public void Test_modification2_hash_set()
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
ModificationWithLocation m1 = new ModificationWithLocation(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new Dictionary <string, IList <string> >(), "modificationType");
ModificationWithLocation m2 = new ModificationWithLocation(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new Dictionary <string, IList <string> >(), "modificationType");
m1.linksToOtherDbs.Add("key", new List <string> {
"value"
});
m2.linksToOtherDbs.Add("key", new List <string> {
"value"
});
HashSet <Modification> mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.True(m1.Equals(m2));
Assert.AreEqual(1, mods.Count);
}
public void Test_modification2_hash_set()
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
ModificationWithLocation m1 = new ModificationWithLocation("id1", "modificationType", motif, TerminusLocalization.Any, new Dictionary <string, IList <string> >());
ModificationWithLocation m2 = new ModificationWithLocation("id1", "modificationType", motif, TerminusLocalization.Any);
m1.linksToOtherDbs.Add("key", new List <string> {
"value"
});
m2.linksToOtherDbs.Add("key", new List <string> {
"value"
});
HashSet <Modification> mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.True(m1.Equals(m2));
Assert.AreEqual(1, mods.Count);
}
public void TestFullProteinReadWrite()
{
Modification mod = new Modification("mod1", "modType1");
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
ModificationWithLocation mod2 = new ModificationWithLocation("mod2", "modType1", motif, TerminusLocalization.Any, null);
ModificationMotif.TryGetMotif("N", out ModificationMotif motif3);
ModificationWithMass mod3 = new ModificationWithMass("mod3", "modType1", motif3, TerminusLocalization.Any, 10, null, null, null);
List <Tuple <string, string> > gene_names = new List <Tuple <string, string> > {
new Tuple <string, string>("a", "b")
};
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 3, new List <Modification> {
mod
} },
{ 4, new List <Modification> {
mod2
} },
{ 5, new List <Modification> {
mod3
} }
};
List <ProteolysisProduct> proteolysisProducts = new List <ProteolysisProduct> {
new ProteolysisProduct(1, 2, "propeptide")
};
string name = "testName";
string full_name = "testFullName";
List <DatabaseReference> databaseReferences = new List <DatabaseReference> {
new DatabaseReference("type1", "id1", new List <Tuple <string, string> > {
new Tuple <string, string>("e1", "e2")
})
};
List <SequenceVariation> sequenceVariations = new List <SequenceVariation> {
new SequenceVariation(3, "Q", "N", "replace Q by N"),
new SequenceVariation(3, 4, "QE", "NN", "replace QE by NN")
};
List <DisulfideBond> disulfideBonds = new List <DisulfideBond> {
new DisulfideBond(1, "ds1"), new DisulfideBond(2, 3, "ds2")
};
Protein p1 = new Protein("SEQENCE",
"a1",
gene_names: gene_names,
oneBasedModifications: oneBasedModifications,
proteolysisProducts: proteolysisProducts,
name: name,
full_name: full_name,
isDecoy: false,
isContaminant: true,
databaseReferences: databaseReferences,
sequenceVariations: sequenceVariations,
disulfideBonds: disulfideBonds,
databaseFilePath: Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"));
// Generate data for files
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
p1
}, Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"));
IEnumerable <string> modTypesToExclude = new List <string>();
IEnumerable <Modification> allKnownModifications = new List <Modification>();
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"bnueiwhf.xml"), true, DecoyType.None, allKnownModifications, true, modTypesToExclude, out Dictionary <string, Modification> unknownModifications);
Assert.AreEqual(p1.Accession, ok[0].Accession);
Assert.AreEqual(p1.BaseSequence, ok[0].BaseSequence);
Assert.AreEqual(p1.DatabaseReferences.First().Id, ok[0].DatabaseReferences.First().Id);
Assert.AreEqual(p1.DatabaseReferences.First().Properties.First().Item1, ok[0].DatabaseReferences.First().Properties.First().Item1);
Assert.AreEqual(p1.DatabaseReferences.First().Properties.First().Item2, ok[0].DatabaseReferences.First().Properties.First().Item2);
