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.Ambiguous)
{
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 = merStringToOriginalAA0PositionToCount.GetValueOrDefault(merString);
originalAA0PositionToCount[originalAA1Position] = 1 + originalAA0PositionToCount.GetValueOrDefault(originalAA1Position);
}
}
return(merStringToOriginalAA0PositionToCount);
}
public 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, MixtureSemantics mixtureSemantics, int offset)
{
AASeq aaSeq = new AASeq(aaSeqAsString, mixtureSemantics, offset);
//aaSeq.Sequence = aaSeq.CreateCharSetList(aaSeqAsString);
//aaSeq.Offset = offset;
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);
}
static public AASeq GetInstance(string aaSeqAsString, List <string> originalAA1PositionTable, MixtureSemantics mixtureSemantics)
{
Helper.CheckCondition(null != originalAA1PositionTable, "must give a position table");
AASeq aaSeq = new AASeq(mixtureSemantics);
aaSeq.Sequence = aaSeq.CreateCharSetList(aaSeqAsString);
Helper.CheckCondition(aaSeq.Count == originalAA1PositionTable.Count, "aaSeq and position table must be same length");
aaSeq._originalAA1PositionTableOrNull = originalAA1PositionTable;
return(aaSeq);
}
//public void CreateSparseFile(string outputFileName, bool keepOneValueVariables)
//{
// CreateSparseFile(outputFileName, keepOneValueVariables);
//}
private Dictionary <string, AASeq> RemoveDeletesAndStopsFromData(bool stopOnStop, 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, stopOnStop, textWriter);
compressedDictionary.Add(caseIdAndAASeq.Key, compressedAASeq);
}
return(compressedDictionary);
}
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));
}
}
}
}
}
public override bool Equals(object obj)
{
AASeq other = obj as AASeq;
if (other == null)
{
return(false);
}
else
{
return(ToString() == other.ToString());
}
}
// /*
// 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);
}
//static public CaseIdToAASeq GetInstance(TextReader textReader, bool mixture)
//{
// return GetInstance(textReader, mixture, 0);
//}
public void Add(string caseId, AASeq aaSeq)
{
Helper.CheckCondition(!_caseIdToAASeq.ContainsKey(caseId), string.Format("caseId {0} appears more than once", caseId));
//!!!1205x
if (null == SequenceLengthOrNull)
{
SequenceLengthOrNull = aaSeq.Count;
}
if (SequenceLengthOrNull != aaSeq.Count)
{
Console.Error.WriteLine("Warning: Not all amino acid sequences are of the same length");
}
_caseIdToAASeq.Add(caseId, aaSeq);
}
public void SplitOnProtein(string niceName, string outputDirectory)
{
Debug.WriteLine(niceName);
Dictionary <string, Dictionary <string, string> > proteinToCaseIdToSequence = new Dictionary <string, Dictionary <string, string> >();
foreach (string caseId in _caseIdToAASeq.Keys)
{
AASeq aaSeq = _caseIdToAASeq[caseId];
string previousProtein = null;
Dictionary <string, StringBuilder> proteinToSequence = new Dictionary <string, StringBuilder>();
for (int aa0Pos = 0; aa0Pos < (int)SequenceLengthOrNull; ++aa0Pos)
{
string posName = aaSeq.OriginalAA1Position(aa0Pos);
string[] posParts = posName.Split('@');
string protein = posParts[0];
StringBuilder sequence = proteinToSequence.GetValueOrDefault(protein);
if (previousProtein != protein)
{
Helper.CheckCondition(sequence.Length == 0, "Expect proteins to be contintiguous");
previousProtein = protein;
}
Set <char> strainAASet = aaSeq[aa0Pos];
sequence.Append(AASeq.AaAsString(strainAASet));
}
foreach (string protein in proteinToSequence.Keys)
{
Dictionary <string, string> caseIdToSequence = proteinToCaseIdToSequence.GetValueOrDefault(protein);
caseIdToSequence.Add(caseId, proteinToSequence[protein].ToString());
}
}
foreach (string protein in proteinToCaseIdToSequence.Keys)
{
