+++ /dev/null
-#if DEBUG && !_DEBUG\r
-#define _DEBUG 1\r
-#endif\r
-\r
-#if _DEBUG && !DEBUG\r
-#define DEBUG 1\r
-#endif\r
-\r
-#if _MSC_VER\r
-#define TIMING 0\r
-#endif\r
-\r
-#define VER_3_52 0\r
-\r
-#ifdef _MSC_VER // Miscrosoft compiler\r
-#pragma warning(disable : 4800) // int-bool conversion\r
-#pragma warning(disable : 4996) // deprecated names like strdup, isatty.\r
-#endif\r
-\r
-extern const char *MUSCLE_LONG_VERSION;\r
-#define SHORT_VERSION "3.8"\r
-\r
-#include <stdlib.h>\r
-#include <string.h>\r
-#include <ctype.h>\r
-#include <stdarg.h>\r
-#include <stdio.h>\r
-\r
-#define DOUBLE_AFFINE 0\r
-#define SINGLE_AFFINE 1\r
-#define PAF 0\r
-\r
-#include "types.h"\r
-#include "intmath.h"\r
-#include "alpha.h"\r
-#include "params.h"\r
-\r
-#ifndef _WIN32\r
-#define stricmp strcasecmp\r
-#define strnicmp strncasecmp\r
-#define _snprintf snprintf\r
-#define _fsopen(name, mode, share) fopen((name), (mode))\r
-#endif\r
-\r
-#if DEBUG\r
-#undef assert\r
-#define assert(b) Call_MY_ASSERT(__FILE__, __LINE__, b, #b)\r
-void Call_MY_ASSERT(const char *file, int line, bool b, const char *msg);\r
-#else\r
-#define assert(exp) ((void)0)\r
-#endif\r
-\r
-extern int g_argc;\r
-extern char **g_argv;\r
-\r
-#define Rotate(a, b, c) { SCORE *tmp = a; a = b; b = c; c = tmp; }\r
-\r
-const double VERY_LARGE_DOUBLE = 1e20;\r
-\r
-extern unsigned g_uTreeSplitNode1;\r
-extern unsigned g_uTreeSplitNode2;\r
-\r
-// Number of elements in array a[]\r
-#define countof(a) (sizeof(a)/sizeof(a[0]))\r
-\r
-// Maximum of two of any type\r
-#define Max2(a, b) ((a) > (b) ? (a) : (b))\r
-\r
-// Maximum of three of any type\r
-#define Max3(a, b, c) Max2(Max2(a, b), c)\r
-\r
-// Minimum of two of any type\r
-#define Min2(a, b) ((a) < (b) ? (a) : (b))\r
-\r
-// Maximum of four of any type\r
-#define Max4(a, b, c, d) Max2(Max2(a, b), Max2(c, d))\r
-\r
-const double VERY_NEGATIVE_DOUBLE = -9e29;\r
-const float VERY_NEGATIVE_FLOAT = (float) -9e29;\r
-\r
-const double BLOSUM_DIST = 0.62; // todo settable\r
-\r
-// insane value for uninitialized variables\r
-const unsigned uInsane = 8888888;\r
-const int iInsane = 8888888;\r
-const SCORE scoreInsane = 8888888;\r
-const char cInsane = (char) 0xcd; // int 3 instruction, used e.g. for unint. memory\r
-const double dInsane = VERY_NEGATIVE_DOUBLE;\r
-const float fInsane = VERY_NEGATIVE_FLOAT;\r
-const char INVALID_STATE = '*';\r
-const BASETYPE BTInsane = (BASETYPE) dInsane;\r
-const WEIGHT wInsane = BTInsane;\r
-\r
-extern double g_dNAN;\r
-\r
-extern unsigned long g_tStart;\r
-\r
-void Quit(const char szFormat[], ...);\r
-void Warning(const char szFormat[], ...);\r
-void TrimBlanks(char szStr[]);\r
-void TrimLeadingBlanks(char szStr[]);\r
-void TrimTrailingBlanks(char szStr[]);\r
-void Log(const char szFormat[], ...);\r
-bool Verbose();\r
-const char *ScoreToStr(SCORE Score);\r
-const char *ScoreToStrL(SCORE Score);\r
-SCORE StrToScore(const char *pszStr);\r
-void Break();\r
-\r
-double VecSum(const double v[], unsigned n);\r