Assert.AreEqual(p1.DatabaseReferences.First().Type, ok[0].DatabaseReferences.First().Type);
Assert.AreEqual(p1.DisulfideBonds.First().Description, ok[0].DisulfideBonds.First().Description);
Assert.AreEqual(p1.DisulfideBonds.First().OneBasedBeginPosition, ok[0].DisulfideBonds.First().OneBasedBeginPosition);
Assert.AreEqual(p1.DisulfideBonds.First().OneBasedEndPosition, ok[0].DisulfideBonds.First().OneBasedEndPosition);
Assert.AreEqual(p1.DisulfideBonds.Last().Description, ok[0].DisulfideBonds.Last().Description);
Assert.AreEqual(p1.DisulfideBonds.Last().OneBasedBeginPosition, ok[0].DisulfideBonds.Last().OneBasedBeginPosition);
Assert.AreEqual(p1.DisulfideBonds.Last().OneBasedEndPosition, ok[0].DisulfideBonds.Last().OneBasedEndPosition);
Assert.AreEqual(p1.FullDescription, ok[0].FullDescription);
Assert.AreEqual(p1.FullName, ok[0].FullName);
Assert.AreEqual(p1.GeneNames, ok[0].GeneNames);
Assert.AreEqual(p1.IsContaminant, ok[0].IsContaminant);
Assert.AreEqual(p1.IsDecoy, ok[0].IsDecoy);
Assert.AreEqual(p1.Length, ok[0].Length);
Assert.AreEqual(p1.Name, ok[0].Name);
Assert.AreEqual(p1.DatabaseFilePath, ok[0].DatabaseFilePath);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0], ok[0].OneBasedPossibleLocalizedModifications[3][0]);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0].id, ok[0].OneBasedPossibleLocalizedModifications[3][0].id);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[3][0].modificationType, ok[0].OneBasedPossibleLocalizedModifications[3][0].modificationType);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[4][0].id, ok[0].OneBasedPossibleLocalizedModifications[4][0].id);
Assert.AreEqual(p1.OneBasedPossibleLocalizedModifications[4][0].modificationType, ok[0].OneBasedPossibleLocalizedModifications[4][0].modificationType);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).linksToOtherDbs, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).linksToOtherDbs);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).motif, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).motif);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).terminusLocalization, (ok[0].OneBasedPossibleLocalizedModifications[4][0] as ModificationWithLocation).terminusLocalization);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).diagnosticIons, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).diagnosticIons);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).neutralLosses, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).neutralLosses);
Assert.AreEqual((p1.OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).monoisotopicMass, (ok[0].OneBasedPossibleLocalizedModifications[5][0] as ModificationWithMass).monoisotopicMass);
Assert.AreEqual(p1.ProteolysisProducts.First().OneBasedBeginPosition, ok[0].ProteolysisProducts.First().OneBasedBeginPosition);
Assert.AreEqual(p1.ProteolysisProducts.First().OneBasedEndPosition, ok[0].ProteolysisProducts.First().OneBasedEndPosition);
Assert.AreEqual(p1.ProteolysisProducts.First().Type, ok[0].ProteolysisProducts.First().Type);
Assert.AreEqual(p1.SequenceVariations.First().Description, ok[0].SequenceVariations.First().Description);
Assert.AreEqual(p1.SequenceVariations.First().OneBasedBeginPosition, ok[0].SequenceVariations.First().OneBasedBeginPosition);
Assert.AreEqual(p1.SequenceVariations.First().OneBasedEndPosition, ok[0].SequenceVariations.First().OneBasedEndPosition);
Assert.AreEqual(p1.SequenceVariations.First().OriginalSequence, ok[0].SequenceVariations.First().OriginalSequence);
Assert.AreEqual(p1.SequenceVariations.First().VariantSequence, ok[0].SequenceVariations.First().VariantSequence);
Assert.AreEqual(p1.SequenceVariations.Last().Description, ok[0].SequenceVariations.Last().Description);
Assert.AreEqual(p1.SequenceVariations.Last().OneBasedBeginPosition, ok[0].SequenceVariations.Last().OneBasedBeginPosition);
Assert.AreEqual(p1.SequenceVariations.Last().OneBasedEndPosition, ok[0].SequenceVariations.Last().OneBasedEndPosition);
Assert.AreEqual(p1.SequenceVariations.Last().OriginalSequence, ok[0].SequenceVariations.Last().OriginalSequence);
Assert.AreEqual(p1.SequenceVariations.Last().VariantSequence, ok[0].SequenceVariations.Last().VariantSequence);
}
