public TurnoverCalculator GetTurnoverCalculator(string peptideSequence)
{
peptideSequence = Peptide.TrimSequence(peptideSequence);
TurnoverCalculator turnoverCalculator;
if (_turnoverCalculators.TryGetValue(peptideSequence, out turnoverCalculator))
{
return(turnoverCalculator);
}
turnoverCalculator = new TurnoverCalculator(Workspace, peptideSequence);
_turnoverCalculators.Add(peptideSequence, turnoverCalculator);
return(turnoverCalculator);
}
private void dataGridView1_CellContentClick(object sender, DataGridViewCellEventArgs e)
{
if (e.RowIndex < 0)
{
return;
}
var row = dataGridView1.Rows[e.RowIndex];
if (e.ColumnIndex == colPeptide.Index)
{
var peptideSequence = row.Cells[e.ColumnIndex].Value as string;
if (string.IsNullOrEmpty(peptideSequence))
{
return;
}
using (var session = Workspace.OpenSession())
{
var peptideAnalysisIds =
session.CreateQuery(
"SELECT pa.Id FROM DbPeptideAnalysis pa WHERE pa.Peptide.Sequence = :sequence")
.SetParameter("sequence", Peptide.TrimSequence(peptideSequence))
.List();
if (peptideAnalysisIds.Count >= 0)
{
PeptideAnalysisFrame.ShowPeptideAnalysis(
TurnoverForm.Instance.LoadPeptideAnalysis((long)peptideAnalysisIds[0]));
}
}
return;
}
if (e.ColumnIndex == colProteinKey.Index)
{
var halfLifeForm = new HalfLifeForm(Workspace)
{
Peptide = Peptide.TrimSequence(Convert.ToString(row.Cells[colPeptide.Index].Value) ?? ""),
ProteinName = Convert.ToString(row.Cells[colProteinName.Index].Value),
MinScore = double.Parse(tbxMinScore.Text),
};
halfLifeForm.Show(DockPanel, DockState);
}
}
private void AddSearchResults(IList <SearchResult> searchResults, Dictionary <string, DbPeptide> peptides, Dictionary <string, DbMsDataFile> dataFiles)
{
String baseMessage = _message;
if (searchResults == null)
{
return;
}
var dbPeptideSearchResults = GetSearchResults();
var modifiedPeptides = new HashSet <DbPeptide>();
var searchResultsToInsert = new Dictionary <SearchResultKey, DbPeptideSpectrumMatch>();
var searchResultsToUpdate = new Dictionary <SearchResultKey, DbPeptideSpectrumMatch>();
using (var session = Workspace.OpenWriteSession())
{
var statementBuilder = new SqlStatementBuilder(session.GetSessionImplementation().Factory.Dialect);
var dbWorkspace = Workspace.LoadDbWorkspace(session);
session.BeginTransaction();
var newPeptides = new Dictionary <String, Dictionary <String, object> >();
foreach (var searchResult in searchResults)
{
var trimmedSequence = Peptide.TrimSequence(searchResult.Sequence);
if (peptides.ContainsKey(trimmedSequence) || newPeptides.ContainsKey(trimmedSequence))
{
continue;
}
newPeptides.Add(trimmedSequence, new Dictionary <string, object>
{
{ "Sequence", trimmedSequence },
{ "FullSequence", searchResult.Sequence },
{ "Version", 1 },
{ "ValidationStatus", 0 }
});
}
if (newPeptides.Count > 0)
{
long maxPeptideId = (long?)session.CreateQuery("SELECT Max(T.Id) FROM DbPeptide T").UniqueResult() ?? 0;
var insertStatements = new List <String>();
foreach (var dict in newPeptides.Values)
{
insertStatements.Add(statementBuilder.GetInsertStatement("DbPeptide", dict));
}
statementBuilder.ExecuteStatements(session, insertStatements);
var criteria = session.CreateCriteria(typeof(DbPeptide))
.Add(Restrictions.Gt("Id", maxPeptideId));
