public void load_save_unlocalized()
{
Loaders.LoadElements();
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
List <Modification> mods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "ptmlist.txt"), out List <(Modification, string)> filteredModificationsWithWarnings).ToList();
foreach (Modification m in mods)
{
if (!Sweet.lollipop.modification_ranks.TryGetValue(Math.Round((double)m.MonoisotopicMass, 5), out int x))
{
Sweet.lollipop.modification_ranks.Add(Math.Round((double)m.MonoisotopicMass, 5), -1);
}
}
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods);
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "stored_mods.modnames"));
tpd.save_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
Modification firstAcetyl = mods.FirstOrDefault(x => x.OriginalId.StartsWith("N-acetyl"));
Assert.AreNotEqual(firstAcetyl.OriginalId, tpd.unlocalized_lookup[firstAcetyl].id);
//Test amending
mods.AddRange(PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "intact_mods.txt"), out filteredModificationsWithWarnings).OfType <Modification>());
Sweet.lollipop.modification_ranks = mods.DistinctBy(m => m.MonoisotopicMass).ToDictionary(m => Math.Round((double)m.MonoisotopicMass, 5), m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods.OfType <Modification>());
tpd.amend_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
}
public void parallel_enter_theoreticals_doesnt_crash()
{
TheoreticalProteoformDatabase db = new TheoreticalProteoformDatabase();
db.populate_aa_mass_dictionary();
List <Modification> var = new List <Modification>();
List <TheoreticalProteoform> ts = new List <TheoreticalProteoform>();
ProteinWithGoTerms p = ConstructorsForTesting.make_a_theoretical().ExpandedProteinList.First();
Parallel.Invoke(
() => db.EnterTheoreticalProteformFamily("SEQ", p, p.OneBasedPossibleLocalizedModifications, p.Accession, ts, 1, var),
() => db.EnterTheoreticalProteformFamily("SEQ", p, p.OneBasedPossibleLocalizedModifications, p.Accession, ts, 1, var)
);
}
public void group_by_mass()
{
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
List <TheoreticalProteoform> pfs_with_mass_redundancy = new List <TheoreticalProteoform>
{
ConstructorsForTesting.make_a_theoretical("", 100.0, 1), // bundled
ConstructorsForTesting.make_a_theoretical("", 100.0, 1), // bundled
ConstructorsForTesting.make_a_theoretical("", 100.1, 1), // different mass
ConstructorsForTesting.make_a_theoretical("", 100.0, 2) // still gets bundled even if different lysine count
};
TheoreticalProteoformGroup[] x = tpd.group_proteoforms_by_mass(pfs_with_mass_redundancy);
Assert.AreEqual(2, x.Length);
}
public void load_save_unlocalized()
{
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
tpd.ready_to_make_database(TestContext.CurrentContext.TestDirectory);
List <ModificationWithMass> mods = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "variable.txt")).OfType <ModificationWithMass>().ToList();
SaveState.lollipop.modification_ranks = mods.ToDictionary(m => m.monoisotopicMass, m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods);
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "stored_mods.modnames"));
tpd.save_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
Assert.AreNotEqual(mods.First().id, tpd.unlocalized_lookup.Values.First().id);
//Test amending
mods.AddRange(PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "intact_mods.txt")).OfType <ModificationWithMass>());
SaveState.lollipop.modification_ranks = mods.DistinctBy(m => m.monoisotopicMass).ToDictionary(m => m.monoisotopicMass, m => - 1);
tpd.unlocalized_lookup = tpd.make_unlocalized_lookup(mods.OfType <ModificationWithMass>());
tpd.amend_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "Mods", "fake_stored_mods.modnames"));
}
public void load_unlocalized_doesntcrash()
{
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
tpd.load_unlocalized_names(Path.Combine(TestContext.CurrentContext.TestDirectory, "asdfghjkl", "fake.txt"));
}
public void test_not_ready_to_make_db_doesnt_crash()
{
TheoreticalProteoformDatabase tpd = new TheoreticalProteoformDatabase();
tpd.get_theoretical_proteoforms(TestContext.CurrentContext.TestDirectory);
}
