private static FileRetentionTimeAlignments CalculateFileRetentionTimeAlignments(
string dataFileName, ResultNameMap <IDictionary <Target, double> > libraryRetentionTimes, IProgressMonitor progressMonitor)
{
var targetTimes = libraryRetentionTimes.Find(dataFileName);
if (targetTimes == null)
{
return(null);
}
var alignments = new List <RetentionTimeAlignment>();
foreach (var entry in libraryRetentionTimes)
{
if (dataFileName == entry.Key)
{
continue;
}
var alignedFile = AlignedRetentionTimes.AlignLibraryRetentionTimes(targetTimes, entry.Value, REFINEMENT_THRESHHOLD, RegressionMethodRT.linear, new CustomCancellationToken(CancellationToken.None, () => progressMonitor.IsCanceled));
if (alignedFile == null || alignedFile.RegressionRefinedStatistics == null ||
!RetentionTimeRegression.IsAboveThreshold(alignedFile.RegressionRefinedStatistics.R, REFINEMENT_THRESHHOLD))
{
continue;
}
var regressionLine = alignedFile.RegressionRefined.Conversion as RegressionLineElement;
if (regressionLine != null)
{
alignments.Add(new RetentionTimeAlignment(entry.Key, regressionLine));
}
}
return(new FileRetentionTimeAlignments(dataFileName, alignments));
}
public static ResultNameMap <RetentionTimeSource> ListSourcesForResults(MeasuredResults results, ResultNameMap <RetentionTimeSource> availableSources)
{
if (results == null)
{
return(ResultNameMap <RetentionTimeSource> .EMPTY);
}
var sourcesForResults = results.Chromatograms
.SelectMany(chromatogramSet => chromatogramSet.MSDataFileInfos)
.Select(availableSources.Find);
return(ResultNameMap.FromNamedElements(sourcesForResults.Where(source => null != source)));
}
public static ResultNameMap <RetentionTimeSource> ListAvailableRetentionTimeSources(SrmSettings settings)
{
if (!settings.TransitionSettings.FullScan.IsEnabled)
{
return(ResultNameMap <RetentionTimeSource> .EMPTY);
}
IEnumerable <RetentionTimeSource> sources = new RetentionTimeSource[0];
foreach (var library in settings.PeptideSettings.Libraries.Libraries)
{
if (library == null || !library.IsLoaded)
{
continue;
}
sources = sources.Concat(library.ListRetentionTimeSources());
}
return(ResultNameMap.FromNamedElements(sources));
}
public static ResultNameMap <IDictionary <Target, double> > ReadAllRetentionTimes(SrmDocument document, ResultNameMap <RetentionTimeSource> sources)
{
var allRetentionTimes = new Dictionary <string, IDictionary <Target, double> >();
foreach (var source in sources)
{
var library = document.Settings.PeptideSettings.Libraries.GetLibrary(source.Value.Library);
if (null == library)
{
continue;
}
LibraryRetentionTimes libraryRetentionTimes;
if (!library.TryGetRetentionTimes(MsDataFileUri.Parse(source.Value.Name), out libraryRetentionTimes))
{
continue;
}
allRetentionTimes.Add(source.Key, libraryRetentionTimes.GetFirstRetentionTimes());
}
return(ResultNameMap.FromDictionary(allRetentionTimes));
}
public override void ReadXml(XmlReader reader)
{
if (null != RetentionTimeAlignments)
{
throw new InvalidOperationException();
}
base.ReadXml(reader);
var retentionTimeAlignments = new List <RetentionTimeAlignment>();
if (reader.IsEmptyElement)
{
reader.Read();
}
else
{
// Read past the property element
reader.Read();
reader.ReadElements(retentionTimeAlignments);
reader.ReadEndElement();
}
RetentionTimeAlignments = ResultNameMap.FromNamedElements(retentionTimeAlignments);
}
public void ReadXml(XmlReader reader)
{
if (RetentionTimeSources != null || FileAlignments != null)
{
throw new InvalidOperationException();
}
var sources = new List <RetentionTimeSource>();
var fileAlignments = new List <FileRetentionTimeAlignments>();