string outputFileName = string.Format(@"{0}\{1}.{2}.aaSeq.txt", outputDirectory, protein, niceName);
using (TextWriter textWriter = File.CreateText(outputFileName))
{
textWriter.WriteLine("cid\taaSeq"); //!!!const
Dictionary <string, string> caseIdToSequence = proteinToCaseIdToSequence[protein];
foreach (string caseId in caseIdToSequence.Keys)
{
textWriter.WriteLine(Helper.CreateTabString(caseId, caseIdToSequence[caseId]));
}
}
}
}
public static NamedSequence GetConsensus(List <NamedSequence> seqs)
{
int len = -1;
//StringBuilder consensusSeq = new StringBuilder();
List <AASeq> aaSeqs = new List <AASeq>();
bool isDna = seqs[0].IsDna();
foreach (NamedSequence seq in seqs)
{
AASeq aaSeq = isDna ? DnaSeq.GetInstance(seq.Sequence, MixtureSemantics.Uncertainty) : AASeq.GetInstance(seq.Sequence, MixtureSemantics.Uncertainty);
len = Math.Max(len, aaSeq.Count);
//if (len < 0)
//{
// len = aaSeq.Count;
//}
//else
//{
// Helper.CheckCondition(len == aaSeq.Count, String.Format("Sequence {0} is a different length from previous sequences", seq.Name));
//}
aaSeqs.Add(aaSeq);
}
//for (int i = 0; i < len; i++)
//{
// Dictionary<string, int> charToCount = new Dictionary<string, int>();
// KeyValuePair<string, int> currentConsensus = new KeyValuePair<string, int>("z", -1);
// foreach (AASeq aaSeq in aaSeqs)
// {
// if (i < aaSeq.Count)
// {
// string residue = aaSeq.SubSeqAA0Pos(i, 1).ToString();
// charToCount[residue] = SpecialFunctions.GetValueOrDefault(charToCount, residue) + 1;
// if (charToCount[residue] > currentConsensus.Value)
// {
// currentConsensus = new KeyValuePair<string, int>(residue, charToCount[residue]);
// }
// }
// }
// consensusSeq.Append(currentConsensus.Key);
//}
AASeq consensusAaSeq = GetAaSeqConsensus(aaSeqs);
NamedSequence consensus = new NamedSequence("consensus", consensusAaSeq.ToString());
return(consensus);
}
public AASeq SubSeqAA0Pos(int aa0Pos, int merLength, bool skipDelete)
{
List <Set <char> > subSequence = new List <Set <char> >();
AASeq aaSeqOut = new AASeq(MixtureSemantics);
aaSeqOut.Sequence = subSequence;
aaSeqOut._originalAA1PositionTableOrNull = new List <string>();
Debug.Assert(aaSeqOut.Offset == 0); // real assert
for (int aa0 = aa0Pos; aa0 < aa0Pos + merLength; ++aa0)
{
Set <char> charSet = Sequence[aa0];
if (!skipDelete || !AASeq.Delete.Equals(charSet))
{
string originalAA1Position = OriginalAA1Position(aa0);
aaSeqOut._originalAA1PositionTableOrNull.Add(originalAA1Position);
subSequence.Add(charSet);
}
}
return(aaSeqOut);
}
public void TriplesAppend(ref Set <string> seenTriple, ref Dictionary <string, List <string> > proteinToTripleList)
{
AASeq aaSeq = GetFirstAASeq();
for (int aa0Pos = 0; aa0Pos < (int)SequenceLengthOrNull; ++aa0Pos)
{
string posName = aaSeq.OriginalAA1Position(aa0Pos);
string[] posParts = posName.Split('@');
string protein = posParts[0];
string hxb2Pos = posParts[2];
string triple = Helper.CreateTabString(protein, hxb2Pos);
if (!seenTriple.Contains(triple))
{
seenTriple.AddNew(triple);
List <string> tripleList = proteinToTripleList.GetValueOrDefault(protein);
tripleList.Add(triple);
}
}
}
public IEnumerable <AASeq> BlowOut()
{
foreach (List <char> possibleSeq in SpecialFunctions.EveryCombination <char>(this.Sequence))
{
List <Set <char> > subSequence = new List <Set <char> >();
AASeq aaSeqOut = new AASeq(MixtureSemantics);
aaSeqOut.Sequence = subSequence;
aaSeqOut._originalAA1PositionTableOrNull = new List <string>();
Debug.Assert(aaSeqOut.Offset == 0); // real assert
for (int aa0 = 0; aa0 < Count; ++aa0)
{
Set <char> charSet = Set <char> .GetInstance(possibleSeq[aa0]);
Helper.CheckCondition(!AASeq.Delete.Equals(charSet), "'delete' not expected");
string originalAA1Position = OriginalAA1Position(aa0);
