align.cxx File Reference

#include "mem.h"
#include "trnsprob.h"
#include "i-hopper.h"
#include <cxxforward.h>
#include <stdio.h>
#include <math.h>

Include dependency graph for align.cxx:

Go to the source code of this file.

Classes
struct	score
struct	fragment
struct	island

Macros
#define	EXTERN
#define	MSIZE   512
#define	ESIZE   36
#define	MINDIST   0.001
#define	MAXDIST   1.000
#define	MAXGAP   16
#define	NOWHERE   (MAXGAP+1)
#define	MINLENGTH   5

Typedefs
typedef struct score	Score
typedef struct fragment	Fragment
typedef struct island	Island

Functions
static void	initScore (double ***pP, double ***pS)
static void	uninitScore (double ***pP, double ***pS)
static void	updateScore (double **P, double **S, double F[N], double X[6], double dist)
static void	initEntropy (double ***EE)
static void	uninitEntropy (double ***EE)
static double	getEntropy (double **E, double m, int l)
static void	updateEntropy (double **P, double **S, double **E)
static Island *	newIsland (char *X, char *Y, int i, int j, int d)
static void	freeIsland (Island **pp)
static void	registerIsland (Island *f)
static Island *	selectUpperIslands (Island *f, int nX, int nY, int *incomplete)
static Island *	selectLowerIslands (Island *f, int *incomplete)
static int	areEqual (Island *a, Island *b)
static int	isUnique (Island *f)
static int	isSignificant (Island *f)
static void	drawLowerPath (Island *f, int nX, char *X, char *XX, int nY, char *Y, char *YY)
static void	drawPath (Island *f, int nX, char *X, char *XX, int nY, char *Y, char *YY)
static void	drawIsland (Island *f)
static double	secS (int i, int j, char X[], int secX[], char Y[], int secY[])
static void	AlignTwo (int nX, char X[], int secX[], char XX[], int nY, char Y[], int secY[], char YY[])
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
static double **	GP
static double **	GS
static Score **	U
static double	Thres
static double	LogThres
static double	Supp
static double	GapA
static double	GapB
static double	GapC
static double	expectedScore
static double **	GE
static Island *	Z
static Island **	ZB
static Island **	ZE
static int	I
static int	J
static int	K

Macro Definition Documentation

#define EXTERN

Definition at line 14 of file align.cxx.

#define MSIZE   512

Definition at line 22 of file align.cxx.

Referenced by getEntropy(), initEntropy(), matrix_config_changed_cb(), and updateEntropy().

#define ESIZE   36

Definition at line 23 of file align.cxx.

Referenced by initEntropy(), and updateEntropy().

#define MINDIST   0.001

Definition at line 27 of file align.cxx.

Referenced by Align().

#define MAXDIST   1.000

Definition at line 28 of file align.cxx.

Referenced by Align().

#define MAXGAP   16

Definition at line 30 of file align.cxx.

Referenced by AlignTwo().

#define NOWHERE   (MAXGAP+1)

Definition at line 31 of file align.cxx.

Referenced by AlignTwo(), create_new_species(), and newIsland().

#define MINLENGTH   5

Definition at line 33 of file align.cxx.

Referenced by isSignificant().

Typedef Documentation

typedef struct score Score

typedef struct fragment Fragment

typedef struct island Island

Function Documentation

static void initScore ( double ***  pP, double ***  pS  )

static

Definition at line 75 of file align.cxx.

References N, N1, and newDoubleMatrix.

Referenced by Align().

static void uninitScore ( double ***  pP, double ***  pS  )

static

Definition at line 84 of file align.cxx.

References freeMatrix.

Referenced by Align().

static void updateScore ( double **  P, double **  S, double  F[N], double  X[6], double  dist  )

static

Definition at line 93 of file align.cxx.

References A, C, G, getTrnsprob(), initTrnsprob(), N, REV, s, T, uninitTrnsprob(), and updateTrnsprob().

Referenced by Align().

static void initEntropy ( double ***  EE )

static

Definition at line 138 of file align.cxx.

References ESIZE, MSIZE, and newDoubleMatrix.

Referenced by Align().

static void uninitEntropy ( double ***  EE )

static

Definition at line 144 of file align.cxx.

References freeMatrix.

Referenced by Align().

static double getEntropy ( double **  E, double  m, int  l  )

static

Definition at line 150 of file align.cxx.

References M, and MSIZE.

Referenced by isSignificant(), and updateEntropy().

static void updateEntropy ( double **  P, double **  S, double **  E  )

static

Definition at line 211 of file align.cxx.

References ESIZE, getEntropy(), LOG_REAL_MIN, M, MSIZE, N, and REAL_MIN.

Referenced by Align().

static Island* newIsland ( char *  X, char *  Y, int  i, int  j, int  d  )

static

Definition at line 323 of file align.cxx.

References fragment::beginX, island::beginX, fragment::beginY, island::beginY, score::down, island::endX, island::endY, expectedScore, island::fragments, GapC, GS, fragment::length, newBlock(), fragment::next, NOWHERE, NULp, s, island::score, and score::up.

Referenced by AlignTwo().

static void freeIsland ( Island **  pp )

static

Definition at line 375 of file align.cxx.

References island::fragments, freeBlock, and fragment::next.

