public override IEnumerable <string> Process(string sourceDatabase)
{
StringBuilder sb = new StringBuilder();
List <int> seqLengths = new List <int>();
List <Sequence> source = new List <Sequence>();
if (contaminantFile != null)
{
Progress.SetMessage("Reading contaminant proteins : " + contaminantFile + " ...");
ReadFile(source, contaminantFile, sb, seqLengths);
}
Progress.SetMessage("Reading " + sourceDatabase + " ...");
ReadFile(source, sourceDatabase, sb, seqLengths);
List <string> shuffledSeqs = UShuffle.Shuffle(sb.ToString(), klet, repeat);
List <string> result = new List <string>();
for (int i = 0; i < repeat; i++)
{
string targetFilename;
if (combined)
{
targetFilename = FileUtils.ChangeExtension(sourceDatabase, MyConvert.Format("SHUFFLED{0}-{1}.fasta", klet, i + 1));
}
else
{
targetFilename = FileUtils.ChangeExtension(sourceDatabase, MyConvert.Format("SHUFFLED{0}-{1}_ONLY.fasta", klet, i + 1));
}
var shuffledSeq = shuffledSeqs[i];
using (StreamWriter sw = new StreamWriter(targetFilename))
{
source.ForEach(m => ff.WriteSequence(sw, m));
int index = 0;
int pos = 0;
foreach (var length in seqLengths)
{
index++;
var name = "SHF_" + index.ToString().PadLeft(8, '0');
var seq = new Sequence(name, shuffledSeq.Substring(pos, length));
pos += length;
ff.WriteSequence(sw, seq);
}
}
result.Add(targetFilename);
}
Progress.SetMessage("Finished.");
return(result);
}
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);
}
}
}
