ct_nlmzip_deflate.cpp File Reference

#include <ncbi_pch.hpp>
#include "ct_nlmzip_i.h"

Include dependency graph for ct_nlmzip_deflate.cpp:

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Classes
struct	config

Macros
#define	HASH_BITS   15
#define	HASH_SIZE   (Uint4)(1<<HASH_BITS)
#define	HASH_MASK   (HASH_SIZE-1)
#define	WMASK   (WSIZE-1)
#define	NIL   0 /* Tail of hash chains */
#define	FAST   4
#define	SLOW   2
#define	TOO_FAR   4096
#define	H_SHIFT   ((HASH_BITS+MIN_MATCH-1)/MIN_MATCH)
#define	max_insert_length   max_lazy_match
#define	EQUAL   0
#define	UPDATE_HASH(h, c)   (h = (((h)<<H_SHIFT) ^ (c)) & HASH_MASK)
#define	INSERT_STRING(s, match_head)
#define	FLUSH_BLOCK(eof)

Typedefs
typedef unsigned short	Pos
typedef Uint4	IPos
typedef struct config	config

Functions
static void	fill_window (void)
static ulg	deflate_fast (void)
static int	longest_match (IPos cur_match)
void	Nlmzip_lm_init (int pack_level, ush *flags)
ulg	Nlmzip_deflate (void)

Variables
static ulg	window_size = (ulg)2* 0x8000
static Uint4	ins_h
static Uint4	prev_length
static Uint4	match_start
static int	eofile
static Uint4	lookahead
static Uint4	max_chain_length
static Uint4	max_lazy_match
static int	compr_level
static Uint4	good_match
static int	nice_match
static config	configuration_table [10]

Macro Definition Documentation

EQUAL

#define EQUAL   0

Definition at line 109 of file ct_nlmzip_deflate.cpp.

FAST

#define FAST   4

Definition at line 86 of file ct_nlmzip_deflate.cpp.

FLUSH_BLOCK

#define FLUSH_BLOCK

(

eof

)

Value:

      Nlmzip_flush_block(Nlmzip_block_start >= 0L \
    ? (char*)&Nlmzip_window[(Uint4)Nlmzip_block_start] \
    : (char*)NULL,(Int4)Nlmzip_strstart-Nlmzip_block_start,(eof))

Definition at line 135 of file ct_nlmzip_deflate.cpp.

H_SHIFT

#define H_SHIFT   ((HASH_BITS+MIN_MATCH-1)/MIN_MATCH)

Definition at line 99 of file ct_nlmzip_deflate.cpp.

HASH_BITS

#define HASH_BITS   15

Definition at line 66 of file ct_nlmzip_deflate.cpp.

HASH_MASK

#define HASH_MASK   (HASH_SIZE-1)

Definition at line 80 of file ct_nlmzip_deflate.cpp.

HASH_SIZE

#define HASH_SIZE   (Uint4)(1<<HASH_BITS)

Definition at line 79 of file ct_nlmzip_deflate.cpp.

INSERT_STRING

#define INSERT_STRING	(		s,
			match_head
	)

Value:

   (UPDATE_HASH(ins_h, Nlmzip_window[(s) + MIN_MATCH-1]), \
    Nlmzip_prev[(s) & WMASK] = match_head = head[ins_h], \
    head[ins_h] = (s))

Definition at line 126 of file ct_nlmzip_deflate.cpp.

max_insert_length

#define max_insert_length   max_lazy_match

Definition at line 106 of file ct_nlmzip_deflate.cpp.

NIL

#define NIL   0 /* Tail of hash chains */

Definition at line 83 of file ct_nlmzip_deflate.cpp.

SLOW

#define SLOW   2

Definition at line 87 of file ct_nlmzip_deflate.cpp.

TOO_FAR

#define TOO_FAR   4096

Definition at line 92 of file ct_nlmzip_deflate.cpp.

UPDATE_HASH

#define UPDATE_HASH	(		h,
			c
	)		(h = (((h)<<H_SHIFT) ^ (c)) & HASH_MASK)

Definition at line 116 of file ct_nlmzip_deflate.cpp.

WMASK

#define WMASK   (WSIZE-1)

Definition at line 81 of file ct_nlmzip_deflate.cpp.

Typedef Documentation

config

typedef struct config config

IPos

typedef Uint4 IPos

Definition at line 149 of file ct_nlmzip_deflate.cpp.

Pos

typedef unsigned short Pos

Definition at line 148 of file ct_nlmzip_deflate.cpp.

Function Documentation

deflate_fast()

static ulg deflate_fast ( void  )

static

Definition at line 399 of file ct_nlmzip_deflate.cpp.

References eofile, fill_window(), FLUSH_BLOCK, ins_h, INSERT_STRING, longest_match(), lookahead, match_start, MAX_DIST, max_insert_length, MIN_LOOKAHEAD, MIN_MATCH, NIL, Nlmzip_block_start, Nlmzip_ct_tally(), Nlmzip_strstart, Nlmzip_window, prev_length, and UPDATE_HASH.

Referenced by Nlmzip_deflate().

fill_window()

static void fill_window ( void  )

static

Definition at line 335 of file ct_nlmzip_deflate.cpp.

References eofile, HASH_SIZE, head, lookahead, match_start, MAX_DIST, n, NIL, Nlmzip_block_start, Nlmzip_prev, Nlmzip_ReadData(), Nlmzip_strstart, Nlmzip_window, window_size, and WSIZE.

