// creates dictionary of a protein to a list of peptides that match
private void FindProteinMatchesWithFasta(Stream fastaFile)
{
var proteinAssociations = new List <KeyValuePair <FastaSequence, List <PeptideDocNode> > >();
var peptidesForMatching = ListPeptidesForMatching();
using (var reader = new StreamReader(fastaFile))
{
foreach (var seq in FastaData.ParseFastaFile(reader))
{
var fasta = new FastaSequence(seq.Name, null, null, seq.Sequence);
var matches = new List <PeptideDocNode>();
foreach (var peptide in peptidesForMatching)
{
// TODO(yuval): does digest matter?
if (fasta.Sequence.IndexOf(peptide.Peptide.Target.Sequence, StringComparison.Ordinal) < 0)
{
continue;
}
matches.Add(peptide);
}
if (matches.Count > 0)
{
proteinAssociations.Add(new KeyValuePair <FastaSequence, List <PeptideDocNode> >(fasta, matches));
}
}
}
SetCheckBoxListItems(proteinAssociations,
Resources.AssociateProteinsDlg_FindProteinMatchesWithFasta_No_matches_were_found_using_the_imported_fasta_file_);
}
/// <summary>
/// Obtain new names from a FASTA file.
/// </summary>
public void UseFastaFile(string fastaFile)
{
try
{
var dictExistToNewName = new Dictionary <string, string>();
using (var reader = new StreamReader(fastaFile))
{
var dictSeqToNames = new Dictionary <string, List <string> >();
foreach (var nodePepGroup in _document.MoleculeGroups)
{
string sequence = nodePepGroup.PeptideGroup.Sequence;
if (string.IsNullOrEmpty(sequence))
{
continue;
}
List <string> names;
if (!dictSeqToNames.TryGetValue(sequence, out names))
{
names = new List <string>();
dictSeqToNames.Add(sequence, names);
}
if (!names.Contains(nodePepGroup.Name))
{
names.Add(nodePepGroup.Name);
}
}
foreach (var seq in FastaData.ParseFastaFile(reader))
{
List <string> names;
if (dictSeqToNames.TryGetValue(seq.Sequence, out names))
{
// Ignore multiple occurrances of the same sequence in the FASTA file
dictSeqToNames.Remove(seq.Sequence);
foreach (var name in names)
{
if (Equals(name, seq.Name))
{
continue;
}
if (dictExistToNewName.ContainsKey(name))
{
throw new IOException(string.Format(Resources.RenameProteinsDlg_UseFastaFile_The_document_contains_a_naming_conflict_The_name__0__is_currently_used_by_multiple_protein_sequences, name));
}
dictExistToNewName.Add(name, seq.Name);
}
}
}
}
_gridViewDriver.Populate(_document.MoleculeGroups
.Where(nodePepGroup => dictExistToNewName.ContainsKey(nodePepGroup.Name))
.Select(nodePepGroup => new RenameProteins
{
CurrentName = nodePepGroup.Name,
NewName = dictExistToNewName[nodePepGroup.Name]
}));
if (NameCount == 0)
{
MessageDlg.Show(this, string.Format(Resources.RenameProteinsDlg_UseFastaFile_No_protein_sequence_matches_found_between_the_current_document_and_the_FASTA_file__0_,
fastaFile));
}
}
catch (IOException x)
{
MessageDlg.Show(this, string.Format(Resources.RenameProteinsDlg_UseFastaFile_Failed_reading_the_file__0__1__,
fastaFile, x.Message));
}
}
