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[jabaws.git] / website / archive / binaries / mac / src / muscle / msa.h
diff --git a/website/archive/binaries/mac/src/muscle/msa.h b/website/archive/binaries/mac/src/muscle/msa.h
deleted file mode 100644 (file)
index c023989..0000000
--- a/website/archive/binaries/mac/src/muscle/msa.h
+++ /dev/null
@@ -1,179 +0,0 @@
-#ifndef        MSA_h\r
-#define MSA_h\r
-\r
-const int MAX_SEQ_NAME = 63;\r
-struct PathEdge;\r
-class TextFile;\r
-class Seq;\r
-class ClusterNode;\r
-class NodeCounts;\r
-class DataBuffer;\r
-\r
-class MSA\r
-       {\r
-public:\r
-       MSA();\r
-       virtual ~MSA();\r
-\r
-public:\r
-// Ways to create an MSA\r
-       void FromFile(TextFile &File);\r
-       void FromFASTAFile(TextFile &File);\r
-       void FromSeq(const Seq &s);\r
-\r
-       void ToFile(TextFile &File) const;\r
-       void ToFASTAFile(TextFile &File) const;\r
-       void ToMSFFile(TextFile &File, const char *ptrComment = 0) const;\r
-       void ToAlnFile(TextFile &File) const;\r
-       void ToHTMLFile(TextFile &File) const;\r
-       void ToPhySequentialFile(TextFile &File) const;\r
-       void ToPhyInterleavedFile(TextFile &File) const;\r
-\r
-       void SetSize(unsigned uSeqCount, unsigned uColCount);\r
-       void SetSeqCount(unsigned uSeqCount);\r
-       char GetChar(unsigned uSeqIndex, unsigned uIndex) const;\r
-       unsigned GetLetter(unsigned uSeqIndex, unsigned uIndex) const;\r
-       unsigned GetLetterEx(unsigned uSeqIndex, unsigned uIndex) const;\r
-       const char *GetSeqName(unsigned uSeqIndex) const;\r
-       unsigned GetSeqId(unsigned uSeqIndex) const;\r
-       unsigned GetSeqIndex(unsigned uId) const;\r
-       bool GetSeqIndex(unsigned uId, unsigned *ptruIndex) const;\r
-       double GetOcc(unsigned uColIndex) const;\r
-       void GetFractionalWeightedCounts(unsigned uColIndex, bool bNormalize,\r
-         FCOUNT fcCounts[], FCOUNT *ptrfcGapStart, FCOUNT *ptrfcGapEnd,\r
-         FCOUNT *fcGapExtend, FCOUNT *ptrfOcc,\r
-         FCOUNT *fcLL, FCOUNT *fcLG, FCOUNT *fcGL, FCOUNT *fcGG) const;\r
-       bool IsGap(unsigned uSeqIndex, unsigned uColIndex) const;\r
-       bool IsWildcard(unsigned uSeqIndex, unsigned uColIndex) const;\r
-       bool IsGapColumn(unsigned uColIndex) const;\r
-       bool ColumnHasGap(unsigned uColIndex) const;\r
-       bool IsGapSeq(unsigned uSeqIndex) const;\r
-\r
-       void SetChar(unsigned uSeqIndex, unsigned uColIndex, char c);\r
-       void SetSeqName(unsigned uSeqIndex, const char szName[]);\r
-       void SetSeqId(unsigned uSeqIndex, unsigned uId);\r
-       bool HasGap() const;\r
-       bool IsLegalLetter(unsigned uLetter) const;\r
-       void GetSeq(unsigned uSeqIndex, Seq &seq) const;\r
-       void Copy(const MSA &msa);\r
-       double GetCons(unsigned uColIndex) const;\r
-       double GetAvgCons() const;\r
-       double GetPctIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const;\r
-       bool GetSeqIndex(const char *ptrSeqName, unsigned *ptruSeqIndex) const;\r
-       void DeleteCol(unsigned uColIndex);\r
-       void DeleteColumns(unsigned uColIndex, unsigned uColCount);\r
-       void CopySeq(unsigned uToSeqIndex, const MSA &msaFrom, unsigned uFromSeqIndex);\r
-       void DeleteSeq(unsigned uSeqIndex);\r
-//     void DeleteEmptyCols(bool bProgress = false);\r
-       bool IsEmptyCol(unsigned uColIndex) const;\r
-\r
-       WEIGHT GetSeqWeight(unsigned uSeqIndex) const;\r
-       WEIGHT GetTotalSeqWeight() const;\r
-       void SetSeqWeight(unsigned uSeqIndex, WEIGHT w) const;\r
-       void NormalizeWeights(WEIGHT wTotal) const;\r
-       bool WeightsSet() const;\r
-\r
-       unsigned GetGCGCheckSum(unsigned uSeqIndex) const;\r
-\r
-       ALPHA GuessAlpha() const;\r
-       void FixAlpha();\r
-\r
-       unsigned UniqueResidueTypes(unsigned uColIndex) const;\r
-\r