-bool IsValidInteger(const char *Str);\r
-bool IsValidSignedInteger(const char *Str);\r
-bool IsValidIdentifier(const char *Str);\r
-bool IsValidFloatChar(char c);\r
-bool isident(char c);\r
-bool isidentf(char c);\r
-\r
-void TreeFromSeqVect(const SeqVect &c, Tree &tree, CLUSTER Cluster,\r
- DISTANCE Distance, ROOT Root, const char *SaveFileName = 0);\r
-void TreeFromMSA(const MSA &msa, Tree &tree, CLUSTER Cluster,\r
- DISTANCE Distance, ROOT Root, const char *SaveFileName = 0);\r
-\r
-void StripGaps(char szStr[]);\r
-void StripWhitespace(char szStr[]);\r
-const char *GetTimeAsStr();\r
-unsigned CalcBLOSUMWeights(MSA &Aln, ClusterTree &BlosumCluster);\r
-void CalcGSCWeights(MSA &Aln, const ClusterTree &BlosumCluster);\r
-void AssertNormalized(const PROB p[]);\r
-void AssertNormalizedOrZero(const PROB p[]);\r
-void AssertNormalized(const double p[]);\r
-bool VectorIsZero(const double dValues[], unsigned n);\r
-void VectorSet(double dValues[], unsigned n, double d);\r
-bool VectorIsZero(const float dValues[], unsigned n);\r
-void VectorSet(float dValues[], unsigned n, float d);\r
-\r
-// @@TODO should be "not linux"\r
-#if _WIN32\r
-double log2(double x); // Defined in <math.h> on Linux\r
-#endif\r
-\r
-double pow2(double x);\r
-double lnTolog2(double ln);\r
-\r
-double lp2(double x);\r
-SCORE SumLog(SCORE x, SCORE y);\r
-SCORE SumLog(SCORE x, SCORE y, SCORE z);\r
-SCORE SumLog(SCORE w, SCORE x, SCORE y, SCORE z);\r
-\r
-double lp2Fast(double x);\r
-double SumLogFast(double x, double y);\r
-double SumLogFast(double x, double y, double z);\r
-double SumLogFast(double w, double x, double y, double z);\r
-\r
-void chkmem(const char szMsg[] = "");\r
-\r
-void Normalize(PROB p[], unsigned n);\r
-void Normalize(PROB p[], unsigned n, double dRequiredTotal);\r
-void NormalizeUnlessZero(PROB p[], unsigned n);\r
-\r
-void DebugPrintf(const char szFormat[], ...);\r
-void SetListFileName(const char *ptrListFileName, bool bAppend);\r
-void ModelFromAlign(const char *strInputFileName, const char *strModelFileName,\r
- double dMaxNIC);\r
-double GetMemUseMB();\r
-double GetRAMSizeMB();\r
-double GetPeakMemUseMB();\r
-void CheckMemUse();\r
-const char *ElapsedTimeAsString();\r
-char *SecsToHHMMSS(long lSecs, char szStr[]);\r
-double GetCPUGHz();\r
-SCORE GetBlosum62(unsigned uLetterA, unsigned uLetterB);\r
-SCORE GetBlosum62d(unsigned uLetterA, unsigned uLetterB);\r
-SCORE GetBlosum50(unsigned uLetterA, unsigned uLetterB);\r
-void AssertNormalizedDist(const PROB p[], unsigned N);\r
-void CmdLineError(const char *Format, ...);\r
-void Fatal(const char *Format, ...);\r
-void InitCmd();\r
-void ExecCommandLine(int argc, char *argv[]);\r
-void DoCmd();\r
-void SetLogFile();\r
-void NameFromPath(const char szPath[], char szName[], unsigned uBytes);\r
-char *strsave(const char *s);\r
-void DistKmer20_3(const SeqVect &v, DistFunc &DF);\r
-void DistKbit20_3(const SeqVect &v, DistFunc &DF);\r
-void DistKmer6_6(const SeqVect &v, DistFunc &DF);\r
-void DistKmer4_6(const SeqVect &v, DistFunc &DF);\r
