null, out firstAdded, out nextAdd);
}
emptyProteinCount = importer.EmptyPeptideGroupCount;
return document;
}
private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection <PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
selectedPath = null;
// Some .blib files provide protein accessions (understood as Molecule List Names fro small molecules).
// If those are provided we will use them as node names.
// TODO(bspratt) for now we will do this only for small molecules since it might be a surprise to proteomics users. We should revisit that decision.
foreach (var proteinName in listMatches.Select(m => m.LibInfo.Protein).Distinct())
{
var listPeptides = new List <PeptideDocNode>();
var hasSmallMolecules = false;
foreach (var match in listMatches.Where(m => Equals(proteinName, m.LibInfo.Protein)))
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return(document);
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
hasSmallMolecules |= !match.NodePep.IsProteomic;
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
// If library provides a RefSpectraProteins table, use that to name the group
// TODO(bspratt) for now we will use RefSpectraProteins names only for small molecules
var genericLibraryPeptidesGroupName = hasSmallMolecules
? Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Molecules
: Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides;
var nodeName = string.IsNullOrEmpty(proteinName) ||
listPeptides.Any(p => p.IsProteomic) // TODO(bspratt) revisit this caution-driven decision
? genericLibraryPeptidesGroupName
: proteinName;
var nodePepGroupNew = FindPeptideGroupDocNode(document, nodeName, null);
if (nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode)nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
document = (SrmDocument)document.ReplaceChild(nodePepGroupNew);
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
nodeName,
string.Empty, listPeptides.ToArray());
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
}
}
return(document);
}