aaSeqOut._originalAA1PositionTableOrNull.Add(originalAA1Position);
subSequence.Add(charSet);
}
yield 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 + valueToNonZeroCount.GetValueOrDefault((bool)containsMer);
}
}
return(merValues);
}
public static AASeq GetAaSeqConsensus(List <AASeq> aaSeqs)
{
int len = -1;
StringBuilder consensusSeq = new StringBuilder();
foreach (AASeq seq in aaSeqs)
{
len = Math.Max(len, seq.Count);
}
for (int pos0 = 0; pos0 < len; pos0++)
{
consensusSeq.Append(AASeq.CountAasAtPos(aaSeqs, pos0)[0].Key);
}
//for (int i = 0; i < len; i++)
//{
// Dictionary<string, int> charToCount = new Dictionary<string, int>();
// KeyValuePair<string, int> currentConsensus = new KeyValuePair<string, int>("z", -1);
// foreach (AASeq aaSeq in aaSeqs)
// {
// if (i < aaSeq.Count)
// {
// string residue = aaSeq.SubSeqAA0Pos(i, 1).ToString();
// charToCount[residue] = charToCount.GetValueOrDefault(residue) + 1;
// if (charToCount[residue] > currentConsensus.Value)
// {
// currentConsensus = new KeyValuePair<string, int>(residue, charToCount[residue]);
// }
// }
// }
// consensusSeq.Append(currentConsensus.Key);
//}
AASeq consensus = AASeq.GetInstance(consensusSeq.ToString(), MixtureSemantics.Uncertainty);
//NamedSequence consensus = new NamedSequence("consensus", consensusSeq.ToString());
return(consensus);
}
static public AASeq GetCompressedInstance(string caseId, AASeq aaSeqIn, bool stopOnStop, TextWriter errorStream)
{
AASeq aaSeqOut = new AASeq(aaSeqIn.MixtureSemantics);
aaSeqOut.Sequence = new List <Set <char> >();
aaSeqOut._originalAA1PositionTableOrNull = new List <string>();
Debug.Assert(aaSeqOut.Offset == 0); // real assert
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);
if (stopOnStop)
{
break;
}
}
else
{
break;
}
}
aaSeqOut.Sequence.Add(set);
aaSeqOut._originalAA1PositionTableOrNull.Add(originalAA1Position);
}
return(aaSeqOut);
}
/// <summary>
/// Skips over deletes. Is allowed to be short if near end of larger sequence
/// </summary>
public AASeq SubSeqCenteredAA1Pos(int aa1Pos, int merLength, out Set <char> centerAA)
{
Helper.CheckCondition(merLength > 0, "merLength must be greater than 0");
int?positionToStartBase1OrNull = FindStartPositionBase1OrNull(aa1Pos);
if (positionToStartBase1OrNull == null)
{
centerAA = AASeq.Delete;
return(SubSeqAA0Pos(0, 0, false));
}
int positionToStartBase0 = positionToStartBase1OrNull.Value - 1;
centerAA = Sequence[positionToStartBase0];
int goalLength = (merLength - 1) / 2;
int leftIndex = FindLeftPosBase0(positionToStartBase0, goalLength);
int rightIndex = FindRightBase0(positionToStartBase0, goalLength);
AASeq result = SubSeqAA0Pos(leftIndex, rightIndex - leftIndex + 1, true);
return(result);
}
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();
}
public bool TrySubSeqAA1Pos(int aa1Pos, int merLength, out AASeq aaSeq)
{
return(TrySubSeqAA0Pos(aa1Pos - 1, merLength, out aaSeq));
}
public static Matrix <string, string, SufficientStatistics> ConvertToMatrix(List <NamedSequence> sequences, MixtureSemantics mix, BinaryOrMultistate dataType, bool keepOneValueVariables)
{
var colNames = sequences.Select(s => s.Name);
//var rowNames = (from posAndAa in sequences.SelectMany(s => s.AASeq)
// where !AASeq.IsMissing(posAndAa.Value)
// let pos = posAndAa.Key
// let aas = posAndAa.Value
// from c in aas
// let merAndPos = pos + "@" + c
// orderby pos, c
// select merAndPos).Distinct();
var rowNames = (from posAndAa in sequences.SelectMany(s => s.AASeq)
where posAndAa.Value.Count == 1 && !AASeq.IsMissing(posAndAa.Value)
let pos = posAndAa.Key
let aas = posAndAa.Value
let c = aas.First()
let merAndPos = pos + "@" + c
orderby pos, c
select merAndPos).Distinct();
var posToRowNames = (from row in rowNames
let pos = (int)Tabulate.GetMerAndPos(row).Value
