index_ungapped.c File Reference

Definitions of functions needed to implement diagonal hash to support ungapped extensions for indexed version of megablast. More...

#include "index_ungapped.h"

Include dependency graph for index_ungapped.c:

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Macros
#define	FP_ENTRY_SIZE   (1024*1024)

Functions
static ir_fp_entry *	ir_fp_entry_destroy (ir_fp_entry *e)
	Free memory block destructor. More...
static ir_fp_entry *	ir_fp_entry_create (void)
	Free memory block constructor. More...
ir_diag_hash *	ir_hash_create (void)
	Hash table constructor. More...
ir_diag_hash *	ir_hash_destroy (ir_diag_hash *hash)
	Hash table destructor. More...
ir_hash_entry *	ir_locate (ir_diag_hash *hash, Uint4 diag, Uint4 key)
	Find a hash table entry for the given diagonal. More...

Detailed Description

Definitions of functions needed to implement diagonal hash to support ungapped extensions for indexed version of megablast.

Definition in file index_ungapped.c.

Macro Definition Documentation

FP_ENTRY_SIZE

#define FP_ENTRY_SIZE   (1024*1024)

Definition at line 37 of file index_ungapped.c.

Function Documentation

ir_fp_entry_create()

static ir_fp_entry* ir_fp_entry_create ( void  )

static

Free memory block constructor.

Returns

Pointer to a newly allocated free memory block.

Definition at line 60 of file index_ungapped.c.

References calloc(), entries, FP_ENTRY_SIZE, i, ir_fp_entry_destroy(), and result.

Referenced by ir_locate().

ir_fp_entry_destroy()

static ir_fp_entry* ir_fp_entry_destroy ( ir_fp_entry *  e )

static

Free memory block destructor.

Parameters

e	Pointer to the block being destroyed.

Returns

NULL.

Definition at line 45 of file index_ungapped.c.

References ir_fp_entry_::entries, and free().

Referenced by ir_fp_entry_create(), and ir_hash_destroy().

ir_hash_create()

ir_diag_hash* ir_hash_create

(

void

)

Hash table constructor.

Returns

A pointer to a fresh copy of a diagonal hash table, or NULL.

Definition at line 82 of file index_ungapped.c.

References calloc(), entries, ir_hash_destroy(), IR_HASH_SIZE, and result.

Referenced by MB_IndexedWordFinder(), and ShortRead_IndexedWordFinder().

ir_hash_destroy()

ir_diag_hash* ir_hash_destroy

(

ir_diag_hash *

hash

)

Hash table destructor.

Parameters

hash	Pointer to the hash table instance to destroy.

Returns

NULL.

Definition at line 99 of file index_ungapped.c.

References free(), ir_fp_entry_destroy(), and ir_fp_entry_::next.

Referenced by ir_hash_create(), MB_IndexedWordFinder(), and ShortRead_IndexedWordFinder().

ir_locate()

ir_hash_entry* ir_locate	(	ir_diag_hash *	hash,
		Uint4	diag,
		Uint4	key
	)

Find a hash table entry for the given diagonal.

Parameters

hash	Pointer to hash table instance.
diag	Diagonal identifier.
key	Hash table key corresponding to the diagonal.

Returns

Pointer to ir_hash_entry representing the diagonal.

Definition at line 119 of file index_ungapped.c.

References ir_diag_data_::diag, ir_hash_entry_::diag_data, fp, ir_fp_entry_create(), ncbi::grid::netcache::search::fields::key, ir_hash_entry_::next, and tmp.