Referenced by AlignTwo().

static void registerIsland ( Island *  f )

static

Definition at line 388 of file align.cxx.

References island::beginX, island::beginY, island::endX, island::endY, island::next, island::nextBeginIndex, island::nextEndIndex, and Z.

Referenced by AlignTwo().

static Island* selectUpperIslands ( Island *  f, int  nX, int  nY, int *  incomplete  )

static

Definition at line 403 of file align.cxx.

References island::beginX, island::beginY, island::endX, island::endY, FALSE, island::hasUpper, island::nextBeginIndex, island::nextSelected, NULp, and TRUE.

Referenced by AlignTwo().

static Island* selectLowerIslands ( Island *  f, int *  incomplete  )

static

Definition at line 422 of file align.cxx.

References island::beginX, island::beginY, island::endX, island::endY, FALSE, island::hasLower, island::nextEndIndex, island::nextSelected, NULp, and TRUE.

Referenced by AlignTwo().

static int areEqual ( Island *  a, Island *  b  )

static

Definition at line 441 of file align.cxx.

References fragment::beginX, island::beginX, fragment::beginY, island::beginY, island::endX, island::endY, FALSE, island::fragments, fragment::length, fragment::next, and TRUE.

Referenced by isUnique().

static int isUnique ( Island *  f )

static

Definition at line 463 of file align.cxx.

References areEqual(), island::beginX, island::beginY, FALSE, island::nextBeginIndex, and TRUE.

Referenced by AlignTwo().

static int isSignificant ( Island *  f )

static

Definition at line 474 of file align.cxx.

References FALSE, island::fragments, GE, getEntropy(), fragment::length, LogThres, MINLENGTH, fragment::next, island::score, and TRUE.

Referenced by AlignTwo().

static void drawLowerPath ( Island *  f, int  nX, char *  X, char *  XX, int  nY, char *  Y, char *  YY  )

static

Definition at line 493 of file align.cxx.

References fragment::beginX, fragment::beginY, decodeBase(), island::fragments, K, fragment::length, island::lower, and fragment::next.

Referenced by drawPath().

static void drawPath ( Island *  f, int  nX, char *  X, char *  XX, int  nY, char *  Y, char *  YY  )

static

Definition at line 510 of file align.cxx.

References fragment::beginX, fragment::beginY, decodeBase(), drawLowerPath(), island::fragments, K, fragment::length, island::lower, fragment::next, and island::upper.

Referenced by AlignTwo().

static void drawIsland ( Island *  f )

static

Definition at line 537 of file align.cxx.

References fragment::beginX, fragment::beginY, island::fragments, length, fragment::next, and island::score.

Referenced by AlignTwo().

static double secS ( int  i, int  j, char  X[], int  secX[], char  Y[], int  secY[]  )

static

Definition at line 564 of file align.cxx.

References expectedScore, GS, and Supp.

Referenced by AlignTwo().

static void AlignTwo ( int  nX, char  X[], int  secX[], char  XX[], int  nY, char  Y[], int  secY[], char  YY[]  )

static

Definition at line 576 of file align.cxx.

References score::down, drawIsland(), drawPath(), expectedScore, FALSE, freeIsland(), GapA, GapB, GS, island::hasLower, island::hasUpper, isSignificant(), isUnique(), island::lower, island::lowerScore, MAXGAP, N, newIsland(), island::next, island::nextSelected, NOWHERE, NULp, registerIsland(), s, score::score, island::score, secS(), selectLowerIslands(), selectUpperIslands(), TRUE, score::up, island::upper, island::upperScore, and Z.

Referenced by Align().

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

double** GP

static

Definition at line 54 of file align.cxx.

Referenced by Align().

double ** GS

static

Definition at line 54 of file align.cxx.

Referenced by Align(), AlignTwo(), newIsland(), and secS().

Score** U

static

Definition at line 67 of file align.cxx.

Referenced by get_load_count(), and level2index().

double Thres

static

Definition at line 69 of file align.cxx.

Referenced by Align().

double LogThres

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and isSignificant().

double Supp

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and secS().

double GapA

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and AlignTwo().

double GapB

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and AlignTwo().

double GapC

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and newIsland().

double expectedScore

static

Definition at line 69 of file align.cxx.

Referenced by Align(), AlignTwo(), newIsland(), and secS().

double ** GE

static

Definition at line 69 of file align.cxx.

Referenced by Align(), and isSignificant().

Island* Z

static

Definition at line 71 of file align.cxx.

Referenced by AlignTwo(), getTrnsprob(), Structure3D::ReadCoOrdinateFile(), and registerIsland().

Island ** ZB

static

Definition at line 71 of file align.cxx.

Island ** ZE

static

Definition at line 71 of file align.cxx.

int I

static

Definition at line 489 of file align.cxx.

Referenced by AW_scalar::AW_scalar(), CheckItemConsistency(), getTrnsprob(), Int< I >::Int(), Int< I >::operator+=(), Int< I >::operator=(), AW_scalar::set_int(), Int< I >::size(), and SQ_GroupData_Impl< I >::SQ_print_on_screen().

int J

static

Definition at line 489 of file align.cxx.

Referenced by getTrnsprob().

int K

static

Definition at line 489 of file align.cxx.

Referenced by drawLowerPath(), drawPath(), and Structure3D::GenerateTertiaryInteractionsDispLists().