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());
}
