public static SrmDocument ApplyRules(SrmDocument document, HashSet <MsDataFileUri> dataFiles, out CommonException <RuleError> error)
{
error = null;
if (!document.Settings.DataSettings.MetadataRuleSets.Any())
{
return(document);
}
try
{
var dataSchema = SkylineDataSchema.MemoryDataSchema(document, DataSchemaLocalizer.INVARIANT);
dataSchema.BeginBatchModifyDocument();
foreach (var ruleSet in document.Settings.DataSettings.MetadataRuleSets)
{
var metadataExtractor = new MetadataExtractor(dataSchema, typeof(ResultFile));
metadataExtractor.ApplyRule(ruleSet, dataFiles);
}
dataSchema.CommitBatchModifyDocument(string.Empty, null);
return(dataSchema.Document);
}
catch (CommonException <RuleError> ex)
{
error = ex;
return(document);
}
}
public static ExportAnnotationSettings AllAnnotations(SrmDocument document)
{
return(EMPTY.ChangeElementTypes(ElementHandler
.GetElementHandlers(SkylineDataSchema.MemoryDataSchema(document, DataSchemaLocalizer.INVARIANT))
.Select(handler => handler.Name))
.ChangeAnnotationNames(
document.Settings.DataSettings.AnnotationDefs.Select(annotationDef => annotationDef.Name))
.ChangePropertyNames(new[] { @"Note" }));
}
public DocumentAnnotationUpdater(SrmDocument document, IProgressMonitor progressMonitor)
{
SkylineDataSchema = SkylineDataSchema.MemoryDataSchema(document, DataSchemaLocalizer.INVARIANT);
_annotationUpdaters = new Dictionary <AnnotationDef.AnnotationTarget, AnnotationUpdater>();
var calculatedAnnotations = document.Settings.DataSettings.AnnotationDefs
.Where(def => null != def.Expression).ToArray();
foreach (AnnotationDef.AnnotationTarget target in Enum.GetValues(typeof(AnnotationDef.AnnotationTarget)))
{
var annotations = ImmutableList.ValueOf(calculatedAnnotations.Where(def => def.AnnotationTargets.Contains(target)));
if (annotations.Count == 0)
{
continue;
}
_annotationUpdaters[target] = new AnnotationUpdater(annotations);
}
AnnotationUpdater transitionResultAnnotationUpdater;
if (_annotationUpdaters.TryGetValue(AnnotationDef.AnnotationTarget.transition_result,
out transitionResultAnnotationUpdater))
{
_transitionResultUpdater = new TransitionResultUpdater
{
AnnotationUpdater = transitionResultAnnotationUpdater,
SkylineDataSchema = SkylineDataSchema
};
}
AnnotationUpdater precursorResultAnnotationUpdater;
if (_annotationUpdaters.TryGetValue(AnnotationDef.AnnotationTarget.precursor_result,
out precursorResultAnnotationUpdater))
{
_precursorResultUpdater = new PrecursorResultUpdater
{
AnnotationUpdater = precursorResultAnnotationUpdater,
SkylineDataSchema = SkylineDataSchema
};
}
RecurseTransitions = _annotationUpdaters.ContainsKey(AnnotationDef.AnnotationTarget.transition) ||
transitionResultAnnotationUpdater != null;
RecursePrecursors =
RecurseTransitions || _annotationUpdaters.ContainsKey(AnnotationDef.AnnotationTarget.precursor) ||
precursorResultAnnotationUpdater != null;
RecurseMolecules =
RecursePrecursors || _annotationUpdaters.ContainsKey(AnnotationDef.AnnotationTarget.peptide);
}
public DocumentAnnotations(SrmDocument document) : this(SkylineDataSchema.MemoryDataSchema(document, SkylineDataSchema.GetLocalizedSchemaLocalizer()))
{
}
public DocumentAnnotations(SrmDocument document) : this(SkylineDataSchema.MemoryDataSchema(document, DataSchemaLocalizer.INVARIANT))
{
}
