static public CaseIdToAASeq GetInstance()
{
CaseIdToAASeq caseId = new CaseIdToAASeq();
caseId._caseIdToAASeq = new Dictionary <string, AASeq>();
return(caseId);
}
// /*
// 1189MB MEPVDPNLEPWNHPGSQPKTPCTNCYCKHCSYHCLVCFQTKGLGISYGRK
// J112MA MEPVDPNLEPWNHPGSQPITACNKCYCKYCSYHCLVCFQTKGLGISYGRK
// 1157M3M MEPVDPNLEPWNHPGSQPKTPCNKCYCKHCSYHCLVCFQTKGLGISYGRK
// 1195MB MEPVDPNLEPWNHPGSQPKTPCNKCYCKYCSYHCLVCFQTKGLGISYGRK
// */
static public CaseIdToAASeq GetInstance(TextReader textReader, MixtureSemantics mixtureSemantics, int offset)
{
CaseIdToAASeq caseIdToAASeq = CaseIdToAASeq.GetInstance();
foreach (Dictionary <string, string> row in SpecialFunctions.TabFileTable(textReader, "cid\taaSeq", false))
{
string caseId = row["cid"]; //!!!const
string aaSeqAsString = row["aaSeq"]; //!!!const
AASeq aaSeq = AASeq.GetInstance(aaSeqAsString, mixtureSemantics, offset);
caseIdToAASeq.Add(caseId, aaSeq);
}
return(caseIdToAASeq);
}
public void WriteAsTable(List <NamedSequence> sequences, TextWriter writer)
{
CaseIdToAASeq cidToAASeq = CaseIdToAASeq.GetInstance();
bool isDna = sequences[0].IsDna();
foreach (NamedSequence seq in sequences)
{
cidToAASeq.Add(seq.Name,
isDna ?
DnaSeq.GetInstance(seq.Sequence, MixtureSemantics) :
AASeq.GetInstance(seq.Sequence, MixtureSemantics));
}
List <string> header = new List <string>(sequences.Count + 1);
header.Add("Var");
header.AddRange(sequences.Select(seq => seq.Name));
writer.WriteLine(header.StringJoin("\t"));
int maxLen = cidToAASeq.Dictionary.Values.Select(aaSeq => aaSeq.Count).Max();
for (int pos0 = 0; pos0 < maxLen; pos0++)
{
foreach (char aa in cidToAASeq.EveryAminoAcid(pos0))
{
string merAndPos = (pos0 + 1) + "@" + aa;
int?[] values = new int?[sequences.Count];
HashSet <int> nonMissingValues = new HashSet <int>();
for (int pidIdx = 0; pidIdx < sequences.Count; pidIdx++)
{
int? value;
Set <char> observedAAs = cidToAASeq.Dictionary[sequences[pidIdx].Name][pos0];
if (observedAAs.Contains('?') || observedAAs.Count == 0 ||
(observedAAs.Count > 1 && MixtureSemantics == MixtureSemantics.Uncertainty && observedAAs.Contains(aa)))
{
value = null;
}
else if (observedAAs.Contains(aa) && (MixtureSemantics != MixtureSemantics.Pure || observedAAs.Count == 1))
{
value = 1;
}
else
{
value = 0;
}
values[pidIdx] = value;
if (value != null)
{
nonMissingValues.Add((int)value);
}
}
if (nonMissingValues.Count > 1 || (KeepOneValueVariables && nonMissingValues.Count == 1 && nonMissingValues.First() == 1))
{
writer.WriteLine(Helper.CreateTabString(merAndPos, values.Select(v => v.HasValue ? v.ToString() : MissingStatistics.GetInstance().ToString()).StringJoin("\t")));
}
}
}
writer.Flush();
}