lex.newick.cpp File Reference

#include <ncbi_pch.hpp>
#include <stdio.h>
#include <string.h>
#include <corelib/stream_utils.hpp>
#include <algo/phy_tree/phy_node.hpp>
#include "newick.tab.hpp"

Include dependency graph for lex.newick.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
struct	yy_buffer_state

Macros
#define	yy_create_buffer   newick_create_buffer
#define	yy_delete_buffer   newick_delete_buffer
#define	yy_scan_buffer   newick_scan_buffer
#define	yy_scan_string   newick_scan_string
#define	yy_scan_bytes   newick_scan_bytes
#define	yy_flex_debug   newick_flex_debug
#define	yy_init_buffer   newick_init_buffer
#define	yy_flush_buffer   newick_flush_buffer
#define	yy_load_buffer_state   newick_load_buffer_state
#define	yy_switch_to_buffer   newick_switch_to_buffer
#define	yyin   newickin
#define	yyleng   newickleng
#define	yylex   newicklex
#define	yyout   newickout
#define	yyrestart   newickrestart
#define	yytext   newicktext
#define	FLEX_SCANNER
#define	YY_FLEX_MAJOR_VERSION   2
#define	YY_FLEX_MINOR_VERSION   5
#define	yyconst
#define	YY_PROTO(proto)   ()
#define	YY_NULL   0
#define	YY_SC_TO_UI(c)   ((unsigned int) (unsigned char) c)
#define	BEGIN   yy_start = 1 + 2 *
#define	YY_START   ((yy_start - 1) / 2)
#define	YYSTATE   YY_START
#define	YY_STATE_EOF(state)   (YY_END_OF_BUFFER + state + 1)
#define	YY_NEW_FILE   yyrestart( yyin )
#define	YY_END_OF_BUFFER_CHAR   0
#define	YY_BUF_SIZE   16384
#define	EOB_ACT_CONTINUE_SCAN   0
#define	EOB_ACT_END_OF_FILE   1
#define	EOB_ACT_LAST_MATCH   2
#define	yyless(n)
#define	unput(c)   yyunput( c, yytext_ptr )
#define	YY_BUFFER_NEW   0
#define	YY_BUFFER_NORMAL   1
#define	YY_BUFFER_EOF_PENDING   2
#define	YY_CURRENT_BUFFER   yy_current_buffer
#define	YY_FLUSH_BUFFER   yy_flush_buffer( yy_current_buffer )
#define	yy_new_buffer   yy_create_buffer
#define	yy_set_interactive(is_interactive)
#define	yy_set_bol(at_bol)
#define	YY_AT_BOL()   (yy_current_buffer->yy_at_bol)
#define	yywrap()   1
#define	YY_SKIP_YYWRAP
#define	yytext_ptr   yytext
#define	YY_DO_BEFORE_ACTION
#define	YY_NUM_RULES   7
#define	YY_END_OF_BUFFER   8
#define	REJECT   reject_used_but_not_detected
#define	yymore()   yymore_used_but_not_detected
#define	YY_MORE_ADJ   0
#define	YY_RESTORE_YY_MORE_OFFSET
#define	INITIAL   0
#define	YY_NO_UNPUT   1
#define	YY_INPUT(buf, result, max_size)
#define	YY_NEVER_INTERACTIVE   1
#define	EXPECT_NUM   1
#define	YY_NO_PUSH_STATE   1
#define	YY_NO_POP_STATE   1
#define	YY_NO_TOP_STATE   1
#define	YY_READ_BUF_SIZE   8192
#define	ECHO   (void) fwrite( yytext, yyleng, 1, yyout )
#define	yyterminate()   return YY_NULL
#define	YY_START_STACK_INCR   25
#define	YY_FATAL_ERROR(msg)   yy_fatal_error( msg )
#define	YY_DECL   int yylex YY_PROTO(( void ))
#define	YY_USER_ACTION
#define	YY_BREAK   break;
#define	YY_RULE_SETUP    YY_USER_ACTION
#define	YY_EXIT_FAILURE   2
#define	yyless(n)

Typedefs
typedef struct yy_buffer_state *	YY_BUFFER_STATE
typedef unsigned int	yy_size_t
typedef unsigned char	YY_CHAR
typedef int	yy_state_type

Functions
void	newickrestart ()
void	newick_switch_to_buffer ()
void	newick_load_buffer_state ()
YY_BUFFER_STATE	newick_create_buffer ()
void	newick_delete_buffer ()
void	newick_init_buffer ()
void	newick_flush_buffer ()
YY_BUFFER_STATE	newick_scan_buffer ()
YY_BUFFER_STATE	newick_scan_string ()
YY_BUFFER_STATE	newick_scan_bytes ()
static void *	yy_flex_alloc ()
static void *	yy_flex_realloc ()
static void	yy_flex_free ()
static yy_state_type	yy_get_previous_state ()
static yy_state_type	yy_try_NUL_trans ()
static int	yy_get_next_buffer ()
static void	yy_fatal_error ()
	USING_SCOPE (ncbi)
static int	input ()
int	newicklex ()
static yy_state_type	yy_try_NUL_trans (yy_current_state) yy_state_type yy_current_state
	if (yy_accept[yy_current_state])
	while (yy_chk[yy_base[yy_current_state]+yy_c] !=yy_current_state)
void	newickrestart (input_file) FILE *input_file
	newick_init_buffer (yy_current_buffer, input_file)
void	newick_switch_to_buffer (new_buffer) YY_BUFFER_STATE new _buffer
	if (yy_current_buffer)
	if (! b) yy_fatal_error("out of dynamic memory in yy_create_buffer()")
	if (! b->yy_ch_buf) yy_fatal_error("out of dynamic memory in yy_create_buffer()")
	newick_init_buffer (b, file)
void	newick_delete_buffer (b) YY_BUFFER_STATE b
	if (b==yy_current_buffer) yy_current_buffer
	if (b->yy_is_our_buffer) yy_flex_free((void *) b -> yy_ch_buf)
	yy_flex_free ((void *) b)
void	newick_flush_buffer (b) YY_BUFFER_STATE b
	if (size< 2||base[size-2] !=0||base[size-1] !=0) return 0
	newick_switch_to_buffer (b)
	for (len=0;yy_str[len];++len)
return	newick_scan_bytes (yy_str, len)
	for (i=0;i< len;++i) buf[i]
static void	yy_fatal_error (msg) char msg[]
	exit (2)
static void *	yy_flex_alloc (size) yy_size_t size
static void *	yy_flex_realloc (ptr, size) void *ptr
static void	yy_flex_free (ptr) void *ptr
void	newick_flex_reset (void)

Variables
int	newickleng
FILE *	newickin = (FILE *) 0
FILE *	newickout = (FILE *) 0
static YY_BUFFER_STATE	yy_current_buffer = 0
static char	yy_hold_char
static int	yy_n_chars = 0
static char *	yy_c_buf_p = (char *) 0
static int	yy_init = 1
static int	yy_start = 0
static int	yy_did_buffer_switch_on_eof = 1
char *	newicktext
static short int	yy_accept [26]
static int	yy_ec [256]
static int	yy_meta [11]
static short int	yy_base [28]
static short int	yy_def [28]
static short int	yy_nxt [41]
static short int	yy_chk [41]
static yy_state_type	yy_last_accepting_state
static char *	yy_last_accepting_cpos
static string	g_Buffer
CNcbiIstream *	g_NewickIstr
char *	yy_cp = yy_c_buf_p
YY_CHAR	yy_c = 1
	yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c]
	yy_is_jam = (yy_current_state == 25)
YY_BUFFER_STATE	newick_create_buffer (file, size) FILE *file
int	size
	b = (YY_BUFFER_STATE) yy_flex_alloc( sizeof( struct yy_buffer_state ) )
b	yy_buf_size = size
b	yy_ch_buf = (char *) yy_flex_alloc( b->yy_buf_size + 2 )
b	yy_is_our_buffer = 1
FILE *	file
b	yy_input_file = file
b	yy_fill_buffer = 1
b	yy_is_interactive = 0
b	yy_buf_pos = &b->yy_ch_buf[0]
b	yy_at_bol = 1
b	yy_buffer_status = 0
YY_BUFFER_STATE	newick_scan_buffer (base, size) char *base
YY_BUFFER_STATE	newick_scan_string (yy_str) char *yy_str
YY_BUFFER_STATE	newick_scan_bytes (bytes, len) char *bytes
int	len
char *	buf
yy_size_t	n = len + 2
int	i

Macro Definition Documentation

BEGIN

#define BEGIN   yy_start = 1 + 2 *

Definition at line 97 of file lex.newick.cpp.

ECHO

#define ECHO   (void) fwrite( yytext, yyleng, 1, yyout )

Definition at line 540 of file lex.newick.cpp.

EOB_ACT_CONTINUE_SCAN

#define EOB_ACT_CONTINUE_SCAN   0

Definition at line 122 of file lex.newick.cpp.

EOB_ACT_END_OF_FILE

#define EOB_ACT_END_OF_FILE   1

Definition at line 123 of file lex.newick.cpp.

EOB_ACT_LAST_MATCH

#define EOB_ACT_LAST_MATCH   2

Definition at line 124 of file lex.newick.cpp.

EXPECT_NUM

#define EXPECT_NUM   1

Definition at line 458 of file lex.newick.cpp.

FLEX_SCANNER

#define FLEX_SCANNER

Definition at line 26 of file lex.newick.cpp.

INITIAL

#define INITIAL   0

Definition at line 394 of file lex.newick.cpp.

REJECT

#define REJECT   reject_used_but_not_detected

Definition at line 388 of file lex.newick.cpp.

unput

#define unput

(

c

)

yyunput( c, yytext_ptr )

Definition at line 153 of file lex.newick.cpp.

YY_AT_BOL

#define YY_AT_BOL

(

)

(yy_current_buffer->yy_at_bol)

Definition at line 280 of file lex.newick.cpp.

YY_BREAK

#define YY_BREAK   break;

Definition at line 599 of file lex.newick.cpp.

YY_BUF_SIZE

#define YY_BUF_SIZE   16384

Definition at line 115 of file lex.newick.cpp.

YY_BUFFER_EOF_PENDING

#define YY_BUFFER_EOF_PENDING   2

Definition at line 216 of file lex.newick.cpp.

YY_BUFFER_NEW

#define YY_BUFFER_NEW   0

Definition at line 204 of file lex.newick.cpp.

YY_BUFFER_NORMAL

#define YY_BUFFER_NORMAL   1

Definition at line 205 of file lex.newick.cpp.

yy_create_buffer

#define yy_create_buffer   newick_create_buffer

Definition at line 2 of file lex.newick.cpp.

YY_CURRENT_BUFFER

#define YY_CURRENT_BUFFER   yy_current_buffer

Definition at line 225 of file lex.newick.cpp.

YY_DECL

#define YY_DECL   int yylex YY_PROTO(( void ))

Definition at line 587 of file lex.newick.cpp.

yy_delete_buffer

#define yy_delete_buffer   newick_delete_buffer

Definition at line 3 of file lex.newick.cpp.

YY_DO_BEFORE_ACTION

#define YY_DO_BEFORE_ACTION

Value:

    yytext_ptr = yy_bp; \
    yyleng = (int) (yy_cp - yy_bp); \
    yy_hold_char = *yy_cp; \
    *yy_cp = '\0'; \
    yy_c_buf_p = yy_cp;

Definition at line 299 of file lex.newick.cpp.

YY_END_OF_BUFFER

#define YY_END_OF_BUFFER   8

Definition at line 307 of file lex.newick.cpp.

YY_END_OF_BUFFER_CHAR

#define YY_END_OF_BUFFER_CHAR   0

Definition at line 112 of file lex.newick.cpp.

YY_EXIT_FAILURE

#define YY_EXIT_FAILURE   2

Definition at line 1536 of file lex.newick.cpp.

YY_FATAL_ERROR

#define YY_FATAL_ERROR

(

msg

)

yy_fatal_error( msg )

Definition at line 580 of file lex.newick.cpp.

yy_flex_debug

#define yy_flex_debug   newick_flex_debug

Definition at line 7 of file lex.newick.cpp.

YY_FLEX_MAJOR_VERSION

#define YY_FLEX_MAJOR_VERSION   2

Definition at line 27 of file lex.newick.cpp.

YY_FLEX_MINOR_VERSION

#define YY_FLEX_MINOR_VERSION   5

Definition at line 28 of file lex.newick.cpp.

yy_flush_buffer

#define yy_flush_buffer   newick_flush_buffer

Definition at line 9 of file lex.newick.cpp.

YY_FLUSH_BUFFER

#define YY_FLUSH_BUFFER   yy_flush_buffer( yy_current_buffer )

Definition at line 254 of file lex.newick.cpp.

yy_init_buffer

#define yy_init_buffer   newick_init_buffer

Definition at line 8 of file lex.newick.cpp.

YY_INPUT

#define YY_INPUT	(		buf,
			result,
			max_size
	)

Value:

{ \
    result = CStreamUtils::Readsome(*g_NewickIstr, buf, max_size); \
    if (result == 0 && !*g_NewickIstr) { \
        result = YY_NULL; \
    } \
}

Definition at line 449 of file lex.newick.cpp.

yy_load_buffer_state

#define yy_load_buffer_state   newick_load_buffer_state

Definition at line 10 of file lex.newick.cpp.

YY_MORE_ADJ

#define YY_MORE_ADJ   0

Definition at line 390 of file lex.newick.cpp.

YY_NEVER_INTERACTIVE

#define YY_NEVER_INTERACTIVE   1

Definition at line 457 of file lex.newick.cpp.

yy_new_buffer

#define yy_new_buffer   yy_create_buffer

Definition at line 264 of file lex.newick.cpp.

YY_NEW_FILE

#define YY_NEW_FILE   yyrestart( yyin )

Definition at line 110 of file lex.newick.cpp.

YY_NO_POP_STATE

#define YY_NO_POP_STATE   1

Definition at line 510 of file lex.newick.cpp.

YY_NO_PUSH_STATE

#define YY_NO_PUSH_STATE   1

Definition at line 509 of file lex.newick.cpp.

YY_NO_TOP_STATE

#define YY_NO_TOP_STATE   1

Definition at line 511 of file lex.newick.cpp.

YY_NO_UNPUT

#define YY_NO_UNPUT   1

Definition at line 439 of file lex.newick.cpp.

YY_NULL

#define YY_NULL   0

Definition at line 84 of file lex.newick.cpp.

YY_NUM_RULES

#define YY_NUM_RULES   7

Definition at line 306 of file lex.newick.cpp.

YY_PROTO

#define YY_PROTO

(

proto

)

()

Definition at line 80 of file lex.newick.cpp.

YY_READ_BUF_SIZE

#define YY_READ_BUF_SIZE   8192

Definition at line 531 of file lex.newick.cpp.

YY_RESTORE_YY_MORE_OFFSET

#define YY_RESTORE_YY_MORE_OFFSET

Definition at line 391 of file lex.newick.cpp.

YY_RULE_SETUP

#define YY_RULE_SETUP    YY_USER_ACTION

Definition at line 602 of file lex.newick.cpp.

YY_SC_TO_UI

#define YY_SC_TO_UI

(

c

)

((unsigned int) (unsigned char) c)

Definition at line 91 of file lex.newick.cpp.

yy_scan_buffer

#define yy_scan_buffer   newick_scan_buffer

Definition at line 4 of file lex.newick.cpp.

yy_scan_bytes

#define yy_scan_bytes   newick_scan_bytes

Definition at line 6 of file lex.newick.cpp.

yy_scan_string

#define yy_scan_string   newick_scan_string

Definition at line 5 of file lex.newick.cpp.

yy_set_bol

#define yy_set_bol

(

at_bol

)

Value:

    { \
    if ( ! yy_current_buffer ) \
        yy_current_buffer = yy_create_buffer( yyin, YY_BUF_SIZE ); \
    yy_current_buffer->yy_at_bol = at_bol; \
    }

Definition at line 273 of file lex.newick.cpp.

yy_set_interactive

#define yy_set_interactive

(

is_interactive

)

Value:

    { \
    if ( ! yy_current_buffer ) \
        yy_current_buffer = yy_create_buffer( yyin, YY_BUF_SIZE ); \
    yy_current_buffer->yy_is_interactive = is_interactive; \
    }

Definition at line 266 of file lex.newick.cpp.

YY_SKIP_YYWRAP

#define YY_SKIP_YYWRAP

Definition at line 284 of file lex.newick.cpp.

YY_START

#define YY_START   ((yy_start - 1) / 2)

Definition at line 103 of file lex.newick.cpp.

YY_START_STACK_INCR

#define YY_START_STACK_INCR   25

Definition at line 575 of file lex.newick.cpp.

YY_STATE_EOF

#define YY_STATE_EOF

(

state

)

(YY_END_OF_BUFFER + state + 1)

Definition at line 107 of file lex.newick.cpp.

yy_switch_to_buffer

#define yy_switch_to_buffer   newick_switch_to_buffer

Definition at line 11 of file lex.newick.cpp.

YY_USER_ACTION

#define YY_USER_ACTION

Definition at line 594 of file lex.newick.cpp.

yyconst

#define yyconst

Definition at line 73 of file lex.newick.cpp.

yyin

#define yyin   newickin

Definition at line 12 of file lex.newick.cpp.

yyleng

#define yyleng   newickleng

Definition at line 13 of file lex.newick.cpp.

yyless [1/2]

#define yyless

(

n

)

Value:

    do \
        { \
        /* Undo effects of setting up yytext. */ \
        *yy_cp = yy_hold_char; \
        YY_RESTORE_YY_MORE_OFFSET \
        yy_c_buf_p = yy_cp = yy_bp + n - YY_MORE_ADJ; \
        YY_DO_BEFORE_ACTION; /* set up yytext again */ \
        } \
    while ( 0 )

Definition at line 1555 of file lex.newick.cpp.

yyless [2/2]

#define yyless

(

n

)

Value:

    do \
        { \
        /* Undo effects of setting up yytext. */ \
        yytext[yyleng] = yy_hold_char; \
        yy_c_buf_p = yytext + n; \
        yy_hold_char = *yy_c_buf_p; \
        *yy_c_buf_p = '\0'; \
        yyleng = n; \
        } \
    while ( 0 )

Definition at line 1555 of file lex.newick.cpp.

yylex

#define yylex   newicklex

Definition at line 14 of file lex.newick.cpp.

yymore

#define yymore

(

)

yymore_used_but_not_detected

Definition at line 389 of file lex.newick.cpp.

yyout

#define yyout   newickout

Definition at line 15 of file lex.newick.cpp.

yyrestart

#define yyrestart   newickrestart

Definition at line 16 of file lex.newick.cpp.

YYSTATE

#define YYSTATE   YY_START

Definition at line 104 of file lex.newick.cpp.

yyterminate

#define yyterminate

(

)

return YY_NULL

Definition at line 570 of file lex.newick.cpp.

yytext

#define yytext   newicktext

Definition at line 17 of file lex.newick.cpp.

yytext_ptr

#define yytext_ptr   yytext

Definition at line 289 of file lex.newick.cpp.

yywrap

#define yywrap

(

)

1

Definition at line 283 of file lex.newick.cpp.

Typedef Documentation

YY_BUFFER_STATE

typedef struct yy_buffer_state* YY_BUFFER_STATE

Definition at line 117 of file lex.newick.cpp.

YY_CHAR

typedef unsigned char YY_CHAR

Definition at line 285 of file lex.newick.cpp.

yy_size_t

typedef unsigned int yy_size_t

Definition at line 159 of file lex.newick.cpp.

yy_state_type

typedef int yy_state_type

Definition at line 287 of file lex.newick.cpp.

Function Documentation

exit()

exit

(

2

)

Referenced by _dblib_check_and_handle_interrupt(), _dblib_handle_err_message(), mu::Test::ParserTester::Abort(), add_test(), CPSGS_Dispatcher::AddProcessor(), dbg_block_allocator::allocate(), dbg_ptr_allocator::allocate(), AndOperationsTest(), CDirectCGIExec::Ask(), BasicFunctionalityTest(), big_test(), bit_decode_func2(), BitBlockTransposeTest(), BitCountChangeTest(), BitEncoderTest(), BitForEachTest(), Blast_CompositionMatrixAdj(), block_cipher_df(), BlockBitEraseTest(), BlockBitInsertTest(), BuildZipIndex(), BvectorBitForEachTest(), BvectorBulkSetTest(), BvectorEraseTest(), BvectorShiftTest(), BZ2_bz__AssertH__fail(), check(), check_ipd_params(), check_ird_params(), Check_SimModel(), CheckAllocLeaks(), CheckBitList(), CheckCompressedDecode(), CheckCountGapRange(), CheckCountRange(), CheckFDLimit(), CheckFetch(), CheckGap2DGap(), CheckGAPMin(), CheckGTSearch(), CheckIntervals(), CheckRangeCopy(), CheckRowNum(), CheckSparseVectorFilter(), CheckSparseVectorGather(), CheckSparseVectorGatherRandom(), CheckSparseVectorRange(), CheckType(), CheckVectors(), chk(), chooseSettings(), cleanup(), cleanUpAndFail(), compare_BV(), compare_BV_set_ref(), compare_SV_set_ref(), CompareEnumerators(), CompareMiniSet(), compareSets(), CompareSparseVector(), CompareStrSparseVector(), ComparisonTest(), configError(), gap_vector::control(), copyFileName(), CBiosampleChkApp::CreateBiosampleUpdateWebService(), ctr_drbg_update_internal(), dbperror(), dbpivot(), dbg_block_allocator::deallocate(), dbg_ptr_allocator::deallocate(), decodeNewickSubtree(), des(), DesrializationTest2(), DetailedCheckVectors(), DetailedCompareBVectors(), DetailedCompareSparseVectors(), detrifurcate(), DNACompressionTest(), DoTest(), CBDB_FileDumperApp::Dump(), CVdbFastaExtractor::DumpAll(), EmptyBVTest(), EnumeratorTest(), err_handler(), establish_login(), ex_display_results(), exec_query(), extend_inputline(), CExonSelectorApplication::ExtractExonsFromSAM(), fastme_run(), fatal(), fatal_error(), FindRank(), GammaEncoderTest(), GAPCheck(), GAPTestStress(), get_encoding_coll(), GetNextExon(), CExonSelectorApplication::GetNextExon(), GetNextTest(), GroupByTest(), hmac5(), hmac_drbg_reseed_core(), ignore_err_handler(), ind_subdbp(), CAltValidator::Init(), insert_test(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::IntegerTemplate(), IntervalsCheck(), LoadBLOB_Table(), LoadBVDump(), bm::LoadBVector(), LoadDemoDB(), loadMatrix(), loadMatrixOLD(), loadNewickTree(), LoadPhoneBook(), LoadVectors(), Log2Test(), main(), CIgBlastnApp::CIgFormatter::Main(), mallocFail(), mbedtls_aes_crypt_cbc_ncbicxx_2_28_3(), mbedtls_aes_crypt_cfb128_ncbicxx_2_28_3(), mbedtls_aes_crypt_cfb8_ncbicxx_2_28_3(), mbedtls_aes_crypt_ctr_ncbicxx_2_28_3(), mbedtls_aes_crypt_ofb_ncbicxx_2_28_3(), mbedtls_aes_setkey_dec_ncbicxx_2_28_3(), mbedtls_camellia_setkey_dec_ncbicxx_2_28_3(), mbedtls_cipher_check_tag_ncbicxx_2_28_3(), mbedtls_ctr_drbg_random_with_add_ncbicxx_2_28_3(), mbedtls_ctr_drbg_reseed_internal(), mbedtls_ctr_drbg_update_ret_ncbicxx_2_28_3(), mbedtls_ctr_drbg_update_seed_file_ncbicxx_2_28_3(), mbedtls_ctr_drbg_write_seed_file_ncbicxx_2_28_3(), mbedtls_des3_crypt_cbc_ncbicxx_2_28_3(), mbedtls_des_crypt_cbc_ncbicxx_2_28_3(), mbedtls_dhm_parse_dhm_ncbicxx_2_28_3(), mbedtls_entropy_add_source_ncbicxx_2_28_3(), mbedtls_entropy_func_ncbicxx_2_28_3(), mbedtls_entropy_write_seed_file_ncbicxx_2_28_3(), mbedtls_hkdf_expand_ncbicxx_2_28_3(), mbedtls_hmac_drbg_random_with_add_ncbicxx_2_28_3(), mbedtls_hmac_drbg_update_ret_ncbicxx_2_28_3(), mbedtls_hmac_drbg_update_seed_file_ncbicxx_2_28_3(), mbedtls_hmac_drbg_write_seed_file_ncbicxx_2_28_3(), mbedtls_md5_ret_ncbicxx_2_28_3(), mbedtls_pkcs12_derivation_ncbicxx_2_28_3(), mbedtls_pkcs12_pbe_ncbicxx_2_28_3(), mbedtls_pkcs12_pbe_sha1_rc4_128_ncbicxx_2_28_3(), mbedtls_pkcs5_pbes2_ncbicxx_2_28_3(), mbedtls_psa_aead_decrypt_ncbicxx_2_28_3(), mbedtls_psa_aead_encrypt_ncbicxx_2_28_3(), mbedtls_ripemd160_ret_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_oaep_encrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsassa_pss_verify_ext_ncbicxx_2_28_3(), mbedtls_sha1_ret_ncbicxx_2_28_3(), mbedtls_sha256_ret_ncbicxx_2_28_3(), mbedtls_sha512_ret_ncbicxx_2_28_3(), mbedtls_ssl_cache_get_ncbicxx_2_28_3(), mbedtls_ssl_cache_set_ncbicxx_2_28_3(), mbedtls_ssl_check_record_ncbicxx_2_28_3(), mbedtls_ssl_cookie_check_ncbicxx_2_28_3(), mbedtls_ssl_get_key_exchange_md_ssl_tls_ncbicxx_2_28_3(), mbedtls_ssl_get_key_exchange_md_tls1_2_ncbicxx_2_28_3(), mbedtls_ssl_parse_finished_ncbicxx_2_28_3(), mbedtls_x509_string_to_names_ncbicxx_2_28_3(), md4(), md5(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::MergeTwoSorted(), mgf_mask(), NewickPrintSubtree(), normal_select(), odbc_check_cols(), odbc_check_no_row(), odbc_check_rows(), odbc_connect(), odbc_db_version_int(), odbc_fatal(), odbc_report_error(), odbc_tds_version_long(), odbc_test_skipped(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::push_back_elements::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::merge_sorted::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::swap_with_other::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::extract_uniq::operator()(), DeBruijn::LargeInt< precision >::operator*(), DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::operator[](), OrOperationsTest(), pcregrep_exit(), pem_aes_decrypt(), pem_des3_decrypt(), pem_des_decrypt(), pem_pbkdf1(), pk_write_ec_private(), CSeqMaskerScoreMeanGlob::PostAdvance(), CBiosampleChkApp::ProcessAsnInput(), ProcessSAM(), psa_asymmetric_decrypt_ncbicxx_2_28_3(), psa_asymmetric_encrypt_ncbicxx_2_28_3(), psa_cipher_decrypt_ncbicxx_2_28_3(), psa_cipher_encrypt_ncbicxx_2_28_3(), psa_cipher_finish_ncbicxx_2_28_3(), psa_cipher_generate_iv_ncbicxx_2_28_3(), psa_cipher_set_iv_ncbicxx_2_28_3(), psa_cipher_setup(), psa_cipher_update_ncbicxx_2_28_3(), psa_copy_key_ncbicxx_2_28_3(), psa_crypto_init_ncbicxx_2_28_3(), psa_crypto_storage_store(), psa_destroy_key_ncbicxx_2_28_3(), psa_export_public_key_ncbicxx_2_28_3(), psa_generate_derived_key_internal(), psa_generate_key_ncbicxx_2_28_3(), psa_hash_compare_ncbicxx_2_28_3(), psa_hash_setup_ncbicxx_2_28_3(), psa_hash_update_ncbicxx_2_28_3(), psa_hash_verify_ncbicxx_2_28_3(), psa_import_key_ncbicxx_2_28_3(), psa_its_get_ncbicxx_2_28_3(), psa_its_set_ncbicxx_2_28_3(), psa_key_agreement_internal(), psa_key_derivation_input_internal(), psa_key_derivation_output_bytes_ncbicxx_2_28_3(), psa_load_persistent_key_into_slot(), psa_load_persistent_key_ncbicxx_2_28_3(), psa_mac_compute_internal(), psa_mac_setup(), psa_mac_sign_finish_ncbicxx_2_28_3(), psa_mac_verify_finish_ncbicxx_2_28_3(), psa_mac_verify_ncbicxx_2_28_3(), psa_raw_key_agreement_ncbicxx_2_28_3(), psa_sign_internal(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::PushBack(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::PushBackElementsFrom(), query(), query_test(), RankFindTest(), CPhyloCSFData::Read(), SPhyloCSFCompactScore::Read(), read_login_info(), readError(), readhdr(), DistanceMatrix::readMat(), ReportODBCError(), rsa_rsassa_pss_sign(), CMkIndexApplication::Run(), CSRSearchApplication::Run(), CCompactSAMApplication::Run(), CExonSelectorApplication::Run(), CAgpValidateApplication::Run(), CDemoApp::Run(), s_Abort(), s_NewHandler(), s_ParseOptions(), s_RunLocalVDBSearch(), s_RunPsiVDBSearch(), bm::SaveBlob(), bm::SaveBVector(), CAgpCompSpanSplitter::SaveRow(), select_rows(), SerializationOperation(), SerializationOperation2Test(), SerializationTest(), SetTest(), ShiftRotateTest(), special_select(), sql_cmd(), ssl_buffer_message(), ssl_handle_id_based_session_resumption(), ssl_load_buffered_message(), ssl_load_buffered_record(), ssl_parse_server_key_exchange(), StressTest(), StressTestAggregatorAND(), StressTestAggregatorOR(), StressTestAggregatorShiftAND(), StressTestStrSparseVector(), SubOperationsTest(), syb_err_handler(), syb_msg_handler(), Test(), test(), test0(), Test0(), test_err(), test_file(), test_params(), test_rows(), test_split(), test_with_dbname(), TestBlockOR(), TestCompressedCollection(), TestCompressSparseSignedVector(), TestCompressSparseVector(), TestEqualSparseVectors(), TestOutput(), TestProc(), TestRandomSubset(), TestRankCompress(), TestResult(), TestSignedSparseSort(), TestSignedSparseVector(), TestSignedSparseVectorScan(), TestSignedSparseVectorSerial(), TestSparseSort(), TestSparseVector(), TestSparseVector_Stress(), TestSparseVectorInserter(), TestSparseVectorScan(), TestSparseVectorSerial(), TestSparseVectorSerialization2(), TestSparseVectorTransform(), TestStrSparseSort(), TestStrSparseVector(), TestStrSparseVectorSerial(), TestTable(), timeout_err_handler(), tls1_prf(), tls_prf_generic(), tooManyBlocks(), unfinished_query_test(), usage(), VerifyCountRange(), WordCmpTest(), SPhyloCSFCompactScore::Write(), CPhyloCSFData::Write(), writeError(), x509_crt_verify_restartable_ca_cb(), CAgpValidateApplication::x_LoadLenFa(), CNetStorageHandler::x_ProcessShutdown(), CAgpValidateApplication::x_ValidateUsingFiles(), and XorOperationsTest().

