public PeptideDocNode UpdateMolecule(IdentityPath parent, PeptideDocNode peptideDocNode)
{
CheckCancelled();
AnnotationUpdater updater;
_annotationUpdaters.TryGetValue(AnnotationDef.AnnotationTarget.peptide, out updater);
var identityPath = new IdentityPath(parent, peptideDocNode.Peptide);
if (updater != null)
{
var peptide = new Databinding.Entities.Peptide(SkylineDataSchema, new IdentityPath(parent, peptideDocNode.Peptide));
var annotations = updater.UpdateAnnotations(peptideDocNode.Annotations, peptide);
if (!Equals(annotations, peptideDocNode.Annotations))
{
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeAnnotations(annotations);
}
}
if (!RecursePrecursors)
{
return(peptideDocNode);
}
var newChildren = peptideDocNode.TransitionGroups.Select(tg => UpdatePrecursor(identityPath, tg)).ToArray();
if (!ArrayUtil.ReferencesEqual(peptideDocNode.Children, newChildren))
{
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren);
}
return(peptideDocNode);
}
public static string GetRowDisplayText(Protein protein, Databinding.Entities.Peptide peptide)
{
var proteomic = protein.DocNode.IsProteomic;
if (peptide != null)
{
return(proteomic ? peptide.Sequence : peptide.MoleculeName);
}
else
{
return(proteomic ? ProteinMetadataManager.ProteinModalDisplayText(protein.DocNode) : protein.Name);
}
}
public bool Matches(SrmDocument document, Protein protein, Databinding.Entities.Peptide peptide, FoldChangeResult foldChangeResult, CutoffSettings cutoffSettings)
{
foreach (var match in matchOptions)
{
switch (match)
{
case MatchOption.ProteinName:
case MatchOption.ProteinAccession:
case MatchOption.ProteinPreferredName:
case MatchOption.ProteinGene:
case MatchOption.PeptideSequence:
case MatchOption.PeptideModifiedSequence:
case MatchOption.MoleculeGroupName:
case MatchOption.MoleculeName:
case MatchOption.CAS:
case MatchOption.HMDB:
case MatchOption.InChiKey:
{
var matchString = GetMatchString(document, protein, peptide);
if (matchString == null || !Regex.IsMatch(matchString, RegExpr))
{
return(false);
}
break;
}
case MatchOption.BelowLeftCutoff:
{
if (!cutoffSettings.FoldChangeCutoffValid || foldChangeResult.Log2FoldChange >= -cutoffSettings.Log2FoldChangeCutoff)
{
return(false);
}
break;
}
case MatchOption.AboveRightCutoff:
{
if (!cutoffSettings.FoldChangeCutoffValid || foldChangeResult.Log2FoldChange <= cutoffSettings.Log2FoldChangeCutoff)
{
return(false);
}
break;
}
case MatchOption.BelowPValueCutoff:
{
if (!cutoffSettings.PValueCutoffValid || foldChangeResult.AdjustedPValue <= Math.Pow(10, -cutoffSettings.PValueCutoff))
{
return(false);
}
break;
}
case MatchOption.AbovePValueCutoff:
{
if (!cutoffSettings.PValueCutoffValid || foldChangeResult.AdjustedPValue >= Math.Pow(10, -cutoffSettings.PValueCutoff))
{
return(false);
}
break;
}
}
}
return(true);
}
public string GetMatchString(SrmDocument document, Protein protein, Databinding.Entities.Peptide peptide)
{
if (protein == null)
{
return(null);
}
var perProtein = peptide == null;
foreach (var m in matchOptions)
{
switch (m)
{
case MatchOption.ProteinName:
case MatchOption.ProteinAccession:
case MatchOption.ProteinPreferredName:
case MatchOption.ProteinGene:
return(GetProteinText(protein, MatchOptionToDisplayMode(m)));
case MatchOption.PeptideSequence:
if (!perProtein)
{
return(peptide.Sequence);
}
break;
case MatchOption.PeptideModifiedSequence:
if (!perProtein)
{
return(peptide.ModifiedSequence.ToString());
}
break;
case MatchOption.MoleculeGroupName:
return(protein.Name);
case MatchOption.MoleculeName:
if (!perProtein)
{
return(peptide.MoleculeName);
}
break;
case MatchOption.CAS:
if (!perProtein)
{
return(peptide.CAS);
}
break;
case MatchOption.HMDB:
if (!perProtein)
{
return(peptide.HMDB);
}
break;
case MatchOption.InChiKey:
if (!perProtein)
{
return(peptide.InChiKey);
}
break;
}
}
if (protein.DocNode.IsProteomic)
{
return(GetRowDisplayText(protein, peptide));
}
return(perProtein ? protein.Name : peptide.MoleculeName);
}
public string GetMatchString(SrmDocument document, Protein protein, Databinding.Entities.Peptide peptide)
{
return(GetRowString(document, protein, peptide, false));
}
private string GetRowString(SrmDocument document, Protein protein, Databinding.Entities.Peptide peptide,
bool showProteinForPeptides)
{
if (protein == null)
{
return(null);
}
var perProtein = peptide == null;
foreach (var m in matchOptions)
{
switch (m)
{
case MatchOption.ProteinName:
case MatchOption.ProteinAccession:
case MatchOption.ProteinPreferredName:
case MatchOption.ProteinGene:
if (!perProtein && showProteinForPeptides)
{
return(string.Format(@"{0} ({1})", GetRowDisplayText(protein, peptide),
GetProteinText(protein, m)));
}
return(GetProteinText(protein, m));
case MatchOption.PeptideSequence:
if (!perProtein)
{
return(peptide.Sequence);
}
break;
case MatchOption.PeptideModifiedSequence:
if (!perProtein)
{
return(peptide.ModifiedSequence.ToString());
}
break;
case MatchOption.MoleculeGroupName:
return(protein.Name);
case MatchOption.MoleculeName:
if (!perProtein)
{
return(peptide.MoleculeName);
}
break;
case MatchOption.CAS:
if (!perProtein)
{
return(peptide.CAS);
}
break;
case MatchOption.HMDB:
if (!perProtein)
{
return(peptide.HMDB);
}
break;
case MatchOption.InChiKey:
if (!perProtein)
{
return(peptide.InChiKey);
}
break;
}
}
return(GetRowDisplayText(protein, peptide));
}
public string GetDisplayString(SrmDocument document, Protein protein, Databinding.Entities.Peptide peptide)
{
return(GetRowString(document, protein, peptide, true));
}