Referenced by deflate_fast(), Nlmzip_deflate(), and Nlmzip_lm_init().

longest_match()

static int longest_match ( IPos  cur_match )

static

Definition at line 249 of file ct_nlmzip_deflate.cpp.

References good_match, int, len, match(), match_start, max_chain_length, MAX_DIST, MAX_MATCH, nice_match, NIL, Nlmzip_prev, Nlmzip_strstart, Nlmzip_window, prev_length, and WMASK.

Referenced by deflate_fast(), and Nlmzip_deflate().

Nlmzip_deflate()

ulg Nlmzip_deflate

(

void

)

Definition at line 561 of file ct_nlmzip_deflate.cpp.

References compr_level, deflate_fast(), eofile, fill_window(), FLUSH_BLOCK, INSERT_STRING, longest_match(), lookahead, match_start, MAX_DIST, max_lazy_match, MIN_LOOKAHEAD, MIN_MATCH, NIL, Nlmzip_block_start, Nlmzip_ct_tally(), Nlmzip_strstart, Nlmzip_window, prev_length, and TOO_FAR.

Referenced by Nlmzip_Compress().

Nlmzip_lm_init()

void Nlmzip_lm_init	(	int	pack_level,
		ush *	flags
	)

Definition at line 494 of file ct_nlmzip_deflate.cpp.

References compr_level, configuration_table, eofile, FAST, fill_window(), flags, config::good_length, good_match, HASH_SIZE, head, ins_h, lookahead, config::max_chain, max_chain_length, config::max_lazy, max_lazy_match, MIN_LOOKAHEAD, MIN_MATCH, config::nice_length, nice_match, Nlmzip_block_start, Nlmzip_ReadData(), Nlmzip_strstart, Nlmzip_window, SLOW, UPDATE_HASH, URCOMPRERR, and WSIZE.

Referenced by Nlmzip_Compress().

Variable Documentation

compr_level

int compr_level

static

Definition at line 191 of file ct_nlmzip_deflate.cpp.

Referenced by Nlmzip_deflate(), and Nlmzip_lm_init().

configuration_table

config configuration_table[10]

static

Initial value:

= { 
    {0,    0,  0,    0},  
    {4,    4,  8,    4},  
    {4,    5, 16,    8},
    {4,    6, 32,   32},
    {4,    4, 16,   16},  
    {8,   16, 32,   32},
    {8,   16, 128, 128},
    {8,   32, 128, 256},
    {32, 128, 258, 1024},
    {32, 258, 258, 4096}  
}

Definition at line 209 of file ct_nlmzip_deflate.cpp.

Referenced by Nlmzip_lm_init().

eofile

int eofile

static

Definition at line 174 of file ct_nlmzip_deflate.cpp.

Referenced by deflate_fast(), fill_window(), Nlmzip_deflate(), and Nlmzip_lm_init().

good_match

Uint4 good_match

static

Definition at line 194 of file ct_nlmzip_deflate.cpp.

Referenced by longest_match(), and Nlmzip_lm_init().

ins_h

Uint4 ins_h

static

Definition at line 166 of file ct_nlmzip_deflate.cpp.

Referenced by deflate_fast(), fill_window(), and Nlmzip_lm_init().

lookahead

Uint4 lookahead

static

Definition at line 175 of file ct_nlmzip_deflate.cpp.

Referenced by deflate_fast(), fill_window(), Nlmzip_deflate(), and Nlmzip_lm_init().

match_start

Uint4 match_start

static

Definition at line 173 of file ct_nlmzip_deflate.cpp.

Referenced by deflate_fast(), fill_window(), longest_match(), Nlmzip_deflate(), and CCompareSeq_locs::x_ComputeOverlapValues().

max_chain_length

Uint4 max_chain_length

static

Definition at line 181 of file ct_nlmzip_deflate.cpp.

Referenced by longest_match(), and Nlmzip_lm_init().

max_lazy_match

Uint4 max_lazy_match

static

Definition at line 188 of file ct_nlmzip_deflate.cpp.

Referenced by Nlmzip_deflate(), and Nlmzip_lm_init().

nice_match

int nice_match

static

Definition at line 197 of file ct_nlmzip_deflate.cpp.

Referenced by longest_match(), and Nlmzip_lm_init().

prev_length

Uint4 prev_length

static

Definition at line 171 of file ct_nlmzip_deflate.cpp.

Referenced by compile_regex(), deflate_fast(), longest_match(), and Nlmzip_deflate().

window_size

ulg window_size = (ulg)2* 0x8000

static

Definition at line 164 of file ct_nlmzip_deflate.cpp.

Referenced by BLAST_FillInitialWordOptions(), BLAST_GetSuggestedWindowSize(), BOOST_AUTO_TEST_CASE(), CalculateLinkHSPCutoffs(), CProSplignTrimmer::CutFromLeft(), CProSplignTrimmer::CutFromRight(), fill_window(), CContigAssembly::FindDiagFromAlignSet(), s_BlastDiagHashInsert(), s_BlastDiagTableNew(), s_BlastEvenGapLinkHSPs(), s_BlastnDiagHashExtendInitialHit(), s_BlastnDiagTableExtendInitialHit(), and CScoringJob::x_WindowAvgScores().