public void Test()
{
PseudoSequenceBuilder builder = new PseudoSequenceBuilder("KR", false);
Sequence seq = new Sequence("TEST", "EISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSK");
builder.Build(seq);
Assert.AreEqual("EISQVFEIALRKNLPVNFEVAERSGPPHMNKFVTVKSVGEFVGEGEGSKK", seq.SeqString);
}
public void Test()
{
PseudoSequenceBuilder builder = new PseudoSequenceBuilder("KR", false);
Sequence seq = new Sequence("TEST", "EISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSK");
builder.Build(seq);
Assert.AreEqual("EISQVFEIALRKNLPVNFEVAERSGPPHMNKFVTVKSVGEFVGEGEGSKK", seq.SeqString);
}
private void ProcessFile(ref int index, StreamWriter sw, string fastaFile, bool isContaminant)
{
FastaFormat ff = new FastaFormat();
using (StreamReader sr = new StreamReader(fastaFile))
{
Progress.SetRange(0, sr.BaseStream.Length);
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
Progress.SetPosition(StreamUtils.GetCharpos(sr));
if (isContaminant)
{
if (!seq.Reference.StartsWith("CON_"))
{
seq.Reference = "CON_" + seq.Reference;
}
}
if (combined)
{
ff.WriteSequence(sw, seq);
}
if (pseudoAminoacid)
{
builder.Build(seq);
}
index++;
Sequence reversedSeq = SequenceUtils.GetReversedSequence(seq.SeqString, index);
ff.WriteSequence(sw, reversedSeq);
}
}
}