foreach (DbPeptide dbPeptide in criteria.List())
{
peptides.Add(dbPeptide.Sequence, dbPeptide);
}
}
foreach (var searchResult in searchResults)
{
var trimmedSequence = Peptide.TrimSequence(searchResult.Sequence);
DbPeptide dbPeptide;
if (!peptides.TryGetValue(trimmedSequence, out dbPeptide))
{
// should not happen
continue;
}
if (searchResult.Filename == null)
{
continue;
}
DbMsDataFile dbMsDataFile;
if (!dataFiles.TryGetValue(searchResult.Filename, out dbMsDataFile))
{
dbMsDataFile = new DbMsDataFile
{
Name = searchResult.Filename,
Label = searchResult.Filename,
};
session.Save(dbMsDataFile);
dataFiles.Add(dbMsDataFile.Name, dbMsDataFile);
}
var key = new SearchResultKey(dbMsDataFile, dbPeptide, searchResult.RetentionTime);
DbPeptideSpectrumMatch dbPeptideSpectrumMatch;
if (dbPeptideSearchResults.TryGetValue(key, out dbPeptideSpectrumMatch))
{
bool changed = false;
if (dbPeptideSpectrumMatch.ModifiedSequence == null && searchResult.ModifiedSequence != null)
{
dbPeptideSpectrumMatch.ModifiedSequence = searchResult.ModifiedSequence;
changed = true;
}
if (!dbPeptideSpectrumMatch.PrecursorMz.HasValue && searchResult.PrecursorMz.HasValue)
{
dbPeptideSpectrumMatch.PrecursorMz = searchResult.PrecursorMz;
dbPeptideSpectrumMatch.PrecursorCharge = searchResult.PrecursorCharge;
changed = true;
}
if (!changed)
{
continue;
}
searchResultsToUpdate[key] = dbPeptideSpectrumMatch;
}
else
{
if (!searchResultsToInsert.TryGetValue(key, out dbPeptideSpectrumMatch))
{
dbPeptideSpectrumMatch = new DbPeptideSpectrumMatch
{
MsDataFile = dbMsDataFile,
Peptide = dbPeptide,
RetentionTime = searchResult.RetentionTime,
PrecursorCharge = searchResult.PrecursorCharge,
PrecursorMz = searchResult.PrecursorMz,
ModifiedSequence = searchResult.ModifiedSequence,
};
searchResultsToInsert.Add(key, dbPeptideSpectrumMatch);
if (!newPeptides.ContainsKey(trimmedSequence))
{
modifiedPeptides.Add(dbPeptide);
}
}
}
}
var statements = new List <string>();
foreach (var dbPeptideSearchResult in searchResultsToInsert.Values)
{
statements.Add(statementBuilder.GetInsertStatement("DbPeptideSpectrumMatch",
new Dictionary <string, object> {
{ "MsDataFile", dbPeptideSearchResult.MsDataFile.Id },
{ "Peptide", dbPeptideSearchResult.Peptide.Id },
{ "RetentionTime", dbPeptideSearchResult.RetentionTime },
{ "ModifiedSequence", dbPeptideSearchResult.ModifiedSequence },
{ "PrecursorMz", dbPeptideSearchResult.PrecursorMz },
{ "PrecursorCharge", dbPeptideSearchResult.PrecursorCharge },
{ "Version", 1 },
}));
}
foreach (var dbPeptideSearchResult in searchResultsToUpdate.Values)
{
statements.Add(statementBuilder.GetUpdateStatement("DbPeptideSearchResult",
new Dictionary <string, object> {
{ "RetentionTime", dbPeptideSearchResult.RetentionTime },
{ "ModifiedSequence", dbPeptideSearchResult.ModifiedSequence },
{ "PrecursorMz", dbPeptideSearchResult.PrecursorMz },
{ "PrecursorCharge", dbPeptideSearchResult.PrecursorCharge },
{ "Version", dbPeptideSearchResult.Version + 1 },
},
new Dictionary <string, object> {
{ "Id", dbPeptideSearchResult.Id.GetValueOrDefault() }
}
));
}
statementBuilder.ExecuteStatements(session, statements);
UpdateProgress(baseMessage + "(Committing transaction)", 99);
session.Transaction.Commit();
}
}