inc/hgap.h File Reference

#include "dnaseq.h"
#include "unfin.h"
#include "jksql.h"

Include dependency graph for hgap.h:

Go to the source code of this file.

Data Structures
struct	hgBac
struct	hgContig
struct	hgNest
struct	hgRange
struct	hgHit
struct	hgScoredHit
struct	hgAliHit
struct	hgBoundedHit
struct	hgAlignment
Typedefs
typedef unsigned int	HGID
Enumerations
enum	{ hgContigPad = 800 }
Functions
void	hgSetDb (char *dbName)
char *	hgGetDb ()
sqlConnection *	hgAllocConn ()
sqlConnection *	hgFreeConn (struct sqlConnection **pConn)
HGID	hgIdQuery (struct sqlConnection *conn, char *query)
HGID	hgRealIdQuery (struct sqlConnection *conn, char *query)
sqlConnection *	hgStartUpdate ()
void	hgEndUpdate (struct sqlConnection **pConn, char *comment,...)
HGID	hgNextId ()
FILE *	hgCreateTabFile (char *tableName)
void	hgLoadTabFile (struct sqlConnection *conn, char *tableName)
hgBac *	hgGetBac (char *acc)
hgContig *	hgGetContig (char *acc, int contigIx)
dnaSeq *	hgContigSeq (struct hgContig *contig)
dnaSeq *	hgRnaSeq (char *acc)
void	hgRnaSeqAndId (char *acc, struct dnaSeq **retSeq, HGID *retId)
dnaSeq *	hgBacOrderedSeq (struct hgBac *bac)
dnaSeq *	hgBacSubmittedSeq (char *acc)
dnaSeq *	hgBacContigSeq (char *acc)
int	hgOffset (struct hgNest *source, int offset, struct hgNest *dest)
int	hgCmpTStart (const void *va, const void *vb)
int	hgCmpTarget (const void *va, const void *vb)
int	hgCmpScore (const void *va, const void *vb)
int	hgCmpQStart (const void *va, const void *vb)
int	hgCmpQuery (const void *va, const void *vb)

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Typedef Documentation

typedef unsigned int HGID

Definition at line 22 of file hgap.h.

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Enumeration Type Documentation

anonymous enum

Enumerator:

hgContigPad

Definition at line 64 of file hgap.h.

    {
    hgContigPad = 800,    /* Number of N's between contigs. */
    };

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Function Documentation

struct sqlConnection* hgAllocConn

(

)

[read]

struct dnaSeq* hgBacContigSeq

(

char *

acc

)

[read]

struct dnaSeq* hgBacOrderedSeq

(

struct hgBac *

bac

)

[read]

struct dnaSeq* hgBacSubmittedSeq

(

char *

acc

)

[read]

int hgCmpQStart	(	const void *	va,
		const void *	vb
	)

int hgCmpQuery	(	const void *	va,
		const void *	vb
	)

int hgCmpScore	(	const void *	va,
		const void *	vb
	)

int hgCmpTarget	(	const void *	va,
		const void *	vb
	)

int hgCmpTStart	(	const void *	va,
		const void *	vb
	)

struct dnaSeq* hgContigSeq

(

struct hgContig *

contig

)

[read]

FILE* hgCreateTabFile

(

char *

tableName

)

void hgEndUpdate	(	struct sqlConnection **	pConn,
		char *	comment,
			...
	)

struct sqlConnection* hgFreeConn

(

struct sqlConnection **

pConn

)

[read]

struct hgBac* hgGetBac

(

char *

acc

)

[read]

struct hgContig* hgGetContig	(	char *	acc,
		int	contigIx
	)			[read]

char* hgGetDb

(

)

HGID hgIdQuery	(	struct sqlConnection *	conn,
		char *	query
	)

void hgLoadTabFile	(	struct sqlConnection *	conn,
		char *	tableName
	)

HGID hgNextId

(

)

int hgOffset	(	struct hgNest *	source,
		int	offset,
		struct hgNest *	dest
	)

HGID hgRealIdQuery	(	struct sqlConnection *	conn,
		char *	query
	)

struct dnaSeq* hgRnaSeq

(

char *

acc

)

[read]

void hgRnaSeqAndId	(	char *	acc,
		struct dnaSeq **	retSeq,
		HGID *	retId
	)

void hgSetDb

(

char *

dbName

)

struct sqlConnection* hgStartUpdate

(

)

[read]

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