public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
if (Equals(id.Name, proteinMetadata.Name))
proteinMetadata = proteinMetadata.ChangeName(null); // Make it clear that the name hasn't been altered
if (Equals(id.Description, proteinMetadata.Description))
proteinMetadata = proteinMetadata.ChangeDescription(null); // Make it clear that the description hasn't been altered
_proteinMetadata = proteinMetadata;
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
if (Equals(id.Name, proteinMetadata.Name))
{
proteinMetadata = proteinMetadata.ChangeName(null); // Make it clear that the name hasn't been altered
}
if (Equals(id.Description, proteinMetadata.Description))
{
proteinMetadata = proteinMetadata.ChangeDescription(null); // Make it clear that the description hasn't been altered
}
_proteinMetadata = proteinMetadata;
}
private SrmDocument AddProteins(SrmDocument document, ref IdentityPath selectedPath)
{
if (tabControl1.SelectedTab != tabPageProteinList)
return document;
var backgroundProteome = GetBackgroundProteome(document);
for (int i = gridViewProteins.Rows.Count - 1; i >= 0; i--)
{
var row = gridViewProteins.Rows[i];
var proteinName = Convert.ToString(row.Cells[colProteinName.Index].Value);
if (String.IsNullOrEmpty(proteinName))
{
continue;
}
var pastedMetadata = new ProteinMetadata(proteinName,
Convert.ToString(row.Cells[colProteinDescription.Index].Value),
NullForEmpty(Convert.ToString(row.Cells[colProteinPreferredName.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinAccession.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinGene.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinSpecies.Index].Value)));
FastaSequence fastaSequence = null;
if (!backgroundProteome.IsNone)
{
ProteinMetadata protdbMetadata;
fastaSequence = backgroundProteome.GetFastaSequence(proteinName, out protdbMetadata);
// Fill in any gaps in pasted metadata with that in protdb
pastedMetadata = pastedMetadata.Merge(protdbMetadata);
}
// Strip any whitespace (tab, newline etc) In case it was copied out of a FASTA file
var fastaSequenceString = new string(Convert.ToString(row.Cells[colProteinSequence.Index].Value).Where(c => !Char.IsWhiteSpace(c)).ToArray());
if (!string.IsNullOrEmpty(fastaSequenceString))
{
try
{
if (fastaSequence == null) // Didn't match anything in protdb
{
fastaSequence = new FastaSequence(pastedMetadata.Name, pastedMetadata.Description,
new ProteinMetadata[0], fastaSequenceString);
}
else
{
if (fastaSequence.Sequence != fastaSequenceString)
{
fastaSequence = new FastaSequence(pastedMetadata.Name, pastedMetadata.Description,
fastaSequence.Alternatives, fastaSequenceString);
}
}
}
catch (Exception exception)
{
ShowProteinError(new PasteError
{
Line = i,
Column = colProteinDescription.Index,
Message = string.Format(Resources.PasteDlg_AddProteins_Invalid_protein_sequence__0__, exception.Message)
});
return null;
}
}
if (fastaSequence == null)
{
ShowProteinError(
new PasteError
{
Line = i,
Message = backgroundProteome.IsNone
? Resources.PasteDlg_AddProteins_Missing_protein_sequence
: Resources.PasteDlg_AddProteins_This_protein_was_not_found_in_the_background_proteome_database
});
return null;
}
var description = pastedMetadata.Description;
if (!string.IsNullOrEmpty(description) && description != fastaSequence.Description)
{
fastaSequence = new FastaSequence(fastaSequence.Name, description, fastaSequence.Alternatives, fastaSequence.Sequence);
}
pastedMetadata = pastedMetadata.ChangeName(fastaSequence.Name).ChangeDescription(fastaSequence.Description); // Make sure these agree
var nodeGroupPep = new PeptideGroupDocNode(fastaSequence, pastedMetadata, new PeptideDocNode[0]);
nodeGroupPep = nodeGroupPep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
var to = selectedPath;
if (to == null || to.Depth < (int)SrmDocument.Level.MoleculeGroups)
document = (SrmDocument)document.Add(nodeGroupPep);
else
{
Identity toId = selectedPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups);
document = (SrmDocument)document.Insert(toId, nodeGroupPep);
}
selectedPath = new IdentityPath(nodeGroupPep.Id);
}
return document;
}
public PeptideGroupDocNode ChangeName(string name)
{
var newMetadata = _proteinMetadata.ChangeName(name);
return(ChangeProteinMetadata(newMetadata));
}