private void ShowPeptideAnalysis(Peptide peptide)
{
using (var session = Workspace.OpenSession())
{
var dbPeptide = session.Load <DbPeptide>(peptide.Id);
var dbPeptideAnalysis = (DbPeptideAnalysis)session
.CreateCriteria(typeof(DbPeptideAnalysis))
.Add(Restrictions.Eq("Peptide", dbPeptide))
.UniqueResult();
if (dbPeptideAnalysis == null)
{
var psmTimesByDataFileId = dbPeptide.PsmTimesByDataFileId(session);
if (psmTimesByDataFileId.Count == 0)
{
MessageBox.Show(
"This peptide cannot be analyzed because it has no search results.",
Program.AppName);
return;
}
if (MessageBox.Show("This peptide has not yet been analyzed. Do you want to analyze it now?", Program.AppName, MessageBoxButtons.OKCancel) == DialogResult.Cancel)
{
return;
}
session.BeginTransaction();
session.Save(dbPeptideAnalysis = Peptide.CreateDbPeptideAnalysis(session, dbPeptide));
foreach (var grouping in psmTimesByDataFileId)
{
MsDataFile msDataFile;
if (!Workspace.MsDataFiles.TryGetValue(grouping.Key, out msDataFile))
{
continue;
}
session.Save(PeptideFileAnalysis.CreatePeptideFileAnalysis(
session, msDataFile, dbPeptideAnalysis, psmTimesByDataFileId));
dbPeptideAnalysis.FileAnalysisCount++;
}
session.Update(dbPeptideAnalysis);
session.Transaction.Commit();
}
var peptideAnalysis = TopographForm.Instance.LoadPeptideAnalysis(dbPeptideAnalysis.GetId());
if (peptideAnalysis == null)
{
return;
}
PeptideAnalysisFrame.ShowPeptideAnalysis(peptideAnalysis);
}
}
public void Run(LongOperationBroker longOperationBroker)
{
using (var session = PeptideAnalysis.Workspace.OpenSession())
{
var peptideAnalysis = session.Get <DbPeptideAnalysis>(PeptideAnalysis.Id);
var peptide = peptideAnalysis.Peptide;
var psmTimesByDataFileId = peptide.PsmTimesByDataFileId(session);
session.BeginTransaction();
foreach (var msDataFile in MsDataFiles)
{
var dbPeptideFileAnalysis = PeptideFileAnalysis.CreatePeptideFileAnalysis(
session, msDataFile, peptideAnalysis, psmTimesByDataFileId);
session.Save(dbPeptideFileAnalysis);
peptideAnalysis.FileAnalysisCount++;
}
session.Update(peptideAnalysis);
session.Save(new DbChangeLog(PeptideAnalysis));
session.Transaction.Commit();
}
PeptideAnalysis.Workspace.DatabasePoller.MergeChangesNow();
}
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();
}
}
}