public void TestAddDigestFeatures()
{
Sequence seq = new Sequence("Test", "AAANESAARBBBNPSBBKFFFNITFFRGGGNDTGGR");
Digest digest = new Digest();
digest.DigestProtease = ProteaseManager.CreateProtease("Trypsin_TestAddDigestFeatures", true, "RK", "P");
digest.ProteinSequence = seq;
digest.MaxMissedCleavages = 0;
digest.AddDigestFeatures();
List <DigestPeptideInfo> peptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(4, peptides.Count);
digest.MaxMissedCleavages = 1;
digest.AddDigestFeatures();
List <DigestPeptideInfo> missedPeptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(7, missedPeptides.Count);
IRangeLocationFilter nglycanFilter = new NGlycanFilter();
digest.MaxMissedCleavages = 0;
digest.Filter = nglycanFilter;
digest.AddDigestFeatures();
List <DigestPeptideInfo> nglycanPeptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(2, nglycanPeptides.Count);
Assert.AreEqual("AAANESAAR", nglycanPeptides[0].PeptideSeq);
Assert.AreEqual("FFFNITFFR", nglycanPeptides[1].PeptideSeq);
}
public void TestNGlycanFilter()
{
NGlycanFilter filter = new NGlycanFilter();
filter.SetSequence(new Seq.Sequence("Test", "AAANESAAR"));
Assert.IsTrue(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "BBBNPSBBK"));
Assert.IsFalse(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "FFFNITFFR"));
Assert.IsTrue(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "GGGNDTGGR"));
Assert.IsFalse(filter.Accept(new RangeLocation(1, 9)));
}
