public void Test_modification4_hash_set()
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
ModificationWithMassAndCf m1 = new ModificationWithMassAndCf(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new ChemicalFormula(), 1.11111d, new Dictionary <string, IList <string> >(), new List <double> {
2.222222
}, new List <double> {
5.55555
}, "modificationType");
ModificationWithMassAndCf m2 = new ModificationWithMassAndCf(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new ChemicalFormula(), 1.11111d, new Dictionary <string, IList <string> >(), new List <double> {
2.222222
}, new List <double> {
5.55555
}, "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.AreEqual(1, mods.Count);
Assert.True(m1.Equals(m2));
}
public static void Test_ModificationWithNoMassWritten()
{
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var mod1 = new ModificationWithMassAndCf("mod", "type", motif, TerminusLocalization.Any, ChemicalFormula.ParseFormula("H"), ChemicalFormula.ParseFormula("H").MonoisotopicMass, null, null, null);
var mod1string = mod1.ToString();
Assert.IsTrue(!mod1string.Contains("MM"));
var modAfterWriteRead = PtmListLoader.ReadModsFromString(mod1string + Environment.NewLine + "//").First() as ModificationWithMassAndCf;
Assert.AreEqual(mod1, modAfterWriteRead);
}
public void DoNotWriteSameModTwiceAndDoNotWriteInHeaderSinceDifferent()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "z.txt")).ToList();
Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> > {
{ 2, sampleModList.OfType <Modification>().ToList() }
}, null, "name", "full_name", false, false, new List <DatabaseReference>(), new List <SequenceVariation>(), new List <DisulfideBond>());
Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType <ModificationWithMass>().Count());
Dictionary <string, HashSet <Tuple <int, Modification> > > dictWithThisMod = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
HashSet <Tuple <int, Modification> > value = new HashSet <Tuple <int, Modification> >();
var modReadFromFile = sampleModList.First() as ModificationWithMassAndCf;
ModificationMotif.TryGetMotif("C", out ModificationMotif motif);
ModificationWithMass newMod = new ModificationWithMassAndCf("Palmitoylation of C", modReadFromFile.modificationType, motif, TerminusLocalization.Any, modReadFromFile.chemicalFormula, modReadFromFile.monoisotopicMass, null, null, null);
Assert.AreEqual(newMod, sampleModList.First());
Assert.AreEqual(sampleModList.First(), newMod);
value.Add(new Tuple <int, Modification>(2, newMod));
dictWithThisMod.Add("accession", value);
var newModResEntries = ProteinDbWriter.WriteXmlDatabase(dictWithThisMod, new List <Protein> {
protein
}, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"));
Assert.AreEqual(0, newModResEntries.Count);
List <Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins3.xml"), true, DecoyType.None, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> um);
Assert.AreEqual(1, new_proteins.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).Count());
}