group row by pos into g
select new KeyValuePair <int, List <string> >(g.Key, g.ToList())).ToDictionary();
Matrix <string, string, SufficientStatistics> m = DenseMatrix <string, string, SufficientStatistics> .CreateDefaultInstance(rowNames, colNames, MissingStatistics.GetInstance());
foreach (var seq in sequences)
{
foreach (var posAndAa in seq.AASeq)
{
int pos = posAndAa.Key;
if (!posToRowNames.ContainsKey(pos))
{
Helper.CheckCondition(AASeq.IsMissing(posAndAa.Value), "Something's wrong. We thinking everyone is missing at position {0}, but {1} has {2}", pos, seq.Name, posAndAa.Value);
continue;
}
var relevantRows = posToRowNames[pos];
bool isMissing = AASeq.IsMissing(posAndAa.Value);
var myRows = posAndAa.Value.Select(c => pos + "@" + c).ToList();
foreach (var row in relevantRows)
{
SufficientStatistics value;
if (isMissing)
{
value = MissingStatistics.GetInstance();
}
else if (!myRows.Contains(row))
{
value = (BooleanStatistics)false; //in all cases, this is false
}
else if (myRows.Count == 1)
{
value = (BooleanStatistics)true;
}
else
{
switch (mix)
{
case MixtureSemantics.Any:
value = (BooleanStatistics)true; break; //Any means we say you have both
case MixtureSemantics.Pure:
value = (BooleanStatistics)false; break; //Pure means we say you have neither
case MixtureSemantics.Uncertainty:
value = MissingStatistics.GetInstance(); break; //Uncertainty says we don't know which you have.
case MixtureSemantics.Distribution:
double pTrue = 1.0 / myRows.Count;
value = MultinomialStatistics.GetInstance(new double[] { 1 - pTrue, pTrue });
break;
default:
throw new NotImplementedException("Missing a case.");
}
}
m.SetValueOrMissing(row, seq.Name, value);
}
}
}
if (!keepOneValueVariables)
{
m = m.SelectRowsView(m.RowKeys.Where(row => m.RowView(row).Values.Distinct().Count() > 1));
}
switch (dataType)
{
case BinaryOrMultistate.Binary:
return(m);
case BinaryOrMultistate.Multistate:
return(new BinaryToMultistateView <string, string, SufficientStatistics>(m, Tabulate.BinaryToMultistateMapping(m), ValueConverter.SufficientStatisticsToMultinomial));
default:
throw new NotImplementedException("Missing a case");
}
}
private AASeq GetFirstAASeq()
{
AASeq firstAASeq = this._caseIdToAASeq.Values.First();
return(firstAASeq);
}
private IEnumerable <string> EveryProtein()
{
AASeq firstAASeq = GetFirstAASeq();
return(firstAASeq.EveryProtein());
}
public IEnumerable <string> SparseLineEnumeration(bool keepOneValueVariables)
{
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");
/*
* 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)SequenceLengthOrNull; ++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];
if (aa0Pos >= aaSeq.Count)
{
continue;
}
//Helper.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);
//if (posName.Contains("68.3B"))
//{
// Console.WriteLine("Found it first");
//}
}
else
{
Helper.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)
{
switch (aaSeq.MixtureSemantics)
{
case MixtureSemantics.Pure:
caseToVal.Add(caseId, false);
valueSet.AddNewOrOld(false);
break;
case MixtureSemantics.Uncertainty:
// Do nothing = missing
break;
case MixtureSemantics.Any:
caseToVal.Add(caseId, true);
valueSet.AddNewOrOld(true);
break;
default:
Helper.CheckCondition(false, "Unknown mixturesemantics " + aaSeq.MixtureSemantics.ToString());
break;
}
}
else
{
caseToVal.Add(caseId, true);
valueSet.AddNewOrOld(true);
}
}
else
{
caseToVal.Add(caseId, false);
valueSet.AddNewOrOld(false);
}
}
Helper.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);
//if (variableName.Contains("68.3B"))
//{
// Console.WriteLine("Found it first");
//}
yield return(Helper.CreateTabString(
variableName, caseIdAndVal.Key, caseIdAndVal.Value ? 1 : 0));
}
}
}
}
}
