public void Reset(IDbConnection conn)
{
diskFilepath = null;
memConn = conn;
memConn.ExecuteNonQuery(@"PRAGMA journal_mode=OFF;
PRAGMA synchronous=OFF;");
SessionFactoryFactory.DropIndexes(memConn);
insertCommandByTable = new List <KeyValuePair <IDbCommand, List <object[]> > >();
for (int i = 0; i <= (int)Table.QonverterSettings; ++i)
{
insertCommandByTable.Add(new KeyValuePair <IDbCommand, List <object[]> >());
}
insertCommandByTable[(int)Table.Protein] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.Protein].Key.CommandText = createInsertSql("Protein", "Id, Accession, Length");
insertCommandByTable[(int)Table.ProteinMetadata] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.ProteinMetadata].Key.CommandText = createInsertSql("ProteinMetadata", "Id, Description");
insertCommandByTable[(int)Table.ProteinData] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.ProteinData].Key.CommandText = createInsertSql("ProteinData", "Id, Sequence");
insertCommandByTable[(int)Table.Peptide] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.Peptide].Key.CommandText = createInsertSql("Peptide", "Id, MonoisotopicMass, MolecularWeight");
insertCommandByTable[(int)Table.PeptideSequences] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideSequences].Key.CommandText = createInsertSql("PeptideSequences", "Id, Sequence");
insertCommandByTable[(int)Table.PeptideInstance] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideInstance].Key.CommandText = createInsertSql("PeptideInstance", "Id, Protein, Peptide, Offset, Length, NTerminusIsSpecific, CTerminusIsSpecific, MissedCleavages");
insertCommandByTable[(int)Table.Analysis] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.Analysis].Key.CommandText = createInsertSql("Analysis", "Id, Name, SoftwareName, SoftwareVersion, StartTime, Type");
insertCommandByTable[(int)Table.AnalysisParameter] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.AnalysisParameter].Key.CommandText = createInsertSql("AnalysisParameter", "Id, Analysis, Name, Value");
insertCommandByTable[(int)Table.SpectrumSourceGroup] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.SpectrumSourceGroup].Key.CommandText = createInsertSql("SpectrumSourceGroup", "Id, Name");
insertCommandByTable[(int)Table.SpectrumSource] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.SpectrumSource].Key.CommandText = createInsertSql("SpectrumSource", "Id, Name, URL, Group_");
insertCommandByTable[(int)Table.SpectrumSourceMetadata] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.SpectrumSourceMetadata].Key.CommandText = createInsertSql("SpectrumSourceMetadata", "Id, MsDataBytes");
insertCommandByTable[(int)Table.SpectrumSourceGroupLink] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.SpectrumSourceGroupLink].Key.CommandText = createInsertSql("SpectrumSourceGroupLink", "Id, Source, Group_");
insertCommandByTable[(int)Table.Spectrum] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.Spectrum].Key.CommandText = createInsertSql("Spectrum", "Id, Index_, NativeID, Source, PrecursorMZ");
insertCommandByTable[(int)Table.PeptideSpectrumMatch] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideSpectrumMatch].Key.CommandText =
createInsertSql("PeptideSpectrumMatch",
"Id, Peptide, Spectrum, Analysis, " +
"ObservedNeutralMass, " +
"MonoisotopicMassError, MolecularWeightError, " +
"Rank, QValue, Charge");
insertCommandByTable[(int)Table.PeptideSpectrumMatchScoreName] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideSpectrumMatchScoreName].Key.CommandText = createInsertSql("PeptideSpectrumMatchScoreName", "Id, Name");
insertCommandByTable[(int)Table.PeptideSpectrumMatchScore] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideSpectrumMatchScore].Key.CommandText = createInsertSql("PeptideSpectrumMatchScore", "PsmId, ScoreNameId, Value");
insertCommandByTable[(int)Table.Modification] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.Modification].Key.CommandText = createInsertSql("Modification", "Id, MonoMassDelta, AvgMassDelta, Name, Formula");
insertCommandByTable[(int)Table.PeptideModification] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.PeptideModification].Key.CommandText = createInsertSql("PeptideModification", "Id, Modification, PeptideSpectrumMatch, Offset, Site");
insertCommandByTable[(int)Table.IntegerSet] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.IntegerSet].Key.CommandText = "INSERT INTO IntegerSet VALUES (?)";
insertCommandByTable[(int)Table.QonverterSettings] = new KeyValuePair <IDbCommand, List <object[]> >(conn.CreateCommand(), new List <object[]>());
insertCommandByTable[(int)Table.QonverterSettings].Key.CommandText = createInsertSql("QonverterSettings", "Id, QonverterMethod, DecoyPrefix, RerankMatches, ScoreInfoByName");
foreach (var itr in insertCommandByTable)
{
createParameters(itr.Key);
itr.Key.Prepare();
}
scoreIdByName = new Dictionary <string, long>();
foreach (var queryRow in conn.ExecuteQuery("SELECT Name, Id FROM PeptideSpectrumMatchScoreName"))
{
scoreIdByName[queryRow.GetString(0)] = queryRow.GetInt64(1);
}
/*diskConn.ExecuteNonQuery("CREATE TABLE IF NOT EXISTS PeptideSequences (Id INTEGER PRIMARY KEY, Sequence TEXT)");
* diskConn.ExecuteNonQuery("CREATE TABLE IF NOT EXISTS IntegerSet (Value INTEGER PRIMARY KEY)");
* currentMaxSequenceLength = diskConn.ExecuteQuery("SELECT IFNULL(MAX(Value),0) FROM IntegerSet").First().GetInt64(0);
*/
memConn.ExecuteNonQuery("CREATE TABLE IF NOT EXISTS PeptideSequences (Id INTEGER PRIMARY KEY, Sequence TEXT)");
transaction = memConn.BeginTransaction();
}
public static ISessionFactory CreateSessionFactory (string path) { return SessionFactoryFactory.CreateSessionFactory(path, new SessionFactoryConfig()); }
public void Reset(string diskFilepath)
{
Reset(SessionFactoryFactory.CreateFile(":memory:"));
this.diskFilepath = diskFilepath;
}