if (reader.IsEmptyElement)
{
reader.Read();
}
else
{
reader.Read();
reader.ReadElements(sources);
reader.ReadElements(fileAlignments);
reader.ReadEndElement();
}
RetentionTimeSources = ResultNameMap.FromNamedElements(sources);
FileAlignments = ResultNameMap.FromNamedElements(fileAlignments);
}
public DocumentRetentionTimes(IEnumerable <RetentionTimeSource> sources, IEnumerable <FileRetentionTimeAlignments> fileAlignments)
: this()
{
RetentionTimeSources = ResultNameMap.FromNamedElements(sources);
FileAlignments = ResultNameMap.FromNamedElements(fileAlignments);
}
private static ResultNameMap <string> ResultMapFromStrings(IEnumerable <string> strings)
{
return(ResultNameMap.FromKeyValuePairs(strings.Select(s => new KeyValuePair <string, string>(s, s))));
}
public FileRetentionTimeAlignments(string dataFileName, IEnumerable <RetentionTimeAlignment> alignments) : base(dataFileName)
{
RetentionTimeAlignments = ResultNameMap.FromNamedElements(alignments);
}
private static FileRetentionTimeAlignments CalculateFileRetentionTimeAlignments(
string dataFileName, ResultNameMap<IDictionary<string, double>> libraryRetentionTimes, IProgressMonitor progressMonitor)
{
var targetTimes = libraryRetentionTimes.Find(dataFileName);
if (targetTimes == null)
{
return null;
}
var alignments = new List<RetentionTimeAlignment>();
foreach (var entry in libraryRetentionTimes)
{
if (dataFileName == entry.Key)
{
continue;
}
var alignedFile = AlignedRetentionTimes.AlignLibraryRetentionTimes(targetTimes, entry.Value, REFINEMENT_THRESHHOLD, ()=>progressMonitor.IsCanceled);
if (alignedFile == null || !RetentionTimeRegression.IsAboveThreshold(alignedFile.RegressionRefinedStatistics.R, REFINEMENT_THRESHHOLD))
{
continue;
}
alignments.Add(new RetentionTimeAlignment(entry.Key, alignedFile.RegressionRefined.Conversion));
}
return new FileRetentionTimeAlignments(dataFileName, alignments);
}
public void ReadXml(XmlReader reader)
{
if (RetentionTimeSources != null || FileAlignments != null)
{
throw new InvalidOperationException();
}
var sources = new List<RetentionTimeSource>();
var fileAlignments = new List<FileRetentionTimeAlignments>();
if (reader.IsEmptyElement)
{
reader.Read();
}
else
{
reader.Read();
reader.ReadElements(sources);
reader.ReadElements(fileAlignments);
reader.ReadEndElement();
}
RetentionTimeSources = ResultNameMap.FromNamedElements(sources);
FileAlignments = ResultNameMap.FromNamedElements(fileAlignments);
}
public static ResultNameMap<IDictionary<string, double>> ReadAllRetentionTimes(SrmDocument document, ResultNameMap<RetentionTimeSource> sources)
{
var allRetentionTimes = new Dictionary<string, IDictionary<string, double>>();
foreach (var source in sources)
{
var library = document.Settings.PeptideSettings.Libraries.GetLibrary(source.Value.Library);
if (null == library)
{
continue;
}
LibraryRetentionTimes libraryRetentionTimes;
if (!library.TryGetRetentionTimes(MsDataFileUri.Parse(source.Value.Name), out libraryRetentionTimes))
{
continue;
}
allRetentionTimes.Add(source.Key, libraryRetentionTimes.GetFirstRetentionTimes());
}
return ResultNameMap.FromDictionary(allRetentionTimes);
}
public static ResultNameMap<RetentionTimeSource> ListSourcesForResults(MeasuredResults results, ResultNameMap<RetentionTimeSource> availableSources)
{
if (results == null)
{
return ResultNameMap<RetentionTimeSource>.EMPTY;
}
var sourcesForResults = results.Chromatograms
.SelectMany(chromatogramSet => chromatogramSet.MSDataFileInfos)
.Select(availableSources.Find);
return ResultNameMap.FromNamedElements(sourcesForResults.Where(source => null != source));
}
