private void UpdateBinary(ISession session, DbMsDataFile dbMsDataFile)
{
if (null != Data.Times && null == dbMsDataFile.Times)
{
dbMsDataFile.Times = Data.Times.ToArray();
}
if (null != Data.TotalIonCurrent && null == dbMsDataFile.TotalIonCurrent)
{
dbMsDataFile.TotalIonCurrent = Data.TotalIonCurrent.ToArray();
}
if (null != Data.MsLevels)
{
var msLevels = Data.MsLevels.ToArray();
if (null != dbMsDataFile.MsLevels && dbMsDataFile.MsLevels.Length == msLevels.Length)
{
for (int i = 0; i < msLevels.Length; i++)
{
if (0 == msLevels[i])
{
msLevels[i] = dbMsDataFile.MsLevels[i];
}
}
}
}
}
protected override void OnShown(EventArgs e)
{
base.OnShown(e);
new PeptideInfoForm(PeptideAnalysis).Show(dockPanel, DockState.Document);
DbPeptideAnalysis dbPeptideAnalysis;
List <AnalysisChromatograms> analyses = new List <AnalysisChromatograms>();
using (ISession session = Workspace.OpenSession())
{
dbPeptideAnalysis = session.Get <DbPeptideAnalysis>(PeptideAnalysis.Id);
}
if (dbPeptideAnalysis.HasChromatograms)
{
HasChromatograms = true;
return;
}
DbMsDataFile msDataFile = TurnoverForm.Instance.EnsureMsDataFile(dbPeptideAnalysis.MsDataFile);
if (msDataFile == null)
{
return;
}
WaitingForChromatograms = true;
tbxStatus.Text = "Generating chromatograms";
progressBar1.Visible = true;
new Action <DbMsDataFile>(GenerateChromatogramsBackground).BeginInvoke(msDataFile, null, null);
}
public MsDataFileData(DbMsDataFile dbMsDataFile)
{
Name = dbMsDataFile.Name;
Label = dbMsDataFile.Label;
Cohort = dbMsDataFile.Cohort;
Sample = dbMsDataFile.Sample;
PrecursorPool = PrecursorPoolValue.ParsePersistedString(dbMsDataFile.PrecursorPool);
TimePoint = dbMsDataFile.TimePoint;
Times = ImmutableList.ValueOf(dbMsDataFile.Times);
TotalIonCurrent = ImmutableList.ValueOf(dbMsDataFile.TotalIonCurrent);
MsLevels = ImmutableList.ValueOf(dbMsDataFile.MsLevels);
}
public MsDataFileData(DbMsDataFile dbMsDataFile)
{
Name = dbMsDataFile.Name;
Label = dbMsDataFile.Label;
Cohort = dbMsDataFile.Cohort;
Sample = dbMsDataFile.Sample;
PrecursorPool = PrecursorPoolValue.ParsePersistedString(dbMsDataFile.PrecursorPool);
TimePoint = dbMsDataFile.TimePoint;
Times = ImmutableList.ValueOf(dbMsDataFile.Times);
TotalIonCurrent = ImmutableList.ValueOf(dbMsDataFile.TotalIonCurrent);
MsLevels = ImmutableList.ValueOf(dbMsDataFile.MsLevels);
}
private void GenerateChromatogramsBackground(DbMsDataFile msDataFile)
{
ChromatogramGenerator chromatogramGenerator = new ChromatogramGenerator(Workspace);
chromatogramGenerator.GenerateChromatograms(msDataFile, new List <AnalysisChromatograms> {
new AnalysisChromatograms(PeptideAnalysis)
}, UpdateChromatogramProgress);
SafeBeginInvoke(delegate
{
HasChromatograms = true;
WaitingForChromatograms = false;
progressBar1.Visible = false;
tbxStatus.Text = "";
});
}
public void TestDbMsDataFile()
{
var dbMsDataFile = new DbMsDataFile
{
Name = "Foo",
MsLevels = new byte[] {0x1, 0x2, 0x1, 0x2},
Times = new [] {0.1, 0.2, 0.3, 0.4}
};
var serializer = new DataContractJsonSerializer(typeof (DbMsDataFile));
var stream = new MemoryStream();
serializer.WriteObject(stream, dbMsDataFile);
var streamAsString = Encoding.UTF8.GetString(stream.GetBuffer(), 0, (int) stream.Length);
Trace.TraceInformation("Serialed as {0}", streamAsString);
stream.Seek(0, SeekOrigin.Begin);
var dbMsDataFile2 = (DbMsDataFile) serializer.ReadObject(stream);
Assert.AreEqual(dbMsDataFile.Name, dbMsDataFile2.Name);
CollectionAssert.AreEqual(dbMsDataFile.MsLevels, dbMsDataFile2.MsLevels);
CollectionAssert.AreEqual(dbMsDataFile.Times, dbMsDataFile2.Times);
}
public void TestDbMsDataFile()
{
var dbMsDataFile = new DbMsDataFile
{
Name = "Foo",
MsLevels = new byte[] { 0x1, 0x2, 0x1, 0x2 },
Times = new [] { 0.1, 0.2, 0.3, 0.4 }
};
var serializer = new DataContractJsonSerializer(typeof(DbMsDataFile));
var stream = new MemoryStream();
serializer.WriteObject(stream, dbMsDataFile);
var streamAsString = Encoding.UTF8.GetString(stream.GetBuffer(), 0, (int)stream.Length);
Trace.TraceInformation("Serialed as {0}", streamAsString);
stream.Seek(0, SeekOrigin.Begin);
var dbMsDataFile2 = (DbMsDataFile)serializer.ReadObject(stream);
Assert.AreEqual(dbMsDataFile.Name, dbMsDataFile2.Name);
CollectionAssert.AreEqual(dbMsDataFile.MsLevels, dbMsDataFile2.MsLevels);
CollectionAssert.AreEqual(dbMsDataFile.Times, dbMsDataFile2.Times);
}
public void Merge(DbMsDataFile dbMsDataFile)
{
