static public AASeq GetCompressedInstance(string caseId, AASeq aaSeqIn, TextWriter errorStream)
{
AASeq aaSeqOut = new AASeq(aaSeqIn.Mixture);
aaSeqOut.Sequence = new List <Set <char> >();
aaSeqOut._originalAA1PositionTableOrNull = new List <string>();
for (int iChar = 0; iChar < aaSeqIn.Count; ++iChar)
{
Set <char> set = aaSeqIn[iChar];
string originalAA1Position = aaSeqIn.OriginalAA1Position(iChar);
if (set.Equals(Delete)) //!!!const
{
continue;
}
if (set.Equals(Stop)) //!!!const
{
if (iChar != aaSeqIn.Count - 1)
{
errorStream.WriteLine("Warning: The sequence for case id '{0}' contains a '*' before the last position", caseId);
}
break;
}
aaSeqOut.Sequence.Add(set);
aaSeqOut._originalAA1PositionTableOrNull.Add(originalAA1Position);
}
return(aaSeqOut);
}
public IEnumerable <string> SparseLineEnumeration(bool keepOneValueVariables)
{
if (_caseIdToAASeq.Count == 0)
{
Debug.Assert(SequenceLength == null); // real assert
yield break;
}
SpecialFunctions.CheckCondition(SequenceLength != null, "This converter to sparse assumes all sequences have the same length");
/*
* n1pos aa pid val
* 880 A 3 F
* 880 A 5 F
* 880 A 9 F
* 880 A 13 F
* 880 A 14 F
* 880 A 15 T
* ...
*/
for (int aa0Pos = 0; aa0Pos < (int)SequenceLength; ++aa0Pos)
{
Set <char> everyAminoAcid = EveryAminoAcid(aa0Pos);
if (!keepOneValueVariables && everyAminoAcid.Count == 1)
{
continue;
}
string posName = null;
foreach (char aa in everyAminoAcid)
{
Set <bool> valueSet = Set <bool> .GetInstance();
Dictionary <string, bool> caseToVal = new Dictionary <string, bool>();
foreach (string caseId in _caseIdToAASeq.Keys)
{
AASeq aaSeq = _caseIdToAASeq[caseId];
//SpecialFunctions.CheckCondition(aaSeq.IsUsingOriginalPositions(), "This converter to sparse assumes all sequences are using their original positions");
Set <char> strainAASet = aaSeq[aa0Pos];
if (posName == null)
{
posName = aaSeq.OriginalAA1Position(aa0Pos);
}
else
{
SpecialFunctions.CheckCondition(posName == aaSeq.OriginalAA1Position(aa0Pos));
}
// missing: e.g. A/Any or A/AB
// 1: e.g. A/A
// 0: e.g. A/B or A/BCD
if (strainAASet.Equals(AASeq.Any))
{
//Do nothing - missing
}
else if (strainAASet.Contains(aa))
{
if (strainAASet.Count > 1)
{
if (aaSeq.Mixture)
{
caseToVal.Add(caseId, false);
valueSet.AddNewOrOld(false);
}
else
{
// Do nothing = missing
}
}
else
{
caseToVal.Add(caseId, true);
valueSet.AddNewOrOld(true);
}
}
else
{
caseToVal.Add(caseId, false);
valueSet.AddNewOrOld(false);
}
}
SpecialFunctions.CheckCondition(posName != null);
if (keepOneValueVariables || valueSet.Count == 2)
{
foreach (KeyValuePair <string, bool> caseIdAndVal in caseToVal)
{
//string variableName = string.Format("{0}@{1}", posName, aa);
string variableName = string.Format("{1}@{0}", posName, aa);
yield return(SpecialFunctions.CreateTabString(
variableName, caseIdAndVal.Key, caseIdAndVal.Value ? 1 : 0));
}
}
}
}
}
