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();
}
}
private void DoCreateAnalyses(char[] excludeAas, int minTracerCount)
{
var peptides = new List<DbPeptide>();
bool includeMissingMs2 = cbxIncludeMissingMS2.Checked;
_statusMessage = "Listing peptides";
using (var session = Workspace.OpenWriteSession())
{
session.CreateCriteria(typeof (DbPeptide)).List(peptides);
for (int i = 0; i < peptides.Count(); i++)
{
_statusMessage = "Peptide " + (i + 1) + "/" + peptides.Count;
_progress = 100 * i / peptides.Count;
if (_cancelled)
{
break;
}
var peptide = peptides[i];
if (peptide.Sequence.IndexOfAny(excludeAas) >= 0)
{
continue;
}
if (Workspace.GetMaxTracerCount(peptide.Sequence) < minTracerCount)
{
continue;
}
var dbPeptideAnalysis = (DbPeptideAnalysis) session.CreateCriteria(typeof (DbPeptideAnalysis))
.Add(Restrictions.Eq("Peptide", peptide)).UniqueResult();
if (dbPeptideAnalysis == null)
{
dbPeptideAnalysis = Peptide.CreateDbPeptideAnalysis(session, peptide);
}
var idList = new List<long>();
if (dbPeptideAnalysis.Id.HasValue)
{
var dataFileIdQuery = session.CreateQuery("SELECT A.MsDataFile.Id FROM " + typeof(DbPeptideFileAnalysis) +
" A WHERE A.PeptideAnalysis.Id = :peptideAnalysisId")
.SetParameter("peptideAnalysisId", dbPeptideAnalysis.Id);
dataFileIdQuery.List(idList);
}
var existingDataFileIds = new HashSet<long>(idList);
var psmTimesByDataFileId = peptide.PsmTimesByDataFileId(session);
if (psmTimesByDataFileId.Count == 0)
{
continue;
}
session.BeginTransaction();
bool newAnalysis;
if (dbPeptideAnalysis.Id.HasValue)
{
newAnalysis = false;
}
else
{
session.Save(dbPeptideAnalysis);
newAnalysis = true;
}
var sqlStatementBuilder = new SqlStatementBuilder(session.GetSessionImplementation().Factory.Dialect);
var insertStatements = new List<string>();
IList<MsDataFile> dataFiles;
if (includeMissingMs2)
{
dataFiles = Workspace.MsDataFiles
.Where(msDataFile => !existingDataFileIds.Contains(msDataFile.Id))
.ToArray();
}
else
{
dataFiles = new List<MsDataFile>();
foreach (var grouping in psmTimesByDataFileId)
{
MsDataFile dataFile;
if (existingDataFileIds.Contains(grouping.Key) || !Workspace.MsDataFiles.TryGetValue(grouping.Key, out dataFile))
{
continue;
}
dataFiles.Add(dataFile);
}
}
foreach (var msDataFile in dataFiles)
{
var dbPeptideFileAnalysis = PeptideFileAnalysis.CreatePeptideFileAnalysis(session, msDataFile, dbPeptideAnalysis, psmTimesByDataFileId);
insertStatements.Add(sqlStatementBuilder.GetInsertStatement("DbPeptideFileAnalysis",
new Dictionary<string, object>
{
{"ChromatogramEndTime", dbPeptideFileAnalysis.ChromatogramEndTime},
{"ChromatogramStartTime", dbPeptideFileAnalysis.ChromatogramStartTime},
{"MsDataFile", msDataFile.Id},
{"PeptideAnalysis", dbPeptideAnalysis.Id},
{"AutoFindPeak", 1},
{"Version",1},
{"PeakCount",0},
{"PsmCount", dbPeptideFileAnalysis.PsmCount},
{"ValidationStatus",0},
}
));
dbPeptideAnalysis.FileAnalysisCount++;
existingDataFileIds.Add(msDataFile.Id);
}
sqlStatementBuilder.ExecuteStatements(session, insertStatements);
session.Update(dbPeptideAnalysis);
if (!newAnalysis)
{
session.Save(new DbChangeLog(Workspace, dbPeptideAnalysis));
}
else
{
var dbWorkspace = Workspace.LoadDbWorkspace(session);
session.Update(dbWorkspace);
}
session.Transaction.Commit();
}
}
}