-void DistPWKimura(const SeqVect &v, DistFunc &DF);\r
-void FastDistKmer(const SeqVect &v, DistFunc &DF);\r
-void DistUnaligned(const SeqVect &v, DISTANCE DistMethod, DistFunc &DF);\r
-double PctIdToMAFFTDist(double dPctId);\r
-double KimuraDist(double dPctId);\r
-void SetFastParams();\r
-void AssertProfsEq(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB);\r
-void ValidateMuscleIds(const MSA &msa);\r
-void ValidateMuscleIds(const Tree &tree);\r
-void TraceBackToPath(int **TraceBack, unsigned uLengthA,\r
- unsigned uLengthB, PWPath &Path);\r
-void BitTraceBack(char **TraceBack, unsigned uLengthA, unsigned uLengthB,\r
- char LastEdge, PWPath &Path);\r
-SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,\r
- bool bLockLeft = false, bool bLockRight = false);\r
-SCORE AlignTwoProfs(\r
- const ProfPos *PA, unsigned uLengthA, WEIGHT wA,\r
- const ProfPos *PB, unsigned uLengthB, WEIGHT wB,\r
- PWPath &Path, ProfPos **ptrPout, unsigned *ptruLengthOut);\r
-void AlignTwoProfsGivenPath(const PWPath &Path,\r
- const ProfPos *PA, unsigned uLengthA, WEIGHT wA,\r
- const ProfPos *PB, unsigned uLengthB, WEIGHT wB,\r
- ProfPos **ptrPOut, unsigned *ptruLengthOut);\r
-void AlignTwoMSAsGivenPathSW(const PWPath &Path, const MSA &msaA, const MSA &msaB,\r
- MSA &msaCombined);\r
-void AlignTwoMSAsGivenPath(const PWPath &Path, const MSA &msaA, const MSA &msaB,\r
- MSA &msaCombined);\r
-SCORE FastScorePath2(const ProfPos *PA, unsigned uLengthA,\r
- const ProfPos *PB, unsigned uLengthB, const PWPath &Path);\r
-SCORE GlobalAlignDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-SCORE GlobalAlignSimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-SCORE GlobalAlignSP(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-SCORE GlobalAlignSPN(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-SCORE GlobalAlignLE(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-void CalcThreeWayWeights(const Tree &tree, unsigned uNode1, unsigned uNode2,\r
- WEIGHT *Weights);\r
-SCORE GlobalAlignSS(const Seq &seqA, const Seq &seqB, PWPath &Path);\r
-bool RefineHoriz(MSA &msaIn, const Tree &tree, unsigned uIters, bool bLockLeft, bool bLockRight);\r
-bool RefineVert(MSA &msaIn, const Tree &tree, unsigned uIters);\r
-SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-\r
-void SetInputFileName(const char *pstrFileName);\r
-void SetIter(unsigned uIter);\r
-void IncIter();\r
-void SetMaxIters(unsigned uMaxIters);\r
-void Progress(unsigned uStep, unsigned uTotalSteps);\r
-void Progress(const char *szFormat, ...);\r
-void SetStartTime();\r
-void ProgressStepsDone();\r
-void SetProgressDesc(const char szDesc[]);\r
-void SetSeqStats(unsigned uSeqCount, unsigned uMaxL, unsigned uAvgL);\r
-\r
-void SetNewHandler();\r
-void SaveCurrentAlignment();\r
-void SetCurrentAlignment(MSA &msa);\r
-void SetOutputFileName(const char *out);\r
-\r
-#if DEBUG\r
-void SetMuscleSeqVect(SeqVect &v);\r
-void SetMuscleInputMSA(MSA &msa);\r
-void ValidateMuscleIds(const MSA &msa);\r
-void ValidateMuscleIds(const Tree &tree);\r
