// find matches using the background proteome
public void UseBackgroundProteome()
{
if (_parent.Document.Settings.PeptideSettings.BackgroundProteome.Equals(BackgroundProteome.NONE))
{
MessageDlg.Show(this, Resources.AssociateProteinsDlg_UseBackgroundProteome_No_background_proteome_defined);
return;
}
_isFasta = false;
_fileName = _parent.Document.Settings.PeptideSettings.BackgroundProteome.DatabasePath;
checkBoxListMatches.Items.Clear();
BackgroundProteome proteome = _parent.Document.Settings.PeptideSettings.BackgroundProteome;
var proteinAssociations = new List <KeyValuePair <FastaSequence, List <PeptideDocNode> > >();
var peptidesForMatching = ListPeptidesForMatching();
IDictionary <String, List <Protein> > proteinsWithSequences = null;
using (var longWaitDlg = new LongWaitDlg())
{
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
{
using (var proteomeDb = proteome.OpenProteomeDb(longWaitBroker.CancellationToken))
{
proteinsWithSequences = proteomeDb.GetDigestion()
.GetProteinsWithSequences(peptidesForMatching.Select(pep => pep.Peptide.Target.Sequence));
}
});
}
if (proteinsWithSequences == null)
{
return;
}
HashSet <String> processedProteinSequence = new HashSet <string>();
foreach (var entry in proteinsWithSequences)
{
foreach (var protein in entry.Value)
{
if (!processedProteinSequence.Add(protein.Sequence))
{
continue;
}
var matches = peptidesForMatching.Where(pep => protein.Sequence.Contains(pep.Peptide.Target.Sequence)).ToList();
if (matches.Count == 0)
{
continue;
}
FastaSequence fastaSequence = proteome.MakeFastaSequence(protein);
if (fastaSequence != null)
{
proteinAssociations.Add(new KeyValuePair <FastaSequence, List <PeptideDocNode> >(fastaSequence, matches));
}
}
}
SetCheckBoxListItems(proteinAssociations,
Resources.AssociateProteinsDlg_UseBackgroundProteome_No_matches_were_found_using_the_background_proteome_);
}
public void SetBackgroundProteome(BackgroundProteome backgroundProteome)
{
_backgroundProteome = backgroundProteome;
}