-       void UnWeight();\r
-\r
-       void GetNodeCounts(unsigned uAlignedColIndex, NodeCounts &Counts) const;\r
-       void ValidateBreakMatrices() const;\r
-       unsigned GetCharCount(unsigned uSeqIndex, unsigned uColIndex) const;\r
-       const char *GetSeqBuffer(unsigned uSeqIndex) const;\r
-       unsigned AlignedColIndexToColIndex(unsigned uAlignedColIndex) const;\r
-       unsigned GetSeqLength(unsigned uSeqIndex) const;\r
-       void GetPWID(unsigned uSeqIndex1, unsigned uSeqIndex2, double *ptrdPWID,\r
-         unsigned *ptruPosCount) const;\r
-\r
-       void GetPairMap(unsigned uSeqIndex1, unsigned uSeqIndex2, int iMap1[],\r
-         int iMap2[]) const;\r
-\r
-       void LogMe() const;\r
-       void ListWeights() const;\r
-\r
-       void GapInfoToDataBuffer(DataBuffer &Buffer) const;\r
-       void GapInfoFromDataBuffer(const DataBuffer &Buffer);\r
-       double GetPctGroupIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const;\r
-\r
-       void Clear()\r
-               {\r
-               Free();\r
-               }\r
-       unsigned GetSeqCount() const\r
-               {\r
-               return m_uSeqCount;\r
-               }\r
-       unsigned GetColCount() const\r
-               {\r
-               return m_uColCount;\r
-               }\r
-\r
-       static bool SeqsEq(const MSA &a1, unsigned uSeqIndex1, const MSA &a2,\r
-         unsigned uSeqIndex2);\r
-\r
-       static void SetIdCount(unsigned uIdCount);\r
-\r
-private:\r
-       friend void SetMSAWeightsMuscle(MSA &msa);\r
-       friend void SetThreeWayWeightsMuscle(MSA &msa);\r
-       void SetHenikoffWeightsPB() const;\r
-       void SetHenikoffWeights() const;\r
-       void SetGSCWeights() const;\r
-       void SetUniformWeights() const;\r
-       void SetClustalWWeights(const Tree &tree);\r
-\r
-       void Free();\r
-       void AppendSeq(char *ptrSeq, unsigned uSeqLength, char *ptrLabel);\r
-       void ExpandCache(unsigned uSeqCount, unsigned uColCount);\r
-       void CalcWeights() const;\r
-       void GetNameFromFASTAAnnotationLine(const char szLine[],\r
-         char szName[], unsigned uBytes);\r
-       void CopyCol(unsigned uFromCol, unsigned uToCol);\r
-       unsigned CalcBLOSUMWeights(ClusterTree &BlosumCluster) const;\r
-       void SetBLOSUMSubtreeWeight(const ClusterNode *ptrNode, double dWeight) const;\r
-       unsigned SetBLOSUMNodeWeight(const ClusterNode *ptrNode, double dMinDist) const;\r
-       void SetSubtreeWeight2(const ClusterNode *ptrNode) const;\r
-       void SetSubtreeGSCWeight(ClusterNode *ptrNode) const;\r
-\r
-       void CalcHenikoffWeightsColPB(unsigned uColIndex) const;\r
-       void CalcHenikoffWeightsCol(unsigned uColIndex) const;\r
-\r
-private:\r
-       unsigned m_uSeqCount;\r
-       unsigned m_uColCount;\r
-       unsigned m_uCacheSeqLength;\r
-       unsigned m_uCacheSeqCount;\r
-       char **m_szSeqs;\r
-       char **m_szNames;\r
-\r
-       static unsigned m_uIdCount;\r
-\r
-       unsigned *m_IdToSeqIndex;\r
-       unsigned *m_SeqIndexToId;\r
-\r
-       WEIGHT *m_Weights;\r
-       };\r
-\r
-void SeqVectFromMSA(const MSA &msa, SeqVect &v);\r
-void DeleteGappedCols(MSA &msa);\r
-void MSAFromColRange(const MSA &msaIn, unsigned uFromColIndex, unsigned uColCount,\r
-  MSA &msaOut);\r
-void MSACat(const MSA &msa1, const MSA &msa2, MSA &msaCat);\r
-void MSAAppend(MSA &msa1, const MSA &msa2);\r
-void MSAFromSeqSubset(const MSA &msaIn, const unsigned uSeqIndexes[], unsigned uSeqCount,\r
-  MSA &msaOut);\r
-void AssertMSAEq(const MSA &msa1, const MSA &msa2);\r
-void AssertMSAEqIgnoreCaseAndGaps(const MSA &msa1, const MSA &msa2);\r
-void MSASubsetByIds(const MSA &msaIn, const unsigned Ids[], unsigned uIdCount,\r
-  MSA &msaOut);\r
-void SetMSAWeightsMuscle(MSA &msa);\r
-void SetClustalWWeightsMuscle(MSA &msa);\r
-void SetThreeWayWeightsMuscle(MSA &msa);\r
-\r
-#endif // MSA_h\r