Merge(new MsDataFileData(dbMsDataFile));
}
public SearchResultKey(DbMsDataFile msDataFile, DbPeptide peptide, double retentionTime)
: this(msDataFile.Id.GetValueOrDefault(), peptide.Id.GetValueOrDefault(), retentionTime)
{
}
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 AddPeptide(Workspace workspace, PeakFinderPeptide peakFinderPeptide)
{
var msDataFile = GetMsDataFile(workspace, peakFinderPeptide.DataFile);
Peptide peptide;
using (var session = workspace.OpenWriteSession())
{
var dbMsDataFile = new DbMsDataFile
{
Name = peakFinderPeptide.DataFile,
Label = peakFinderPeptide.DataFile,
};
if (msDataFile == null)
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
var dbPeptide = (DbPeptide)
session.CreateCriteria <DbPeptide>().Add(Restrictions.Eq("Sequence",
peakFinderPeptide.PeptideSequence)).
UniqueResult();
if (dbPeptide == null)
{
dbPeptide = new DbPeptide
{
FullSequence = peakFinderPeptide.PeptideSequence,
Sequence = peakFinderPeptide.PeptideSequence,
};
session.BeginTransaction();
session.Save(dbPeptide);
session.Transaction.Commit();
}
session.BeginTransaction();
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.FirstDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MinCharge,
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
});
if (peakFinderPeptide.LastDetectedTime != peakFinderPeptide.FirstDetectedTime)
{
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.LastDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MaxCharge,
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
});
}
session.Transaction.Commit();
peptide = new Peptide(workspace, dbPeptide);
}
MsDataFileUtil.InitMsDataFile(workspace, msDataFile);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
if (peptideAnalysis == null)
{
Assert.Fail();
}
PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
}
public void TestChromatogramGenerator()
{
String dbPath = Path.Combine(TestContext.TestDir, "test" + Guid.NewGuid() + ".tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetN15Enrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
var dbMsDataFile = new DbMsDataFile
{
Name = "20090724_HT3_0",
};
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
Assert.IsTrue(MsDataFileUtil.InitMsDataFile(workspace, msDataFile));
DbPeptide dbPeptide;
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
dbPeptide = new DbPeptide
{
Protein = "TestProtein",
Sequence = "YLAAYLLLVQGGNAAPSAADIK",
FullSequence = "K.YLAAYLLLVQGGNAAPSAADIK.A",
};
session.Save(dbPeptide);
var searchResult = new DbPeptideSpectrumMatch
{
Peptide = dbPeptide,
MsDataFile = session.Load <DbMsDataFile>(msDataFile.Id),
PrecursorCharge = 3,
RetentionTime = 20.557 * 60,
};
session.Save(searchResult);
session.Transaction.Commit();
}
var peptide = new Peptide(workspace, dbPeptide);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
peptideAnalysis.IncChromatogramRefCount();
var peptideFileAnalysis = PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
workspace.DatabasePoller.LoadAndMergeChanges(null);
peptideAnalysis.IncChromatogramRefCount();
var chromatogramGenerator = new ChromatogramGenerator(workspace);
chromatogramGenerator.Start();
while (peptideFileAnalysis.ChromatogramSet == null)
{
Thread.Sleep(100);
}
var chromatogramDatas = peptideFileAnalysis.GetChromatograms();
Assert.IsFalse(chromatogramDatas.Chromatograms.Count == 0);
chromatogramGenerator.Stop();
while (chromatogramGenerator.IsThreadAlive)
{
Thread.Sleep(100);
}
}
public SearchResultKey(DbMsDataFile msDataFile, DbPeptide peptide, double retentionTime)
: this(msDataFile.Id.GetValueOrDefault(), peptide.Id.GetValueOrDefault(), retentionTime)
{
}
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();
}
}
public MsDataFile(Workspace workspace, DbMsDataFile dbMsDataFile) : this(workspace, dbMsDataFile.GetId(), new MsDataFileData(dbMsDataFile))
{
}
private void AddPeptide(Workspace workspace, PeakFinderPeptide peakFinderPeptide)
{
var msDataFile = GetMsDataFile(workspace, peakFinderPeptide.DataFile);
Peptide peptide;
using (var session = workspace.OpenWriteSession())
{
var dbMsDataFile = new DbMsDataFile
{
Name = peakFinderPeptide.DataFile,
Label = peakFinderPeptide.DataFile,
};
if (msDataFile == null)
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
var dbPeptide = (DbPeptide)
session.CreateCriteria<DbPeptide>().Add(Restrictions.Eq("Sequence",
peakFinderPeptide.PeptideSequence)).
