public void TestCrosslinkWithModifications() { CrosslinkLibraryKey libKey = CrosslinkSequenceParser.ParseCrosslinkLibraryKey( "C[+57.02146]C[+57.02146]TKPESER-EKVLTSSAR-[+138.0681@4,2]", 1); Assert.AreEqual(2, libKey.PeptideLibraryKeys.Count); Assert.AreEqual("C[+57.02146]C[+57.02146]TKPESER", libKey.PeptideLibraryKeys[0].ModifiedSequence); Assert.AreEqual("EKVLTSSAR", libKey.PeptideLibraryKeys[1].ModifiedSequence); Assert.AreEqual("+138.0681", libKey.Crosslinks[0].Name); Assert.AreEqual(2, libKey.Crosslinks[0].Positions.Count); Assert.AreEqual(ImmutableList.Singleton(4), libKey.Crosslinks[0].Positions[0]); Assert.AreEqual(ImmutableList.Singleton(2), libKey.Crosslinks[0].Positions[1]); }
public void TestCrosslinkSequenceParser() { CrosslinkLibraryKey libKey = CrosslinkSequenceParser.ParseCrosslinkLibraryKey("VTIAQGGVLPNIQAVLLPKK-TESHHKACGK-[+138.0681@19,6]", 1); Assert.AreEqual(2, libKey.PeptideLibraryKeys.Count); Assert.AreEqual("VTIAQGGVLPNIQAVLLPKK", libKey.PeptideLibraryKeys[0].ModifiedSequence); Assert.AreEqual("TESHHKACGK", libKey.PeptideLibraryKeys[1].ModifiedSequence); Assert.AreEqual(1, libKey.Crosslinks.Count); Assert.AreEqual("+138.0681", libKey.Crosslinks[0].Name); Assert.AreEqual(2, libKey.Crosslinks[0].Positions.Count); Assert.AreEqual(ImmutableList.Singleton(19), libKey.Crosslinks[0].Positions[0]); Assert.AreEqual(ImmutableList.Singleton(6), libKey.Crosslinks[0].Positions[1]); }
public override IEnumerable <AAModInfo> GetCurrentSequenceInfos() { if (_sequences.Current != null) { CrosslinkLibraryKey crosslinkLibraryKey = CrosslinkSequenceParser.TryParseCrosslinkLibraryKey(_sequences.Current, 0); if (crosslinkLibraryKey != null) { return(crosslinkLibraryKey.PeptideLibraryKeys.SelectMany(peptideLibraryKey => EnumerateAaModInfos(peptideLibraryKey.ModifiedSequence))); } } return(EnumerateAaModInfos(_sequences.Current ?? string.Empty)); }
public static bool IsValidPeptideSequence(string seq) { return(IsExSequence(seq) || null != CrosslinkSequenceParser.TryParseCrosslinkLibraryKey(seq, 0)); }
private static void VerifySupported(string libKeyString, bool expectedSupported) { var libKey = CrosslinkSequenceParser.ParseCrosslinkLibraryKey(libKeyString, 1); Assert.AreEqual(expectedSupported, libKey.IsSupportedBySkyline()); }