for() [1/2]

for

(

)

for() [2/2]

for

(

len

= 0;yy_str[len];++len

)

Referenced by BLAST_AffineGreedyAlign(), BLAST_GreedyAlign(), BlastHitSavingParametersUpdate(), BlastResCompStr(), BlastRPSScanSubject(), BOOST_AUTO_TEST_CASE(), BZ2_decompress(), gen_bitlen(), generateMTFValues(), inflateBack(), init_block(), CTable2AsnContext::MakeGenomeCenterId(), mbedtls_x509_serial_gets_ncbicxx_2_28_3(), mpi_montmul(), mz_zip_reader_read_central_dir(), Messenger::RemoveHighlights(), s_AdjustEvaluesForComposition(), s_BlastHSPBestHitRun(), s_BlastSmallNaExtend(), s_BlastSmallNaExtendAlignedOneByte(), s_GetAlignParams(), s_ImportFromHitlist(), s_NaLookup(), s_SetupQueryInfoForReevaluateTest(), s_TarChecksum(), s_VT_Open(), CBamCoverageGraphPanel::SetBamFiles(), tinfl_decompress(), Messenger::ToggleHighlights(), and CQueueDataBase::x_DumpQueueOrClass().

if() [1/7]

if

(

!

b

)

if() [2/7]

if

(

! b->

yy_ch_buf

)

if() [3/7]

if

(

b->

yy_is_our_buffer

)

-> yy_ch_buf)

if() [4/7]

if ( b  = =yy_current_buffer )

new

if() [5/7]

if

(

)

if() [6/7]

if

(

yy_accept

[yy_current_state]

)

Definition at line 1081 of file lex.newick.cpp.

References yy_cp, yy_current_state, yy_last_accepting_cpos, and yy_last_accepting_state.

Referenced by _bcp_get_col_data(), _blk_get_col_data(), _ct_handle_client_message(), _ct_handle_server_message(), hashtable< _Val, _Key, _HF, _ExK, _EqK, _All >::_M_copy_from(), _SQLFetch(), _SQLGetDiagField(), Messenger::AddHighlights(), CTL_Cmd::AssignCmdParam(), BLAST_LinkHsps(), BLAST_PreliminarySearchEngine(), BlastChooseNaExtend(), BlastNaWordFinder(), blk_bind(), buffer_add_row(), CPhyloTreePS::CalcForces(), CConnTest::CheckFWConnections(), CkSegmentSet(), compile_branch(), CONN_GetSOCK(), ConnNetInfo_ParseURL(), continue_logging_in(), convert_to_usc2le_string(), copy_output_until_stop(), AlignmentManager::CreateMultipleFromPairwiseWithIBM(), CreateNewPairwiseAlignmentsByBlockExtension(), ct_bind(), ct_cmd_props(), ct_con_props(), CTLibContext::CTLIB_srverr_handler(), dbgetnull(), dbtxptr(), dbtxtimestamp(), deflate_stored(), deflateInit2_(), deflateResetKeep(), AlignmentUtility::DoIBM(), DoSocketWait(), DP_GlobalBlockAlign(), DP_GlobalBlockAlignGeneric(), fill_window(), GenBankIndex(), CCgiRequest::GetCGIEntries(), BlockMultipleAlignment::GetCharacterAt(), BlockMultipleAlignment::GetCharacterTraitsAt(), GetFeatNameAndLoc(), CLinkedFeatsGroup::GetHTMLActiveAreas(), CDirEntry::GetType(), GICache_Dump(), GICache_GetAccFreqTab(), bm::bvector< Alloc >::enumerator::go_up(), gzclose_w(), gzprintf(), inflate(), inflate_codes(), inflateBack(), inflateEnd(), inflateGetDictionary(), inflateGetHeader(), inflatePrime(), inflateReset2(), inflateResetKeep(), inflateSetDictionary(), inflateStateCheck(), inflateSync(), inflateValidate(), InitialEntry(), JumperNaWordFinder(), LookupTableOptionsNew(), CTable2AsnContext::MakeGenomeCenterId(), match(), mbedtls_cipher_aead_decrypt(), mbedtls_cipher_aead_encrypt(), mbedtls_cipher_crypt_ncbicxx_2_28_3(), mbedtls_cipher_free_ncbicxx_2_28_3(), mbedtls_md_hmac_finish_ncbicxx_2_28_3(), mbedtls_md_hmac_reset_ncbicxx_2_28_3(), mbedtls_pk_write_pubkey_ncbicxx_2_28_3(), mbedtls_ssl_encrypt_buf_ncbicxx_2_28_3(), mbedtls_ssl_prepare_handshake_record_ncbicxx_2_28_3(), mbedtls_ssl_read_ncbicxx_2_28_3(), mbedtls_x509_get_rsassa_pss_params_ncbicxx_2_28_3(), MD4Update(), MD5Update(), mdb_cmp_memnr(), mdb_cursor_del0(), mdb_cursor_put(), mdb_env_copyfd1(), mdb_env_open2(), mdb_env_set_mapsize(), mdb_freelist_save(), mdb_node_add(), mdb_page_alloc(), mdb_page_new(), mdb_page_spill(), mdb_txn_begin(), fix_pub::MergeNonPubmedPubIds(), mz_zip_reader_extract_to_mem_no_alloc(), mz_zip_validate_file(), mz_zip_writer_add_from_zip_reader(), mz_zip_writer_add_to_central_dir(), NcbiGetHostIfConfEx(), odbc_set_return_params(), odbc_set_return_status(), odbc_sql2tds(), bm::bvector< Alloc >::optimize_gap_size(), pcre_dfa_exec(), pcre_exec(), CTbl2AsnApp::ProcessTopEntry(), CBDB_Cache::Purge(), QSIndex(), python::RetrieveModuleFileName(), CPubseqGatewayApp::Run(), s_BlastEvenGapLinkHSPs(), s_BlastGreedyAlignMemAlloc(), s_BlastNaHashLookupRetieveHits(), s_BlastnDiagTableExtendInitialHit(), s_BuildScoreList(), s_CalculateScoreVectorSize(), s_Close(), s_Connect(), s_CreateHttpConnector(), s_Destroy(), s_FillReturnCutoffsInfo(), s_FindSpliceJunctionsForGap(), s_FwdCompareLinkedHSPSets(), s_gethostbyname_(), s_GetLString(), s_GetNextInfo(), s_InitalizeDllProj(), s_ParseHeader(), s_ProcessOptionalSettings(), s_Read_(), s_ReleaseToFreePages(), s_Reset(), s_RPSPreliminarySearchEngine(), s_ShiftWin1(), s_SmallNaLookup(), s_Update(), s_VT_Close(), s_VT_Descr(), s_VT_Flush(), s_VT_Read(), s_VT_Wait(), s_VT_Write(), TestFixture::ScanCheckHitsCore(), TestFixture::ScanMaxHitsTestCore(), TestFixture::ScanOffsetTestCore(), sendMTFValues(), FileMessenger::SendPendingCommands(), SERV_WriteInfo(), set_nottype_bits(), set_type_bits(), CHistogramGlyph::SetAxisRange(), CBamCoverageGraphPanel::SetBamFiles(), bm::bvector< Alloc >::enumerator::skip(), SPHIPatternSearchBlkNew(), SQLGetData(), SQLGetTypeInfo(), ssl_buffer_message(), ssl_check_client_reconnect(), ssl_parse_client_hello(), ssl_parse_record_header(), tdefl_compress_normal(), tdefl_flush_block(), tds_datecrack(), tds_generic_get(), tds_money_to_string(), tds_msdatetime_put(), tds_numeric_put(), tds_process_login_tokens(), tds_row_free(), tds_sybbigtime_put(), tds_variant_get(), test(), CPhyloTreePS::Update(), updatewindow(), VDBSRC_GetSeq2na(), x509_crt_check_san(), x509_profile_check_key(), x_AddInfo(), CPhyloTreePS::x_ApplyRepulsiveForcesHashed(), CBlobCacher::x_CacheMapRecs(), CBlobCacher::x_CacheMetaRec(), x_DataToGiData(), x_Finalize(), CGeneFileWriter::x_Gene2Accn_Filter(), CAlnVecRow::x_HitTest(), SDiagMessage::x_OldWrite(), CDisplaySeqalign::x_PrintDefLine(), CTar::x_ReadAndProcess(), CMakeProfileDBApp::x_RPS_DbClose(), CGapsEditor::x_SetGapParameters(), x_UpdatePort(), CValidError_bioseq::x_ValidateCDSVDJCmatch(), and CSparseGraph::x_WriteMap().

if() [7/7]

if

(

yy_current_buffer

)

Definition at line 1242 of file lex.newick.cpp.

References yy_buffer_state::yy_buf_pos, yy_c_buf_p, yy_current_buffer, yy_hold_char, yy_buffer_state::yy_n_chars, and yy_n_chars.

input()

static int input ( )

static

Definition at line 1147 of file lex.newick.cpp.

References EOB_ACT_CONTINUE_SCAN, EOB_ACT_END_OF_FILE, EOB_ACT_LAST_MATCH, offset, yy_c_buf_p, yy_ch_buf, yy_did_buffer_switch_on_eof, YY_END_OF_BUFFER_CHAR, yy_get_next_buffer(), yy_hold_char, yy_n_chars, YY_NEW_FILE, yyin, yyrestart, yytext_ptr, and yywrap.

Referenced by _mm_movemask_epi8(), _mm_movemask_pd(), _mm_movemask_pi8(), _mm_movemask_ps(), CMultiFileInput::AddFilenames(), CTableSortMultiChoice::AddLevels(), aes_crypt_cbc_wrap(), aes_crypt_cfb128_wrap(), aes_crypt_ctr_wrap(), aes_crypt_ecb_wrap(), aes_crypt_ofb_wrap(), aes_crypt_xts_wrap(), xslt::stylesheet::apply(), arc4_crypt_stream_wrap(), AssignFuzzy(), AssignFuzzyLocalVariation(), blowfish_crypt_cbc_wrap(), blowfish_crypt_cfb64_wrap(), blowfish_crypt_ctr_wrap(), blowfish_crypt_ecb_wrap(), BOOST_AUTO_TEST_CASE(), CDebugDumpViewer::Bpt(), SRequestBuilder::Build(), camellia_crypt_cbc_wrap(), camellia_crypt_cfb128_wrap(), camellia_crypt_ctr_wrap(), camellia_crypt_ecb_wrap(), CapitalizeAfterApostrophe(), CBlastnNode::CBlastnNode(), CBlastnNodeArgs::CBlastnNodeArgs(), CBlastpNode::CBlastpNode(), CBlastpNodeArgs::CBlastpNodeArgs(), CBlastxNode::CBlastxNode(), CBlastxNodeArgs::CBlastxNodeArgs(), ccm_auth_crypt(), chacha20_stream_wrap(), chachapoly_crypt_and_tag(), NAutomation::SCommandImpl::Check(), check_ascii(), NAutomation::CAutomationObject::CheckCall(), CheckDuplicates(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::const_lower_bound(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::const_upper_bound(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::construct_hashes(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::construct_values(), CBlastDBAliasApp::ConvertGiFile(), CCountries::CountryFixupItem(), CPssmEngine::CPssmEngine(), CDbIndex_Factory::Create(), CSubAnnotationPanel::Create5ColFeatTable(), CBlastDBAliasApp::CreateAliasFile(), CreateAsnConn_Service(), CreateAsnConn_ServiceEx(), CreateBlastMatrix(), CRPSBlastNodeArgs::CRPSBlastNodeArgs(), CRPSTBlastnNodeArgs::CRPSTBlastnNodeArgs(), CTblastnNode::CTblastnNode(), CTblastnNodeArgs::CTblastnNodeArgs(), dbpivot(), des3_crypt_cbc_wrap(), des3_crypt_ecb_wrap(), des_crypt_cbc_wrap(), des_crypt_ecb_wrap(), CDbIndex_Factory::do_create(), CDbIndex_Factory::do_create_1_2(), NAutomation::CArgument::Exec(), SSimpleCommandImpl::Exec(), SVariadicCommandImpl::Exec(), ctll::fixed_string< N >::fixed_string(), SRequestBuilder::SReader< CJson_ConstObject >::ForEachTSE(), SRequestBuilder::SReader< CArgs >::ForEachTSE(), SRequestBuilder::SReader< SPsgCgiEntries >::ForEachTSE(), CFormatGuess::Format(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::get_current_term(), get_no_padding(), get_one_and_zeros_padding(), get_pkcs_padding(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::get_previous_term(), get_zeros_and_len_padding(), get_zeros_padding(), SRequestBuilder::SReader< CJson_ConstObject >::GetAbsPathRef(), SRequestBuilder::SReader< CJson_ConstObject >::GetAccSubstitution(), SRequestBuilder::SReader< CArgs >::GetAccSubstitution(), SRequestBuilder::SReader< SPsgCgiEntries >::GetAccSubstitution(), SRequestBuilder::SReader< CJson_ConstObject >::GetBioId(), SRequestBuilder::SReader< CArgs >::GetBioId(), SRequestBuilder::SReader< SPsgCgiEntries >::GetBioId(), SRequestBuilder::SReader< CJson_ConstObject >::GetBioIdResolution(), SRequestBuilder::SReader< CArgs >::GetBioIdResolution(), SRequestBuilder::SReader< SPsgCgiEntries >::GetBioIdResolution(), SRequestBuilder::SReader< CJson_ConstObject >::GetBioIds(), SRequestBuilder::SReader< CArgs >::GetBioIds(), SRequestBuilder::SReader< SPsgCgiEntries >::GetBioIds(), SRequestBuilder::SReader< CArgs >::GetBioIdType(), SRequestBuilder::SReader< SPsgCgiEntries >::GetBioIdType(), SRequestBuilder::SReader< CJson_ConstObject >::GetBlobId(), SRequestBuilder::SReader< CArgs >::GetBlobId(), SRequestBuilder::SReader< SPsgCgiEntries >::GetBlobId(), SRequestBuilder::SReader< CJson_ConstObject >::GetChunkId(), SRequestBuilder::SReader< CArgs >::GetChunkId(), SRequestBuilder::SReader< SPsgCgiEntries >::GetChunkId(), CMultiFileInput::GetFilenames(), GetFirstInitial(), SRequestBuilder::SReader< CJson_ConstObject >::GetIpg(), SRequestBuilder::SReader< CArgs >::GetIpg(), SRequestBuilder::SReader< SPsgCgiEntries >::GetIpg(), CTableSortMultiChoice::GetLevels(), CPssmCddInputTest::GetMsaSize(), SRequestBuilder::SReader< CJson_ConstObject >::GetNamedAnnots(), SRequestBuilder::SReader< CArgs >::GetNamedAnnots(), SRequestBuilder::SReader< SPsgCgiEntries >::GetNamedAnnots(), SRequestBuilder::SReader< CJson_ConstObject >::GetNucleotide(), SRequestBuilder::SReader< CArgs >::GetNucleotide(), SRequestBuilder::SReader< SPsgCgiEntries >::GetNucleotide(), CPssmCreateTestFixture::GetNumAlignedSequences(), CPssmCddInputTest::GetNumHits(), SRequestBuilder::SReader< CJson_ConstObject >::GetProtein(), SRequestBuilder::SReader< CArgs >::GetProtein(), SRequestBuilder::SReader< SPsgCgiEntries >::GetProtein(), SRequestBuilder::SReader< CJson_ConstObject >::GetResendTimeout(), SRequestBuilder::GetResolveParams(), CParseTextOptionsDlg::GetSelectedText(), CParseTextOptions::GetSelectedText(), SRequestBuilder::SReader< CJson_ConstObject >::GetSNPScaleLimit(), SRequestBuilder::SReader< CArgs >::GetSNPScaleLimit(), SRequestBuilder::SReader< SPsgCgiEntries >::GetSNPScaleLimit(), SRequestBuilder::SReader< CJson_ConstObject >::GetSpecified(), SRequestBuilder::SReader< CArgs >::GetSpecified(), SRequestBuilder::SReader< SPsgCgiEntries >::GetSpecified(), CPssmCddInputTest::GetSubjectMsaIndex(), GetTextEncodingForm(), SRequestBuilder::SReader< CJson_ConstObject >::GetUserArgs(), SRequestBuilder::SReader< CArgs >::GetUserArgs(), SRequestBuilder::SReader< SPsgCgiEntries >::GetUserArgs(), NAutomation::CCommand::Help(), SCommandGroupImpl::Help(), CTaxValidationAndCleanup::IncrementalSpecificHostMapUpdate(), CTaxValidationAndCleanup::IncrementalStrainMapUpdate(), CQualLookupMap::IncrementalUpdate(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::insert_sort_indices(), LaunchAdapterJob(), CGenBankLoadOptionPanel::LoadSettings(), main(), CBlastnNode::Main(), CBlastpNode::Main(), CBlastxNode::Main(), CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CTblastnNode::Main(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::make_indices(), CDbIndex::MakeIndex(), MakeLoc(), mbedtls_aes_crypt_cbc_ncbicxx_2_28_3(), mbedtls_aes_crypt_cfb128_ncbicxx_2_28_3(), mbedtls_aes_crypt_cfb8_ncbicxx_2_28_3(), mbedtls_aes_crypt_ctr_ncbicxx_2_28_3(), mbedtls_aes_crypt_ecb_ncbicxx_2_28_3(), mbedtls_aes_crypt_ofb_ncbicxx_2_28_3(), mbedtls_aes_crypt_xts_ncbicxx_2_28_3(), mbedtls_aes_decrypt_ncbicxx_2_28_3(), mbedtls_aes_encrypt_ncbicxx_2_28_3(), mbedtls_arc4_crypt_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_cbc_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_cfb64_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_ctr_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_ecb_ncbicxx_2_28_3(), mbedtls_camellia_crypt_cbc_ncbicxx_2_28_3(), mbedtls_camellia_crypt_cfb128_ncbicxx_2_28_3(), mbedtls_camellia_crypt_ctr_ncbicxx_2_28_3(), mbedtls_camellia_crypt_ecb_ncbicxx_2_28_3(), mbedtls_ccm_auth_decrypt_ncbicxx_2_28_3(), mbedtls_ccm_encrypt_and_tag_ncbicxx_2_28_3(), mbedtls_ccm_star_auth_decrypt_ncbicxx_2_28_3(), mbedtls_ccm_star_encrypt_and_tag_ncbicxx_2_28_3(), mbedtls_chacha20_crypt_ncbicxx_2_28_3(), mbedtls_chacha20_update_ncbicxx_2_28_3(), mbedtls_chachapoly_auth_decrypt_ncbicxx_2_28_3(), mbedtls_chachapoly_encrypt_and_tag_ncbicxx_2_28_3(), mbedtls_chachapoly_update_ncbicxx_2_28_3(), mbedtls_cipher_aead_decrypt(), mbedtls_cipher_aead_encrypt(), mbedtls_cipher_auth_decrypt_ext_ncbicxx_2_28_3(), mbedtls_cipher_auth_decrypt_ncbicxx_2_28_3(), mbedtls_cipher_auth_encrypt_ext_ncbicxx_2_28_3(), mbedtls_cipher_auth_encrypt_ncbicxx_2_28_3(), mbedtls_cipher_crypt_ncbicxx_2_28_3(), mbedtls_cipher_update_ncbicxx_2_28_3(), mbedtls_ct_rsaes_pkcs1_v15_unpadding_ncbicxx_2_28_3(), mbedtls_des3_crypt_cbc_ncbicxx_2_28_3(), mbedtls_des3_crypt_ecb_ncbicxx_2_28_3(), mbedtls_des_crypt_cbc_ncbicxx_2_28_3(), mbedtls_des_crypt_ecb_ncbicxx_2_28_3(), mbedtls_dhm_read_public_ncbicxx_2_28_3(), mbedtls_gcm_auth_decrypt_ncbicxx_2_28_3(), mbedtls_gcm_crypt_and_tag_ncbicxx_2_28_3(), mbedtls_gcm_update_ncbicxx_2_28_3(), mbedtls_internal_aes_decrypt_ncbicxx_2_28_3(), mbedtls_internal_aes_encrypt_ncbicxx_2_28_3(), mbedtls_md5_ncbicxx_2_28_3(), mbedtls_md5_ret_ncbicxx_2_28_3(), mbedtls_md5_update_ncbicxx_2_28_3(), mbedtls_md5_update_ret_ncbicxx_2_28_3(), mbedtls_md_hmac_ncbicxx_2_28_3(), mbedtls_md_hmac_update_ncbicxx_2_28_3(), mbedtls_md_ncbicxx_2_28_3(), mbedtls_md_update_ncbicxx_2_28_3(), mbedtls_pk_decrypt_ncbicxx_2_28_3(), mbedtls_pk_encrypt_ncbicxx_2_28_3(), mbedtls_poly1305_mac_ncbicxx_2_28_3(), mbedtls_poly1305_update_ncbicxx_2_28_3(), mbedtls_ripemd160_ncbicxx_2_28_3(), mbedtls_ripemd160_ret_ncbicxx_2_28_3(), mbedtls_ripemd160_update_ncbicxx_2_28_3(), mbedtls_ripemd160_update_ret_ncbicxx_2_28_3(), mbedtls_rsa_pkcs1_decrypt_ncbicxx_2_28_3(), mbedtls_rsa_pkcs1_encrypt_ncbicxx_2_28_3(), mbedtls_rsa_private_ncbicxx_2_28_3(), mbedtls_rsa_public_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_oaep_decrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_oaep_encrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_pkcs1_v15_decrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_pkcs1_v15_encrypt_ncbicxx_2_28_3(), mbedtls_sha1_ncbicxx_2_28_3(), mbedtls_sha1_ret_ncbicxx_2_28_3(), mbedtls_sha1_update_ncbicxx_2_28_3(), mbedtls_sha1_update_ret_ncbicxx_2_28_3(), mbedtls_sha256_ncbicxx_2_28_3(), mbedtls_sha256_ret_ncbicxx_2_28_3(), mbedtls_sha256_update_ncbicxx_2_28_3(), mbedtls_sha256_update_ret_ncbicxx_2_28_3(), mbedtls_sha512_ncbicxx_2_28_3(), mbedtls_sha512_ret_ncbicxx_2_28_3(), mbedtls_sha512_update_ncbicxx_2_28_3(), mbedtls_sha512_update_ret_ncbicxx_2_28_3(), mbedtls_xtea_crypt_cbc_ncbicxx_2_28_3(), mbedtls_xtea_crypt_ecb_ncbicxx_2_28_3(), ctll::parser< Grammar, input, ActionSelector, IgnoreUnknownActions >::move(), CGridCommandLineInterfaceApp::NetScheduleSanityCheck(), CCountries::NewFixCountry(), CTableSortMultiChoice::OnBrowseBtn(), CGenBankLoadOptionPanel::OnRecentAccClicked(), compile_time_bits::TInsertSorter< _Traits, _AllowDuplicates >::Less::operator()(), pearson_hash_int2byte(), pearson_hash_int2short(), poly1305_process(), PositiveSign(), CObjectsSniffer::Probe(), CObjectsSniffer::ProbeAny(), CObjectsSniffer::ProbeASN1_Bin(), CObjectsSniffer::ProbeText(), process_string(), NAutomation::CAutomationProc::ProcessMessage(), CTAbleValApp::ProcessOneFile(), psa_asymmetric_decrypt_ncbicxx_2_28_3(), psa_asymmetric_encrypt_ncbicxx_2_28_3(), psa_cipher_decrypt_ncbicxx_2_28_3(), psa_cipher_encrypt_ncbicxx_2_28_3(), psa_cipher_update_ncbicxx_2_28_3(), psa_driver_wrapper_cipher_decrypt_ncbicxx_2_28_3(), psa_driver_wrapper_cipher_encrypt_ncbicxx_2_28_3(), psa_driver_wrapper_cipher_update_ncbicxx_2_28_3(), psa_driver_wrapper_hash_compute_ncbicxx_2_28_3(), psa_driver_wrapper_hash_update_ncbicxx_2_28_3(), psa_driver_wrapper_mac_compute_ncbicxx_2_28_3(), psa_driver_wrapper_mac_update_ncbicxx_2_28_3(), psa_driver_wrapper_sign_message_ncbicxx_2_28_3(), psa_driver_wrapper_verify_message_ncbicxx_2_28_3(), psa_hash_compare_ncbicxx_2_28_3(), psa_hash_compute_ncbicxx_2_28_3(), psa_hash_update_ncbicxx_2_28_3(), psa_mac_compute_internal(), psa_mac_compute_ncbicxx_2_28_3(), psa_mac_update_ncbicxx_2_28_3(), psa_mac_verify_ncbicxx_2_28_3(), psa_sign_internal(), psa_sign_message_builtin_ncbicxx_2_28_3(), psa_sign_message_ncbicxx_2_28_3(), psa_verify_internal(), psa_verify_message_builtin_ncbicxx_2_28_3(), psa_verify_message_ncbicxx_2_28_3(), PsiBlastComputePssmFromAlignment(), SJobIODump::Read(), ReadContainer(), ReadFastaFileMap(), ReadIntoUtf8(), ReadMap(), CRebase::ReadNARFormat(), ReadSequencesToBlast(), CPssmCddInputTest::RemoveMultipleCdHits(), CParseTextOptions::RemoveSelectedText(), CFindASN1Dlg::ReplaceLinebreaks(), ReplaceNoCase(), CFindASN1Dlg::ReplaceValue(), CTaxValidationAndCleanup::ReportSpecificHostErrors(), rsa_alt_decrypt_wrap(), rsa_decrypt_wrap(), rsa_encrypt_wrap(), CDeltaBlastApp::Run(), CPsiBlastApp::Run(), CSeedTopApp::Run(), CTblastxApp::Run(), CBlastDBAliasApp::Run(), CIgBlastpApp::Run(), CMagicBlastApp::Run(), CRMBlastnApp::Run(), CVecScreenApp::Run(), CTax4BlastDemo::Run(), CBlastInputDemoApplication::Run(), CCacheIndexCopyApp::Run(), CGuideTreeApplication::Run(), CVDBBlastnApp::Run(), CVDBTblastnApp::Run(), CMultipatternApp::Run(), CObjConvProfile::Run(), CSampleNetScheduleClient::Run(), s_CheckInputSize(), s_Create5ColFeatTable(), s_ReadAndTestQueryFromString(), s_ReadAndTestQueryFromString_CFastaReader(), s_ReplaceGIs(), CUpdateMultiSeq_Dlg::s_ReportIdenticalPairs(), s_SearchInSeqText(), s_SplitArrayOf8(), CGenBankLoadOptionPanel::SaveSettings(), ScanFastaFile(), CSuspect_rule_set::Screen(), CMultipatternSearch::Search(), SSnpFilter::SerializeFrom(), CConvertAuthorToConsortiumWhereConstraint::SetConstraint(), CNetBLASTLoadOptionPanel::SetInput(), CBamLoadOptionPanel::SetInput(), CGenBankLoadOptionPanel::SetInput(), CJob::SetInput(), COpenViewManager::SetInputObjects(), CGridJobBatchSubmitter::SetJobInput(), CGridClient::SetJobInput(), CGridCgiContext::SetJobInput(), CAsnExporter::SetObjects(), CAlignTabExporter::SetObjects(), CFastaAlignExporter::SetObjects(), CPhyExporter::SetObjects(), C5ColExporter::SetObjects(), CAgpExporter::SetObjects(), CFastaExporter::SetObjects(), CFlatFileExporter::SetObjects(), CGffExporter::SetObjects(), CGtfExporter::SetObjects(), CWiggleExporter::SetObjects(), skip_one_input_sequence(), CNetScheduleSubmitter::SubmitJobBatch(), sUpdateCase(), tds7_send_login(), tds_readpassphrase(), CFormatGuess::TestFormatXml(), ToAsciiStdString(), CDoiLookup::Transcode(), CSubAnnotationPanel::TransferDataToWindow(), TSeqLocVector2Bioseqs(), SJobIODump::Write(), CMultiFileInput::x_AddFilenameRow(), CTableSortMultiChoice::x_AddLevelRow(), CMakeBlastDBApp::x_AddSequenceData(), CDiscRepApp::x_ConstructOutputName(), CBlastDBAliasApp::x_ConvertSeqIDFile(), CObjConvProfile::x_CreateRelatedMap(), CMultiFileInput::x_DeleteFilename(), CTableSortMultiChoice::x_DeleteLevel(), CHtmlTooltipFormatter::x_FindAllOccurences(), CFormatGuess::x_FindJsonStringLimits(), CClustalOmegaToolJob::x_GetCommandLine(), CClustalwToolJob::x_GetCommandLine(), CKalignToolJob::x_GetCommandLine(), CMafftToolJob::x_GetCommandLine(), CMuscleToolJob::x_GetCommandLine(), CDebugDumpViewer::x_GetInput(), x_GetNextAttribute(), CAltitudePanel::x_GetNumber(), CBlastVdbCmdApp::x_GetQueries(), CConvert2BlastMaskApplication::x_GetReader(), SegMaskerApplication::x_GetReader(), CAlignedFeatureGraph::x_GetRecsSortedByLength(), CMakeBlastDBApp::x_GuessFileType(), CCompressedFile::x_GuessFormat(), CBlastDBCmdApp::x_InitBlastDB_TaxIdList(), CMixedStrands::x_InitDialog(), CHtmlTooltipFormatter::x_InsertSpaces(), CSplitQueryTestFixture::x_ParseConfigLine(), CBlastDBCmdApp::x_ProcessBatchEntry(), CBlastDBCmdApp::x_ProcessBatchEntry_NoDup(), CBlastDBCmdApp::x_ProcessBatchPig(), CRpsAuxFile::x_ReadFromFile(), CObjectsSniffer::x_ReadObject(), CFeatureTblFr::x_RefreshTable(), CBlastnApp::x_RunMTBySplitDB(), CBlastpApp::x_RunMTBySplitDB(), CBlastxApp::x_RunMTBySplitDB(), CRPSBlastApp::x_RunMTBySplitDB(), CRPSTBlastnApp::x_RunMTBySplitDB(), CTblastnApp::x_RunMTBySplitDB(), CBlastnApp::x_RunMTBySplitQuery(), CBlastpApp::x_RunMTBySplitQuery(), CBlastxApp::x_RunMTBySplitQuery(), CRPSBlastApp::x_RunMTBySplitQuery(), CRPSTBlastnApp::x_RunMTBySplitQuery(), CTblastnApp::x_RunMTBySplitQuery(), CMultiFileInput::x_SendFileTxtChangedEvt(), CFeaturePanel::x_StartAssemblyJob(), CSeqTextPanel::x_StartSearch(), CFormatGuess::x_TestInput(), CObjectsSniffer::x_TryReadObject(), CGff2Record::xAssignAttributesFromGff(), xMultiPatternSearch(), and xTryTextFile().