-#else\r
-#define SetMuscleSeqVect(x) /* empty */\r
-#define SetMuscleInputMSA(x) /* empty */\r
-#define ValidateMuscleIds(x) /* empty */\r
-#endif\r
-\r
-void ProcessArgVect(int argc, char *argv[]);\r
-void ProcessArgStr(const char *Str);\r
-void Usage();\r
-void SetParams();\r
-\r
-void SortCounts(const FCOUNT fcCounts[], unsigned SortOrder[]);\r
-unsigned ResidueGroupFromFCounts(const FCOUNT fcCounts[]);\r
-FCOUNT SumCounts(const FCOUNT Counts[]);\r
-\r
-bool FlagOpt(const char *Name);\r
-const char *ValueOpt(const char *Name);\r
-void DoMuscle();\r
-void ProfDB();\r
-void DoSP();\r
-void ProgAlignSubFams();\r
-void Run();\r
-void ListParams();\r
-void OnException();\r
-void SetSeqWeightMethod(SEQWEIGHT Method);\r
-SEQWEIGHT GetSeqWeightMethod();\r
-WEIGHT GetMuscleSeqWeightById(unsigned uId);\r
-void ListDiagSavings();\r
-void CheckMaxTime();\r
-const char *MaxSecsToStr();\r
-unsigned long GetStartTime();\r
-\r
-void ProgressiveAlign(const SeqVect &v, const Tree &GuideTree, MSA &a);\r
-ProgNode *ProgressiveAlignE(const SeqVect &v, const Tree &GuideTree, MSA &a);\r
-\r
-void CalcDistRangeKmer6_6(const MSA &msa, unsigned uRow, float Dist[]);\r
-void CalcDistRangeKmer20_3(const MSA &msa, unsigned uRow, float Dist[]);\r
-void CalcDistRangeKmer20_4(const MSA &msa, unsigned uRow, float Dist[]);\r
-void CalcDistRangePctIdKimura(const MSA &msa, unsigned uRow, float Dist[]);\r
-void CalcDistRangePctIdLog(const MSA &msa, unsigned uRow, float Dist[]);\r
-\r
-void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[], MSA &a);\r
-void MakeRootMSABrenner(SeqVect &v, const Tree &GuideTree, ProgNode Nodes[], MSA &a);\r
-\r
-void Refine();\r
-void Local();\r
-void Profile();\r
-void PPScore();\r
-void UPGMA2(const DistCalc &DC, Tree &tree, LINKAGE Linkage);\r
-\r
-char *GetFastaSeq(FILE *f, unsigned *ptrSeqLength, char **ptrLabel,\r
- bool DeleteGaps = true);\r
-SCORE SW(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-void TraceBackSW(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, const SCORE *DPM_, const SCORE *DPD_, const SCORE *DPI_,\r
- unsigned uPrefixLengthAMax, unsigned uPrefixLengthBMax, PWPath &Path);\r
-void DiffPaths(const PWPath &p1, const PWPath &p2, unsigned Edges1[],\r
- unsigned *ptruDiffCount1, unsigned Edges2[], unsigned *ptruDiffCount2);\r
-void SetPPScore(bool bRespectFlagOpts = true);\r
-void SetPPScore(PPSCORE p);\r
-SCORE GlobalAlignDimer(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
- unsigned uLengthB, PWPath &Path);\r
-bool MissingCommand();\r
-void Credits();\r
-void ProfileProfile(MSA &msa1, MSA &msa2, MSA &msaOut);\r
-void MHackStart(SeqVect &v);\r
-void MHackEnd(MSA &msa);\r
-void WriteScoreFile(const MSA &msa);\r
-char ConsensusChar(const ProfPos &PP);\r
-void Stabilize(const MSA &msa, MSA &msaStable);\r
-void MuscleOutput(MSA &msa);\r
-PTR_SCOREMATRIX ReadMx(TextFile &File);\r
-void MemPlus(size_t Bytes, char *Where);\r
-void MemMinus(size_t Bytes, char *Where);\r
git://source.jalview.org / jabaws.git / blobdiff