/// <summary>
/// Returns candidates for grouping by annotation by the annotation target. (usually replicates)
/// </summary>
public static string[] FindGroupsByTarget(SrmSettings settings, AnnotationDef.AnnotationTarget target)
{
var replicateAnnotations = settings.DataSettings.AnnotationDefs
.Where(annotationDef => annotationDef.AnnotationTargets.Contains(target));
return(replicateAnnotations.Select(a => a.Name).ToArray());
}
public static Type RowTypeFromAnnotationTarget(AnnotationDef.AnnotationTarget annotationTarget)
{
switch (annotationTarget)
{
case AnnotationDef.AnnotationTarget.protein:
return(typeof(Protein));
case AnnotationDef.AnnotationTarget.peptide:
return(typeof(Databinding.Entities.Peptide));
case AnnotationDef.AnnotationTarget.precursor:
return(typeof(Precursor));
case AnnotationDef.AnnotationTarget.transition:
return(typeof(Databinding.Entities.Transition));
case AnnotationDef.AnnotationTarget.replicate:
return(typeof(Replicate));
case AnnotationDef.AnnotationTarget.precursor_result:
return(typeof(PrecursorResult));
case AnnotationDef.AnnotationTarget.transition_result:
return(typeof(TransitionResult));
default:
return(null);
}
}
private Annotations AddAnnotations(Annotations annotations, AnnotationDef.AnnotationTarget annotationTarget)
{
annotations = annotations.ChangeAnnotation("Text", annotationTarget + ":" + _counter++);
if (DocumentAnnotations.NOTE_TARGETS.Contains(annotationTarget))
{
annotations = annotations.ChangeNote("Note" + _counter++);
}
annotations =
annotations.ChangeAnnotation("Number", (_counter++ *.1).ToString(CultureInfo.InvariantCulture));
if (0 != (_elementCount & 2))
{
_counter++;
annotations = annotations.ChangeAnnotation("TrueFalse", "TrueFalse");
}
annotations = annotations.ChangeAnnotation(GetAnnotationTargetName(annotationTarget),
annotationTarget + ":" + _counter++);
return(annotations);
}
/// <summary>
/// Remove annotations from the Annotations object which do not apply to the particular target,
/// or are calculated.
/// Also uses the StringPool to reduce duplicated strings.
/// </summary>
public Annotations ScrubAnnotations(Annotations annotations, AnnotationDef.AnnotationTarget target)
{
if (annotations.IsEmpty)
{
return(annotations);
}
var newAnnotations = annotations.ListAnnotations().AsEnumerable();
if (null != _validAnnotationNames)
{
var validNames = _validAnnotationNames[target];
newAnnotations = newAnnotations.Where(kvp => validNames.Contains(kvp.Key));
}
newAnnotations = newAnnotations.Select(kvp => new KeyValuePair <string, string>(
StringPool.GetString(kvp.Key), kvp.Value));
return(new Annotations(StringPool.GetString(annotations.Note), newAnnotations, annotations.ColorIndex));
}
public AnnotationTargetItem(AnnotationDef.AnnotationTarget annotationTarget, SrmDocument.DOCUMENT_TYPE modeUI)
{
AnnotationTarget = annotationTarget;
ModeUI = modeUI;
}
public AnnotationTargetAttribute(AnnotationDef.AnnotationTarget target)
{
AnnotationTarget = target;
}
private string GetAnnotationTargetName(AnnotationDef.AnnotationTarget annotationTarget)
{
Assert.IsTrue(Enum.IsDefined(typeof(AnnotationDef.AnnotationTarget), annotationTarget));
return(annotationTarget.ToString());
}
public AnnotationTargetItem(AnnotationDef.AnnotationTarget annotationTarget)
{
AnnotationTarget = annotationTarget;
}
/// <summary>
/// Gets possible values for an annotation.
/// </summary>
public static string[] GetPossibleAnnotations(SrmSettings settings, string group, AnnotationDef.AnnotationTarget target)
{
var annotation = settings.DataSettings.AnnotationDefs.FirstOrDefault(annotationDef => annotationDef.AnnotationTargets.Contains(target) && annotationDef.Name == group);
if (annotation == null)
{
return(new string[0]);
}
switch (annotation.Type)
{
case AnnotationDef.AnnotationType.text:
case AnnotationDef.AnnotationType.number:
return(settings.MeasuredResults == null ? new string[0] : settings.MeasuredResults.Chromatograms
.Select(c => c.Annotations.GetAnnotation(group)).Distinct().Where(s => s != null).ToArray());
case AnnotationDef.AnnotationType.value_list:
return(annotation.Items.ToArray());
case AnnotationDef.AnnotationType.true_false:
return(new[] { Resources.AnnotationHelper_GetReplicateIndicices_True, Resources.AnnotationHelper_GetReplicateIndicices_False });
default:
return(new string[0]); // Should never happen
}
}
private static void AddAnnotations(Configuration configuration, SrmSettings settings, AnnotationDef.AnnotationTarget annotationTarget, Type persistentClass)
{
var mapping = configuration.GetClassMapping(persistentClass);
foreach (var annotationDef in settings.DataSettings.AnnotationDefs)
{
if (!annotationDef.AnnotationTargets.Contains(annotationTarget))
{
continue;
}
string columnName = AnnotationDef.GetColumnName(annotationDef.Name);
Type accessorType;
switch (annotationDef.Type)
{
case AnnotationDef.AnnotationType.number:
accessorType = typeof(NumberAnnotationPropertyAccessor);
break;
case AnnotationDef.AnnotationType.true_false:
accessorType = typeof(BoolAnnotationPropertyAccessor);
break;
default:
accessorType = typeof(AnnotationPropertyAccessor);
break;
}
AddColumn(mapping, columnName, accessorType);
}
}