UniqueResult();
if (dbPeptide == null)
{
dbPeptide = new DbPeptide
{
FullSequence = peakFinderPeptide.PeptideSequence,
Sequence = peakFinderPeptide.PeptideSequence,
};
session.BeginTransaction();
session.Save(dbPeptide);
session.Transaction.Commit();
}
session.BeginTransaction();
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.FirstDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MinCharge,
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
});
if (peakFinderPeptide.LastDetectedTime != peakFinderPeptide.FirstDetectedTime)
{
session.Save(new DbPeptideSpectrumMatch
{
RetentionTime = peakFinderPeptide.LastDetectedTime * 60,
PrecursorCharge = peakFinderPeptide.MaxCharge,
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
});
}
session.Transaction.Commit();
peptide = new Peptide(workspace, dbPeptide);
}
MsDataFileUtil.InitMsDataFile(workspace, msDataFile);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
if (peptideAnalysis == null)
{
Assert.Fail();
}
PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
}
public bool IsRejected(DbMsDataFile msDataFile)
{
return(_rejectedMsDataFileIds.Contains(msDataFile.Id.Value));
}
public void TestChromatogramGenerator()
{
String dbPath = Path.Combine(TestContext.TestDir, "test" + Guid.NewGuid() + ".tpg");
using (var sessionFactory = SessionFactoryFactory.CreateSessionFactory(dbPath, SessionFactoryFlags.CreateSchema))
{
using (var session = sessionFactory.OpenSession())
{
session.BeginTransaction();
DbWorkspace dbWorkspace = new DbWorkspace
{
TracerDefCount = 1,
};
session.Save(dbWorkspace);
DbTracerDef dbTracerDef = TracerDef.GetN15Enrichment();
dbTracerDef.Workspace = dbWorkspace;
dbTracerDef.Name = "Tracer";
session.Save(dbTracerDef);
session.Save(new DbSetting
{
Workspace = dbWorkspace,
Name = SettingEnum.data_directory.ToString(),
Value = GetDataDirectory()
});
session.Transaction.Commit();
}
}
Workspace workspace = new Workspace(dbPath);
workspace.SetTaskScheduler(TaskScheduler.Default);
var dbMsDataFile = new DbMsDataFile
{
Name = "20090724_HT3_0",
};
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
session.Save(dbMsDataFile);
session.Transaction.Commit();
}
workspace.DatabasePoller.LoadAndMergeChanges(null);
var msDataFile = workspace.MsDataFiles.FindByKey(dbMsDataFile.GetId());
Assert.IsTrue(MsDataFileUtil.InitMsDataFile(workspace, msDataFile));
DbPeptide dbPeptide;
using (var session = workspace.OpenWriteSession())
{
session.BeginTransaction();
dbPeptide = new DbPeptide
{
Protein = "TestProtein",
Sequence = "YLAAYLLLVQGGNAAPSAADIK",
FullSequence = "K.YLAAYLLLVQGGNAAPSAADIK.A",
};
session.Save(dbPeptide);
var searchResult = new DbPeptideSpectrumMatch
{
Peptide = dbPeptide,
MsDataFile = session.Load<DbMsDataFile>(msDataFile.Id),
PrecursorCharge = 3,
RetentionTime = 20.557 * 60,
};
session.Save(searchResult);
session.Transaction.Commit();
}
var peptide = new Peptide(workspace, dbPeptide);
var peptideAnalysis = peptide.EnsurePeptideAnalysis();
peptideAnalysis.IncChromatogramRefCount();
var peptideFileAnalysis = PeptideFileAnalysis.EnsurePeptideFileAnalysis(peptideAnalysis, msDataFile);
workspace.DatabasePoller.LoadAndMergeChanges(null);
peptideAnalysis.IncChromatogramRefCount();
var chromatogramGenerator = new ChromatogramGenerator(workspace);
chromatogramGenerator.Start();
while (peptideFileAnalysis.ChromatogramSet == null)
{
Thread.Sleep(100);
}
var chromatogramDatas = peptideFileAnalysis.GetChromatograms();
Assert.IsFalse(chromatogramDatas.Chromatograms.Count == 0);
chromatogramGenerator.Stop();
while (chromatogramGenerator.IsThreadAlive)
{
Thread.Sleep(100);
}
}
