private static Dictionary <string, Dictionary <string, int> > CreateMerStringToOriginalAA0PositionToCount(int merLength, TextWriter textWriterForWarnings, Dictionary <string, AASeq> caseToCompressedAASeq)
{
Dictionary <string, Dictionary <string, int> > merStringToOriginalAA0PositionToCount = new Dictionary <string, Dictionary <string, int> >();
foreach (string caseId in caseToCompressedAASeq.Keys)
{
AASeq aaSeq = caseToCompressedAASeq[caseId];
Set <string> SeenIt = new Set <string>();
foreach (AASeq mer in aaSeq.SubSeqEnumeration(merLength))
{
if (mer.Ambiguious)
{
continue;
}
string merString = mer.ToString();
if (SeenIt.Contains(merString))
{
textWriterForWarnings.WriteLine("Warning: Mer '{0}' appears again in case '{1}'", merString, caseId);
}
SeenIt.AddNewOrOld(merString);
string originalAA1Position = mer.OriginalAA1Position(0);
Dictionary <string, int> originalAA0PositionToCount = SpecialFunctions.GetValueOrDefault(merStringToOriginalAA0PositionToCount, merString);
originalAA0PositionToCount[originalAA1Position] = 1 + SpecialFunctions.GetValueOrDefault(originalAA0PositionToCount, originalAA1Position);
}
}
return(merStringToOriginalAA0PositionToCount);
}
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);
}
static public AASeq GetInstance(string aaSeqAsString, bool mixture)
{
AASeq aaSeq = new AASeq(mixture);
aaSeq.Sequence = CreateSequence(aaSeqAsString);
return(aaSeq);
}
internal IEnumerable <AASeq> SubSeqEnumeration(int merLength)
{
for (int startIndex = 0; startIndex <= Sequence.Count - merLength; ++startIndex)
{
AASeq aaSeqOut = SubSeqAA0Pos(startIndex, merLength);
yield return(aaSeqOut);
}
}
static public AASeq GetInstance(string aaSeqAsString, List <string> originalAA1PositionTable, bool mixture)
{
AASeq aaSeq = new AASeq(mixture);
aaSeq.Sequence = CreateSequence(aaSeqAsString);
SpecialFunctions.CheckCondition(aaSeq.Count == originalAA1PositionTable.Count, "aaSeq and position table must be same length");
aaSeq._originalAA1PositionTableOrNull = originalAA1PositionTable;
return(aaSeq);
}
public bool TrySubSeqAA0Pos(int aa0Pos, int merLength, out AASeq aaSeq)
{
if (aa0Pos < 0 || aa0Pos + merLength > this.Sequence.Count)
{
aaSeq = null;
return(false);
}
aaSeq = SubSeqAA0Pos(aa0Pos, merLength);
return(true);
}
//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);
}
public void Add(string caseId, AASeq aaSeq)
{
SpecialFunctions.CheckCondition(!_caseIdToAASeq.ContainsKey(caseId), string.Format("caseId {0} appears more than once", caseId));
if (null == SequenceLength)
{
SequenceLength = aaSeq.Count;
}
if (SequenceLength != aaSeq.Count)
{
Console.WriteLine("Warning: Not all amino acid sequences are of the same length");
}
_caseIdToAASeq.Add(caseId, aaSeq);
}
public override bool Equals(object obj)
{
AASeq other = obj as AASeq;
if (other == null)
{
return(false);
}
else
{
return(Sequence == other.Sequence);
}
}
// /*
// 1189MB MEPVDPNLEPWNHPGSQPKTPCTNCYCKHCSYHCLVCFQTKGLGISYGRK
// J112MA MEPVDPNLEPWNHPGSQPITACNKCYCKYCSYHCLVCFQTKGLGISYGRK
// 1157M3M MEPVDPNLEPWNHPGSQPKTPCNKCYCKHCSYHCLVCFQTKGLGISYGRK
// 1195MB MEPVDPNLEPWNHPGSQPKTPCNKCYCKYCSYHCLVCFQTKGLGISYGRK
// */
static public CaseIdToAASeq GetInstance(TextReader textReader, bool mixture)
{
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, mixture);
caseIdToAASeq.Add(caseId, aaSeq);
}
return(caseIdToAASeq);
}
public AASeq SubSeqAA0Pos(int aa0Pos, int merLength)
{
List <Set <char> > subSequence = SpecialFunctions.SubList(Sequence, aa0Pos, merLength);
AASeq aaSeqOut = new AASeq(Mixture);
aaSeqOut.Sequence = subSequence;
aaSeqOut._originalAA1PositionTableOrNull = new List <string>();
for (int aa0 = aa0Pos; aa0 < aa0Pos + merLength; ++aa0)
{
string originalAA1Position = OriginalAA1Position(aa0);
aaSeqOut._originalAA1PositionTableOrNull.Add(originalAA1Position);
}
return(aaSeqOut);
}
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 + SpecialFunctions.GetValueOrDefault(valueToNonZeroCount, (bool)containsMer);
}
}
return(merValues);
}
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));
}
}
}
}
}
public bool TrySubSeqAA1Pos(int aa1Pos, int merLength, out AASeq aaSeq)
{
return(TrySubSeqAA0Pos(aa1Pos - 1, merLength, out aaSeq));
}
