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();
}
