sim4.h File Reference

#include <iostream.h>

Go to the source code of this file.

Classes
struct	msp
class	exon
struct	intron
struct	coordinates
class	edit_script
class	edit_script_list
struct	edit
struct	ValNode
struct	spliced
class	sim4_stats
class	sim4Args
Defines
#define	DEFAULT_NUM_I   3
#define	DIST_CUTOFF   3
#define	DEFAULT_MIN_COV   .8
#define	MININT   -99999
#define	MIN_INTRON   30
#define	MAX_INTRON   20000
#define	MAX_GRINIT   500
#define	MAX_INTERNAL_GAP   50
#define	LL   60
#define	DEFAULT_DRANGE   10
#define	DEFAULT_WEIGHT   100
#define	DEFAULT_W   15
#define	DEFAULT_X   12
#define	DEFAULT_K   18
#define	DEFAULT_C   16
#define	P   .2
#define	min(x, y)   ((x>y) ? (y):(x))
#define	max(x, y)   ((x<y) ? (y):(x))
#define	START_SIG   ((G_score >= abs(C_score)) ? "GT" : "CT")
#define	END_SIG   ((G_score >= abs(C_score)) ? "AG" : "AC")
#define	MATCH   1
#define	MISMATCH   -5
#define	L   8
#define	DELETE   1
#define	INSERT   2
#define	SUBSTITUTE   3
#define	INTRON   4
#define	O_INTRON   5
Typedefs
typedef struct msp *	Msp_ptr
typedef exon *	Exon_ptr
typedef struct intron *	Intron_ptr
typedef struct intron	Intron
typedef struct exon	Exon
typedef struct coordinates	coords
typedef void *	Pointer
typedef struct ValNode *	ValNodePtr
typedef int	signal_t [4][4]
typedef struct spliced	splice_t
typedef sim4_stats	sim4_stats_t
Enumerations
enum	{ FALSE = 0, TRUE = 1 }
enum	{ INIT = 0, PERM = 1, TEMP = 2 }
enum	comparisonType { EST_GEN = 1, GEN_EST = 2 }
enum	{ FWD = 0, BWD = 1, BOTH = 2 }
enum	{ OK = 0, FREE_START = 1, FREE_END = 2, FREE_BOTH_ENDS = 3 }

---

Define Documentation

#define DEFAULT_C   16

Referenced by exon_cores(), and sim4Args::sim4Args().

#define DEFAULT_DRANGE   10

Referenced by sim4Args::sim4Args().

#define DEFAULT_K   18

Referenced by sim4Args::sim4Args().

#define DEFAULT_MIN_COV   .8

#define DEFAULT_NUM_I   3

#define DEFAULT_W   15

Referenced by sim4Args::sim4Args().

#define DEFAULT_WEIGHT   100

Referenced by sim4Args::sim4Args().

#define DEFAULT_X   12

Referenced by sim4Args::sim4Args().

#define DELETE   1

Referenced by align_path(), find_ends(), greedy(), and pluri_align().

#define DIST_CUTOFF   3

Referenced by sim4Args::sim4Args().

#define END_SIG   ((G_score >= abs(C_score)) ? "AG" : "AC")

Referenced by SIM4().

#define INSERT   2

Referenced by align_path(), find_ends(), greedy(), pluri_align(), and S2A().

#define INTRON   4

*ACU *AGU *AUU *CAU *CCU *CGU *CUU *GAU *GCU *GGU *GUU *UAU *UCU *UGU L   8

Referenced by bld_table(), checkstop(), computeDerivative(), Coverdepth::findDip(), link_msps(), load_seq(), GModel< T >::maxIntronLength(), msp2exons(), newmem(), feature::nojunkGene(), and Coverdepth::searchDip().

#define LL   60

#define MATCH   1

Referenced by extend_hit(), and msp2exons().

#define max	(	x,
		y		)	((x<y) ? (y):(x))

#define MAX_GRINIT   500

Referenced by SIM4().

#define MAX_INTERNAL_GAP   50

Referenced by compact_list(), and msp2exons().

#define MAX_INTRON   20000

#define min	(	x,
		y		)	((x>y) ? (y):(x))

#define MIN_INTRON   30

Referenced by link_msps().

#define MININT   -99999

Referenced by align_get_dist(), and link_msps().

#define MISMATCH   -5

Referenced by extend_hit(), and msp2exons().

#define O_INTRON   5

*ACU *AGU *AUU *CAU *CCU * P   .2

Referenced by compact_list(), good_ratio(), greedy(), merge(), msp2exons(), pluri_align(), print_align(), and SIM4().

#define START_SIG   ((G_score >= abs(C_score)) ? "GT" : "CT")

Referenced by SIM4().

#define SUBSTITUTE   3

Referenced by align_path(), find_ends(), greedy(), pluri_align(), and S2A().

---

Typedef Documentation

typedef struct coordinates coords

typedef struct exon Exon

typedef exon* Exon_ptr

typedef struct intron Intron

typedef struct intron * Intron_ptr

typedef struct msp * Msp_ptr

typedef void* Pointer

typedef int signal_t[4][4]

typedef sim4_stats sim4_stats_t

typedef struct spliced splice_t

typedef struct ValNode * ValNodePtr

---

Enumeration Type Documentation

anonymous enum

Enumerator:

FALSE
TRUE

anonymous enum

Enumerator:

INIT
PERM
TEMP

anonymous enum

Enumerator:

FWD
BWD
BOTH

anonymous enum

Enumerator:

OK
FREE_START
FREE_END
FREE_BOTH_ENDS

enum comparisonType

Enumerator:

EST_GEN
GEN_EST