public IEnumerable <string> SparseLineMerEnumeration(bool keepOneValueVariables, int merLength)
{
if (_caseIdToAASeq.Count == 0)
{
Debug.Assert(SequenceLengthOrNull == null); // real assert
yield break;
}
Helper.CheckCondition(SequenceLengthOrNull != null, "This converter to sparse assumes all sequences have the same length");
Dictionary <string, AASeq> caseToCompressedAASeq = RemoveDeletesAndStopsFromData(false, Console.Error);
foreach (string mer in EveryUnambiguousStopFreeMer(merLength, caseToCompressedAASeq))
{
Regex merAsRegex = AASeq.CreateMerRegex(mer); //!!!look for similar code elsewhere
foreach (string protein in EveryProtein())
{
Set <bool> valueSet = Set <bool> .GetInstance();
Dictionary <string, bool> caseToVal = new Dictionary <string, bool>();
foreach (string caseId in caseToCompressedAASeq.Keys)
{
AASeq aaSeq = caseToCompressedAASeq[caseId];
Helper.CheckCondition(aaSeq.MixtureSemantics == MixtureSemantics.Uncertainty, "Code does not expect Mixture semantics");
bool?containsOrNull = aaSeq.ContainsMer(mer, merAsRegex, protein);
if (null == containsOrNull)
{
continue;
}
else if ((bool)containsOrNull)
{
caseToVal.Add(caseId, true);
valueSet.AddNewOrOld(true);
}
else
{
caseToVal.Add(caseId, false);
valueSet.AddNewOrOld(false);
}
}
if (keepOneValueVariables || valueSet.Count == 2)
{
foreach (KeyValuePair <string, bool> caseIdAndVal in caseToVal)
{
string variableName = protein + "@" + mer;
yield return(Helper.CreateTabString(
variableName, caseIdAndVal.Key, caseIdAndVal.Value ? 1 : 0));
}
}
}
}
}
private Dictionary <string, bool> FindMerValues(string merAsString, Dictionary <string, AASeq> caseToCompressedAASeq, out Dictionary <bool, int> valueToNonZeroCount)
{
Regex merAsRegex = AASeq.CreateMerRegex(merAsString);
Dictionary <string, bool> merValues = new Dictionary <string, bool>();
valueToNonZeroCount = new Dictionary <bool, int>();
foreach (KeyValuePair <string, AASeq> caseIdAndCompressedAASeq in caseToCompressedAASeq)
{
string caseId = caseIdAndCompressedAASeq.Key;
AASeq compressedAASeq = caseIdAndCompressedAASeq.Value;
bool?containsMer = compressedAASeq.ContainsMer(merAsString, merAsRegex);
if (null != containsMer)
{
merValues.Add(caseId, (bool)containsMer);
valueToNonZeroCount[(bool)containsMer] = 1 + valueToNonZeroCount.GetValueOrDefault((bool)containsMer);
}
}
return(merValues);
}
