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Mac binaries
[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
new file mode 100644 (file)
index 0000000..c023989
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/msa.h
@@ -0,0 +1,179 @@
+#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