newick_create_buffer()

YY_BUFFER_STATE newick_create_buffer

(

)

newick_delete_buffer() [1/2]

void newick_delete_buffer

(

)

newick_delete_buffer() [2/2]

void newick_delete_buffer

(

b

)

References b.

newick_flex_reset()

void newick_flex_reset

(

void

)

Definition at line 1652 of file lex.newick.cpp.

References BEGIN, and newickrestart().

Referenced by ReadNewickTree().

newick_flush_buffer() [1/2]

void newick_flush_buffer

(

)

newick_flush_buffer() [2/2]

void newick_flush_buffer

(

b

)

References b, and YY_END_OF_BUFFER_CHAR.

newick_init_buffer() [1/3]

void newick_init_buffer

(

)

newick_init_buffer() [2/3]

void newick_init_buffer	(	b	,
		file
	)

newick_init_buffer() [3/3]

newick_init_buffer	(	yy_current_buffer	,
		input_file
	)

newick_load_buffer_state()

void newick_load_buffer_state

(

)

Definition at line 1265 of file lex.newick.cpp.

References yy_buffer_state::yy_buf_pos, yy_c_buf_p, yy_current_buffer, yy_hold_char, yy_buffer_state::yy_input_file, yy_buffer_state::yy_n_chars, yy_n_chars, yyin, and yytext_ptr.

newick_scan_buffer()

YY_BUFFER_STATE newick_scan_buffer

(

)

newick_scan_bytes() [1/2]

YY_BUFFER_STATE newick_scan_bytes

(

)

newick_scan_bytes() [2/2]

return newick_scan_bytes	(	yy_str	,
		len
	)

newick_scan_string()

YY_BUFFER_STATE newick_scan_string

(

)

newick_switch_to_buffer() [1/3]

void newick_switch_to_buffer

(

)

newick_switch_to_buffer() [2/3]

newick_switch_to_buffer

(

b

)

newick_switch_to_buffer() [3/3]

void newick_switch_to_buffer ( new_buffer  )

new

References yy_current_buffer.

newicklex()

int newicklex

(

void

)

Definition at line 605 of file lex.newick.cpp.

References BEGIN, YYSTYPE::dblval, ECHO, EOB_ACT_CONTINUE_SCAN, EOB_ACT_END_OF_FILE, EOB_ACT_LAST_MATCH, EXPECT_NUM, g_Buffer, i, INITIAL, int, LABEL, newicklval, NUM, YYSTYPE::strval, yy_accept, yy_base, YY_BREAK, YY_BUF_SIZE, YY_BUFFER_NEW, YY_BUFFER_NORMAL, yy_buffer_state::yy_buffer_status, yy_c, yy_c_buf_p, yy_buffer_state::yy_ch_buf, yy_ch_buf, yy_chk, yy_cp, yy_create_buffer, yy_current_buffer, yy_current_state, yy_def, yy_did_buffer_switch_on_eof, YY_DO_BEFORE_ACTION, yy_ec, YY_END_OF_BUFFER, YY_FATAL_ERROR, yy_get_next_buffer(), yy_get_previous_state(), yy_hold_char, yy_init, yy_buffer_state::yy_input_file, yy_last_accepting_cpos, yy_last_accepting_state, yy_load_buffer_state, yy_meta, YY_MORE_ADJ, yy_buffer_state::yy_n_chars, yy_n_chars, YY_NEW_FILE, yy_nxt, YY_RESTORE_YY_MORE_OFFSET, YY_RULE_SETUP, YY_SC_TO_UI, YY_START, yy_start, YY_STATE_EOF, yy_try_NUL_trans(), yyin, yyout, yyterminate, yytext, yytext_ptr, and yywrap.

newickrestart() [1/2]

void newickrestart

(

)

Referenced by newick_flex_reset().

newickrestart() [2/2]

void newickrestart

(

input_file

)

References YY_BUF_SIZE, yy_create_buffer, yy_current_buffer, and yyin.

USING_SCOPE()

USING_SCOPE

(

ncbi

)

while()

while

(

yy_chk+yy_c] !

[yy_base[yy_current_state] = yy_current_state

)

Definition at line 1086 of file lex.newick.cpp.

References int, yy_c, yy_current_state, yy_def, and yy_meta.

Referenced by deflate(), CSequenceOfTypeInfoFunctionsI::EraseAllElements(), NNIupdateAverages(), CGridCommandLineInterfaceApp::Run(), s_BlastCompressedAaScanSubject(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_DynamicSGenCodeNodeArray_BinSearch(), and ssl_check_key_curve().

yy_fatal_error() [1/2]

static void yy_fatal_error ( )

static

yy_fatal_error() [2/2]

static void yy_fatal_error ( msg  )

static

yy_flex_alloc() [1/2]

static void* yy_flex_alloc ( )

static

yy_flex_alloc() [2/2]

static void* yy_flex_alloc ( size  )

static

References size.

yy_flex_free() [1/3]

yy_flex_free

(

(void *)

b

)

yy_flex_free() [2/3]

static void yy_flex_free ( )

static

yy_flex_free() [3/3]

static void yy_flex_free ( ptr  )

static

yy_flex_realloc() [1/2]

static void* yy_flex_realloc ( )

static

Referenced by yy_get_next_buffer().

yy_flex_realloc() [2/2]

static void* yy_flex_realloc ( ptr  , size    )

static

References size.

yy_get_next_buffer()

static int yy_get_next_buffer ( )

static

Definition at line 904 of file lex.newick.cpp.

References b, EOB_ACT_CONTINUE_SCAN, EOB_ACT_END_OF_FILE, EOB_ACT_LAST_MATCH, i, int, rapidjson::source, yy_buffer_state::yy_buf_size, YY_BUFFER_EOF_PENDING, yy_buffer_state::yy_buffer_status, yy_c_buf_p, yy_buffer_state::yy_ch_buf, yy_current_buffer, YY_END_OF_BUFFER_CHAR, YY_FATAL_ERROR, yy_buffer_state::yy_fill_buffer, yy_flex_realloc(), YY_INPUT, YY_MORE_ADJ, yy_buffer_state::yy_n_chars, yy_n_chars, YY_READ_BUF_SIZE, yyin, yyrestart, and yytext_ptr.

Referenced by input(), and newicklex().

yy_get_previous_state()

static yy_state_type yy_get_previous_state ( )

static

Definition at line 1036 of file lex.newick.cpp.

References int, yy_accept, yy_base, yy_c, yy_c_buf_p, yy_chk, yy_cp, yy_current_state, yy_def, yy_ec, yy_last_accepting_cpos, yy_last_accepting_state, yy_meta, YY_MORE_ADJ, yy_nxt, YY_SC_TO_UI, yy_start, and yytext_ptr.

Referenced by newicklex().

yy_try_NUL_trans() [1/2]

static yy_state_type yy_try_NUL_trans ( )

static

Referenced by newicklex().

yy_try_NUL_trans() [2/2]

static yy_state_type yy_try_NUL_trans ( yy_current_state  )

static

References yy_is_jam.

Variable Documentation

b

return b = (YY_BUFFER_STATE) yy_flex_alloc( sizeof( struct yy_buffer_state ) )

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbimisc.hpp, and /home/coremake/doxygen/cxx/include/util/data_histogram.hpp.

Definition at line 1285 of file lex.newick.cpp.

