protected internal override LibraryKeyProto ToLibraryKeyProto()
{
var libraryKeyProto = new LibraryKeyProto()
{
KeyType = LibraryKeyProto.Types.KeyType.Crosslink,
Charge = Charge
};
foreach (var peptideLibraryKey in PeptideLibraryKeys)
{
libraryKeyProto.CrosslinkedSequences.Add(peptideLibraryKey.ModifiedSequence);
}
foreach (var crosslinker in Crosslinks)
{
var crosslinkProto = new LibraryKeyProto.Types.Crosslinker()
{
Name = crosslinker.Name
};
foreach (var positions in crosslinker.Positions)
{
var positionsProto = new LibraryKeyProto.Types.Positions();
positionsProto.Position.AddRange(positions);
crosslinkProto.Positions.Add(positionsProto);
}
libraryKeyProto.Crosslinkers.Add(crosslinkProto);
}
return(libraryKeyProto);
}
public static LibraryKey Read(ValueCache valueCache, Stream stream)
{
int length = PrimitiveArrays.ReadOneValue <int>(stream);
byte[] buffer = new byte[length];
stream.Read(buffer, 0, length);
var proto = new LibraryKeyProto();
proto.MergeFrom(new CodedInputStream(buffer));
switch (proto.KeyType)
{
case LibraryKeyProto.Types.KeyType.Peptide:
return(new PeptideLibraryKey(proto.ModifiedSequence, proto.Charge).ValueFromCache(valueCache));
case LibraryKeyProto.Types.KeyType.PrecursorMz:
return(new PrecursorLibraryKey(proto));
case LibraryKeyProto.Types.KeyType.SmallMolecule:
return(new MoleculeLibraryKey(valueCache, proto));
case LibraryKeyProto.Types.KeyType.Crosslink:
return(new CrosslinkLibraryKey(proto));
}
return(null);
}
public PrecursorLibraryKey(LibraryKeyProto libraryKeyProto)
{
Mz = libraryKeyProto.PrecursorMz;
if (0 != libraryKeyProto.RetentionTime)
{
RetentionTime = libraryKeyProto.RetentionTime;
}
}
public CrosslinkLibraryKey(LibraryKeyProto libraryKeyProto)
{
PeptideLibraryKeys = ImmutableList.ValueOf(libraryKeyProto.CrosslinkedSequences
.Select(sequence => new PeptideLibraryKey(sequence, 0)));
Crosslinks = ImmutableList.ValueOf(libraryKeyProto.Crosslinkers.Select(crosslinkProto =>
new Crosslink(crosslinkProto.Name, crosslinkProto.Positions.Select(pos => pos.Position.ToArray()))));
Charge = libraryKeyProto.Charge;
}
internal MoleculeLibraryKey(ValueCache valueCache, LibraryKeyProto libraryKeyProto) : this(
valueCache,
SmallMoleculeLibraryAttributes.Create(
valueCache.CacheValue(libraryKeyProto.MoleculeName),
valueCache.CacheValue(libraryKeyProto.ChemicalFormula),
libraryKeyProto.InChiKey, libraryKeyProto.OtherKeys),
Adduct.FromString(libraryKeyProto.Adduct, Adduct.ADDUCT_TYPE.non_proteomic, null))
{
}
