public Digestion Digest(IProtease protease, String name, String description, ProgressMonitor progressMonitor)
{
DbOrganism organism;
DbDigestion digestion;
List <DbProtein> proteins;
using (ISession session = ProteomeDb.OpenWriteSession())
{
organism = GetEntity(session);
session.BeginTransaction();
digestion = new DbDigestion
{
Name = name,
Description = description,
Organism = organism,
MaxMissedCleavages = protease.MaxMissedCleavages
};
session.Save(digestion);
if (!progressMonitor.Invoke("Listing proteins", 0))
{
return(null);
}
proteins = new List <DbProtein>(organism.Proteins);
Dictionary <String, long> digestedPeptideIds
= new Dictionary <string, long>();
const String sqlPeptide =
"INSERT INTO ProteomeDbDigestedPeptide (Digestion, MissedCleavages, Sequence, Version) VALUES(@Digestion,@MissedCleavages,@Sequence,1);select last_insert_rowid();";
var commandPeptide = session.Connection.CreateCommand();
commandPeptide.CommandText = sqlPeptide;
commandPeptide.Parameters.Add(new SQLiteParameter("@Digestion"));
commandPeptide.Parameters.Add(new SQLiteParameter("@MissedCleavages"));
commandPeptide.Parameters.Add(new SQLiteParameter("@Sequence"));
const String sqlPeptideProtein =
"INSERT INTO ProteomeDbDigestedPeptideProtein (StartIndex, Peptide, Protein, Version) VALUES(?,?,?,1);";
var commandProtein = session.Connection.CreateCommand();
commandProtein.CommandText = sqlPeptideProtein;
commandProtein.Parameters.Add(new SQLiteParameter("@StartIndex"));
commandProtein.Parameters.Add(new SQLiteParameter("@Peptide"));
commandProtein.Parameters.Add(new SQLiteParameter("@Protein"));
for (int i = 0; i < proteins.Count; i++)
{
if (!progressMonitor.Invoke("Digesting " + proteins.Count
+ " proteins", 100 * i / proteins.Count))
{
return(null);
}
Protein protein = new Protein(this, proteins[i]);
foreach (DigestedPeptide digestedPeptide in protease.Digest(protein))
{
if (digestedPeptide.Sequence.Length > MAX_PEPTIDE_LENGTH)
{
continue;
}
long digestedPeptideId;
if (!digestedPeptideIds.TryGetValue(digestedPeptide.Sequence, out digestedPeptideId))
{
((SQLiteParameter)commandPeptide.Parameters[0]).Value = digestion.Id;
((SQLiteParameter)commandPeptide.Parameters[1]).Value = digestedPeptide.MissedCleavages;
((SQLiteParameter)commandPeptide.Parameters[2]).Value = digestedPeptide.Sequence;
digestedPeptideId = Convert.ToInt64(commandPeptide.ExecuteScalar());
digestedPeptideIds.Add(digestedPeptide.Sequence, digestedPeptideId);
}
((SQLiteParameter)commandProtein.Parameters[0]).Value = digestedPeptide.Index;
((SQLiteParameter)commandProtein.Parameters[1]).Value = digestedPeptideId;
((SQLiteParameter)commandProtein.Parameters[2]).Value = proteins[i].Id;
commandProtein.ExecuteNonQuery();
}
}
if (!progressMonitor.Invoke("Committing transaction", 99))
{
return(null);
}
session.Transaction.Commit();
progressMonitor.Invoke(
"Digested " + proteins.Count + " proteins into " + digestedPeptideIds.Count + " unique peptides",
100);
return(new Digestion(this, digestion));
}
}