public int CompareTo(object obj)
{
AASequence other = (AASequence)obj;
int min = Math.Min(sequence.Length, other.sequence.Length);
for (int i = 0; i < min; i++)
{
if (sequence[i] != other.sequence[i])
{
if (sequence[i] < other.sequence[i])
{
return(-1);
}
return(1);
}
}
if (sequence.Length != other.sequence.Length)
{
if (sequence.Length < other.sequence.Length)
{
return(-1);
}
return(1);
}
if (len != other.len)
{
if (len < other.len)
{
return(-1);
}
return(1);
}
return(0);
}
public Protein(BinaryReader reader)
{
sequence = AASequence.Read(reader).ToString();
sequenceData = new Sequence(sequence);
accession = FileUtil.ReadString(reader);
description = FileUtil.ReadString(reader);
molecularWeight = reader.ReadDouble();
}
public static AASequence Read(BinaryReader reader)
{
try {
AASequence result = new AASequence();
result.len = reader.ReadInt32();
result.sequence = new ulong[reader.ReadInt32()];
for (int i = 0; i < result.sequence.Length; i++)
{
result.sequence[i] = reader.ReadUInt64();
}
return(result);
}catch (EndOfStreamException) {
return(null);
}
}
public static Peptide Read(BinaryReader reader)
{
Peptide result = new Peptide();
result.sequence = AASequence.Read(reader);
if (result.sequence == null)
{
return(null);
}
result.monoIsotopicMass = reader.ReadDouble();
int nproteins = reader.ReadInt32();
for (int i = 0; i < nproteins; i++)
{
result.proteinIndices.Add(reader.ReadInt32());
result.proteinOffsets.Add(reader.ReadInt32());
result.residueBefore.Add(reader.ReadByte());
result.residueAfter.Add(reader.ReadByte());
}
result.fixedModifications = PeptideModificationState.Read(reader);
return(result);
}
public override bool Equals(object obj)
{
if (this == obj)
{
return(true);
}
if (obj is AASequence)
{
AASequence other = (AASequence)obj;
if (other.len != len)
{
return(false);
}
for (int i = 0; i < sequence.Length; i++)
{
if (sequence[i] != other.sequence[i])
{
return(false);
}
}
return(true);
}
return(false);
}
public Peptide(string sequence)
{
this.sequence = new AASequence(sequence);
monoIsotopicMass = MonoIsotopicMass;
fixedModifications = new PeptideModificationState(sequence.Length);
}
