//public void CreateSparseFile(string outputFileName, bool keepOneValueVariables)
//{
// CreateSparseFile(outputFileName, keepOneValueVariables);
//}
private Dictionary <string, AASeq> RemoveDeletesAndStopsFromData(TextWriter textWriter)
{
Dictionary <string, AASeq> compressedDictionary = new Dictionary <string, AASeq>();
foreach (KeyValuePair <string, AASeq> caseIdAndAASeq in _caseIdToAASeq)
{
AASeq compressedAASeq = AASeq.GetCompressedInstance(caseIdAndAASeq.Key, caseIdAndAASeq.Value, textWriter);
compressedDictionary.Add(caseIdAndAASeq.Key, compressedAASeq);
}
return(compressedDictionary);
}