public int[] GetSequenceCoverage(IEnumerable <IAminoAcidSequence> peptides)
{
int[] bits = new int[Length];
string leucineSequence = RepresentativeProtein.GetLeucineSequence();
foreach (IAminoAcidSequence pep in peptides)
{
int start_index = 0;
while (true)
{
int index = leucineSequence.IndexOf(pep.GetLeucineSequence(), start_index);
start_index = index + 1;
if (index < 0)
{
break;
}
for (int aa = index; aa < index + pep.Length; aa++)
{
bits[aa]++;
}
}
}
return(bits);
}
public string ToParsimonyProteins(ExperimentGroup exp, bool duplexQuant = false, bool useOnlyCompleteSets = false)
{
StringBuilder sb = new StringBuilder(512);
sb.AppendFormat("{0},{1},{2},{3:G4},{4:G4},{5:G4},{6},{7},{8},{9},", Name, Description, LongestProteinLen, SequenceCoverage, RepresentativeProtein.CalculateSequenceCoverage(Peptides.Where(pep => !pep.IsShared)), SequenceRedundacy, Count, UniquePeptides, Peptides.Count, Peptides.Count(pep => pep.IsShared));
if (exp != null)
{
int psms;
HashSet <Peptide> uniquepeps;
UniquePeptidesPerGroup.TryGetValue(exp, out uniquepeps);
PsmsPerGroup.TryGetValue(exp, out psms);
sb.Append(psms);
sb.Append(',');
if (uniquepeps != null)
{
sb.Append(uniquepeps.Count);
}
sb.Append(',');
sb.Append(uniquepeps.Count(pep => pep.IsShared));
sb.Append(',');
}
sb.Append(PScore.ToString(CultureInfo.InvariantCulture));
if (exp != null && exp.UseQuant)
{
Quantitation quant;
if (Quantitation.TryGetValue(exp.Name, out quant))
{
sb.Append(',');
sb.Append(quant.PSMs);
sb.Append(',');
sb.Append(quant.UniquePeptides.Count);
sb.Append(',');
sb.Append(quant.ToOutput(duplexQuant, exp.MeidanLog2Ratio, useOnlyCompleteSets));
}
else
{
sb.Append(",0,0");
for (int i = 0; i < exp.QuantPlex * 4; i++)
{
sb.Append(",-");
}
if (duplexQuant)
{
sb.Append(",N/A,N/A");
}
}
}
if (ProteinHoarder.AnnotationType != AnnotationType.None)
{
sb.Append(',');
sb.Append(ProteinIdsString());
sb.Append(',');
sb.Append(GeneNamesString());
}
return(sb.ToString());
}