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#ifndef MULTALN_H
#define MULTALN_H
#ifdef _MSC_VER
#pragma warning(disable: 4996) // deprecated functions
#define _CRT_SECURE_NO_DEPRECATE 1
#endif
#include <vector>
#include <memory.h>
#include <limits.h>
#include <ctype.h>
#include <math.h>
#include "types.h"
#include "params.h"
#include "myassert.h"
#ifndef _MSC_VER
#define stricmp strcasecmp
#define strnicmp strncasecmp
#define _snprintf snprintf
#define _fsopen(name, mode, share) fopen((name), (mode))
#endif
enum
{
BIT_MM = 0x00,
BIT_DM = 0x01,
BIT_IM = 0x02,
BIT_xM = 0x03,
BIT_DD = 0x00,
BIT_MD = 0x04,
// ID not allowed
BIT_xD = 0x04,
BIT_II = 0x00,
BIT_MI = 0x08,
// DI not allowed
BIT_xI = 0x08,
};
// NX=Nucleotide alphabet
enum NX
{
NX_A,
NX_C,
NX_G,
NX_T,
NX_U = NX_T,
NX_N,
NX_GAP
};
const size_t MAX_ALPHA = 4;
const size_t MAX_ALPHA_EX = 6;
const size_t g_AlphaSize = 4;
typedef float BASETYPE;
typedef BASETYPE FCOUNT;
typedef BASETYPE SCORE;
typedef float SCOREMATRIX[32][32];
typedef SCOREMATRIX *PTR_SCOREMATRIX;
extern PTR_SCOREMATRIX g_ptrScoreMatrix;
static inline bool BTEq2(BASETYPE b1, BASETYPE b2)
{
double diff = fabs(b1 - b2);
if (diff < 0.0001)
return true;
double sum = fabs(b1) + fabs(b2);
return diff/sum < 0.005;
}
static inline bool BTEq(double b1, double b2)
{
return BTEq2((BASETYPE) b1, (BASETYPE) b2);
}
static inline bool ScoreEq(SCORE s1, SCORE s2)
{
return BTEq(s1, s2);
}
extern SCORE g_scoreGapOpen;
extern SCORE g_scoreGapExtend;
const unsigned uInsane = UINT_MAX;
const double dInsane = -9e-9;
const BASETYPE BTInsane = (BASETYPE) -9e-9;
const SCORE MINUS_INFINITY = (SCORE) -1e37;
#include "utils.h"
#include "seq.h"
#include "seqvect.h"
#include "msa.h"
#include "tree.h"
#include "distfunc.h"
#include "pwpath.h"
#include "estring.h"
#include "profile.h"
#include "distcalc.h"
extern unsigned g_CharToLetter[];
extern unsigned g_CharToLetterEx[];
extern char g_LetterToChar[];
extern char g_LetterExToChar[];
extern char g_UnalignChar[];
extern char g_AlignChar[];
extern bool g_IsWildcardChar[];
extern bool g_IsResidueChar[];
#define CharToLetter(c) (g_CharToLetter[(unsigned char) (c)])
#define CharToLetterEx(c) (g_CharToLetterEx[(unsigned char) (c)])
#define LetterToChar(u) (g_LetterToChar[u])
#define LetterExToChar(u) (g_LetterExToChar[u])
#define IsResidueChar(c) (g_IsResidueChar[(unsigned char) (c)])
#define IsGapChar(c) ('-' == (c) || '.' == (c))
#define IsWildcardChar(c) (g_IsWildcardChar[(unsigned char) (c)])
#define AlignChar(c) (g_AlignChar[(unsigned char) (c)])
#define UnalignChar(c) (g_UnalignChar[(unsigned char) (c)])
void GetGuideTree(const SeqVect &Seqs, Tree &GuideTree);
void KmerDist(const SeqVect &Seqs, DistFunc &DF);
void ProgressiveAlign(const SeqVect &Seqs, const Tree &GuideTree, MSA &Aln);
SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,
unsigned uLengthB, PWPath &Path);
void BitTraceBack(char **TraceBack, unsigned uLengthA, unsigned uLengthB,
char LastEdge, PWPath &Path);
SCORE AlignProfiles(
const ProfPos *PA, unsigned uLengthA,
const ProfPos *PB, unsigned uLengthB,
PWPath &Path, ProfPos **ptrPout, unsigned *ptruLengthOut);
void AlignTwoProfsGivenPath(const PWPath &Path,
const ProfPos *PA, unsigned uPrefixLengthA,
const ProfPos *PB, unsigned uPrefixLengthB,
ProfPos **ptrPOut, unsigned *ptruLengthOut);
void MakeRootMSA(const SeqVect &v, const Tree &GuideTree, ProgNode Nodes[],
MSA &Aln);
void MultipleAlign(SeqVect &Seqs, MSA &Aln);
void UPGMA(const DistCalc &DC, Tree &tree);
void GetConsSeq(const MSA &Aln, double MinCons, int *ptrStartCol,
int *ptrEndCol, Seq &ConsSeq);
void GetConsSymbols(const MSA &Aln, Seq &ConsSymbols);
#endif // MULTALN_H
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