public static SrmDocument RecalculateAlignments(SrmDocument document, IProgressMonitor progressMonitor)
{
var newSources = ListAvailableRetentionTimeSources(document.Settings);
var newResultsSources = ListSourcesForResults(document.Settings.MeasuredResults, newSources);
var allLibraryRetentionTimes = ReadAllRetentionTimes(document, newSources);
var newFileAlignments = new List <FileRetentionTimeAlignments>();
IProgressStatus progressStatus = new ProgressStatus(@"Aligning retention times"); // CONSIDER: localize? Will users see this?
foreach (var retentionTimeSource in newResultsSources.Values)
{
progressStatus = progressStatus.ChangePercentComplete(100 * newFileAlignments.Count / newResultsSources.Count);
progressMonitor.UpdateProgress(progressStatus);
try
{
var fileAlignments = CalculateFileRetentionTimeAlignments(retentionTimeSource.Name, allLibraryRetentionTimes, progressMonitor);
newFileAlignments.Add(fileAlignments);
}
catch (OperationCanceledException)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return(null);
}
}
var newDocRt = new DocumentRetentionTimes(newSources.Values, newFileAlignments);
var newDocument = document.ChangeSettings(document.Settings.ChangeDocumentRetentionTimes(newDocRt));
Debug.Assert(IsLoaded(newDocument));
progressMonitor.UpdateProgress(progressStatus.Complete());
return(newDocument);
}
public bool Equals(DocumentRetentionTimes other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Equals(other.RetentionTimeSources, RetentionTimeSources) &&
Equals(other.FileAlignments, FileAlignments));
}
public void TestSettings()
{
var settings = SrmSettingsList.GetDefault();
var documentRetentionTimes =
new DocumentRetentionTimes(
new[] {new RetentionTimeSource("foo", "fooLibrary"), },
new[] {new FileRetentionTimeAlignments("foo", new RetentionTimeAlignment[0])}
);
var settings2 = settings.ChangeDocumentRetentionTimes(documentRetentionTimes);
Assert.AreNotEqual(settings, settings2);
Assert.AreEqual(documentRetentionTimes, settings2.DocumentRetentionTimes);
var settings3 =
settings2.ChangeDataSettings(new DataSettings(new[]{new AnnotationDef("foo", AnnotationDef.AnnotationTargetSet.Singleton(AnnotationDef.AnnotationTarget.transition_result), AnnotationDef.AnnotationType.true_false, new string[0])}));
Assert.AreNotEqual(settings2, settings3);
Assert.AreEqual(settings2.DocumentRetentionTimes, settings3.DocumentRetentionTimes);
Assert.AreNotEqual(settings.DocumentRetentionTimes, settings3.DocumentRetentionTimes);
}
protected override bool LoadBackground(IDocumentContainer container, SrmDocument document, SrmDocument docCurrent)
{
SrmDocument docNew, docOrig;
do
{
docOrig = container.Document;
var loadMonitor = new LoadMonitor(this, container, docOrig);
docNew = DocumentRetentionTimes.RecalculateAlignments(docOrig, loadMonitor);
if (null == docNew)
{
EndProcessing(docOrig);
return(false);
}
}while (!CompleteProcessing(container, docNew, docOrig));
return(true);
}
public SrmSettings ChangeDocumentRetentionTimes(DocumentRetentionTimes prop)
{
return ChangeProp(ImClone(this), im => im.DocumentRetentionTimes = prop);
}
public SrmSettings(string name, PeptideSettings peptideSettings, TransitionSettings transitionSettings, DataSettings dataSettings, DocumentRetentionTimes documentRetentionTimes)
: base(name)
{
PeptideSettings = peptideSettings;
TransitionSettings = transitionSettings;
DataSettings = dataSettings;
DocumentRetentionTimes = documentRetentionTimes;
// Create cached calculator instances
CreatePrecursorMassCalcs();
CreateFragmentMassCalcs();
}
protected override string IsNotLoadedExplained(SrmDocument document)
{
return(DocumentRetentionTimes.IsNotLoadedExplained(document));
}
public bool Equals(DocumentRetentionTimes other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other.RetentionTimeSources, RetentionTimeSources) &&
Equals(other.FileAlignments, FileAlignments);
}
public static SrmDocument RecalculateAlignments(SrmDocument document, IProgressMonitor progressMonitor)
{
var newSources = ListAvailableRetentionTimeSources(document.Settings);
var newResultsSources = ListSourcesForResults(document.Settings.MeasuredResults, newSources);
var allLibraryRetentionTimes = ReadAllRetentionTimes(document, newSources);
var newFileAlignments = new List<FileRetentionTimeAlignments>();
var progressStatus = new ProgressStatus("Aligning retention times"); // Not L10N? Will users see this?
foreach (var retentionTimeSource in newResultsSources.Values)
{
progressStatus = progressStatus.ChangePercentComplete(100*newFileAlignments.Count/newResultsSources.Count);
progressMonitor.UpdateProgress(progressStatus);
try
{
var fileAlignments = CalculateFileRetentionTimeAlignments(retentionTimeSource.Name, allLibraryRetentionTimes, progressMonitor);
newFileAlignments.Add(fileAlignments);
}
catch (OperationCanceledException)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
var newDocRt = new DocumentRetentionTimes(newSources.Values, newFileAlignments);
var newDocument = document.ChangeSettings(document.Settings.ChangeDocumentRetentionTimes(newDocRt));
Debug.Assert(IsLoaded(newDocument));
progressMonitor.UpdateProgress(progressStatus.Complete());
return newDocument;
}