Referenced by _mm_add_epi16(), _mm_add_epi32(), _mm_add_epi64(), _mm_add_epi8(), _mm_add_pd(), _mm_add_ps(), _mm_add_sd(), _mm_add_si64(), _mm_add_ss(), _mm_adds_epi16(), _mm_adds_epi8(), _mm_adds_epu16(), _mm_adds_epu8(), _mm_addsub_pd(), _mm_addsub_ps(), _mm_alignr_epi8(), _mm_and_pd(), _mm_and_ps(), _mm_and_si128(), _mm_andnot_pd(), _mm_andnot_ps(), _mm_andnot_si128(), _mm_avg_epu16(), _mm_avg_epu8(), _mm_avg_pu16(), _mm_avg_pu8(), _mm_blend_ps(), _mm_blendv_epi8(), _mm_blendv_pd(), _mm_blendv_ps(), _mm_ceil_sd(), _mm_ceil_ss(), _mm_clmulepi64_si128(), _mm_cmpeq_epi16(), _mm_cmpeq_epi32(), _mm_cmpeq_epi64(), _mm_cmpeq_epi8(), _mm_cmpeq_pd(), _mm_cmpeq_ps(), _mm_cmpeq_sd(), _mm_cmpeq_ss(), _mm_cmpge_pd(), _mm_cmpge_ps(), _mm_cmpge_sd(), _mm_cmpge_ss(), _mm_cmpgt_epi16(), _mm_cmpgt_epi32(), _mm_cmpgt_epi64(), _mm_cmpgt_epi8(), _mm_cmpgt_pd(), _mm_cmpgt_ps(), _mm_cmpgt_sd(), _mm_cmpgt_ss(), _mm_cmple_pd(), _mm_cmple_ps(), _mm_cmple_sd(), _mm_cmple_ss(), _mm_cmplt_epi16(), _mm_cmplt_epi32(), _mm_cmplt_epi8(), _mm_cmplt_pd(), _mm_cmplt_ps(), _mm_cmplt_sd(), _mm_cmplt_ss(), _mm_cmpneq_pd(), _mm_cmpneq_ps(), _mm_cmpneq_sd(), _mm_cmpneq_ss(), _mm_cmpnge_pd(), _mm_cmpnge_ps(), _mm_cmpnge_sd(), _mm_cmpnge_ss(), _mm_cmpngt_pd(), _mm_cmpngt_ps(), _mm_cmpngt_sd(), _mm_cmpngt_ss(), _mm_cmpnle_pd(), _mm_cmpnle_ps(), _mm_cmpnle_sd(), _mm_cmpnle_ss(), _mm_cmpnlt_pd(), _mm_cmpnlt_ps(), _mm_cmpnlt_sd(), _mm_cmpnlt_ss(), _mm_cmpord_pd(), _mm_cmpord_ps(), _mm_cmpord_sd(), _mm_cmpord_ss(), _mm_cmpunord_pd(), _mm_cmpunord_ps(), _mm_cmpunord_sd(), _mm_cmpunord_ss(), _mm_comieq_sd(), _mm_comieq_ss(), _mm_comige_sd(), _mm_comige_ss(), _mm_comigt_sd(), _mm_comigt_ss(), _mm_comile_sd(), _mm_comile_ss(), _mm_comilt_sd(), _mm_comilt_ss(), _mm_comineq_sd(), _mm_comineq_ss(), _mm_cvt_pi2ps(), _mm_cvt_si2ss(), _mm_cvtpi32_ps(), _mm_cvtpi32x2_ps(), _mm_cvtsd_ss(), _mm_cvtsi32_sd(), _mm_cvtsi64_sd(), _mm_cvtsi64_ss(), _mm_cvtss_sd(), _mm_div_pd(), _mm_div_ps(), _mm_div_sd(), _mm_div_ss(), _mm_dp_pd(), _mm_dp_ps(), _mm_floor_sd(), _mm_floor_ss(), _mm_hadd_epi16(), _mm_hadd_epi32(), _mm_hadd_pd(), _mm_hadd_pi16(), _mm_hadd_pi32(), _mm_hadd_ps(), _mm_hadds_epi16(), _mm_hadds_pi16(), _mm_hsub_epi16(), _mm_hsub_epi32(), _mm_hsub_pd(), _mm_hsub_pi16(), _mm_hsub_pi32(), _mm_hsub_ps(), _mm_hsubs_epi16(), _mm_hsubs_pi16(), _mm_madd_epi16(), _mm_maddubs_epi16(), _mm_maddubs_pi16(), _mm_maskmove_si64(), _mm_maskmoveu_si128(), _mm_max_epi16(), _mm_max_epi32(), _mm_max_epi8(), _mm_max_epu16(), _mm_max_epu32(), _mm_max_epu8(), _mm_max_pd(), _mm_max_pi16(), _mm_max_ps(), _mm_max_pu8(), _mm_max_sd(), _mm_max_ss(), _mm_min_epi16(), _mm_min_epi32(), _mm_min_epi8(), _mm_min_epu16(), _mm_min_epu32(), _mm_min_epu8(), _mm_min_pd(), _mm_min_pi16(), _mm_min_ps(), _mm_min_pu8(), _mm_min_sd(), _mm_min_ss(), _mm_move_sd(), _mm_move_ss(), _mm_mpsadbw_epu8(), _mm_mul_epi32(), _mm_mul_epu32(), _mm_mul_pd(), _mm_mul_ps(), _mm_mul_sd(), _mm_mul_ss(), _mm_mul_su32(), _mm_mulhi_epi16(), _mm_mulhi_epu16(), _mm_mulhi_pu16(), _mm_mulhrs_epi16(), _mm_mulhrs_pi16(), _mm_mullo_epi16(), _mm_mullo_epi32(), _mm_or_pd(), _mm_or_ps(), _mm_or_si128(), _mm_packs_epi16(), _mm_packs_epi32(), _mm_packus_epi16(), _mm_packus_epi32(), _mm_round_sd(), _mm_round_ss(), _mm_sad_epu8(), _mm_sad_pu8(), _mm_shuffle_epi8(), _mm_shuffle_pi8(), _mm_shuffle_ps_0011(), _mm_shuffle_ps_0022(), _mm_shuffle_ps_0101(), _mm_shuffle_ps_0321(), _mm_shuffle_ps_1001(), _mm_shuffle_ps_1010(), _mm_shuffle_ps_1032(), _mm_shuffle_ps_1133(), _mm_shuffle_ps_2001(), _mm_shuffle_ps_2010(), _mm_shuffle_ps_2032(), _mm_shuffle_ps_2103(), _mm_shuffle_ps_2200(), _mm_shuffle_ps_2301(), _mm_shuffle_ps_3202(), _mm_shuffle_ps_3210(), _mm_sign_epi16(), _mm_sign_epi32(), _mm_sign_epi8(), _mm_sign_pi16(), _mm_sign_pi32(), _mm_sign_pi8(), _mm_sqrt_sd(), _mm_storel_epi64(), _mm_sub_epi16(), _mm_sub_epi32(), _mm_sub_epi64(), _mm_sub_epi8(), _mm_sub_pd(), _mm_sub_ps(), _mm_sub_sd(), _mm_sub_si64(), _mm_sub_ss(), _mm_subs_epi16(), _mm_subs_epi8(), _mm_subs_epu16(), _mm_subs_epu8(), _mm_testc_si128(), _mm_testz_si128(), _mm_unpackhi_epi16(), _mm_unpackhi_epi32(), _mm_unpackhi_epi64(), _mm_unpackhi_epi8(), _mm_unpackhi_pd(), _mm_unpackhi_ps(), _mm_unpacklo_epi16(), _mm_unpacklo_epi32(), _mm_unpacklo_epi64(), _mm_unpacklo_epi8(), _mm_unpacklo_pd(), _mm_unpacklo_ps(), _mm_xor_pd(), _mm_xor_ps(), _mm_xor_si128(), _PHIPatternWordsBitwiseAnd(), _PHIPatternWordsBitwiseOr(), _PHIPatternWordsLeftShift(), _sse2neon_vmull_p64(), SBaseStat::add_base(), SBaseStats::add_base(), SBaseStats::add_base_raw(), PeriodicTableClass::AddElement(), CGraphContainer::AddGraph(), BlockIntersector::addOneAlignment(), CAlnMultiPane::AddTitle(), CSeqGraphicPane::AddTitle(), CClickableSortUniqueCount::AddToListCtrl(), AggregatorTest(), algs(), AllTests(), bm::and_values_kleene(), CMemStore::Append(), CBinaryListBuilder::AppendIdList(), CRemoveUnindexedFeatures::apply(), CConvertComment::ApplyToComment(), CModelCompare::AreSimilar(), CChainerArgUtil::ArgsToChainer(), CCassQueryList::AttachSlot(), CSequenceEditingEventHandler::Autodef(), CCleanup::AutodefId(), CEditingBtnsPanel::AutodefOptions(), bm::avx2_bit_count(), BackboneCellFree(), CModelCompare::BadOverlapTest(), BarcodeTestBioseq(), BarcodeTestFails(), BDB_compare_prefix(), CResultSet::BindBlobToVariant(), CVariant::Bit(), BitRangeAllSetTest(), BitString(), BLAST_Gcd(), BLAST_Gdb3(), Blast_RedoAlignmentCore_MT(), BLAST_SpougeEtoS(), Blast_TrueAaToStdTargetFreqs(), bm::block_find_interval_end(), bm::block_find_interval_start(), bm::block_find_reverse(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::Bool(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::Bool(), rapidjson::internal::Hasher< Encoding, Allocator >::Bool(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::Bool(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::Bool(), BOOST_AUTO_TEST_CASE(), BSearchContextInfo(), BSearchInt4(), CHitClustering::Build(), BvectorEraseTest(), BvectorFindReverseTest(), BvectorIncTest(), BvectorShiftTest(), bwfi(), BZ2_bzclose(), BZ2_bzerror(), BZ2_bzread(), BZ2_bzRead(), BZ2_bzReadClose(), BZ2_bzReadGetUnused(), BZ2_bzwrite(), BZ2_bzWrite(), BZ2_bzWriteClose(), BZ2_bzWriteClose64(), CalcBitCount32(), CalcDistanceSquare(), CalcMD5(), alp_sim::calculate_lambda(), ConservationColorer::CalculateBasicConservationColors(), ConservationColorer::CalculateFitConservationColors(), CalculatePSSMScore(), CModelCompare::CanBeConnectedIntoOne(), ccm_auth_crypt(), CDBInterfacesFileConnParams::CDBInterfacesFileConnParams(), CFloatingFrame::CFloatingFrame(), chacha20_quarter_round(), CSeqTable_multi_data::ChangeToBit_bvector(), CStickyTooltipHandler::checkChildFocus(), CheckCollectionDate(), CChainer::CChainerImpl::CheckCompatibility(), rapidjson::internal::Schema< SchemaDocumentType >::CheckDoubleMultipleOf(), CheckFocusInOrgs(), CheckForENV(), CheckForExemption(), CValidError_bioseq::CheckForMissingChromosome(), CheckForUnusualFullLengthOrgs(), CheckNeedSYNFocus(), CTreeMinimalSet< TNode, TSet, TNodeList >::CheckNodeList(), CheckPropagatedCDSLocation(), CheckQualsInSourceFeat(), CHttpReply::CDataTrigger::CheckResetTriggered(), CheckSourceFeatLocFuzz(), rapidjson::internal::CheckWithinHalfULP(), CAlignCollapser::ClipNotSupportedFlanks(), BlockMultipleAlignment::Clone(), cmp_labels(), subfuse::CmpEntry(), cmpTableValues(), CSeqScores::CodingScore(), NTweakExon::Collapse(), CGlState::Color3d(), IRender::Color3d(), CGlState::Color3f(), IRender::Color3f(), CGlState::Color4d(), IRender::Color4d(), CGlRenderDebug::Color4f(), CGlState::Color4f(), IRender::Color4f(), comp_buttons(), compare_BV(), compare_BV_set_ref(), compare_seqids(), MoleculeIdentifier::CompareIdentifiers(), CDiscrepancyContext::CompareRefs(), CompareRowsByEValue(), CompareRowsByIdentifier(), CompareRowsByScore(), CompareRowsFloatGV(), CompareRowsFloatHighlights(), CompareRowsFloatPDB(), CompareSequencesByIdentifier(), CompareSparseVector(), CompareUpdatesByIdentifier(), CompareUpdatesByScore(), dtl::Diff< elem, vector< elem >, Compare< elem > >::composeUnifiedHunks(), CompressNcbi2na(), CNAnnotFilter::Consume(), variation::Contains(), CCleanup::ConvertPubFeatsToPubDescs(), CCleanup::ConvertSrcFeatsToSrcDescs(), CorrectIntervalOrder(), CModelCompare::CountCommonSplices(), CButtonPanel::CreateButton(), CTaskTablePanel::CreateControls(), Threader::CreateCorDef(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), CreatePairwiseSeqAlignFromMultipleRow(), CRgbaColor::CRgbaColor(), cs_locale(), CSeqDB_BasePath::CSeqDB_BasePath(), CSeqDB_Path::CSeqDB_Path(), CTooltipFrame::CTooltipFrame(), DefVsHTGKeywords(), BlockMultipleAlignment::DeleteRow(), DescendingModelOrder(), DescendingModelOrderP(), DescendingModelOrderPConsistentCoverage(), bm::iterator_deserializer< BV, SerialIterator >::deserialize(), bm::compressed_collection_deserializer< CBC >::deserialize(), DetailedCompareSparseVectors(), rapidjson::internal::BigInteger::Difference(), DirectCompareFunction(), CResultSet::DisableBind(), CPrintOptions::DisableGouraudShading(), IImageGrabber::DisableGouraudShading(), CTreeQueryExec::DisableUndo(), HitDistributor::distribute(), DoCylinderPlacementTransform(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), CGlWidgetBase::DoPopupMenu(), ChemicalGraph::DrawAll(), OpenGLRenderer::DrawHalfWorm(), CChainer::DropAlignmentInfo(), DynamicUint4Array_AreEqual(), ecp_group_load(), ecp_mul_mxz(), CAlignMap::EditedSequence(), EmptyBVTest(), EnumeratorTest(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::equal(), CSeq_id_Textseq_Info::TKey::EqualAcc(), EqualPrimerSets(), estimate_jaccard(), estimate_jaccard2(), NSnpAnnot::EstimateSNPCount(), CReportNode::Ext(), CGeneModel::Extend(), fix_pub::ExtractConsortiums(), BlockMultipleAlignment::ExtractRows(), F(), fill_orgref(), CRgbaGradColorTable::FillGradient(), FillInAlignmentData(), FillSetsIntervals(), CAlignCleanup::FillUnaligned(), CAlignCollapser::FilterAlignments(), DeBruijn::CDBGraphDigger::FilterNeighbors(), bm::rsc_sparse_vector< Val, SV >::find_rank(), CBarcodeTool::FindBarcodeFeats(), FindDuplicatePrimers(), CSeqDBNegativeList::FindGi(), CProSplign::FindGlobalAlignment(), CSeqDBNegativeList::FindSi(), CSeqDBNegativeList::FindTi(), util::Fingerprint(), FrAlign(), FrAlignFNog1(), CGeneModel::FrameShifts(), FrBackAlign(), CRegistryFile::FromConfigFile(), CGeneModel::FShiftedLen(), CAlignMap::FShiftedLen(), fta_check_embl_moltype(), fta_check_exception(), fta_check_replace_regulatory(), fta_get_trna_from_product(), fta_if_special_org(), fta_remark_is_er(), fta_remove_keywords(), fta_tpa_keywords_check(), bm::gap_bitset_or_any(), GAPTestStress(), generate_bvector(), rapidjson::GenericValue< rapidjson::Encoding, rapidjson::Allocator >::GenericValue(), CBDB_FieldInt8::Get(), CBDB_FieldUint8::Get(), CBDB_FieldInt4::Get(), CBDB_FieldInt2::Get(), CBDB_FieldUint2::Get(), CBDB_FieldUint4::Get(), CBDB_FieldFloat::Get(), CBDB_FieldDouble::Get(), get_LSH_hashes(), get_LSH_hashes5(), get_sub(), bm::random_subset< BV >::get_subset(), GetAlignedResidueIndexes(), GetAlignmentByBestNeighbor(), SBamIndexRefIndex::GetAlnOverStarts(), GetAverage(), GetBarcodeValues(), NSnp::GetBitfield(), BlockMultipleAlignment::GetBlockAfter(), BlockMultipleAlignment::GetBlockBefore(), BlockMultipleAlignment::GetBlockList(), BlockMultipleAlignment::GetBlocks(), GetBLOSUM62Score(), CSplign::SAlignedCompartment::GetBox(), CAlignCollapser::GetCollapsedAlgnments(), CReorderSequencesDlg::GetCommand(), variation::GetCommonPrefixLen(), variation::GetCommonSuffixLen(), GetDRlineDataSP(), GetEmblBlockXref(), BlockMultipleAlignment::GetFirstAlignedBlockPosition(), CProteinAlignText::GetGenomicBounds(), Threader::GetGeometryViolations(), GetHexChar(), CGeneModel::GetInDels(), CBDB_FieldSimpleInt< Uint2 >::GetInt(), GetIntFuzzPtr(), GetLocalGeneByLocus(), BlockMultipleAlignment::GetMarkedBlockNumbers(), BlockMultipleAlignment::GetModifiableUngappedAlignedBlocks(), GetNextTest(), CValidErrorFormat::GetObjectLabel(), GetOptionsForSet(), ConservationColorer::GetProfileIndexAndResidue(), GetRandomNumbers(), BlockMultipleAlignment::GetRelativeAlignmentFraction(), GetResidue(), CGeneralScoreMatrix::GetScore(), CCassConnection::GetSizeEstimates(), GetSourceDbtag(), CCompartApp::CCompartment::GetSpan(), CSeq_bond::GetStart(), CSeq_bond::GetStop(), CVariant::GetString(), CIndexSuperHeader_Base::GetSystemEndianness(), CTextSelectItem::GetText(), CBamIndex::GetTotalFileRange(), CTaxon1::GetTypeMaterial(), CBDB_FieldSimpleInt< Uint2 >::GetUint(), GetUnalignedRegionLength(), BlockMultipleAlignment::GetUngappedAlignedBlocks(), CMolInfoField::GetVal(), CSeqDBGiList::GiToOid(), GlbAlign(), Hash128to64(), util::Hash128to64(), CNCBlobAccessor::HasPutSucceeded(), CModelCompare::HaveCommonExonOrIntron(), HEAP_Attach(), HEAP_Create(), HEAP_Free(), HEAP_FreeFast(), HEAP_Idle(), HEAP_Trim(), IBoundaryShape::Hide(), CSubtreeBoundary::Hide(), IGridTableAdapter::HideUnselected(), huft_build(), importance_sampling::importance_sampling(), UpdateViewer::ImportStructure(), CFeatureGenerator::SImplementation::SMapper::IncludeSourceLocs(), inflate_block(), inflate_codes(), inflate_dynamic(), inflate_stored(), CSeqScores::Init(), CMemStore::Insert(), CVectorSet< CSupportInfo >::insert(), BlockMultipleAlignment::InsertBlockAfter(), BlockMultipleAlignment::InsertBlockBefore(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::IntegerTemplate(), CSeqScores::IntergenicScore(), IntersectByMaster(), CInDelInfo::IntersectingWith(), CHitElemGlyph::Intersects(), Intervals_RangesTest(), IntervalsCheck(), IntervalsEnumeratorCheck(), InvertInto(), invmod(), bm::is_interval(), CGene::IsAllowedAlternative(), CGeneModel::isCompatible(), IsFirstResidueOfABlock(), variation_ref::IsFirstSubsetOfSecond(), isGoodIntron(), CDataType::IsPrimitive(), IsSPROTAccession(), CDataType::IsStdType(), IsValidAccessPrefix(), key_equal(), KleeneLogicAndStressTest(), KleeneLogicOrStressTest(), KleeneLogicTest(), CGene::LargeCdsOverlap(), DeBruijn::LargeInt< precision >::LargeInt(), LclAlign(), CSeqScores::LeftAlignmentBoundary(), LeftAndLongFirst(), less(), AMatrix_base::LinearTransform(), StructureSet::LoadAlignmentsAndStructures(), StructureSet::LoadMaster(), CEditObjectSeq_desc::LocationChange(), main(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), CGLFrameBuffer::MakeCurrent(), CBamIndex::MakeEstimatedCoverageAnnot(), CBam2Seq_graph::MakeSeq_annot(), CAlignMap::MapAtoB(), MapDependentToMaster(), CAlignMap::MapRangeAtoB(), BlockModelPair::mask(), MatchExceptSpaceColon(), Splines::max_abs(), mbedtls_arc4_crypt_ncbicxx_2_28_3(), mbedtls_ct_memcmp_ncbicxx_2_28_3(), mbedtls_gf128mul_x_ble(), mbedtls_mpi_add_int_ncbicxx_2_28_3(), mbedtls_mpi_div_int_ncbicxx_2_28_3(), mbedtls_mpi_mod_int_ncbicxx_2_28_3(), mbedtls_mpi_mul_int_ncbicxx_2_28_3(), mbedtls_mpi_sub_int_ncbicxx_2_28_3(), mbedtls_psa_safer_memcmp(), MD4Transform(), MD5Transform(), mdb_cmp(), mdb_cmp_cint(), mdb_cmp_int(), mdb_cmp_long(), mdb_cmp_memn(), mdb_cmp_memnr(), mdb_dcmp(), BlockMultipleAlignment::MergeAlignment(), AlignmentManager::MergeUpdates(), rapidjson::internal::GenericRegex< Encoding, Allocator >::Min(), rapidjson::internal::Min3(), Splines::min_abs(), min_max(), minhash_query(), CTreeMinimalSet< TNode, TSet, TNodeList >::MinimalSet(), mmed3(), DeBruijn::CDBGraphDigger::MostLikelyExtension(), CCleanup::MoveOneFeatToPubdesc(), SequenceViewerWidget_SequenceArea::MoveRubberband(), mul64(), rapidjson::internal::BigInteger::MulAdd64(), multmodp(), myMin(), BlockMultipleAlignment::NAlignedBlocks(), NCBI_LinearSolution(), NcbiGetHostIfConfEx(), NcbiGetHostIP(), NcbiIsInIPRange(), CRCache::CRVPool::newBlock(), newick_delete_buffer(), newick_flush_buffer(), CCassQuery::NextRow(), Nlm_StrICmp(), Nlm_StringCmp(), Nlm_StringCSpn(), Nlm_StringICmp(), Nlm_StringNCmp(), Nlm_StringNICmp(), Nlm_StringPBrk(), Nlm_StringSpn(), Nlm_StrIPCmp(), Nlm_StrNICmp(), Nlm_StrNIPCmp(), NlmKarlinLambdaNR(), NNIEdgeTest(), CSeqScores::NonCodingScore(), CReportNode::NoRec(), odbc_dstr_swap(), CCleanup::OkToPromoteNpPub(), StructureWindow::OnAlignStructures(), CHttpReply::CDataTrigger::OnData(), OneExonCompare(), OneRowOk(), CwxTableListCtrl::OnGetItemAttr(), SequenceViewerWindow::OnHighlight(), CProjectTreeCtrl::OnKeyUp(), CBarcodePanel::OnPaint(), CSeqGraphicWidget::OnSetSeqMarkerDlg(), CSeqGraphicWidget::OnSetSeqMarkerForSelDlg(), CTcpWorker::OnTcpConnection(), bm::op_and(), bm::op_or(), bm::op_xor(), CSeqScores::OpenCodingRegion(), CSeqScores::OpenIntergenicRegion(), CSeqScores::OpenNonCodingRegion(), CBGZFPos::operator!=(), CSafeFlags< Enum >::operator!=(), CWGSDb_Impl::SProtAccInfo::operator!=(), CSeq_id_Textseq_Info::TKey::operator!=(), CSeq_id_General_Str_Info::TKey::operator!=(), pythonpp::operator%(), CSafeFlags< Enum >::operator&(), operator&(), CSafeFlags< Enum >::operator&=(), CCddInputData::compare_hits_by_seqid_eval::operator()(), compare_hit_seq1_start::operator()(), compare_hit_seq2_idx::operator()(), compare_hit_score::operator()(), compare_hit_redundant::operator()(), compare_hit_start::operator()(), s_ByAccVerLen::operator()(), CConstRefCSeqId_LessThan::operator()(), GModelOrder::operator()(), SAlignOrder::operator()(), MultiExonsCompare::operator()(), CWriteDB_PackedStringsCompare::operator()(), CCddInputData::compare_hitseg_range::operator()(), CAlignCollapser::GenomicGapsOrder::operator()(), SGeneInfoListSorter::operator()(), TQueryMessagesLessComparator::operator()(), TQueryMessagesEqualComparator::operator()(), TQueryMessagesComparator::operator()(), seq_align_pairs_first::operator()(), compare_alignments_fwrev_first::operator()(), compare_alignments_revfw_first::operator()(), SLessByInfo::operator()(), eq_seqid::operator()(), PSeq_locLess::operator()(), PSeq_locStrandLess::operator()(), compare_tree_edge_descending::operator()(), CCompareByFind::operator()(), CCompareByCat::operator()(), SOpLess_Second::operator()(), CPhyTreeFormatter::compare_nodes_by_seqid::operator()(), LeftAndLongFirstOrder::operator()(), limited_resource_map< TVDBRowId, CRef< SAmbiguityInfo >, size_t >::SLess::operator()(), limited_size_map< string, CRef< CSlot > >::SLess::operator()(), CMultiAligner::compare_sseg_db_idx::operator()(), CAddFluComments::SCompareStr::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_plus::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_minus::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_or::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_xor::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_and::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_less::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_lesseq::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_equals::operator()(), CSeq_id_General_Str_Info::PKeyLess::operator()(), AlignIdOrder::operator()(), CCddInputData::compare_range::operator()(), tree< T, tree_node_allocator >::compare_nodes< StrictWeakOrdering >::operator()(), RangeOrder::operator()(), CTreeSet2NodeListFunc< TTreeNode, TSet, TNodeList >::operator()(), SUvNgHttp2_TlsImpl::SIncomingData::operator()(), StrLenAdd::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::push_back_elements::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::merge_sorted::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_plusaffect::operator()(), DeBruijn::IntegerTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::Integer_xoraffect::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::swap_with_other::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::extract_uniq::operator()(), LeftAndLongFirstOrderForAligns::operator()(), pythonpp::operator*(), rapidjson::internal::DiyFp::operator*(), pythonpp::operator+(), pythonpp::operator-(), operator-(), pythonpp::operator/(), CBGZFPos::operator<(), CWGSDb_Impl::SProtAccInfo::operator<(), CSeq_id_Textseq_Info::TKey::operator<(), operator<<(), CBGZFPos::operator<=(), CBGZFPos::operator==(), CBlastOptionsLocal::operator==(), CSafeFlags< Enum >::operator==(), CFeatureGenerator::SImplementation::SExon::operator==(), CWGSDb_Impl::SProtAccInfo::operator==(), CSeq_id_Textseq_Info::TKey::operator==(), CSeq_id_General_Str_Info::TKey::operator==(), CBGZFPos::operator>(), CBGZFPos::operator>=(), CSafeFlags< Enum >::operator^(), operator^(), CSafeFlags< Enum >::operator^=(), CSafeFlags< Enum >::operator|(), operator|(), CSafeFlags< Enum >::operator|=(), bm::or_values_kleene(), OriginalOrder(), OrOperationsTest(), CRWStreambuf::overflow(), CConn_Streambuf::overflow(), SSnpFilter::Passes(), pivot_key_equal(), PixDistanceSquare(), CSeqGlyph::PointInRect(), CReorderSequencesDlg::PopulateSet(), CGnomonAnnotator::Predict(), CCassConnection::Prepare(), CAlignCleanup::PreserveRows(), CParse::PrintInfo(), ProcFeatBlk(), CSeqScores::ProtNumber(), SequenceDisplay::ProximitySort(), bm::encoder::put_16(), bm::encoder::put_32(), COStreamBuffer::PutInt4(), COStreamBuffer::PutInt8(), putShortMSB(), COStreamBuffer::PutUint4(), COStreamBuffer::PutUint8(), NBestPlacement::Rank(), RankRangeSplitTest(), CJson_WalkHandler::Read(), SEmbeddedStreamReaderWriter::Read(), CMemStore::Read(), ReadBlock(), ReadBytes(), ReadCassandraSatInfo(), ReadId(), ReadNumber(), ReadOctetString(), UpdateViewer::ReadSequencesFromFile(), ReadString(), ReadValue(), AlignmentManager::RealignAllDependentStructures(), StructureObject::RealignStructure(), CHMM_State::RegionStop(), BlockMultipleAlignment::RemoveBlock(), BlockIntersector::removeOneAlignment(), CReorderSequencesDlg::ReorderById(), BlockMultipleAlignment::ReorderRows(), CCleanup::RescueSiteRefPubs(), Residue::Residue(), CChain::RestoreReasonableConfirmedStart(), RSIndexTest(), CBlastKmer::Run(), CSeqDescrRetrievalJob::Run(), CDbapiTest::Run(), CTest::Run(), CProjBulderApp::Run(), CMysqlDemoApp::Run(), s_AbsMax(), s_AddGraphToMap(), s_AddToRPSBucket(), s_AddWordHit(), s_AlignmentCmp(), s_AlignSeqOrder(), s_AmbiguousMatch(), s_ApproxEqual(), s_BlastNaHashLookupFinalize(), s_BUF_IO(), variation_ref::CVariationUtil::s_CatLiterals(), variation::CVariationUtil::s_CatLiterals(), s_CollectAllLeaves(), s_CompareChainsByOid(), s_CompareChainsByScore(), s_CompareOffsetPairsByDiagQuery(), s_ComparePairs(), variation_ref::CVariationUtil::s_CountMatches(), variation::CVariationUtil::s_CountMatches(), s_CreateHeap(), s_CreateRotatedFont(), s_DoPubsMatch(), s_DynamicSGenCodeNodeArray_BinSearch(), s_FromHex(), s_Get_LSH_index_hashes(), s_Get_LSH_index_hashes5(), s_GetNormalizedString(), s_GetNucIdentityMismatch(), s_GetOptionsForSet(), s_GetOverlapCost(), s_GetRandomNumbers(), s_HEAP_Collect(), s_HEAP_Find(), s_HEAP_Free(), s_HEAP_Link(), s_HEAP_Take(), s_HEAP_Walk(), s_MatchesBoundary(), s_MatchesMask(), s_MinhashSequences(), s_NaHashLookupScanSubjectForWordCounts(), s_Ncbi4naToNcbi2na(), s_NeedFeatureClause(), s_NoCaseEqual(), s_NormalizeLinkageEvidenceString(), CMacroFunction_RefreshDefline::s_RefreshDeflineCommand(), LbsmLookup::s_Resolve(), s_SGenCodeNodeCompare(), s_ShiftGapsRight(), s_SortDbSize(), s_StrandsConsistent(), s_StripToPattern(), s_ToString(), s_UpdateAdler32(), compile_time_bits::ct_crc32< poly >::SaltedHash(), same_domain(), SameCitation_PubEquivMatch_Logic(), CSeq_id_Textseq_Info::TKey::SameHash(), CSeq_id_Textseq_Info::TKey::SameHashNoVer(), NTweakExon::SameIdAndStrand(), SameOrientation(), SameWithdrawn(), bm::random_subset< BV >::sample(), CSymDustMasker::save_masked_regions(), CPhyloPdfGrabber::SaveTooltips(), SBamRangeBlock::SBamRangeBlock(), CGlRender::ScaleInvarient(), CGlState::ScaleInvarient(), PssmScorer::score(), ScoreDifferenceSort(), AlignmentUtility::ScoreRowByPSSM(), BlockMultipleAlignment::SelectBlocks(), SeqDB_JoinDelim(), variation::SeqsMatch(), CRgbaColor::Set(), CBDB_FieldSimpleFloat< float >::Set(), CBDB_FieldSimpleInt< Uint2 >::Set(), CPhyloNodeData::SetAlreadyDrawn(), CBoundaryParms::SetAxisAligned(), CRgbaColor::SetBlue(), CGLCanvas::SetClearColor(), CChain::SetConfirmedEnds(), CProjectTreePanel::SetCopyMode(), CAlnVecMultiDataSource::SetCreateConsensus(), CTableImportListCtrl::SetDisplayTypeHeader(), IPhyloTreeRender::SetDistanceBarLowerLeft(), CBoundaryParms::SetDrawBoundaryEdge(), CGlRenderBuffer< T >::SetDrawEnabled(), CTooltipFrame::SetElementActive(), CBDB_FieldSimple< Uint2 >::SetField(), CFieldChoicePanel::SetFieldType(), CTableImportListCtrl::SetFixedWidthUseFields(), CDiscrepancySet::SetGui(), CClonePlacementGlyph::SetHideLabel(), CFeatGlyph::SetHideLabel(), CSegmentGlyph::SetHideLabel(), CVcfGlyph::SetHideLabel(), CGridWidget::SetHideUnselected(), CPhyloTreeWidget::SetHideUnselected(), CTreeBoundaryNode::SetIncludeLabels(), CFeedbackReport::SetIncludeLog(), CBoundaryParms::SetIncludeTextArea(), CTableImportColumn::SetIsCurrent(), CQueryNodeValue::SetIsDataField(), CGlRenderPdf::SetIsGreyscale(), CPdf::SetIsGreyscale(), CSVGRenderer::SetIsGreyscale(), CTreeTriFanNode::SetLabelVisibility(), CMagicBlastOptionsHandle::SetLookupDbFilter(), CPrintOptions::SetMarginBottom(), CTableImportColumn::SetMatchColumn(), CTableDelimiterRules::SetMergeDelimiters(), CTableDelimiterRules::SetMultipleSpacesOnly(), CTableImportColumn::SetOneBased(), CMouseZoomHandler::SetPanOnMouseDown(), CTooltipFrame::SetPinned(), CGlWidgetPane::SetPopupMenuDisplayed(), IImageGrabber::SetPrintingGuidesEnabled(), CAttribMenuItem::SetReadOnly(), CAlignFilter::SetRemoveDuplicates(), CTreeGraphicsModel::SetRenderTooltips(), CClusterer::SetReportSingletons(), CGlPreviewSetupWidget::SetRotated(), CTreeGraphicsModel::SetRotateLabels(), CPsiBlastArgs::SetSaveLastPssm(), CGridWidget::SetSelectAll(), CPhyloTreeWidget::SetSelectAll(), CPhyloSelectionSet::SetSelected(), CRichTextHandle::SetSelectionEnabled(), CHtmlWindowtHandle::SetSelectionEnabled(), CSeqTextConfig::SetShow(), CPhyloTreeScheme::SetSolidColorLeaves(), CFeedbackReport::SetSubscribe(), CTaxon1Node::SetSubtreeLoaded(), CBoundaryParms::SetTextBox(), CSeqGraphicPane::SetVectorMode(), CGlRenderNode::SetVisible(), CPhyloNodeData::SetVisible(), sGetWarningMsg(), bm::bvector< Alloc >::shift_left(), CSeqGraphicHairline::ShowDownwardHairline(), CBarcodeTool::ShowReport(), CAlignMap::ShrinkToRealPoints(), CAlignMap::ShrinkToRealPointsOnEdited(), Splines::signTest(), bm::random_subset< BV >::simple_pick(), CSeqDBGiList::SiToOid(), SkipComments(), SkipEndOfLine(), SkipWhiteSpace(), SkipWhiteSpaceAndGetChar(), SOCK_ntoa(), UpdateViewer::SortByPSSM(), SortCluster(), SortClusterSeqs(), CAlignCleanup::SortInputsByScore(), SourceFeatStructFillIn(), CFeatGapInfo::Split(), bm::sse2_and(), bm::sse2_bit_block_calc_count_change(), bm::sse2_bit_count(), bm::sse2_bit_count_op(), bm::sse2_or(), bm::sse2_sub(), bm::sse2_xor(), bm::sse42_bit_block_calc_count_change(), bm::sse4_bit_count(), bm::sse4_bit_count_op(), SSeqRangeArrayLessThanOrEqual(), SSeqRangeIntersectsWith(), CPhyloForce::StartRendering(), IPhyloTreeRender::StartRendering(), CSeq_annot_Info::StartSortedIterator(), CSeqScores::StopInside(), StressTest(), StressTestAggregatorAND(), StressTestAggregatorAND_SUB(), CSuspect_rule::StringMatchesSuspectProductRule(), StripCDSComment(), StripParens(), SubOperationsTest(), CReportNode::Summ(), CDiscrepancyVisitorImpl< _Name >::Summarize(), BlockMultipleAlignment::SumOfAlignedBlockWidths(), rapidjson::internal::Swap(), CAlignShadow::SwapQS(), sx_FindFirstNonZeroBit(), sx_FindNextNonZeroBit(), sx_Get_4na(), CHitFilter< THit >::sx_GetEndsInRange(), sx_Is2na(), SyntaxTest(), bm::aggregator< BV >::test_gap_blocks_and(), bm::aggregator< BV >::test_gap_blocks_sub(), TestBasicMatrix(), TestCompressSparseGather(), TestCompressSparseSignedVector(), TestCompressSparseVector(), TestEqualSparseVectors(), TestFindFirst(), TestHasZeroByte(), TestSignedSparseVectorScan(), TestSignedSparseVectorScanGT(), TestSignedSparseVectorSerial(), TestSparseVector(), TestSparseVectorScan(), TestSparseVectorScanGT(), TestSparseVectorSerial(), TestSQueue(), TestStrSparseVector(), TestStrSparseVector_FindEq(), TestStrSparseVectorSerial(), CSeqDBGiList::TiToOid(), CLessTypeInfo::ToBool(), TotalFrameShift(), CMD5::Transform(), ProjectCDS::transform_align(), CFeatGapInfo::Trim(), TrimAlignment::TrimProtein(), TrimAlignment::TrimTranscript(), rapidjson::internal::u32toa(), rapidjson::internal::u64toa(), uhash(), UngetNonWhiteSpace(), CGlBuffer20< T >::UnmapBuffer(), UnpackDPResult(), sse42_crc32::update(), compile_time_bits::ct_crc32< poly >::update(), tabled_crc32::update(), compile_time_bits::ct_crc32< poly >::update4(), BlockMultipleAlignment::UpdateBlockMap(), BlockMultipleAlignment::UpdateBlockMapAndColors(), IColumnScoringMethod::UpdateSettings(), CPhyloCircularCladogram::UseMinimalRotation(), UTIL_Adler32_Update(), CSerialFacetContainer::Validate(), CFarPointerSeq::ValidateAlignment(), CSerialFacetImpl::ValidateContainerElements(), CChain::ValidPolyA(), Convert::ValueToCassCollection< bool >(), VariBandAlign(), verify_all_one_ranges(), VerifyCountRange(), WeDontNeedToJoinThis(), bm::wordcmp(), SEmbeddedStreamReaderWriter::Write(), CMemStore::Write(), CObjectOStreamAsnBinary::WriteBitString(), CNCBlobStorage::WriteBlobStat(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::WriteBool(), TNCBufferType::WriteBool(), CSrvSocketTask::WriteBool(), x509_name_cmp(), x509_string_cmp(), CWGSDb_Impl::SAmbiguityInfo::x_AddAmbiguities(), CTooltipFrame::x_AddButton(), CSGAnnotJob::x_AddGraphToMap(), CCleanupApp::x_BatchExtendCDS(), x_BlastDatabaseOptions_cmp(), x_BlastEffectiveLengthsOptions_cmp(), x_BlastScoringOptions_cmp(), CTooltipFrame::x_BreakIntoLines(), CVecscreen::x_BuildHtmlBar(), CBlastKmerBuildIndex::x_BuildIndex(), CValuesCount::x_byCount(), CHitClustering::x_CanCombine(), CPhyloImageGrabber::x_CaptureImage(), CNewCleanup_imp::x_CleanupGenbankBlock(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFeatGlyph::x_DrawFeatureBar(), CAlignGlyph::x_DrawIntronsAndInternalUnalignedRegions(), CAttribTableColumnIdPanel::x_EnableColumnEditControls(), CTableColumnIdPanel::x_EnableColumnEditControls(), CPhyloSaveSelectiondlg::x_EnableCurrentSelection(), CAttribTableDelimitersPanel::x_EnableMergeSplitWidgets(), CAttribTableColumnIdPanel::x_EnableNonFormatEditControls(), CTableColumnIdPanel::x_EnableNonFormatEditControls(), CSnpJob::x_FetchGraphs(), CBamRefSequencesPanel::x_FillList(), CVcfRefSequencesPanel::x_FillList(), NAdapterSearch::CSimpleUngappedAligner::x_GetBetterOf(), CWriteDB_Impl::x_GetBioseqBinaryHeader(), CVcfGlyph::x_GetClinVarToolTip(), CSVGRenderer::x_GetGradientColors(), CTL_BCPInCmd::x_GetStringValue(), x_HEAP_Walk(), x_json_value_equals(), CTSE_Split_Info::x_LoadChunks(), x_LookupTableOptions_cmp(), x_MatchesMask(), CNewCleanup_imp::x_MoveNPTitle(), CBlastTabular::x_PartialDeserialize(), CBlastKmer::x_ProcessQuery(), CSplign::x_ProcessTermSegm(), x_PushPairVec(), x_QuerySetupOptions_cmp(), CFeaturePanel::x_RenderTitleBar(), CMakeProfileDBApp::x_Run(), x_safe_memcmp(), x_safe_strcmp(), CBlastKmer::x_SearchMultipleQueries(), CWriteDB_LMDB::x_Split(), x_tr(), CGlTextureFont::x_Truncate(), DTDParser::x_Type(), CRawSeqToDeltaSeqByLoc::x_UpdateRows(), CGridWidget::x_UpdateRowsToSelection(), ASNParser::x_Value(), DTDParser::x_Value(), CSeqGlyph::x_Visible_V(), CBlastKmerBuildIndex::x_WriteDataFile(), CBedImportData::xInitializeRgb(), XMLCheckQualifiers(), XMLDefVsHTGKeywords(), XorOperationsTest(), CRgbaColor::YuvToRgb(), and yy_get_next_buffer().

buf

buf[len]

Initial value:

{
    YY_BUFFER_STATE b

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp, /home/coremake/doxygen/cxx/include/util/buffer_writer.hpp, and /home/coremake/doxygen/cxx/src/objtools/data_loaders/asn_cache/buffer_writer.hpp.

