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#ifndef MSA_H
#define MSA_H
const int MAX_SEQ_NAME = 63;
struct PathEdge;
class TextFile;
class Seq;
class ClusterNode;
class NodeCounts;
class DataBuffer;
class MSA
{
public:
MSA();
virtual ~MSA();
public:
// Ways to create an MSA
void FromFile(TextFile &File);
void FromFASTAFile(TextFile &File);
void FromSeq(const Seq &s);
void ToFile(TextFile &File) const;
void ToFASTAFile(TextFile &File) const;
void ToMSFFile(TextFile &File, const char *ptrComment = 0) const;
void ToAlnFile(TextFile &File) const;
void ToHTMLFile(TextFile &File) const;
void ToPhySequentialFile(TextFile &File) const;
void ToPhyInterleavedFile(TextFile &File) const;
void SetSize(unsigned uSeqCount, unsigned uColCount);
void SetSeqCount(unsigned uSeqCount);
char GetChar(unsigned uSeqIndex, unsigned uIndex) const;
unsigned GetLetter(unsigned uSeqIndex, unsigned uIndex) const;
unsigned GetLetterEx(unsigned uSeqIndex, unsigned uIndex) const;
const char *GetSeqName(unsigned uSeqIndex) const;
unsigned GetSeqId(unsigned uSeqIndex) const;
unsigned GetSeqIndex(unsigned uId) const;
bool GetSeqIndex(unsigned uId, unsigned *ptruIndex) const;
double GetOcc(unsigned uColIndex) const;
void GetFractionalWeightedCounts(unsigned uColIndex, bool bNormalize,
FCOUNT fcCounts[], FCOUNT *ptrfcGapStart, FCOUNT *ptrfcGapEnd,
FCOUNT *fcGapExtend, FCOUNT *ptrfOcc,
FCOUNT *fcLL, FCOUNT *fcLG, FCOUNT *fcGL, FCOUNT *fcGG) const;
bool IsGap(unsigned uSeqIndex, unsigned uColIndex) const;
bool IsWildcard(unsigned uSeqIndex, unsigned uColIndex) const;
bool IsGapColumn(unsigned uColIndex) const;
bool ColumnHasGap(unsigned uColIndex) const;
bool IsGapSeq(unsigned uSeqIndex) const;
void SetChar(unsigned uSeqIndex, unsigned uColIndex, char c);
void SetSeqName(unsigned uSeqIndex, const char szName[]);
void SetSeqId(unsigned uSeqIndex, unsigned uId);
bool HasGap() const;
bool IsLegalLetter(unsigned uLetter) const;
void GetSeq(unsigned uSeqIndex, Seq &seq) const;
void Copy(const MSA &msa);
double GetCons(unsigned uColIndex) const;
double GetAvgCons() const;
double GetPctIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const;
bool GetSeqIndex(const char *ptrSeqName, unsigned *ptruSeqIndex) const;
void DeleteCol(unsigned uColIndex);
void DeleteColumns(unsigned uColIndex, unsigned uColCount);
void CopySeq(unsigned uToSeqIndex, const MSA &msaFrom, unsigned uFromSeqIndex);
void DeleteSeq(unsigned uSeqIndex);
// void DeleteEmptyCols(bool bProgress = false);
bool IsEmptyCol(unsigned uColIndex) const;
unsigned GetGCGCheckSum(unsigned uSeqIndex) const;
unsigned UniqueResidueTypes(unsigned uColIndex) const;
void GetNodeCounts(unsigned uAlignedColIndex, NodeCounts &Counts) const;
void ValidateBreakMatrices() const;
unsigned GetCharCount(unsigned uSeqIndex, unsigned uColIndex) const;
const char *GetSeqBuffer(unsigned uSeqIndex) const;
unsigned AlignedColIndexToColIndex(unsigned uAlignedColIndex) const;
unsigned GetSeqLength(unsigned uSeqIndex) const;
void GetPWID(unsigned uSeqIndex1, unsigned uSeqIndex2, double *ptrdPWID,
unsigned *ptruPosCount) const;
void GetPairMap(unsigned uSeqIndex1, unsigned uSeqIndex2, int iMap1[],
int iMap2[]) const;
void LogMe() const;
void GapInfoToDataBuffer(DataBuffer &Buffer) const;
void GapInfoFromDataBuffer(const DataBuffer &Buffer);
double GetPctGroupIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const;
void Clear()
{
Free();
}
unsigned GetSeqCount() const
{
return m_uSeqCount;
}
unsigned GetColCount() const
{
return m_uColCount;
}
static bool SeqsEq(const MSA &a1, unsigned uSeqIndex1, const MSA &a2,
unsigned uSeqIndex2);
static void SetIdCount(unsigned uIdCount);
private:
void Free();
void AppendSeq(char *ptrSeq, unsigned uSeqLength, char *ptrLabel);
void ExpandCache(unsigned uSeqCount, unsigned uColCount);
void GetNameFromFASTAAnnotationLine(const char szLine[],
char szName[], unsigned uBytes);
void CopyCol(unsigned uFromCol, unsigned uToCol);
private:
unsigned m_uSeqCount;
unsigned m_uColCount;
unsigned m_uCacheSeqLength;
unsigned m_uCacheSeqCount;
char **m_szSeqs;
char **m_szNames;
static unsigned m_uIdCount;
unsigned *m_IdToSeqIndex;
unsigned *m_SeqIndexToId;
};
void SeqVectFromMSA(const MSA &msa, SeqVect &v);
void DeleteGappedCols(MSA &msa);
void MSAFromColRange(const MSA &msaIn, unsigned uFromColIndex, unsigned uColCount,
MSA &msaOut);
void MSACat(const MSA &msa1, const MSA &msa2, MSA &msaCat);
void MSAAppend(MSA &msa1, const MSA &msa2);
void MSAFromSeqSubset(const MSA &msaIn, const unsigned uSeqIndexes[], unsigned uSeqCount,
MSA &msaOut);
void AssertMSAEq(const MSA &msa1, const MSA &msa2);
void AssertMSAEqIgnoreCaseAndGaps(const MSA &msa1, const MSA &msa2);
void MSASubsetByIds(const MSA &msaIn, const unsigned Ids[], unsigned uIdCount,
MSA &msaOut);
void SetMSAWeightsMuscle(MSA &msa);
void SetClustalWWeightsMuscle(MSA &msa);
void SetThreeWayWeightsMuscle(MSA &msa);
#endif // MSA_H
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