public override bool Equals(object obj)
{
AASeq other = obj as AASeq;
if (other == null)
{
return(false);
}
else
{
return(ToString() == other.ToString());
}
}
public static NamedSequence GetConsensus(List <NamedSequence> seqs)
{
int len = -1;
//StringBuilder consensusSeq = new StringBuilder();
List <AASeq> aaSeqs = new List <AASeq>();
bool isDna = seqs[0].IsDna();
foreach (NamedSequence seq in seqs)
{
AASeq aaSeq = isDna ? DnaSeq.GetInstance(seq.Sequence, MixtureSemantics.Uncertainty) : AASeq.GetInstance(seq.Sequence, MixtureSemantics.Uncertainty);
len = Math.Max(len, aaSeq.Count);
//if (len < 0)
//{
// len = aaSeq.Count;
//}
//else
//{
// Helper.CheckCondition(len == aaSeq.Count, String.Format("Sequence {0} is a different length from previous sequences", seq.Name));
//}
aaSeqs.Add(aaSeq);
}
//for (int i = 0; i < len; i++)
//{
// Dictionary<string, int> charToCount = new Dictionary<string, int>();
// KeyValuePair<string, int> currentConsensus = new KeyValuePair<string, int>("z", -1);
// foreach (AASeq aaSeq in aaSeqs)
// {
// if (i < aaSeq.Count)
// {
// string residue = aaSeq.SubSeqAA0Pos(i, 1).ToString();
// charToCount[residue] = SpecialFunctions.GetValueOrDefault(charToCount, residue) + 1;
// if (charToCount[residue] > currentConsensus.Value)
// {
// currentConsensus = new KeyValuePair<string, int>(residue, charToCount[residue]);
// }
// }
// }
// consensusSeq.Append(currentConsensus.Key);
//}
AASeq consensusAaSeq = GetAaSeqConsensus(aaSeqs);
NamedSequence consensus = new NamedSequence("consensus", consensusAaSeq.ToString());
return(consensus);
}