Definition at line 1454 of file lex.newick.cpp.

Referenced by _bcp_readfmt_colinfo(), _blk_get_col_data(), _SQLGetInfo(), _tr_flush_block(), _tr_stored_block(), CRWStreambuf::_Xsgetn_s(), CConn_Streambuf::_Xsgetn_s(), CPushback_Streambuf::_Xsgetn_s(), CCompressionStreambuf::_Xsgetn_s(), CPageBuffers::Add(), add_couple(), CProteinAlignText::AddDNAText(), CArchiveZip::AddEntryFromMemory(), CChecksum::AddFile(), CWriteDB_IsamIndex::AddHash(), CProteinAlignText::AddProtText(), CGRPCClientContext::AddStandardNCBIMetadata(), CChecksum::AddStream(), CAttribMenu::AddSubMenuUnique(), adler32(), adler32_z(), AllTests(), CVariant::Append(), CSimpleBufferT< char >::append(), append_string(), CArchive::AppendFileFromMemory(), CCassPrm::Assign(), bm::avx2_gap_bfind(), bm::avx2_gap_test(), BDB_Hash(), CCassQuery::BindBytes(), BitEncoderTest(), Blast_PerrorEx(), BlastScoreBlkProteinMatrixRead(), CSimpleBlobStore::BlobDescriptor(), block_cipher_df(), BOOST_AUTO_TEST_CASE(), BUF_Append(), BUF_AppendEx(), BUF_Destroy(), BUF_Erase(), BUF_Peek(), BUF_PeekAt(), BUF_PeekAtCB(), BUF_Prepend(), BUF_PrependEx(), BUF_Pushback(), BUF_Read(), BUF_SetChunkSize(), BUF_Size(), BUF_Write(), buffer_add_row(), buffer_alloc(), buffer_count(), buffer_current_index(), buffer_delete_rows(), buffer_free(), buffer_idx2row(), buffer_idx_increment(), buffer_index_valid(), buffer_is_full(), buffer_reset(), buffer_row2idx(), buffer_row_address(), buffer_save_row(), buffer_set_capacity(), buffer_struct_print(), buffer_transfer_bound_data(), BV_Serialize(), BZ2_bzread(), BZ2_bzRead(), BZ2_bzwrite(), BZ2_bzWrite(), cacher_read(), cacher_write(), bm::compressed_buffer_collection< BV >::calc_stat(), CalcMD5(), CTestSeqBasedMethod::CalculateScores(), CColorTableMethod::CalculateScores(), CCddBookRefToBvString(), CDiagRestorer::CDiagRestorer(), check_attr_ard(), check_attr_ird(), check_chars(), check_hex(), CheckData(), CheckGBBlock(), CheckOneDenDiag(), CheckRangeDeserial(), CheckTwoDenDiags(), CNcbiApplogApp::Cmd_Generate(), CNetCacheReader::CNetCacheReader(), CompareSparseVector(), compressor_header(), compressor_write(), bm::compute_serialization_size(), ComputeFileChecksum_deprecated(), ConfigDSN(), CONN_Read(), ConnNetInfo_Log(), bm::miniset< A, N >::convert_buf(), convert_to_upper(), pub_report::ConvertPMCtoPMID(), CSymLink::Copy(), CORE_GetUsername(), CORE_GetUsernameEx(), crc32(), crc32_z(), CSymLink::Create(), CreateConfigurableFile(), CGlShader::CreateShader(), CPagerViewButtons::CreateSubNodes(), ct_config(), SH2S_IoStream::DataSourceRead(), dbclrbuf(), DBLB_GetServer(), dbreadtext(), dbresults(), DbxrefQualToDbtag(), CGBenchFeedbackAttachment::DecodeData(), bm::decoder_base::decoder_base(), DeleteFields(), derive_mpi(), bm::sparse_vector_deserializer< bm::str_sparse_vector >::deserialize(), bm::deserialize(), bm::operation_deserializer< bvector_type >::deserialize(), bm::deserializer< BV, DEC >::deserialize(), bm::operation_deserializer< BV >::deserialize(), bm::compressed_collection_deserializer< CBC >::deserialize(), CBDB_ExtBlobMap::Deserialize(), CBDB_BlobMetaContainer::Deserialize(), bm::sparse_vector_deserializer< SV >::deserialize(), CBDB_BvSplitDictStore< Key, Dictionary, BvStore, BV >::Deserialize(), CBDB_BvStore< TBV >::Deserialize(), bm::sparse_vector_deserializer< SV >::deserialize_planes(), bm::deserialize_range(), bm::operation_deserializer< bvector_type >::deserialize_range(), bm::operation_deserializer< BV >::deserialize_range(), bm::sparse_vector_deserializer< SV >::deserialize_range(), bm::sparse_vector_deserializer< SV >::deserialize_structure(), bm::sparse_vector_deserializer< SV >::deserialize_sv(), bm::operation_deserializer< BV >::deserialize_xor(), bm::operation_deserializer< BV >::deserialize_xor_range(), DetailedCompareSparseVectors(), CSeqMaskerIstatFactory::DiscoverStatType(), CConnTest::DispatcherOkay(), dns_a(), dns_txt(), CEUtilsUpdaterBase::DoPubSearch(), CGlCurve< Curve >::DrawBuffered(), SequenceViewerWidget_SequenceArea::DrawCell(), DSOCK_RecvMsg(), CBDB_FileDumper::Dump(), dump(), CDumpSysInfo::DumpSystemInfo(), ecdh_calc_secret_internal(), ecdh_make_params_internal(), ecdh_make_public_internal(), ecdh_read_params_internal(), ecdh_read_public_internal(), ecdsa_sign_det_restartable(), ecdsa_sign_restartable(), ecdsa_signature_to_asn1(), ecdsa_verify_restartable(), CExtraEncoder::Encode(), entropy_gather_internal(), CExecute::Exec(), CPipe::ExecWait(), ExportTest(), CArchiveZip::ExtractEntryToMemory(), CArchive::ExtractFileToMemory(), CFetchURL::Fetch(), CBDB_FileCursor::Fetch(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::Fetch(), CBDB_LobFile::Fetch(), CBDB_BLobFile::Fetch(), CBDB_FileCursor::FetchFirst(), CBlobMetaDB::FetchMeta(), CDbapiTestSpeedApp::FetchResults(), CCassQuery::FieldGetBlobValue(), bm::file_load_compressed_collection(), bm::file_load_svector(), bm::file_save_compressed_collection(), bm::file_save_svector(), fill_chars(), fill_hex(), FillTestBuffer(), CArchiveZip::FinalizeMemory(), CNcbiApplicationAPI::FindProgramExecutablePath(), CImageUtil::FlipY(), CCompressionStreambuf::Flush(), bm::for_each_gap_blk(), bm::for_each_gap_blk_range(), bm::for_each_gap_dbit(), fta_build_structured_comment(), fta_fix_tpa_keywords(), fta_parse_buf(), fta_parse_structured_comment(), fta_parse_tpa_tsa_block(), fta_process_con_slice(), fta_tpa_keywords_check(), fta_vnp_structured_comment(), FtaErrGetMsgCodes(), g_CORE_Sprintf(), g_VersionStr(), bm::gap_add_value(), bm::gap_any_range(), bm::gap_bfind(), bm::gap_bit_count(), bm::gap_bit_count_range(), bm::gap_bit_count_range_hint(), bm::gap_bit_count_to(), bm::gap_bit_count_unr(), bm::gap_bitset_or_any(), bm::gap_bitset_or_count(), bm::gap_bitset_sub_any(), bm::gap_bitset_sub_count(), bm::gap_bitset_xor_any(), bm::gap_bitset_xor_count(), bm::gap_block_find(), bm::gap_capacity(), bm::gap_control_sum(), bm::gap_convert_to_arr(), bm::gap_convert_to_bitset(), bm::gap_convert_to_bitset_smart(), bm::gap_find_first(), bm::gap_find_interval_end(), bm::gap_find_interval_start(), bm::gap_find_last(), bm::gap_find_prev(), bm::gap_free_elements(), bm::gap_init_range_block(), bm::gap_insert(), bm::gap_invert(), bm::gap_is_all_one(), bm::gap_is_all_one_range(), bm::gap_is_all_zero(), bm::gap_is_interval(), bm::gap_length(), bm::gap_level(), bm::gap_limit(), bm::gap_set_all(), bm::gap_set_array(), bm::gap_set_value(), bm::gap_set_value_cpos(), bm::gap_shift_l1(), bm::gap_shift_r1(), bm::gap_split(), bm::gap_test(), bm::gap_test_unr(), GAPCheck(), GenerateCompressedBufferCollection(), CBDB_FieldFixedByteString::Get(), CBDB_FieldLString::Get(), bm::heap_matrix< Val, ROWS, COLS, BVAlloc >::get(), bm::decoder_little_endian::get_16(), bm::decoder::get_16(), bm::decoder_little_endian::get_32(), bm::decoder::get_32(), get_art(), GetAccVerHistCompletionHeader(), GetAccVerHistoryHeader(), CObjFingerprint::GetAlignSignature(), CGnomonEngine::GetAnnot(), CEUtils_Request::GetBaseURL(), GetBioseqChunks(), GetBioseqCompletionHeader(), GetBioseqInfoHeader(), GetBioseqMessageHeader(), GetBioseqRecordId(), CPubseqReader::GetBlob(), CSQLITE_Statement::GetBlob(), CBlobStorage_NetCache::GetBlobAsString(), GetBlobChunkHeader(), GetBlobCompletionHeader(), GetBlobExcludeHeader(), GetBlobMessageHeader(), GetBlobPropCompletionHeader(), GetBlobPropHeader(), GetBlobPropMessageHeader(), GetBlobReader(), GetCitBookOld(), CObjFingerprint::GetComponentSignature(), GetCurrentProcessTimes(), CDir::GetCwd(), CNetCacheAPI::GetData(), CBDB_BLobFile::GetData(), CBDB_LobFile::GetData(), CAppExplorerDataObject::GetDataHere(), CBDB_FieldString::GetDataLength(), CBDB_FieldLString::GetDataLength(), CObjFingerprint::GetFeatSignature(), CBDB_FileCursor::GetFieldConvert(), CFtglFontManager::GetFont(), CObjFingerprint::GetGraphSignature(), CUnixFeature::GetGroupGIDByName(), CUnixFeature::GetGroupNameByGID(), CCacheHashedContent::GetHashedContent(), CObjFingerprint::GetHistogramSignature(), CDiagContext::GetHost(), CTaskServer::GetHostByIP(), CTaskServer::GetHostName(), GetIPGMessageHeader(), GetIPGResolveHeader(), CPager::GetItemInfo(), CAsnBinCompressed::GetJobStreamProperties(), GetMD5Digest(), CChecksum::GetMD5Digest(), CCacheHashedContent::GetMediatorKeyContent(), CMergeBitsetBlob< BV >::GetMergeBuffer(), GetNamedAnnotationCompletionHeader(), GetNamedAnnotationHeader(), GetNamedAnnotationMessageCompletionHeader(), GetNamedAnnotationMessageHeader(), CSocket::GetPeerAddress(), CHttpRequest::GetPeerIP(), GetPerNamedAnnotationResultsHeader(), GetPerNAResultsCompletionHeader(), GetProcessorMessageCompletionHeader(), GetProcessorMessageHeader(), GetProcessorProgressMessageHeader(), GetPublicCommentCompletionHeader(), GetPublicCommentHeader(), GetQSFromFile(), CHttpRequest::GetRawBuffer(), CSeqDBExpert::GetRawSeqAndAmbig(), GetReplyCompletionHeader(), GetReplyMessageHeader(), CObjFingerprint::GetRsiteSignature(), CParamsPanel::GetSelectedIndices(), CConversionResultPanel::GetSelectedIndices(), CParamsPanel::GetSelectedObjects(), CParamsPanel::GetSelection(), CConversionResultPanel::GetSelection(), CMAPanel::GetSelection(), CDataMiningPanel::GetSelection(), CSelectionPanel::GetSelection(), CSelectionView::GetSelection(), GetSeqData(), CObjFingerprint::GetSeqLocSignature(), GetSequenceProtein(), CBlastSeqVectorOM::GetStrandData(), IBlastSeqVector::GetStrandData(), CSQLITE_Statement::GetString(), CDiagContext::GetStringUID(), CTableDataBase::GetTableTypeId(), CAttribIntMenuItem::GetText(), CAttribFloatMenuItem::GetText(), CAttribIntMenuItem::GetTextValue(), CAttribFloatMenuItem::GetTextValue(), GetTheQualValue(), CDirEntry::GetTime(), CCurrentProcess::GetTimes(), CAlnStatGlyph::GetTooltip(), CGuiObjectInfoSeq_align::GetToolTip(), GetTSEBlobChunkHeader(), GetTSEBlobCompletionHeader(), GetTSEBlobExcludeHeader(), GetTSEBlobMessageHeader(), GetTSEBlobPropCompletionHeader(), GetTSEBlobPropHeader(), GetTSEBlobPropMessageHeader(), CCompressionUtil::GetUI2(), CCompressionUtil::GetUI4(), CUnixFeature::GetUserNameByUID(), CUnixFeature::GetUserUIDByName(), CObjFingerprint::GetVcfVariantSignature(), CSQLITE3_Cache::GetWriteStream(), CProjBulderApp::Gui_ConfirmConfiguration(), CProjBulderApp::Gui_ConfirmProjects(), gz_load(), gz_read(), gz_write(), gzfread(), gzfwrite(), gzgetc(), gzgets(), gzputc(), gzread(), gzwrite(), CCgiWatchFile::HasChanged(), CProSplign::CImplementation::HasStartOnNuc(), CProSplign::CImplementation::HasStopOnNuc(), CSocketAPI::HostPortToString(), IBISAnnotateDialog::IBISAnnotateDialog(), IdentifySlnGUID(), inflateSync(), bm::miniset< A, N >::init_bitbuf(), bm::miniset< A, N >::init_gapbuf(), CFastCgiThreadedRequest::inProcessor(), CBDB_BLobFile::Insert(), InsertItemInListView(), InsertItemInReportView(), InterpolativeCodingTest(), CTaskServer::IPToString(), CAsnBinCompressed::IsLZOStream(), mu::ParserComplex::IsVal(), mu::ParserInt::IsVal(), CJson_WalkHandler::Key(), load_file(), bm::sparse_vector_deserializer< SV >::load_null_plane(), bm::sparse_vector_deserializer< SV >::load_planes_off_table(), CBDB_RangeMap< TBV >::LoadFreeList(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::LoadIdDeMux(), CDirEntry::LookupLink(), main(), CSeqDBTest2Thread::Main(), CSeqDBTest3Thread::Main(), CAsyncDiagThread::Main(), Make_GI_or_PDB_String_CN3D(), make_ntlm_v2_hash(), SBamUtil::MakeFloat(), SBamUtil::MakeUint2(), SBamUtil::MakeUint4(), SBamUtil::MakeUint8(), mbedtls_aes_rk_offset(), mbedtls_asn1_write_bitstring_ncbicxx_2_28_3(), mbedtls_asn1_write_named_bitstring_ncbicxx_2_28_3(), mbedtls_asn1_write_octet_string_ncbicxx_2_28_3(), mbedtls_asn1_write_raw_buffer_ncbicxx_2_28_3(), mbedtls_ct_mem_move_to_left(), mbedtls_ctr_drbg_update_seed_file_ncbicxx_2_28_3(), mbedtls_ctr_drbg_write_seed_file_ncbicxx_2_28_3(), mbedtls_debug_print_buf_ncbicxx_2_28_3(), mbedtls_debug_print_crt_ncbicxx_2_28_3(), mbedtls_dhm_parse_dhmfile_ncbicxx_2_28_3(), mbedtls_ecdh_calc_secret_ncbicxx_2_28_3(), mbedtls_ecdh_make_params_ncbicxx_2_28_3(), mbedtls_ecdh_make_public_ncbicxx_2_28_3(), mbedtls_ecdh_read_params_ncbicxx_2_28_3(), mbedtls_ecdh_read_public_ncbicxx_2_28_3(), mbedtls_ecdsa_sign_det_ext_ncbicxx_2_28_3(), mbedtls_ecdsa_sign_det_ncbicxx_2_28_3(), mbedtls_ecdsa_sign_ncbicxx_2_28_3(), mbedtls_ecdsa_verify_ncbicxx_2_28_3(), mbedtls_ecp_point_read_binary_ncbicxx_2_28_3(), mbedtls_ecp_point_write_binary_ncbicxx_2_28_3(), mbedtls_ecp_read_key_ncbicxx_2_28_3(), mbedtls_ecp_tls_read_group_id_ncbicxx_2_28_3(), mbedtls_ecp_tls_read_group_ncbicxx_2_28_3(), mbedtls_ecp_tls_read_point_ncbicxx_2_28_3(), mbedtls_ecp_tls_write_group_ncbicxx_2_28_3(), mbedtls_ecp_tls_write_point_ncbicxx_2_28_3(), mbedtls_ecp_write_key_ncbicxx_2_28_3(), mbedtls_entropy_func_ncbicxx_2_28_3(), mbedtls_entropy_update_seed_file_ncbicxx_2_28_3(), mbedtls_entropy_write_seed_file_ncbicxx_2_28_3(), mbedtls_hmac_drbg_update_seed_file_ncbicxx_2_28_3(), mbedtls_hmac_drbg_write_seed_file_ncbicxx_2_28_3(), mbedtls_md_file_ncbicxx_2_28_3(), mbedtls_mpi_read_binary_le_ncbicxx_2_28_3(), mbedtls_mpi_read_binary_ncbicxx_2_28_3(), mbedtls_mpi_write_binary_le_ncbicxx_2_28_3(), mbedtls_mpi_write_binary_ncbicxx_2_28_3(), mbedtls_mpi_write_string_ncbicxx_2_28_3(), mbedtls_net_accept_ncbicxx_2_28_3(), mbedtls_net_recv_ncbicxx_2_28_3(), mbedtls_net_recv_timeout_ncbicxx_2_28_3(), mbedtls_net_send_ncbicxx_2_28_3(), mbedtls_oid_get_numeric_string_ncbicxx_2_28_3(), mbedtls_pem_read_buffer_ncbicxx_2_28_3(), mbedtls_pem_write_buffer_ncbicxx_2_28_3(), mbedtls_pk_load_file_ncbicxx_2_28_3(), mbedtls_pk_parse_keyfile_ncbicxx_2_28_3(), mbedtls_pk_parse_public_keyfile_ncbicxx_2_28_3(), mbedtls_pk_write_key_der_ncbicxx_2_28_3(), mbedtls_pk_write_key_pem_ncbicxx_2_28_3(), mbedtls_pk_write_pubkey_der_ncbicxx_2_28_3(), mbedtls_pk_write_pubkey_pem_ncbicxx_2_28_3(), mbedtls_platform_zeroize_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_oaep_decrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsaes_pkcs1_v15_decrypt_ncbicxx_2_28_3(), mbedtls_rsa_rsassa_pss_verify_ext_ncbicxx_2_28_3(), mbedtls_ssl_check_record_ncbicxx_2_28_3(), mbedtls_ssl_context_load_ncbicxx_2_28_3(), mbedtls_ssl_context_save_ncbicxx_2_28_3(), mbedtls_ssl_flush_output_ncbicxx_2_28_3(), mbedtls_ssl_parse_finished_ncbicxx_2_28_3(), mbedtls_ssl_read_ncbicxx_2_28_3(), mbedtls_ssl_session_load_ncbicxx_2_28_3(), mbedtls_ssl_session_save_ncbicxx_2_28_3(), mbedtls_ssl_ticket_parse_ncbicxx_2_28_3(), mbedtls_ssl_write_ncbicxx_2_28_3(), mbedtls_strerror_ncbicxx_2_28_3(), mbedtls_x509_crl_info_ncbicxx_2_28_3(), mbedtls_x509_crl_parse_der_ncbicxx_2_28_3(), mbedtls_x509_crl_parse_file_ncbicxx_2_28_3(), mbedtls_x509_crl_parse_ncbicxx_2_28_3(), mbedtls_x509_crt_parse_der_internal(), mbedtls_x509_crt_parse_der_ncbicxx_2_28_3(), mbedtls_x509_crt_parse_der_nocopy_ncbicxx_2_28_3(), mbedtls_x509_crt_parse_der_with_ext_cb_ncbicxx_2_28_3(), mbedtls_x509_crt_parse_file_ncbicxx_2_28_3(), mbedtls_x509_crt_parse_ncbicxx_2_28_3(), mbedtls_x509_crt_verify_info_ncbicxx_2_28_3(), mbedtls_x509_csr_info_ncbicxx_2_28_3(), mbedtls_x509_csr_parse_der_ncbicxx_2_28_3(), mbedtls_x509_csr_parse_file_ncbicxx_2_28_3(), mbedtls_x509_csr_parse_ncbicxx_2_28_3(), mbedtls_x509_dn_gets_ncbicxx_2_28_3(), mbedtls_x509_key_size_helper_ncbicxx_2_28_3(), mbedtls_x509_serial_gets_ncbicxx_2_28_3(), mbedtls_x509_sig_alg_gets_ncbicxx_2_28_3(), mbedtls_x509write_crt_der_ncbicxx_2_28_3(), mbedtls_x509write_crt_pem_ncbicxx_2_28_3(), mbedtls_x509write_crt_set_authority_key_identifier_ncbicxx_2_28_3(), mbedtls_x509write_crt_set_basic_constraints_ncbicxx_2_28_3(), mbedtls_x509write_crt_set_key_usage_ncbicxx_2_28_3(), mbedtls_x509write_crt_set_ns_cert_type_ncbicxx_2_28_3(), mbedtls_x509write_crt_set_subject_key_identifier_ncbicxx_2_28_3(), mbedtls_x509write_csr_der_ncbicxx_2_28_3(), mbedtls_x509write_csr_pem_ncbicxx_2_28_3(), mbedtls_x509write_csr_set_key_usage_ncbicxx_2_28_3(), mbedtls_x509write_csr_set_ns_cert_type_ncbicxx_2_28_3(), MD4Transform(), MD4Update(), MD5Transform(), MD5Update(), mdb_assert_fail(), mdb_env_cwalk(), mdb_reader_list(), mdb_strerror(), MEMORY_CreateConnectorEx(), MergeNoteQual(), MIME_ComposeContentTypeEx(), ASNDataManager::MonitorAlignments(), bm::compressed_buffer_collection< BV >::move_buffer(), mycmp(), myGetPrivateProfileString(), mz_zip_reader_read_central_dir(), mz_zip_writer_init_file_v2(), mz_zip_writer_write_zeros(), NcbiAddrToDNS(), NcbiAddrToString(), NcbiDumpIPRange(), NcbiGetCgiClientIPEx(), NcbiGetCgiClientIPv6Ex(), NcbiGetHostIfConfEx(), NcbiGetHostIP(), NcbiGetline(), NcbiIPv4ToString(), NcbiIPv6ToString(), NcbiIsLocalIPEx(), NcbiLog_GetHostName(), NcbiLog_Perf(), NcbiLog_UpdateOnFork(), NcbiLogP_GenerateHitID(), NcbiLogP_GenerateSID(), NcbiLogP_PerfStr(), NcbiMessagePlusError(), NcbiStreamToString(), CMultiSourceWriterImpl::NewStreamBuf(), CCassConnection::NewTimeUUID(), Nlm_MemFill(), Nlmzip_copy_block(), Nlmzip_flush_block(), CDirEntry::NormalizePath(), odbc_buf_free(), odbc_buf_get(), odbc_convert_datetime_to_binary(), odbc_db_is_microsoft(), odbc_db_version(), odbc_driver_is_freetds(), odbc_get_sqlchar(), odbc_get_sqlwchar(), odbc_populate_ird(), odbc_quote_metadata(), odbc_setenv(), odbc_stat_execute(), odbc_tds2sql(), odbc_tds_convert_wide_iso(), odbc_unquote(), SUv_Tcp::OnAlloc(), CBDBEnvKeeperConnectionHandler::OnMessage(), SUvNgHttp2_SessionBase::OnRead(), SUv_Tcp::OnRead(), SUvNgHttp2_TlsImpl::OnRecv(), CJaegerTracer::OnRequestStart(), SUvNgHttp2_TlsImpl::OnSend(), CLZOCompressionFile::Open(), CZipCompressionFile::Open(), CArchiveZip::OpenMemory(), SGetHttpDefaultRetries::operator()(), CBDB_FieldFixedByteString::operator=(), CBDB_FieldLString::operator=(), bm::serializer< BV >::optimize_serialize_destroy(), CHttpGetParser::Parse(), parse_int8(), parse_numeric(), pem_aes_decrypt(), pem_des3_decrypt(), pem_des_decrypt(), pk_parse_key_pkcs8_encrypted_der(), pk_write_ec_pubkey(), PopDiagPostPrefix(), CConnTest::PostCheck(), prdbresults_state(), prdbretcode(), prepare_call(), CSrvTime::Print(), bm::print_bvector_stat(), print_gap(), CNCActiveSyncControl::PrintState(), CPdfNumber::PrintTo(), CNCStat::PrintToLogs(), CNCStat::PrintToSocket(), ProcessStream(), prresult_type(), prretcode(), PSGToString(), CStreamUtils::Pushback(), CSocketReaderWriter::Pushback(), CStreamReader::Pushback(), CSocket::Pushback(), PushDiagPostPrefix(), bm::encoder::put_16(), bm::encoder::put_32(), put_ascii(), put_iso1(), put_ucs4be(), put_ucs4le(), put_utf16be(), put_utf16le(), put_utf8(), CNetCacheAPI::PutData(), QSIndex(), query_test(), CBGZFStream::Read(), CPhyloCSFData::Read(), CBamIndex::Read(), CCharVectorFunctions< Char >::Read(), SUvNgHttp2_TlsNoOp::Read(), SUvNgHttp2_TlsImpl::Read(), CNetICacheClient::Read(), CBDB_Cache::Read(), CSQLITE3_Cache::Read(), CAsyncWriteCache::Read(), Ctbl_seg::Read(), Ctbl_feat::Read(), NDirectNetStorageImpl::CObj::Read(), CBDB_BLobStream::Read(), CFileIO::Read(), CCgiEntryReader::Read(), CStreamReader::Read(), CStringReader::Read(), CBDB_BlobReaderWriter::Read(), CDB_Result_Reader::Read(), CBDB_CacheIReader::Read(), SFileTrackDownload::Read(), CMemoryReader::Read(), CSocketReaderWriter::Read(), CStringOrBlobStorageReader::Read(), CFileReader::Read(), CFileReaderWriter::Read(), CBlobReader::Read(), CTransmissionReader::Read(), CCGIStreamReader::Read(), CxBlobReader::Read(), CReaderOfLines::Read(), SPSG_BlobReader::Read(), CTarReader::Read(), CDataChunkReader::Read(), SH2S_ReaderWriter::Read(), CNetCacheReader::Read(), CPipeHandle::Read(), CNamedPipeHandle::Read(), CNamedPipe::Read(), NDirectNetStorageImpl::CRONetCache::Read(), NDirectNetStorageImpl::CROFileTrack::Read(), CPipe::Read(), CBZip2CompressionFile::Read(), CLZOCompressionFile::Read(), CCompressionIStream::Read(), CCompressionIOStream::Read(), CZipCompressionFile::Read(), CVariant::Read(), CSrvSocketTask::Read(), CResultSet::Read(), CSocket::Read(), read_buf(), read_string(), CObjectIStreamAsn::ReadAnyContent(), readBlob(), CBDB_MergeStore< BStore >::ReadBlob(), CBDB_MergeStoreAsync< BStore >::ReadBlob(), CBDB_ExtBlobStore< TBV >::ReadBlob(), readBlobAsChar(), CJson_Document::ReadBuffered(), CSeqDBSeqFile::ReadBytes(), CSeqDBHdrFile::ReadBytes(), CSeqDBRawFile::ReadBytes(), CObjectIStream::ReadCompressedBitString(), CBDB_File::ReadCursor(), CSrvSocketTask::ReadData(), SH2S_ReaderWriter::ReadImpl(), ReadIntoUtf8(), CSocket::ReadLine(), readline(), CNetICacheClient::ReadPart(), CStreamUtils::Readsome(), ReadStringFromStream(), ReadStrWithLen(), CDatagramSocket::Recv(), RemoveSourceFeatSpaces(), RemoveSpacesAndCommas(), CMergeBitsetBlob< BV >::Reset(), revcmp(), bm::heap_matrix< Val, ROWS, COLS, BVAlloc >::row(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::row(), CDbapiTest::Run(), CAVApp::Run(), CCompartApplication::Run(), CBDB_SplitTest::Run(), CDbapiTestSpeedApp::RunSample(), s_AddInt(), s_AddZeroPadInt(), s_AddZeroPadInt2(), s_AppendInt4(), s_AppStart(), s_AsnRead(), s_AsnWrite(), s_BUF_IO(), s_BufHash(), s_CheckGZipHeader(), s_CheckLZOHeader(), s_CompactBuffer(), s_Compress(), s_CONN_IO(), s_CONN_Read(), s_CONN_ReadPersist(), s_Connect_(), s_CopyData(), s_CP(), s_CreateConnectorMemory(), SH2S_Session::s_DataSourceRead(), s_Decompress(), s_DisplayCheckbox(), s_DisplayCheckboxChecked(), s_DisplayStructureOverview(), SDiagMessage::s_EscapeNewlines(), s_Extra(), s_ExtraStr(), s_FTPMdtm(), s_FTPRename(), s_FTPSize(), s_FTPSyst(), s_GetAlignmentTooltip(), s_GetCRC32(), s_GetDiskSpace_PANFS(), CMacroFunction_AuthorFix::s_GetFirstNameInitialsWithoutStops(), s_gethostbyname_(), s_GetOneNexusSizeComment(), s_GetSubHitID(), s_GetTimeStr(), s_GetToolkitRCLogLocation(), s_HEAP_Id(), s_HexDumpFile(), s_HttpUrlDecode(), s_ID(), s_InitAPI_(), CMacroFunction_AuthorFix::s_InsertInitialPeriods(), s_LoadLocalIPs(), s_LoadSingleService(), s_LOG_Handler(), s_LookupHost(), s_MakeFrom(), s_MakeOverflowFileName(), s_MbedTlsError(), s_MbedTlsInit(), s_MbedTlsRead(), s_ModeAsString(), s_Ncbi2naRevCmp(), s_Ncbi4naRevCmp(), s_OffsetAsString(), s_on_ipc_alloc(), s_on_ipc_connection(), SUv_Tcp::s_OnAlloc(), SUv_Tcp::s_OnRead(), SUvNgHttp2_TlsImpl::s_OnRecv(), SUvNgHttp2_TlsImpl::s_OnSend(), s_Print1Dig(), s_Print2Digs(), s_Print3Digs(), s_Print4Digs(), s_Print6Digs(), s_PrintMessage(), s_ProgressCallback(), s_QueueLogWrite(), s_Read(), s_Read_(), s_ReadBufToString(), s_ReadData(), s_ReadFileString(), s_ReadFromSocket(), s_ReadFullResponse(), s_ReadMagic(), s_Readsome(), s_ReadStrFromBUF(), s_ReadUInt32(), s_ReadUInt64(), s_Recv(), s_RecvMsg(), s_SendRcpt(), s_SeqDbGetSequence(), s_SeqDBMapNcbiNA8ToBlastNA8(), s_SetCurThread(), s_SetPrimitiveData(), s_SOCK_IO(), s_SockRead(), s_SockReadResponse(), s_SockWrite(), s_StripToPattern(), s_Uint8ToString(), SDiagMessage::s_UnescapeNewlines(), s_UpdateCRC32(), s_VT_Read(), s_VT_Write(), s_Write(), s_WriteBuffer(), s_WriteGZipFooter(), s_WriteGZipHeader(), s_WriteInt4(), s_WriteInt8BE(), s_WriteInt8LE(), s_WriteLog(), s_WriteLZOHeader(), s_WriteNoPending(), s_WriteToNamedPipe(), s_WriteToSocket(), s_ZipExtractCallback(), CBDB_RangeMap< TBV >::Save(), xml::impl::save_to_stream_cb(), xml::impl::save_to_string_cb(), CProjectStorage::SaveRawData(), ScanSequence(), SDiagMessage::SDiagMessage(), SeqToDelta(), SerializationCompressionLevelsTest(), CBDB_ExtBlobMap::Serialize(), CBDB_BlobMetaContainer::Serialize(), CCgiRequest::Serialize(), bm::serializer< BV >::serialize(), bm::serialize(), bm::compressed_collection_serializer< CBC >::serialize(), bm::sparse_vector_serializer< SV >::serialize(), CDataFrame< MAX_SIZE >::Serialize(), CSeqDictionary< Alphabet >::Serialize(), CPSGS_SatInfoChunksVerFlavorId2Info::Serialize(), CPSGS_IdModifiedVerFlavorId2Info::Serialize(), SERV_Print(), SERV_PrintFirewallPorts(), SERV_SetImplicitServerType(), bm::set_gap_level(), CBDB_BufferManager::SetAllNull(), CConn_Streambuf::setbuf(), CGlRenderBuffer< T >::SetBuffer(), CQueryEval_BV_Value< BV >::SetBuffer(), CBDB_Field::SetBuffer(), CAppExplorerDataObject::SetData(), SetDiagPostPrefix(), CBDB_FieldFixedByteString::SetMaxVal(), CBDB_FieldString::SetMaxVal(), CBDB_FieldLString::SetMaxVal(), CBDB_FieldFixedByteString::SetMinVal(), CBDB_BufferManager::SetNullBit(), SetupQueries_OMF(), NtlookupTestFixture::SetUpQuery(), TestFixture::SetUpQuery(), NuclWordFinderTextFixture::setupSequences(), TestFixture::SetUpSubject(), sGenerateFields(), CObjectIStreamJson::SkipByteBlock(), SOCK_gethostbyaddr(), SOCK_gethostbyaddrEx(), SOCK_gethostname(), SOCK_gethostnameEx(), SOCK_GetPeerAddressString(), SOCK_GetPeerAddressStringEx(), SOCK_HostPortToString(), SOCK_HostPortToStringEx(), SOCK_ntoa(), SOCK_Read(), CNetCacheReader::SocketRead(), bm::sparse_vector_deserialize(), SPGetPEValue(), SPSGS_BlobId::SPSGS_BlobId(), SPValidateEcnum(), bm::sse2_gap_bfind(), bm::sse2_gap_test(), bm::sse42_gap_bfind(), bm::sse42_gap_test(), ssl_calc_finished_tls(), ssl_calc_finished_tls_sha256(), ssl_calc_finished_tls_sha384(), ssl_context_load(), ssl_load_six_bytes(), ssl_parse_alpn_ext(), ssl_parse_client_hello(), ssl_parse_encrypt_then_mac_ext(), ssl_parse_extended_ms_ext(), ssl_parse_max_fragment_length_ext(), ssl_parse_record_header(), ssl_parse_renegotiation_info(), ssl_parse_server_hello(), ssl_parse_servername_ext(), ssl_parse_session_ticket_ext(), ssl_parse_supported_elliptic_curves(), ssl_parse_supported_point_formats(), ssl_parse_supported_point_formats_ext(), ssl_parse_truncated_hmac_ext(), ssl_session_load(), ssl_session_save(), ssl_ticket_gen_key(), ssl_update_checksum_md5sha1(), ssl_update_checksum_sha256(), ssl_update_checksum_sha384(), ssl_update_checksum_start(), ssl_write_alpn_ext(), ssl_write_client_hello(), ssl_write_encrypt_then_mac_ext(), ssl_write_extended_ms_ext(), ssl_write_hostname_ext(), ssl_write_max_fragment_length_ext(), ssl_write_real(), ssl_write_renegotiation_ext(), ssl_write_server_hello(), ssl_write_session_ticket_ext(), ssl_write_supported_elliptic_curves_ext(), ssl_write_supported_point_formats_ext(), ssl_write_truncated_hmac_ext(), NDirectNetStorageImpl::CObj::StartRead(), NDirectNetStorageImpl::CNotFound::StartRead(), NDirectNetStorageImpl::CNetCache::StartRead(), NDirectNetStorageImpl::CFileTrack::StartRead(), NDirectNetStorageImpl::CNetCache::StartWrite(), NDirectNetStorageImpl::CFileTrack::StartWrite(), CStreamUtils::Stepback(), CBDB_ExtBlobStore< TBV >::StoreBlob(), CCompressionUtil::StoreUI2(), CCompressionUtil::StoreUI4(), str(), StressTestStrSparseVector(), CJson_WalkHandler::String(), string_to_int(), string_to_int8(), string_to_uint8(), CSeqConvert_imp::Subseq(), syncsearch(), tds71_do_login(), tds7_put_query_params(), tds_alloc_packet(), tds_ascii_to_ucs2(), tds_connection_read(), tds_connection_write(), tds_convert_int8(), tds_convert_string(), tds_convert_uint8(), tds_convert_unique(), tds_generic_put(), tds_get_homedir(), tds_get_locale(), tds_getmac(), tds_goodread(), tds_msdatetime_put(), tds_numeric_put(), tds_put_buf(), tds_put_login_string(), tds_put_n(), tds_put_param_as_string(), tds_quote_and_put(), tds_readpassphrase(), tds_realloc_packet(), tds_send_emulated_rpc(), tds_socket_read(), tds_socket_write(), tds_strftime(), tds_swap_bytes(), tds_vasprintf(), tdsdump_do_dump_buf(), tdsdump_start(), gap_vector::temp_invert(), test(), Test(), test0(), test_err(), test_split(), TestCompressedCollection(), TestCompressSparseVector(), TestCompressSparseVectorSerial(), TestEqualSparseVectors(), TestInsert(), TestName(), CBDB_BufferManager::TestNullBit(), TestSignedSparseVectorSerial(), TestSIMDUtils(), TestSparseVector(), TestSparseVectorSerial(), TestSparseVectorSerialization2(), TestStrSparseVector(), TestStrSparseVector_FindEq(), TestStrSparseVectorSerial(), to_native(), ToJsonString(), CBDB_FieldLString::ToString(), SCass_BlobId::ToString(), CNetCacheWriter::Transmit(), CNetCacheWriter::TransmitImpl(), CAlnVec::TransposeSequences(), uInt64_toAscii(), uncompress2(), unfinished_query_test(), unlookup(), CCache_blob::UnPack(), unpack_rr(), CMD5::Update(), sse42_crc32::update(), CCharHistogram::UpdateHistogram(), CCharHistogram::UpdateHistogramWithDelim(), CBlobMetaDB::UpdateInsert(), CBDB_BLobFile::UpdateInsert(), CNetCacheWriter::UploadCacheFile(), URL_ConnectEx(), CValidError_bioseq::ValidateSeqDescContext(), VDBSRC_Init2naReader(), SUvNgHttp2_TlsImpl::Write(), SDiagMessage::Write(), NDirectNetStorageImpl::CObj::Write(), CBDB_BLobStream::Write(), CFileIO::Write(), CStreamWriter::Write(), CBDB_BlobReaderWriter::Write(), SFileTrackUpload::Write(), CSocketReaderWriter::Write(), CFileWriter::Write(), CFileReaderWriter::Write(), CBlobWriter::Write(), CWriter_HTMLEncoder::Write(), CChecksumStreamWriter::Write(), CMultiWriter::Write(), CTransmissionWriter::Write(), CCgiStreamWrapperWriter::Write(), CNetCacheWriter::Write(), CBDB_CacheIWriter::Write(), CxBlobWriter::Write(), CMD5StreamWriter< Buffer >::Write(), CStringOrWriter::Write(), SH2S_ReaderWriter::Write(), CNamedPipeHandle::Write(), CNamedPipe::Write(), SIoStreamEmbeddedStreamReaderWriter::Write(), NDirectNetStorageImpl::CWONetCache::Write(), NDirectNetStorageImpl::CWOFileTrack::Write(), CBZip2CompressionFile::Write(), CLZOCompressionFile::Write(), CCompressionOStream::Write(), CCompressionIOStream::Write(), CZipCompressionFile::Write(), CSrvSocketTask::Write(), CSocket::Write(), impl::SBufferWriter_Write< ncbi::CSimpleBufferT< T > >::Write(), impl::SBufferWriter_Write< std::vector< T > >::Write(), impl::SBufferWriter_Write< T >::Write(), SUv_Write::Write(), CObjectOStreamAsn::WriteBitString(), CObjectOStreamAsnBinary::WriteBitString(), CObjectOStreamJson::WriteBitString(), CObjectOStreamXml::WriteBitString(), CNCBlobStorage::WriteBlobStat(), CSrvSocketTask::WriteData(), CNCBlobStorage::WriteDbInfo(), SNetServerConnectionImpl::WriteLine(), CFileHandleDiagHandler::WriteMessage(), CFileDiagHandler::WriteMessage(), CMsvcConfigure::WriteNcbiconfMsvcSite(), CBDB_Cache::WriteOverflow(), TNCBufferType::WriteText(), x509_crt_parse_der_core(), x509_get_certificate_policies(), x509_info_cert_policies(), x509_info_cert_type(), x509_info_ext_key_usage(), x509_info_key_usage(), x509_info_subject_alt_name(), x509write_csr_der_internal(), CDllResolver::x_AddExtraDllPath(), CWriteDB_IsamIndex::x_AddString(), CWriteDB_IsamIndex::x_AddStringData(), CSimpleBufferT< char >::x_Allocate(), CRPCClient_Base::x_Ask(), x_Authenticate(), x_BadMagic(), x_BlockTEA_Decode(), x_BlockTEA_Encode(), CCacheHashedContent::x_CheckHashContent(), CQueueDataBase::x_CheckOpenPreconditions(), CBamRefSeqIterator::x_CheckRC(), CBamAlignIterator::x_CheckRC(), x_ClassStr(), CCompression::x_CompressFile(), CDiagContext::x_CreateUID_AsyncSafe(), x_CredInfo(), CBDB_RawFile::x_DB_CPut(), CBDB_RawFile::x_DB_Put(), CCompression::x_DecompressFile(), x_Descr(), CDeflineGenerator::x_DescribeClones(), CGlCurve< Curve >::x_DrawRecursiveBuffered(), x_DumpHdr(), CSeqSearch::x_ExpandPattern(), x_FixupUserHeader(), x_FlagsStr(), x_FTPCompleteUpload(), x_FTPDir(), x_FTPEprt(), x_FTPEpsv(), x_FTPParseMdtm(), x_FTPParseReply(), x_FTPPasv(), x_FTPPollCntl(), x_FTPPort(), x_FTPXfer(), x_GetChar(), CDisplaySeqalign::x_GetGeneLinkUrl(), CEutilsClient::x_GetHostName(), CLDS2_Database::x_GetLdsSeqId(), CDiagContext::x_GetNextHitID(), CSplignApp::x_GetNextPair(), CBamRefSeqIterator::x_GetString(), CBamAlignIterator::x_GetString(), x_GetValue(), CSaveImagesSetupDlg::x_Init(), x_IPv4ToString(), x_IPv6ToString(), x_IsUrlAccessible(), x_json_serialize_string(), x_json_serialize_to_buffer(), x_json_serialize_to_buffer_pretty(), x_json_serialize_to_buffer_r(), x_json_serialize_to_string(), x_json_serialize_to_string_pretty(), CMultiAligner::x_LoadBlockBoundaries(), CHTMLPage::x_LoadTemplate(), CHTMLPage::x_LoadTemplateLib(), x_MbedTlsPull(), CMergeVolumes::x_MergeVolume(), x_Namespace(), SDiagMessage::x_NewWrite(), x_Num(), SDiagMessage::x_OldWrite(), CPhyloTreeMaxDirectChildDist::x_OnStep(), x_OpcodeStr(), CCleanupApp::x_OpenOStream(), CFastCgiThreadedRequest::x_ParseEnv(), x_Port(), CDisplaySeqalign::x_PrintDefLine(), CHTMLPage::x_PrintTemplate(), CCgiRequest::x_ProcessInputStream(), CSoapServerApplication::x_ProcessWsdlRequest(), CStreamUtils::x_Pushback(), x_Pushback(), x_PushbackBuf(), x_RcodeStr(), CCgiWatchFile::x_Read(), CConn_Streambuf::x_Read(), CRWStreambuf::x_Read(), SPSG_BlobReader::x_Read(), CSeqDBExtFile::x_ReadBytes(), CBDB_ExtBlobStore< TBV >::x_ReadCache(), x_ReadChunkHead(), x_ReadChunkTail(), CBlastDbBlob::x_ReadIntFixed(), x_Readsome(), CColumnarVCFReaderApp::x_ReadVCFBlob(), IPhyloTreeRender::x_RenderCircularVbo(), IPhyloTreeRender::x_RenderSplineVbo(), x_ReqMethod(), x_SaveStr(), CWorkspaceAutoSaver::x_SaveWorkspace(), x_Scheme(), x_Sendmail_InitEnv(), x_ServiceName(), x_SetupConnectionParams(), x_TypeStr(), x_UpdateDtabInArgs(), x_UpdateHost(), CRNAValidator::x_ValidateTrnaCodons(), x_VerifyReply(), x_WriteBuf(), CFastaOstream::x_WriteBuffer(), CCgiStreamWrapperWriter::x_WriteChunk(), CBlastDbBlob::x_WriteIntFixed(), CBlastDbBlob::x_WriteIntFixed_LE(), CBDB_CacheIWriter::x_WriteOverflow(), CBlastDbBlob::x_WriteString(), CBlastDbBlob::x_WriteVarInt(), XMLAccessionsCheck(), XMLConcatSubTags(), XMLGetSegment(), XMLGetTagValue(), XMLInitialEntry(), XMLKeywordsCheck(), XMLRestoreSpecialCharacters(), CConn_Streambuf::xsgetn(), CPushback_Streambuf::xsgetn(), CCompressionStreambuf::xsgetn(), CRWStreambuf::xsgetn(), CCompressionStreambuf::xsputn(), CRWStreambuf::xsputn(), CConn_Streambuf::xsputn(), CPushback_Streambuf::xsputn(), xTryProductRules(), xx_LoadLocalIPs(), and CDiagRestorer::~CDiagRestorer().

