public bool ImportResultsFile(MsDataFileUri replicateFile, string replicateName, DateTime? importBefore, DateTime? importOnOrAfter, OptimizableRegression optimize, bool append, bool disableJoining) { if (string.IsNullOrEmpty(replicateName)) replicateName = replicateFile.GetFileNameWithoutExtension(); if(_doc.Settings.HasResults && _doc.Settings.MeasuredResults.ContainsChromatogram(replicateName)) { if (!append) { // CONSIDER: Error? Check if the replicate contains the file? // It does not seem right to just continue on to export a report // or new method without the results added. _out.WriteLine(Resources.CommandLine_ImportResultsFile_Warning__The_replicate__0__already_exists_in_the_given_document_and_the___import_append_option_is_not_specified___The_replicate_will_not_be_added_to_the_document_, replicateName); return true; } // If we are appending to an existing replicate in the document // make sure this file is not already in the replicate. ChromatogramSet chromatogram; int index; _doc.Settings.MeasuredResults.TryGetChromatogramSet(replicateName, out chromatogram, out index); string replicateFileString = replicateFile.ToString(); if (chromatogram.MSDataFilePaths.Any(filePath=>StringComparer.OrdinalIgnoreCase.Equals(filePath, replicateFileString))) { _out.WriteLine(Resources.CommandLine_ImportResultsFile__0______1___Note__The_file_has_already_been_imported__Ignoring___, replicateName, replicateFile); return true; } } return ImportResultsFile(replicateFile, replicateName, importBefore, importOnOrAfter, optimize, disableJoining); }
public double[] GetAlignedRetentionTimes(MsDataFileUri filePath, string peptideSequence, ExplicitMods explicitMods) { string basename = filePath.GetFileNameWithoutExtension(); var fileAlignments = DocumentRetentionTimes.FileAlignments.Find(basename); return GetAlignedRetentionTimes(new RetentionTimeAlignmentIndices(fileAlignments), peptideSequence, explicitMods); }
public double[] GetRetentionTimes(MsDataFileUri filePath, string peptideSequence, ExplicitMods explicitMods, RetentionTimeAlignmentIndex alignmentIndex = null) { string basename = filePath.GetFileNameWithoutExtension(); var source = DocumentRetentionTimes.RetentionTimeSources.Find(basename); if (source == null) { return new double[0]; } var library = PeptideSettings.Libraries.GetLibrary(source.Library); if (library == null) { return new double[0]; } var modifiedSequences = GetTypedSequences(peptideSequence, explicitMods) .Select(typedSequence => typedSequence.ModifiedSequence); int? index = (alignmentIndex != null ? alignmentIndex.FileIndex : null); var times = library.GetRetentionTimesWithSequences(source.Name, modifiedSequences, ref index).ToArray(); if (alignmentIndex != null) alignmentIndex.FileIndex = index; return times; }
public double[] GetRetentionTimesNotAlignedTo(MsDataFileUri fileNotAlignedTo, string peptideSequence, ExplicitMods explicitMods) { var times = new List<double>(); string basename = fileNotAlignedTo.GetFileNameWithoutExtension(); var fileAlignments = DocumentRetentionTimes.FileAlignments.Find(basename); var modifiedSequences = GetTypedSequences(peptideSequence, explicitMods) .Select(typedSequence => typedSequence.ModifiedSequence).ToArray(); foreach (var library in PeptideSettings.Libraries.Libraries) { if (null == library) { continue; } foreach (var source in library.ListRetentionTimeSources()) { if (MeasuredResults.IsBaseNameMatch(source.Name, basename)) { continue; } if (null != fileAlignments) { if (null != fileAlignments.RetentionTimeAlignments.Find(source.Name)) { continue; } } int? indexIgnore = null; times.AddRange(library.GetRetentionTimesWithSequences(source.Name, modifiedSequences, ref indexIgnore)); } } return times.ToArray(); }