public XmlFastaSequence(FastaSeqV01 sequence, XmlPeptide[] peptides)
{
Name = sequence.Id;
if (sequence.Descriptions.Length > 0)
{
Description = sequence.Descriptions[0];
List<XmlAlternativeProtein> alternatives = new List<XmlAlternativeProtein>();
for (int i = 1; i < sequence.Descriptions.Length; i++)
{
string desc = sequence.Descriptions[i].Trim();
int space = desc.IndexOf(' ');
if (space > 0)
alternatives.Add(new XmlAlternativeProtein(desc.Substring(0, space), desc.Substring(space + 1)));
else
alternatives.Add(new XmlAlternativeProtein(desc, null));
}
if (alternatives.Count > 0)
Alternatives = alternatives.ToArray();
}
PeptideList = sequence.PeptideList;
Sequence = FormatAA(sequence.AA);
Peptides = peptides;
}
public PepV01(FastaSeqV01 fastaSequence, int begin, int end, int missedCleavages,
double mh, double? rt)
: this(fastaSequence, begin, end, missedCleavages)
{
MassH = mh;
PredictedRetentionTime = rt;
}
public PepV01(FastaSeqV01 fastaSequence, int begin, int end, int missedCleavages)
{
_fastaSequence = fastaSequence;
Begin = begin;
End = end;
MissedCleavages = missedCleavages;
// Derived value
Sequence = _fastaSequence.AA.Substring(Begin, End - Begin);
}
public PepV01 GetModel(FastaSeqV01 sequence)
{
double mh = NeutralMass + BioMassCalc.MassProton;
return new PepV01(sequence, Begin, End, MissedCleavages, mh, PredictedRetentionTime);
}