file

FILE* file

Definition at line 1337 of file lex.newick.cpp.

Referenced by _bcp_check_eof(), CProjBulderApp::AddCustomConfH(), CProjBulderApp::AddCustomMetaData(), CBamUIDataSource::AddDataLoader(), CSNPDataLoader_Impl::AddFixedFile(), CSNPDataLoader_Impl::AddFixedFileOnce(), CCodeGenerator::AddType(), CUpdateAlign::apply(), CLoadStructComments::apply(), CLoadSecondaryAccessions::apply(), boost::assertion_failed(), CDebugDumpViewer::Bpt(), CRemoteAppLauncher::CanExec(), CBAMDataLoader::CBAMDataLoader(), CBGZFStream::CBGZFStream(), CConn_FTPDownloadStream::CConn_FTPDownloadStream(), CConn_FTPUploadStream::CConn_FTPUploadStream(), CDBInterfacesFileConnParams::CDBInterfacesFileConnParams(), CDiagCompileInfo::CDiagCompileInfo(), CFileDBEngine::CFileDBEngine(), check_lib(), CRR_Util::CheckExistanceAndPermissions(), CGeneFileUtils::CheckExistence(), CheckStaticType(), CHugeAsnReader::CHugeAsnReader(), CInvalidChoiceSelection::CInvalidChoiceSelection(), CBDB_Env::CleanLog(), CFile::CompareTextContents(), CArrayHolder::Convert(), CMacroFlowEditor::CopyDefaultLibrary(), ColumnarVcfCache::CreateBlob(), SRemoteApp::SRequest::CreateFilesNode(), CDirEntry::CreateTmpFile(), CSaveHitMatrixPdfDlg::CSaveHitMatrixPdfDlg(), CSeqDB_Path::CSeqDB_Path(), CSeqIdGuesser::CSeqIdGuesser(), CSeqidlistRead::CSeqidlistRead(), CSimpleDictionary::CSimpleDictionary(), CSmartFileTextToolbar::CSmartFileTextToolbar(), CSNPBlobId::CSNPBlobId(), CSNPDataLoader_Impl::CSNPDataLoader_Impl(), CSNPSeqInfo::CSNPSeqInfo(), CStaticArraySearchBase< NStaticArray::PKeyValuePair< SStaticPair< KeyType, ValueType > >, less< KeyType > >::CStaticArraySearchBase(), debug_print_line_by_line(), debug_print_pk(), debug_send_line(), CReadBlastApp::dumpAlignment(), C5ColObjectLoader::Execute(), CAgpObjectLoader::Execute(), CAsnObjectLoader::Execute(), CBedObjectLoader::Execute(), CFastaObjectLoader::Execute(), CGBFlatFileObjectLoader::Execute(), CGffObjectLoader::Execute(), CPhyObjectLoader::Execute(), CPslObjectLoader::Execute(), CRMObjectLoader::Execute(), CTextAlignObjectLoader::Execute(), CVcfObjectLoader::Execute(), CWigObjectLoader::Execute(), pythonpp::CEngine::ExecuteFile(), ExtractFileName(), CDataType::FileName(), CWinMaskConfig::FillIdList(), get_desktop_file(), CWGSFileInfo::SAccFileInfo::GetContigIterator(), CSeqDB::GetDiskUsage(), GetFavoritesFile(), CWGSDataLoader_Impl::GetFileInfoByGi(), CWGSDataLoader_Impl::GetFileInfoByProtAcc(), CSplitCacheApp::GetFileName(), CMultiFileInput::GetFilenames(), CFtglFontManager::GetFont(), CBamDb::GetHeaderText(), CSeqIdGuesser::GetIdStrings(), CGeneFileUtils::GetLength(), CBamUIDataSource::GetLoaderName(), CSNPDataLoader::SLoaderParams::GetLoaderName(), CSNPDataLoader::GetLoaderNameFromArgs(), CSeqDBAtlas::GetMemoryFile(), CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce(), CWGSFileInfo::SAccFileInfo::GetProteinIterator(), CCSRADataLoader_Impl::GetRecordsOnce(), CCSRADataLoader_Impl::GetRefSeqInfo(), CWGSFileInfo::SAccFileInfo::GetScaffoldIterator(), CBlastSeqidlistFile::GetSeqidlist(), CBlastSeqidlistFile::GetSeqidlistInfo(), CImageIO::GetTypeFromMagic(), gzbuffer(), gzclearerr(), gzclose(), gzclose_r(), gzclose_w(), gzdirect(), gzeof(), gzerror(), gzflush(), gzfread(), gzfwrite(), gzgetc(), gzgetc_(), gzgets(), gzoffset(), gzoffset64(), gzprintf(), gzputc(), gzputs(), gzread(), gzrewind(), gzseek(), gzseek64(), gzsetparams(), gztell(), gztell64(), gzungetc(), gzwrite(), CAuthorNamesContainer::ImportAuthorsFromFile(), CRemoteAppJobFactory< TJob, TListener, kName >::Init(), init_common(), CMsvcSite::IsLibOk(), CWGSFileInfo::SAccFileInfo::IsMigrated(), CTbl2AsnApp::LoadAnnotMap(), CTbl2AsnApp::LoadCMTFile(), CTbl2AsnApp::LoadDSCFile(), CTbl2AsnApp::LoadPEPFile(), CTbl2AsnApp::LoadPRTFile(), CTbl2AsnApp::LoadRNAFile(), CDiscrepancyDlg::LoadSettings(), CwxExportAlnmultiImgDlg::LoadSettings(), CwxExportVectorImageDlg::LoadSettings(), CwxSavePdfBaseDlg::LoadSettings(), CLoadStructComments::LoadSingle(), CTableImportDataSource::LoadTable(), CLoadStructComments::LoadWithAccessions(), LOG_Write(), CDiagMatcher::MatchFile(), mbedtls_debug_print_buf_ncbicxx_2_28_3(), mbedtls_debug_print_crt_ncbicxx_2_28_3(), mbedtls_debug_print_ecp_ncbicxx_2_28_3(), mbedtls_debug_print_mpi_ncbicxx_2_28_3(), mbedtls_debug_print_msg_ncbicxx_2_28_3(), mbedtls_debug_print_ret_ncbicxx_2_28_3(), mbedtls_debug_printf_ecdh_internal(), mbedtls_debug_printf_ecdh_ncbicxx_2_28_3(), mbedtls_error_add(), mbedtls_platform_entropy_poll_ncbicxx_2_28_3(), mdb_assert_fail(), CAgpconvertApplication::CAsnvalRunner::Notify(), odbc_check_cols(), odbc_check_res(), odbc_check_rows(), odbc_command_proc(), odbc_report_error(), odbc_reset_statement_proc(), CMacroFlowEditor::OnExportMenuClick(), CMacroFlowEditor::OnExportStepsClick(), CSuspectProductRulesEditor::OnFileAdd(), CSuspectProductRulesEditor::OnFileLoad(), CSuspectProductRulesEditor::OnFileSaveAs(), CMacroFlowEditor::OnImportMenuClick(), CMacroFlowEditor::OnInputFile(), CMacroFlowEditor::OnOpenClick(), CSmartFileTextToolbar::OnSaveAsBtn(), CMacroFlowEditor::OnSaveAsClick(), CwxSavePdfBaseDlg::OnSaveClick(), CwxExportAlnmultiImgDlg::OnSaveClick(), CwxExportVectorImageDlg::OnSaveClick(), CSuspectProductRulesEditor::OnShowDiffs(), CIndexerOpenViewExtension::OnViewOpen(), CBGZFStream::Open(), CHugeAsnReader::Open(), CHugeFastaReader::Open(), OpenFileBrowser(), CTLSHandler::OpenInputFile(), CTLSHandler::OpenOutputFile(), CTestNameToInfoMapLoader::operator()(), xml::event_parser::parse_file(), Path(), CAppPopup::PopupFile(), CBam2GraphApp::ProcessFile(), CPsgPerfApplication::ProcessFile(), CTAbleValApp::ProcessOneFile(), DTDParser::PushEntityLexer(), CBamHeader::Read(), CReadBlastApp::ReadBlast(), CImageIO::ReadImage(), CImageIO::ReadImageInfo(), CReadBlastApp::ReadPreviousAcc(), CReadBlastApp::ReadRRNA2(), CImageIO::ReadSubImage(), CReadBlastApp::ReadTagMap(), CReadBlastApp::ReadTRNA2(), ReadVDBFile(), CProjBulderApp::RegisterGeneratedFile(), CSNPDataLoader::RegisterInObjectManager(), CMetaRegistry::SEntry::Reload(), CBDB_RawFile::Rename(), CExceptionReporterStream::Report(), report_bcp_error(), ReportIncorrectOrder(), ReportODBCError(), ReportUnsafeStaticType(), CFileDBEngine::RollbackTransaction(), CPrt2FsmApp::Run(), CAgpFastaComparator::Run(), COmssa2pepxmlApplication::Run(), CMultipatternApp::Run(), CTestApplication::Run(), ASNIOTestApp::Run(), CSeqAnnotSplicerApp::Run(), s_AddOneDataFile(), s_CheckGumbelParams(), s_CheckSorted(), s_CollectFileInfo(), s_Dump(), s_DumpSparse(), s_DumpZero(), s_FileContents2String(), s_GetDBTree(), CSeqDBGiMask::s_GetFileRange(), s_GetFtpHostAndFile(), s_GetProductRules(), s_InitializeECNumberMaps(), s_InitializeInstitutionCollectionCodeMaps(), s_InitializeOrgRefMap(), s_InitializeStructuredCommentRules(), CMacroFunction_StringConstraints::s_IsSynonymFile(), s_LoadECNumberTable(), s_LoadLocalIPs(), s_LoadSeqAnnot(), s_LogSocketError(), s_LogWithErrno(), s_LogWithErrStr(), s_PositionAsString(), s_Read(), s_ReadHeader(), s_ReadObject(), s_ReadRecord(), s_ReadVCFAssembly(), s_SetLogFilesDir(), s_WriteHeader(), s_WriteRecord(), SAccGuide::SAccGuide(), SDiagMessage::SDiagMessage(), search_interface_file(), CRemoteAppRequest::Send(), CBrowserUtils::SendToBrowser(), SeqDB_FileIntegrityAssert(), CCodeGenerator::SetCombiningFileName(), CNcbiDiag::SetFile(), CDiagCompileInfo::SetFile(), CCodeGenerator::SetFileListFileName(), CFileAutoLoader::SetFormatManager(), CBamLoadOptionPanel::SetIndexFiles(), SourceFileExt(), CSrvDiagMsg::StartOldStyle(), CSrvDiagMsg::StartSrvLog(), tds_get_home_file(), tdsdump_do_dump_buf(), tdsdump_do_log(), tdsdump_start(), TruncateCache(), CFileManifest::Validate(), CLBLASTParamsPanel::ValidateLocalDatabase(), SDiagMessage::Write(), CImageIO::WriteImage(), CMsvcConfigure::WriteNcbiconfMsvcSite(), CImageIO::WriteSubImage(), CTar::x_AppendFile(), CDiagFilter::x_CheckFile(), CDebugDumpViewer::x_CheckLocation(), CVcfLoadingJob::x_CreateProjectItems(), CBamUIDataSource::x_GetBamInputs(), CBamUIDataSource::x_GetCSraInputs(), CSeqDB::x_GetDBFilesMetaData(), CBlastDBAliasApp::x_GetDbsToAggregate(), CSNPDataLoader_Impl::x_GetFileInfo(), CSeqDBColumn::x_GetFileRange(), CConn_FTPDownloadStream::x_InitDownload(), CGICacheReader::x_Initialize(), CConn_FTPUploadStream::x_InitUpload(), CGBProjectTool::x_LoadGeneralData(), CColumnarVCFReaderApp::x_LoadVCFFile(), CUpdateAlign::x_MapNonPresentIDs(), CUpdateAlign::x_ReadAlign(), CVDBAliasNode::x_ReadValues(), CWiggleExportJob::x_RecalculateGraph(), CVDBAliasNode::x_ResolveVDBList(), CStaticArraySearchBase< NStaticArray::PKeyValuePair< SStaticPair< KeyType, ValueType > >, less< KeyType > >::x_Set(), BlastdbCopyApplication::x_ShouldCopyPIGs(), BlastdbCopyApplication::x_ShouldParseSeqIds(), CStaticArraySearchBase< NStaticArray::PKeyValuePair< SStaticPair< KeyType, ValueType > >, less< KeyType > >::x_Validate(), xTryProductRules(), and xTryTextFile().

g_Buffer

string g_Buffer

static

Definition at line 445 of file lex.newick.cpp.

Referenced by newicklex().

g_NewickIstr

CNcbiIstream* g_NewickIstr

extern

Definition at line 126 of file newick.tab.cpp.

Referenced by ReadNewickTree().

i

int i

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp, and /home/coremake/doxygen/cxx/include/util/data_histogram.hpp.

Definition at line 1456 of file lex.newick.cpp.

