i-hopper.h File Reference

#include "defs.h"

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Macros
#define	EXT

Functions
void	Align (int nX, char X[], int secX[], char **XX, int nY, char Y[], int secY[], char **YY, int freqs, double fT, double fC, double fA, double fG, double rTC, double rTA, double rTG, double rCA, double rCG, double rAG, double dist, double supp, double gapA, double gapB, double gapC, double thres)

Variables
EXT const char *	Error

Macro Definition Documentation

#define EXT

Definition at line 17 of file i-hopper.h.

Function Documentation

void Align	(	int	nX,
		char	X[],
		int	secX[],
		char **	XX,
		int	nY,
		char	Y[],
		int	secY[],
		char **	YY,
		int	freqs,
		double	fT,
		double	fC,
		double	fA,
		double	fG,
		double	rTC,
		double	rTA,
		double	rTG,
		double	rCA,
		double	rCG,
		double	rAG,
		double	dist,
		double	supp,
		double	gapA,
		double	gapB,
		double	gapC,
		double	thres
	)

Definition at line 799 of file align.cxx.

References AlignTwo(), decodeBase(), encodeBase(), expectedScore, freeBlock, freeMatrix, GapA, GapB, GapC, GE, GP, GS, initEntropy(), initScore(), LogThres, MAXDIST, MINDIST, N, newBlock(), newMatrix(), newVector, normalizeBaseFreqs(), normalizeRateParams(), s, Supp, Thres, uninitEntropy(), uninitScore(), updateEntropy(), and updateScore().

Referenced by main().

Variable Documentation

EXT const char* Error

Definition at line 22 of file i-hopper.h.