Referenced by _bcp_exec_in(), _bcp_exec_out(), _bcp_free_columns(), _bcp_read_hostfile(), _bcp_readfmt_colinfo(), CStructuredCommentsReader::_BuildStructuredComment(), res_traits< Res >::_codons(), res_traits< EResidue >::_codons(), _cs_convert_ex(), _ct_bind_data(), CTabDelimitedValidator::_MakeColumns(), _mm_aesenclast_si128(), _mm_aeskeygenassist_si128(), _mm_minpos_epu16(), _mm_prefetch(), _mm_round_pd(), CTabDelimitedValidator::_OperateRows(), _pcre_ord2utf(), _PHIBlastFindHitsShort(), _PHIPatternWordsBitwiseAnd(), _PHIPatternWordsBitwiseOr(), _PHIPatternWordsLeftShift(), _PSIAlignedBlockNew(), _PSIAllocateMatrix(), _PSICalculateNormalizedSequenceWeights(), _PSIComputeAlignedRegionLengths(), _PSIComputeFreqRatios(), _PSIComputeFreqRatiosFromCDs(), _PSIComputePositionExtents(), _PSIConvertFreqRatiosToPSSM(), _PSIDeallocateMatrix(), _PSIGetAlignedSequencesForPosition(), _PSIMatrixFrequencyRatiosNew(), _PSIPackedMsaGetNumberOfAlignedSeqs(), _PSIPurgeAlignedRegion(), _PSIScaleMatrix(), _PSISequenceLengthWithoutX(), _PSIStructureGroupCustomization(), StructureBase::_RemoveChild(), CTabDelimitedValidator::_ReportXML(), res_traits< Res >::_rev_codons(), res_traits< EResidue >::_rev_codons(), _SQLAllocDesc(), _SQLFetch(), _SQLFreeDesc(), _sse2neon_vmull_p64(), CProtProp::AACount(), CMSPeak::AboveThresh(), Matrix< T >::absRelApprox(), CSeqScores::AcceptorScore(), CSeqDBImpl::AccessionsToOids(), CSeqDBLMDBSet::AccessionsToOids(), CSeqDBImpl::AccessionToOids(), CSeqDBLMDBSet::AccessionToOids(), AccsCmp(), CDockManager::ActivateClients(), CDockContainer::ActivateClients(), CResolvedTypeSet::Add(), CSeqsRange::Add(), CInt_fuzz::Add(), SSeqTableContent::Add(), CBBox< 3 >::Add(), SChunkInfo::Add(), CPointerPot::Add(), CPosToIndex::Add(), CRegExFSA::Add(), SSparseIndex::Add(), add64(), bm::sparse_vector_scanner< bm::rsc_sparse_vector >::add_agg_char(), bm::bit_vistor_copy_functor< BV >::add_bits(), bm::bit_visitor_callback_adaptor< VCBT, size_type >::add_bits(), bm::bit_visitor_back_inserter_adaptor< BII, size_type >::add_bits(), TestDecodeFunctor::add_bits(), add_entry(), add_name(), add_one_and_zeros_padding(), add_pair_to_block(), add_pkcs_padding(), bm::bit_visitor_callback_adaptor< VCBT, size_type >::add_range(), bm::bit_visitor_back_inserter_adaptor< BII, size_type >::add_range(), TestDecodeFunctor::add_range(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::back_insert_iterator::add_remap_stat(), SBaseStats::add_stat(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::back_insert_iterator::add_value(), add_zeros_and_len_padding(), add_zeros_padding(), CPatternStats::AddAccRuns(), CAlignCollapser::AddAlignment(), AlignmentCollection::AddAlignment(), CMultAlign::AddAlignment(), CAmbiguityContext::AddAmbiguity(), AddBioseqToTable(), ConservationColorer::AddBlock(), SequenceDisplay::AddBlockBoundaryRows(), AddColumnsToFeatureTable(), AddCommandsForScopedObjects(), CProjectTreeBuilder::AddDatatoolSourcesDepends(), CBoyerMooreMatcher::AddDelimiters(), CArgDescriptions::CPrintUsage::AddDetails(), PeriodicTableClass::AddElement(), DTDParser::AddElementContent(), CBioseq_set_Info::AddEntry(), NAdapterSearch::CPairedEndAdapterDetector::CConsensusPattern::AddExemplar(), AddFeatureSeqTableRowToSeqEntry(), AddFeatureSeqTableToSeqEntry(), AddFeatureToSeqTable(), CMultiFileInput::AddFilenames(), CBamLoadOptionPanel::AddFilenames(), addFlagsFromEnvVar(), CQueryExec::AddFunc(), CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), Messenger::AddHighlights(), CMSPeak::AddHit(), CBuildDatabase::AddIds(), CPagerView::AddImageString(), CPagerView::AddInactiveImageString(), CIndexedDb_New::AddIndexInfo(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::AddInsertions(), CAttribMenu::AddInt(), CRasterizer< A >::AddInterval(), CAttribMenu::AddIntReadOnly(), CSearch< LEGACY, NHITS >::AddIonsToHit(), CFormatItemOStream::AddItem(), CGBDocument::AddItems(), CMsvcPrjProjectContext::AdditionalIncludeDirectories(), CMsvcPrjProjectContext::AdditionalLinkerOptions(), CTableSortMultiChoice::AddLevels(), CHandleRangeMap::AddLocation(), CReadBlastApp::addLoctoSimpleSeq(), CBlastQueryVector::AddMask(), Sequence::AddMMDBAnnotTag(), CSearch< LEGACY, NHITS >::AddModsToHit(), CAccPatternCounter::AddName(), BlockModel::addOffset(), ResidueProfiles::addOneRow(), AddProblemsColumnToFeatureSeqTable(), CDensityMap< CntType >::AddRange(), CDensityMap< CntType >::AddRanges(), TaxTreeData::addRows(), AlignmentCollection::addRowSources(), SAccGuide::AddRule(), CSuspectProductRulesEditor::AddRule(), SeqTree::addSelectionFields(), CBlastQueryFilteredFrames::AddSeqLoc(), CLinkUtils::AddSequenceLinks(), CBuildDatabase::AddSequences(), SequenceTable::addSequences(), CPhyloSelectionSetMgr::AddSet(), CExportTableDlg::AddSourceToTable(), CAlignFormatUtil::AddSpace(), SMMStat::AddStats(), CRunOfDigits::AddString(), AddSupport(), CSrcTablePrimerColumn::AddToBioSource(), CClickableSortUniqueCount::AddToBulkEditList(), CDockManager::AddToDefaultLocation(), CClickableSortUniqueCount::AddToListCtrl(), CWindowManagerService::AddToolBarContext(), OpenGLRenderer::AddTransparentSpheresForList(), CApplyEditconvertPanel::AddUndo(), CHit::AddUpSubHits(), StyleManager::AddUserStyle(), mu::ParserByteCode::AddVal(), mu::ParserByteCode::AddVar(), CTriPerimeter::AddVertex(), CWinMaskConfig::AddWinMaskArgs(), CTextFsm< MatchType >::AddWord(), CEditSequence::AdjustFeatureLocations(), CPaintSequence::AdjustFeatureRange(), CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked(), CPaintSequence::AdjustProtFeatRange(), CEditSequence::AdjustProtFeatureLocations(), AdjustSpecificHostForTaxServer(), AdvancedStringCompare(), aes_gen_tables(), agg_equal(), agg_next(), agg_shift_right_and(), bm::sparse_vector_scanner< SV, S_FACTOR >::aggregate_AND_OR_slices(), bm::sparse_vector_scanner< SV, S_FACTOR >::aggregate_OR_slices(), CNCMMStats::AggregateUsage(), bm::aggregator_pipeline_execute(), AggregatorTest(), algIntSORTFunction(), algs(), algSortQuickCallbackIndex(), ALIGN_EX(), AlignFNog(), AlignmentDisplay::AlignmentDisplay(), AlignmentIsSupportedBySR(), AlignmentSet::AlignmentSet(), AlignModelToSeqalign(), bm::all_set< T >::all_set_block::all_set_block(), bm::blocks_manager< Alloc >::alloc_arena(), bm::blocks_manager< Alloc >::alloc_top_subblock(), CSeedRoots::Allocate(), AMatrix_base::Allocate(), CObjectMemoryPool::Allocate(), bm::basic_bmatrix< BV >::allocate_rows(), CCdCore::AllResiduesInRangeAligned(), alp_data::alp_data(), AnalyzeDllData(), CCyclicDepends::AnalyzeProjItemNew(), AndOperationsTest(), bm::aggregator< BV >::any_carry_overs(), bm::bvector< Alloc >::any_range(), CHitList::Append(), CMSModSpecSet::Append(), CObjectList::Append(), CSymResolver::Append(), append_indent(), MultipleAlignment::appendAlignment(), CSeqTableGrid::AppendCols(), rapidjson::internal::TokenHelper< Stack, Ch >::AppendIndexToken(), CUICommandRegistry::AppendMenuItems(), CObjectIStreamAsn::AppendStringData(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::AppendToken(), CFuseJoinsInLocs::apply(), CMergeBiosources::apply(), CLoadSecondaryAccessions::apply(), CCombineAdjacentGaps::apply_impl(), CRawSeqToDeltaSeqByLoc::apply_impl(), bm::xor_scanner< BV >::apply_xor_match_vector(), ApplyDBLinkValuesTableToSeqEntry(), mu::ParserBase::ApplyFunc(), CDockManager::ApplyLayout(), mu::ParserBase::ApplyNumFunc(), CExpansionRule::ApplyRule(), mu::ParserBase::ApplyStrFunc(), CApplySubpanel::ApplyToAll(), CEditSubpanel::ApplyToAll(), CRemoveSubpanel::ApplyToAll(), CSwapSubpanel::ApplyToAll(), CConvertSubpanel::ApplyToAll(), CParseSubpanel::ApplyToAll(), CChangeCaseSubpanel::ApplyToAll(), CConvertComment::ApplyToComment(), CApplySubpanel::ApplyToSelected(), CEditSubpanel::ApplyToSelected(), CRemoveSubpanel::ApplyToSelected(), CSwapSubpanel::ApplyToSelected(), CConvertSubpanel::ApplyToSelected(), CParseSubpanel::ApplyToSelected(), CChangeCaseSubpanel::ApplyToSelected(), CRemoveEmptyGenomeProjectsDB::ApplyToUserObject(), CRemoveDuplicateStructuredComment::ApplyToUserObject(), CRemoveEmptyStructuredComment::ApplyToUserObject(), CModifyStructuredComment::ApplyToUserObject(), CNcbiApplicationAPI::AppMain(), Matrix< T >::approx(), AlignmentCollection::AreNonOverlapping(), CBDB_BufferManager::ArrangePtrsPacked(), CBDB_BufferManager::ArrangePtrsUnpacked(), mu::ParserByteCode::AsciiDump(), CSplignFormatter::AsExonTable(), CDistanceMatrix::AsMatrix(), CFastaReader::AssembleSeq(), CSplignFormatter::AsSeqAlignSet(), CCompartmentAccessor< THit >::AsSeqAlignSet(), CSeq_id_Descr::Assign(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::assign(), CClassTypeInfo::Assign(), bm::blocks_manager< Alloc >::assign_gap(), bm::blocks_manager< Alloc >::assign_gap_check(), CGffRecord::AssignAttributesCore(), CGffRecord::AssignAttributesExtended(), CSeqDB_BitSet::AssignBit(), CSeqDB_BitSet::AssignBitRange(), CHitMatrixGraph::AssignColorsByScore(), AssignDefaultPatterns(), CTimeSpan::AssignFromSmartString(), rapidjson::internal::Schema< SchemaDocumentType >::AssignIfExist(), CCassPrm::AsStringForDebug(), CSRSearch::CMismatchResultsInfo::at(), atd(), AtomSet::AtomSet(), CGBDocument::AttachProjectItems(), CBlobSplitterImpl::AttachToSkeleton(), DTDParser::AttribBlock(), CAlnMultiRenderer::AutoFitColumns(), CDiscrepancyVisitorImpl< _Name >::Autofix(), AutoMap(), mu::Parser::Avg(), bm::avx2_bit_block_xor(), bm::avx2_gap_sum_arr(), bm::avx2_set_block_bits2(), bm::avx2_setbit_to256(), bm::avx2_shift_r1_and(), BackAlignNog(), CContigAssembly::BandedGlobalAlignment(), BASE64_Decode(), BASE64_Encode(), BasicFunctionalityTest(), bcp_columns(), bcp_options(), BDB_batch_delete_recs(), BDB_Compare(), BDB_find_field(), CObjectIStreamXml::BeginChoiceVariant(), CObjectIStreamJson::BeginClassMember(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::BeginValue(), BelongToExon(), CContigAssembly::BestLocalSubAlignment(), bm::sparse_vector_scanner< SV, S_FACTOR >::bfind(), bm::sparse_vector_scanner< SV, S_FACTOR >::bfind_eq_str(), bm::sparse_vector_scanner< bm::rsc_sparse_vector >::bfind_eq_str_impl(), bm::sv_sample_index< SV >::bfind_range(), big_test(), rapidjson::internal::BigInteger::BigInteger(), impl::binary_to_hex_string(), bm::sparse_vector_scanner< SV, S_FACTOR >::bind(), BioTreeForestConvert2Container(), bm::bvector< Alloc >::bit_and(), bm::basic_bmatrix< BV >::bit_and_rows(), bm::bit_array_compute_gaps(), bm::bit_block_and(), bm::bit_block_erase(), bm::bit_block_find(), bm::bit_block_init_and_2way(), bm::bit_block_insert(), bm::bit_block_rotate_left_1(), bm::bit_block_rotate_left_1_unr(), bm::bit_block_shift_l1(), bm::bit_block_shift_l1_unr_min(), bm::bit_block_shift_r1(), bm::bit_block_shift_r1_and(), bm::bit_block_shift_r1_unr_min(), bm::bit_block_sub(), bm::bit_block_xor(), bm::bit_find_first(), bm::bit_find_first_diff(), bm::bit_find_first_if_1(), bm::bit_find_last(), bm::bit_iblock_make_pcv(), bm::bit_iblock_reduce(), bm::bit_import_u32(), bm::operation_functions< T >::bit_operation_count(), bm::bvector< Alloc >::bit_or(), bm::bvector< Alloc >::bit_or_and(), bm::bit_recomb(), bm::bvector< Alloc >::bit_sub(), bm::basic_bmatrix< BV >::bit_sub_rows(), bm::bvector< Alloc >::bit_xor(), BitBlockTransposeTest(), CSeqMaskerUtil::BitCount(), BitCountChange(), BitCountChangeTest(), BitEncoderTest(), BitForEachRangeFuncTest(), BitForEachTest(), BitRangeAllSetTest(), BitString(), CdBlaster::blast(), Blast_AdjustScores(), Blast_ApplyPseudocounts(), Blast_CalcFreqRatios(), Blast_CalcLambdaFullPrecision(), Blast_CompositionWorkspaceNew(), BLAST_ComputeLengthAdjustment(), BLAST_ComputeTraceback_MT(), BLAST_CreateMixedFrameDNATranslation(), Blast_EntropyOldFreqNewContext(), Blast_FillResidueProbability(), Blast_FindDustFilterLoc(), Blast_FindRepeatFilterLoc(), Blast_FreqRatioToScore(), BLAST_GappedAlignmentWithTraceback(), BLAST_GetAllTranslations(), BLAST_GetAlphaBeta(), Blast_GetCompositionRange(), BLAST_GetGappedScore(), Blast_GetJointProbsForMatrix(), BLAST_GetProteinGapExistenceExtendParams(), Blast_GetRelativeEntropy(), BLAST_GetStandardAaProbabilities(), Blast_HitListMerge(), Blast_HSPListGetEvalues(), Blast_HSPListPurgeHSPsWithCommonEndpoints(), Blast_HSPListSubjectBestHit(), Blast_HSPResultsApplyMasklevel(), Blast_HSPStreamResultBatchReset(), Blast_Int4MatrixFromFreq(), Blast_KarlinBlkNuclGappedCalc(), Blast_KarlinLambdaNR(), BLAST_Log1p(), Blast_MappingResultsFree(), Blast_MaskUnsupportedAA(), BLAST_Matrix::BLAST_Matrix(), Blast_MatrixEntropy(), Blast_MatrixInfoNew(), Blast_PrelimEditBlockToGapEditScript(), Blast_ReadAaComposition(), Blast_RedoAlignmentCore_MT(), BLAST_RombergIntegrate(), Blast_SemiGappedAlign(), BLAST_SetupPartialFetching(), Blast_TargetFreqEntropy(), BlastAaLookupFinalize(), BlastAaLookupTableNew(), BlastBuildSearchResultSet(), BlastCompo_EarlyTermination(), BlastCompressBlastnaSequence(), BlastCompressedAaLookupTableDestruct(), BlastCompressedAaLookupTableNew(), BlastEffectiveLengthsOptions_IsSearchSpaceSet(), BlastHitList2SeqAlign_OMF(), BlastHSPCBSStreamClose(), BlastHSPStreamBatchRead(), BlastHSPStreamClose(), BlastHSPStreamMerge(), BlastInitialWordParametersNew(), BlastKarlinLHtoK(), BlastKmerBreakUpSequence(), BlastKmerGetCompressedTranslationTable(), BlastKmerGetKmerSet(), BlastKmerGetKmerSet2(), BlastKmerGetKmerSetStats(), BlastKmerVerifyIndex(), BlastNaExtendJumper(), BlastNaHashLookupTableNew(), BLASTPrelminSearchHitListToStdSeg(), BlastQueryInfoGetEffSearchSpace(), BlastQueryInfoNew(), BlastQueryInfoSetEffSearchSpace(), BlastRPSScanSubject(), BlastScoreBlkNucleotideMatrixRead(), BlastScoreBlkProteinMatrixLoad(), BlastScoringOptionsSetMatrix(), BlastSeqLocCombine(), BlastSeqLocListReverse(), BlastSeqSrcSetRangesArgBuild(), BlastSparseUint1ArrayNew(), blk_bind(), CSimpleBlobStore::BlobDescriptor(), block_cipher_df(), bm::block_init_digest0(), bm::block_ptr_array_range(), bm::block_to_global_index(), BlockBitEraseTest(), BlockBitInsertTest(), BlockIntersector::BlockIntersector(), BlockLevelTest(), BlockModel::blockMatch(), BlockModel::BlockModel(), blowfish_dec(), blowfish_enc(), bNNI(), BOOST_AUTO_TEST_CASE(), BOOST_AUTO_TEST_SUITE_END(), BOOST_FIXTURE_TEST_CASE(), CGridCellWrapStringRenderer::BreakLines(), bsPutUChar(), bsPutUInt32(), buffer_add_row(), buffer_delete_rows(), buffer_free(), buffer_row2idx(), buffer_transfer_bound_data(), CSeqDictionaryBuilder< Alphabet >::Build(), CBuildAlnVecJob::Build(), CHitClustering::Build(), bm::build_jaccard_similarity_batch(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::build_octet_remap(), bm::sv_serialization_plan_builder< SV >::build_plan(), bm::sparse_vector_serializer< SV >::build_plane_digest(), bm::bvector< Alloc >::build_rs_index(), buildAveragesTable(), BuildBigGoodNucProtSet(), BuildBlastAncillaryData(), TKmerMethods< TKmerCounts >::BuildCompressedTranslation(), WSDLParser::BuildDataTree(), BuildGoodEcoSetWithAlign(), CProjectTreeBuilder::BuildOneProjectTree(), CAlnMixSequences::BuildRows(), BuildSmallGenomeSet(), CStringUtil::BuildString(), CAlignFormatUtil::BuildUserUrl(), BvectorBitForEachTest(), BvectorBulkSetTest(), BvectorInsertTest(), BvectorShiftTest(), BVImportTest(), bwfi(), CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl(), BytesToUint8(), BZ2_blockSort(), BZ2_decompress(), BZ2_hbAssignCodes(), BZ2_hbCreateDecodeTables(), BZ2_hbMakeCodeLengths(), CAA::CAA(), CAbortBlocker::CAbortBlocker(), bm::aggregator< BV >::cache_gap_block(), CachedTaxonomyLookupCommand(), CSeqAnnotFromFasta::CacheSequences(), bm::blocks_manager< Alloc >::calc_arena_stat(), bm::calc_block_digest0(), bm::basic_bmatrix< BV >::calc_effective_rows_not_null(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::calc_octet_stat(), bm::blocks_manager< Alloc >::calc_serialization_null_full(), bm::compressed_buffer_collection< BV >::calc_stat(), bm::bvector< Alloc >::calc_stat(), bm::basic_bmatrix< BV >::calc_stat(), CalcBeginMask(), CLadder::CalcDelta(), variation::CalcEffectForProt(), CalcEndMask(), CGraphUtils::CalcGraphLevels(), ColumnResidueProfile::calcInformationContent(), CClassTypeInfoBase::CalcMayContainType(), CalcMD5(), CSearch< LEGACY, NHITS >::CalcModIndex(), CMSSpectrumMatch::CalcNormalTopHit(), DM_BlastScore::CalcPairwiseScoresOnTheFly(), CMSSpectrumMatch::CalcPoisson(), CMSSpectrumMatch::CalcPoissonMean(), CMSSpectrumMatch::CalcPoissonTopHit(), CMSSpectrumMatch::CalcPvalue(), CMSSpectrumMatch::CalcPvalueTopHit(), CCompositeTextItem::CalcSize(), variation::CalcSOTermsForProt(), CDepthCollection::CalcStats(), bm::similarity_batch< SDESCR >::calculate(), alp_sim::calculate_C(), alp_sim::calculate_FSC(), CUpdateSeq_Input::CalculateAlignmentForUnitTest(), CalculateContactScore(), CChain::CalculateDropLimits(), CScatterGraph::CalculateLimits(), CHTML_table::CalculateNumberOfColumns(), CalculatePSSMScore(), ResidueProfiles::calculateRowWeights(), CQualityScoringMethod::CalculateScores(), CSimpleScoringMethod::CalculateScores(), CSNPScoringMethod::CalculateScores(), CMatrixScoringMethod::CalculateScores(), CNonSynonymousScoringMethod::CalculateScores(), Threader::CalculateScores(), CTestSeqBasedMethod::CalculateScores(), CColorTableMethod::CalculateScores(), CChainer::CChainerImpl::CalculateSpliceWeights(), CChain::CalculateSupportAndWeightFromMembers(), CAlignCommon::CAlignCommon(), CAlignInfo::CAlignInfo(), CAlignMap::CAlignMap(), CAlignModel::CAlignModel(), CAlignShadow::CAlignShadow(), CAlignStrandSorter::CAlignStrandSorter(), callout(), python::CCursor::callproc(), CContigAssembly::CAlnStats::CAlnStats(), CAmbigDataBuilder::CAmbigDataBuilder(), CAssignColumnValueDlg::CanAssignColumn(), CCassQueryList::Cancel(), CSchedulerEngine::CancelJob(), CCopyColumnDlg::CanCopyColumn(), CTypesIteratorBase< Parent >::CanEnter(), CSeqMap::CanResolveRange(), CTypesIteratorBase< Parent >::CanSelect(), CArg_DateTime::CArg_DateTime(), carry64(), CAssemblyObjectLoader::CAssemblyObjectLoader(), CBBox< 3 >::CBBox(), CBlastAncillaryData::CBlastAncillaryData(), CBlastDB_SeqFormatter::CBlastDB_SeqFormatter(), CBlastDbBioseqSource::CBlastDbBioseqSource(), CBlastDbFormatter::CBlastDbFormatter(), CBLASTParams::CBLASTParams(), CBlastTabular::CBlastTabular(), CBoundaryShapeRectBase::CBoundaryShapeRectBase(), CBoyerMooreMatcher::CBoyerMooreMatcher(), CBucketPool< Value, Lock, RPool >::CBucketPool(), CChain::CChain(), CCloneConcordancySorter::CCloneConcordancySorter(), CClusterDBSource::CClusterDBSource(), ccm_auth_crypt(), CCoil_ComputeScores(), CCompartOptions::CCompartOptions(), python::CConnection::CConnection(), CContextTranslator::CContextTranslator(), CDB_Bit::CDB_Bit(), DeBruijn::CDBGraph::CDBGraph(), CDbvarClinicalAsstSorter::CDbvarClinicalAsstSorter(), CDbvarPilotSorter::CDbvarPilotSorter(), CDbvarQualitySorter::CDbvarQualitySorter(), CDbvarSamplesetTypeSorter::CDbvarSamplesetTypeSorter(), CDbvarValidationSorter::CDbvarValidationSorter(), CddIdString(), CDDSplashDialog::CDDSplashDialog(), CDiagHit::CDiagHit(), CDisambiguator::CDisambiguator(), CDocsumTableModel::CDocsumTableModel(), CEditScript::CEditScript(), CEndpointKey::CEndpointKey(), pythonpp::CEngine::CEngine(), StructureSet::CenterViewOnAlignedResidues(), StructureSet::CenterViewOnStructure(), CExonParameters::CExonParameters(), CFillTypes::CFillTypes(), CFindGapIntronRow::CFindGapIntronRow(), CFlatFileSeqIterator::CFlatFileSeqIterator(), CGen_code_table_imp::CGen_code_table_imp(), CGeneralScoreMatrix::CGeneralScoreMatrix(), CFactory< Type >::CgiFactory(), CGlDrawScale::CGlDrawScale(), CGRCStatusSorter::CGRCStatusSorter(), CGrowableListCtrl::CGrowableListCtrl(), chacha20_block(), CExonSelectorApplication::ChainExons(), ChangeCountryColonToComma(), CCountries::ChangeExtraColonsToCommas(), CSeqTable_multi_data::ChangeToBit(), CSeqTable_multi_data::ChangeToBit_bvector(), variation::CVariationUtil::ChangeToDelins(), variation_ref::CVariationUtil::ChangeToDelins(), CDiagFilter::Check(), bm::blocks_manager< Alloc >::check_allocate_block(), check_attr_ard(), check_attr_ird(), check_escape(), alp_sim::check_K_criterion(), alp_sim::check_K_criterion_during_killing(), check_mix_pages_range(), bm::bvector< Alloc >::check_or_next(), bm::check_pair_vect_vbr(), compile_time_bits::bitset_traits< _Ty, _Size, u_type >::check_range(), Check_SimModel(), CheckAccession(), CheckAdjacentSpliceSites(), CCustomTree::CheckAll(), CAlignCollapser::CheckAndInsert(), CheckBioseqEndsForNAndGap(), CheckBitList(), CheckBV_AND_OR(), CStickyTooltipHandler::checkChildFocus(), CChainer::CChainerImpl::CheckCompatibility(), CheckCompressedDecode(), CheckCountGapRange(), Splines::checkCubicSplineMonotonicity(), CheckDupEntries(), CheckDuplicates(), CheckErrors(), CheckForBadLocalIdChars(), CheckForEmptySequences(), CheckForFreqRatioFile(), CPrimerTableCommandConverter::CheckForMixedValues(), SPSG_BlobReader::CheckForNewChunks(), CStickyTooltipHandler::CheckForNewTip(), CGLFrameBuffer::checkFramebufferAvailability(), CheckGAPMin(), CheckGTSearch(), rapidjson::internal::Schema< SchemaDocumentType >::CheckInt(), CheckLineType(), CDataTypeModule::CheckNames(), CBDB_BufferManager::CheckNullConstraint(), CIndexedDb_Old::CheckOid(), CheckPrintPubProblems(), CheckQualsInSourceFeat(), CheckRangeDeserial(), CBarcodeTool::CheckRow(), CheckSeqIdInDD(), CheckSourceFeatCoverage(), CheckSourceFeatLocAccs(), CSourceRequirements::CheckSourceQuals(), CheckSparseVectorFilter(), CheckSparseVectorGather(), CheckSparseVectorGatherRandom(), CheckSparseVectorRange(), COligoSpecificityCheck::CheckSpecificity(), CheckSpliceSite(), CheckSTRAND(), CheckStrSVCompare(), CheckTPG(), rapidjson::internal::Schema< SchemaDocumentType >::CheckUint(), CChoiceDataType::CheckValue(), CRealDataType::CheckValue(), CUniSequenceDataType::CheckValue(), ChemicalGraph::ChemicalGraph(), CHitGlyph::CHitGlyph(), CRemoveSequencesDlg::ChooseSequence(), chooseSettings(), CHTML_br::CHTML_br(), CAlnMapPrinter::Chunks(), CIgAnnotation::CIgAnnotation(), CIgAnnotationInfo::CIgAnnotationInfo(), CCigar::CigarString(), CIndexedDb_New::CIndexedDb_New(), CIndexedDb_Old::CIndexedDb_Old(), CIntronParameters::CIntronParameters(), CEUtilsUpdaterBase::CitMatch(), CJobStatusTracker::CJobStatusTracker(), CkCdRegion(), CkLocusLinePos(), CkQualMatchToken(), CkSegmentSet(), CLadder::CLadder(), CClassTypeInfoBase::ClassesById(), CClassTypeInfoBase::ClassesByName(), CDataType::ClassName(), CLatLonCountryMap::CLatLonCountryMap(), CAlignCollapser::CleanSelfTranscript(), CFileLoadManager::CleanUI(), CSeedRoots::CleanUp(), CGb_qual::CleanupAndRepairInference(), CleanupSeparators(), bitvec< unsigned int >::clear(), CSpatialHash2D< std::vector< int > >::Clear(), CCustomTree::Clear(), CAlignSeqTableModel::Clear(), CHitClustering::Clear(), CGroupMapWidget::Clear(), mpmc_bounded_queue_w< size_t, kNotifyQueueLen >::clear(), DynProgProb::clear(), CMatrix3< T >::Clear(), CMatrix4< T >::Clear(), pythonpp::CDictHelper< T >::clear(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::clear_all(), bm::basic_bmatrix< BV >::clear_column(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::clear_range(), bm::bvector< Alloc >::clear_range_no_check(), CGlModel2D::ClearAll(), ClearAllTest(), CGlModel2D::ClearArrays(), CLadder::ClearHits(), CAlignInfo::ClearIIC(), CFindGapIntronRow::ClearIIC(), CStatement::ClearParamList(), OpenGLRenderer::ClearTransparentSpheresForList(), CleaveOffByTail(), CBarcodeTool::ClickLink(), CAlignCollapser::ClipESTorSR(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), pythonpp::CList::CList(), TFileSet< base_stream, eFiles, _options... >::Clone(), bm::blocks_manager< Alloc >::clone_assign_block(), bm::blocks_manager< Alloc >::clone_gap_block(), CWriteDB_Impl::Close(), CWindowManager::CloseClients(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::CloseVolumes(), CLorentz::ClosingScore(), CAlnVecPrinter::ClustalStyle(), CMatrix3< T >::CMatrix3(), CMatrix4< T >::CMatrix4(), CMC3_CodingRegion< order >::CMC3_CodingRegion(), CNcbiApplogApp::Cmd_Generate(), CArrayString< PREFIX >::Cmp(), CWriteDB_LMDB::SKeyValuePair::cmp_key(), cmp_labels(), CMsvcPrjProjectContext::CMsvcPrjProjectContext(), CNcbi2naRandomizer::CNcbi2naRandomizer(), CNcbiTable< TValue, TRow, TColumn >::CNcbiTable(), CNetBlastSubmittingJob::CNetBlastSubmittingJob(), CNonSynonymousScoringMethod::CNonSynonymousScoringMethod(), CObjectStack::CObjectStack(), CGen_code_table::CodonToIndex(), COffsetData_Factory::COffsetData_Factory(), CFeaturesGroup::CollapseAll(), CSequenceGroup::CollapseAll(), CPhyloTreeDataSource::CollapseByDistance(), CPhyloTreeDataSource::CollapseSelected(), CAlignCollapser::CollapsIdentical(), CRegExFSA::Collect(), CCustomTree::CollectAll(), CNCMMStats::CollectAllStats(), CDataTypeModule::CollectAllTypeinfo(), CFileModules::CollectAllTypeinfo(), CFileSet::CollectAllTypeinfo(), CollectAttributes(), CBioseqEditorFactory::CollectBioseqEditorCommands(), WSDLParser::CollectDataObjects(), CollectDllsDepends(), SBamIndexRefIndex::CollectEstimatedCoverage(), CFeatGapInfo::CollectGaps(), CEditSequenceEnds::CollectLabels(), CRemoveSequencesDlg::CollectLabels(), CRBSubpanel::CollectLabels(), CAlnVec::CollectNucleotideFrequences(), CollectNucleotideFrequences(), CBlobSplitterImpl::CollectPieces(), CAlnVec::CollectProteinFrequences(), CollectProteinFrequences(), CollectSubNames(), CSrvStat::CollectThreads(), CNCStat::CollectThreads(), CChain::CollectTrustedmRNAsProts(), CSimpleMakeFileContents::CollectValues(), CCustomTree::CollectVisible(), CwxTableListCtrl::ColumnHiddenToIndex(), CwxTableListCtrl::ColumnIndexToHidden(), CwxTableListCtrl::ColumnIndexToVisible(), CwxTableListCtrl::ColumnVisibleToIndex(), CTableImportListCtrl::ColumnWidthsUpdated(), TSearchMessages::Combine(), CSRSearch::combine(), bm::aggregator< BV >::combine_and(), bm::aggregator< BV >::combine_and_horizontal(), bm::aggregator< BV >::combine_and_sub(), bm::aggregator< BV >::combine_and_sub_horizontal(), bm::bvector< Alloc >::combine_operation(), bm::bvector< Alloc >::combine_operation_and(), bm::bvector< Alloc >::combine_operation_block_and(), bm::bvector< Alloc >::combine_operation_block_and_or(), bm::bvector< Alloc >::combine_operation_block_or(), bm::bvector< Alloc >::combine_operation_block_sub(), bm::bvector< Alloc >::combine_operation_block_xor(), bm::bvector< Alloc >::combine_operation_or(), bm::bvector< Alloc >::combine_operation_sub(), bm::bvector< Alloc >::combine_operation_xor(), bm::aggregator< BV >::combine_or(), bm::aggregator< BV >::combine_or_horizontal(), bm::aggregator< BV >::combine_shift_right_and(), CAlignRangeCollection< CAlignRange< TSeqPos > >::CombineAbutting(), CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::CombineAbutting(), SrcEditDialog::CombineColumns(), CombineColumns(), CChainer::CChainerImpl::CombineCompatibleChains(), CFixForTransSplicing::CombineFeatures(), bm::sv_sample_index< SV >::common_prefix_length(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::common_prefix_length(), NStr::CommonPrefixSize(), NStr::CommonSuffixSize(), CDense_seg::Compact(), CBDB_RawFile::CompactEx(), CPhyloCSFData::CompactFullScores(), CMSPeak::Compare(), CMSMatchedPeakSet::Compare(), rapidjson::internal::BigInteger::Compare(), bm::bvector< Alloc >::compare(), bm::bvector_mini< A >::compare(), CBDB_BufferManager::Compare(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::compare(), compile_time_bits::Compare(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::compare_nomap(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::compare_remap(), bm::bvector< >::iterator_base::compare_state(), bm::sparse_vector_scanner< SV, S_FACTOR >::compare_str(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::compare_str(), compare_SV_set_ref(), CompareAccsV(), CMultiAlignerTest::CompareDomainHits(), CAnnotCompare::CompareFeats(), CompareMiniSet(), compile_time_bits::CompareNocase(), CDiscrepancyContext::CompareRefs(), SeqTree::compareSequenceCompositions(), CMSPeak::CompareSortedRank(), CompareSparseVector(), CompareStrSparseVector(), CMSPeak::CompareTop(), CompareValLists(), ComparisonTest(), CExonSelectorApplication::CompatiblePair(), CCompactSAMApplication::CompatiblePair(), compile_branch(), bm::aggregator< BV >::pipeline< Opt >::complete(), CTL_Connection::CompleteBlobDescriptors(), BlockModel::completeModelExtendsIntoUnallowedGappedRegion(), CCgiStatistics::Compose_Entries(), ComposeInto(), dtl::Diff< elem, vector< elem >, Compare< elem > >::composeUnifiedHunks(), bm::rank_compressor< BV >::compress(), compress(), bm::rank_compressor< BV >::compress_by_source(), CId2Compressor::CompressChunk(), CompressNcbi2na(), CSequence::CompressSequences(), bm::compute_h64_mask(), bm::compute_s_block_descr(), bm::xor_scanner< BV >::compute_xor_complexity_descr(), CBDB_BufferManager::ComputeBufferSize(), CClusterer::ComputeClusters(), CClusterer::ComputeClustersFromLinks(), TKmerMethods< TKmerCounts >::ComputeDistLinks(), TKmerMethods< TKmerCounts >::ComputeDistMatrix(), CEntropyCalculator::ComputeEntropy(), CPhyloTreeDataSource::ComputeLengthsFromRoot(), CDistances::ComputeMatrix(), ComputeNormalizedProteinEntropy(), CDUpdater::ComputePercentIdentity(), ComputeScoresFromProbs(), CBoundaryShapeRectBase::ComputeShape(), CBoundaryShapeRectBase::ComputeShapeWithLabels(), CBoundaryShapeTri::ComputeShapeWithLabels(), CEntropyCalculator::ComputeSlidingWindowEntropy(), ComputeTableIndex(), NJ_TreeAlgorithm::ComputeTree(), SLC_TreeAlgorithm::ComputeTree(), ConfigureLogging(), CONN_ReadLine(), IPhyloTreeRender::CProjectionExtents::ConsolidateExtents(), CBDB_BufferManager::Construct(), bm::sv_sample_index< SV >::construct(), OpenGLRenderer::ConstructLogo(), CComponentSearchForm::ConstructQuery(), CCpgSearchForm::ConstructQuery(), CFeatureSearchForm::ConstructQuery(), COrfSearchForm::ConstructQuery(), CSequenceSearchForm::ConstructQuery(), CVcfSearchForm::ConstructQuery(), BlockModel::contain(), CClipboard::Contains(), CLadder::Contains(), CGeneModel::Continuous(), CColorPanel::ContrastBG(), CColorPanel::ContrastFG(), gap_vector::control(), Convert(), CConvertImpToRNA::Convert(), CConvertImpToGene::Convert(), CArrayHolder::Convert(), convert_1_to_2(), convert_1_to_4(), convert_datetime2server(), bm::blocks_manager< Alloc >::convert_gap2bitset(), Convert_GC_Assembly_Seq_loc_TopLevel(), convert_to_upper(), CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), RowSourceTable::convertFromCDRows(), CCdsToMatPeptide::ConvertInner(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CPepXML::ConvertModifications(), CPepXML::ConvertModSetting(), NMacroUtil::ConvertMultiSpaces(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), ConvertPSSMToBLASTMatrix(), DMAlignedOptimalScore::convertScoreToDistance(), CSeq_loc_Conversion::ConvertSimpleMix(), CUnculTaxTool::ConvertSpeciesSpecificNote(), RowSourceTable::convertToCDRows(), CDirEntry::ConvertToOSPath(), ConvertToPairwise(), CTableImportDataSource::ConvertToSeqAnnot(), bm::blocks_manager< Alloc >::copy(), Vector< T >::copy(), copy(), LocalMaxStatMatrix::copy(), Matrix< T >::copy(), DynProgProb::copy(), bm::blocks_manager< Alloc >::copy_bit_block(), copy_data_to_host_var(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::copy_from(), bm::basic_bmatrix< BV >::copy_from(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::copy_from(), bm::blocks_manager< Alloc >::copy_to_arena(), CDemoHook::CopyChoiceVariant(), CDemoHook::CopyClassMember(), CObjectOStream::CopyClassRandom(), CObjectOStream::CopyClassSequential(), ViewerBase::CopyDataFromStack(), CMacroFlowEditor::CopyDefaultLibrary(), CBDB_BufferManager::CopyFieldsFrom(), CopyResult(), CdPssmInput::copyRow(), MultipleAlignment::copyRowSource(), CObjectOStreamAsnBinary::CopyString(), CObjectOStreamXml::CopyStringStore(), CObjectOStreamAsnBinary::CopyStringValue(), alp_reg::correction_of_errors(), CorrectWindowRect(), bm::bvector< Alloc >::count(), bm::rs_index< BVAlloc >::count(), bm::count_nz(), bm::bvector< Alloc >::count_to(), bm::bvector< Alloc >::count_to_test(), CMSPeak::CountAAIntervals(), CAnnotPieces::CountAnnotObjects(), SChunkInfo::CountAnnotObjects(), SrcEditDialog::CountColumnRowConflicts(), CountColumnRowConflicts(), CBinaryKmerCounts::CountCommonKmers(), CModelCompare::CountCommonSplices(), CMSHit::CountHits(), CMSHit::CountHitsByType(), CMSHit::CountMods(), CSearch< LEGACY, NHITS >::CountModSites(), CNucProp::CountNmers(), CSeqAnnotFromFasta::CountNonAlphaToPositions(), CountRangeTest(), CdPssmInput::countResiduesInRow(), CAgpErrEx::CountTotals(), CountWords(), CPager::CPager(), cpal(), CParse::CParse(), cpll(), CPrefetchSequence::CPrefetchSequence(), CPrintTaxFields::CPrintTaxFields(), cprl(), CProSplignTrimmer::CProSplignTrimmer(), CPSeq::CPSeq(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPssmInputGapsInQuery::CPssmInputGapsInQuery(), CPssmInputWithSingleCD::CPssmInputWithSingleCD(), CPssmInputWithTwoCDs::CPssmInputWithTwoCDs(), CQueryDataPerChunk::CQueryDataPerChunk(), CQueryExec::CQueryExec(), CRawSeqDBSource::CRawSeqDBSource(), CAlignRowGraphCont::Create(), CSeqMaskerIstatFactory::create(), CFeatureSeqTableColumnBaseFactory::Create(), CMakeDbPosMatrix::Create(), CSubjectsSequenceCoverage::Create(), SNcbiApplogKeywordsInit::Create(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), create_tables(), CAlnMap::CreateAlignFromRange(), CreateAlignRow(), CreateAlignSetFromAnchoredAln(), CreateAlignSetFromPairwiseAln(), CreateAnchoredAlnFromAln(), CArgDescriptions::CreateArgs(), CMSModSpecSet::CreateArrays(), StyleManager::CreateASNStyleDictionary(), ColumnarVcfCache::CreateBlob(), CHttpFormData::CreateBoundary(), CSeqMaskerOstatOpt::createCacheBitArray(), CSelectDescription::CreateComponent(), CAlnVec::CreateConsensus(), CAlnVecMultiDataSource::CreateConsensus(), CRunToolDlg::CreateControls(), CAddLinkageToGaps::CreateControls(), CAdjustFeaturesForGaps::CreateControls(), CApplyGCode::CreateControls(), CBulkMolinfoEditDlg::CreateControls(), CCorrectIntervalOrder::CreateControls(), CFarPointerSeq::CreateControls(), CMolInfoEditDlg::CreateControls(), CRawSeqToDeltaSeqByLoc::CreateControls(), CRemoveDescDlg::CreateControls(), CRemoveFeaturesDlg::CreateControls(), CRemoveGeneXrefs::CreateControls(), CRemoveSeqFromAlignDlg::CreateControls(), CReorderSequencesDlg::CreateControls(), CRevCompSequencesDlg::CreateControls(), CRNANamePanel::CreateControls(), CSeqIdFixDlg::CreateControls(), SrcEditDialog::CreateControls(), CSuppressGenes::CreateControls(), CAddSuspectProductRule::CreateControls(), CScoringMethodsDlg::CreateControls(), CAlignmentAssistant::CreateControls(), CGBQualPanel::CreateControls(), CISOJTALookupDlg::CreateControls(), CNonAsciiCharacterReplacement::CreateControls(), CNonAsciiReplacementPanel::CreateControls(), CRawSeqToDeltaByNPanel::CreateControls(), CColorPanel::CreateControls(), CBondPanel::CreateControls(), CMolInfoPanel::CreateControls(), CSitePanel::CreateControls(), CAssignColumnValueDlg::CreateControls(), CCopyColumnDlg::CreateControls(), CSelectSequenceDlg::CreateControls(), CDescTypeSubpanel::CreateControlsMiddle(), CJniUtil::CreateCStyleArgs(), CRealDataType::CreateDefault(), CSeq_align::CreateDensegFromStdseg(), CreateDllBuildTree(), DTDParser::CreateEmbeddedName(), DTDElement::CreateEmbeddedName(), CProjBulderApp::CreateFeaturesAndPackagesFiles(), SRemoteApp::SRequest::CreateFilesNode(), CProjectItemsTree::CreateFrom(), AlignmentSet::CreateFromMultiple(), Threader::CreateGibScd(), CAutoDef::CreateIDOptions(), CSeqUtils::CreateIdStr(), CLadder::CreateLadder(), CLadderContainer::CreateLadderArrays(), CMSMatchedPeakSet::CreateMatchedPeakSet(), CreateMimeFromBiostruc(), CSequence::CreateMsa(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), CreateNewPairwiseAlignmentsByBlockExtension(), CreateObjectLocation(), CPhrap_Seq::CreatePadsFeat(), CPrintSetupDlg::CreatePaperTypeChoice(), rapidjson::internal::Schema< SchemaDocumentType >::CreateParallelValidator(), CDir::CreatePath(), Threader::CreateQrySeq(), Threader::CreateRcxPtl(), CDirEntry::CreateRelativePath(), CAlnMultiModel::CreateRows(), rapidjson::GenericSchemaDocument< ValueT, Allocator >::CreateSchemaRecursive(), rapidjson::internal::Schema< SchemaDocumentType >::CreateSchemaValidators(), CSeqMap::CreateSeqMapForSeq_loc(), CreateSparseAlign(), CPageList::CreateSubNodes(), CPagerView::CreateSubNodes(), CDbapiCursorApp::CreateTable(), CHTMLPage::CreateTemplate(), CNCMMSizePool_Getter::CreateTlsObject(), CAsnViewContext::CreateTooltipWindow(), CChoiceDataType::CreateTypeInfo(), CHelloReplyCommand::CreateView(), CEditObjectSeq_feat::CreateWindowImpl(), CResultSetMetaData::CResultSetMetaData(), CReverseAndComplement< T >::CReverseAndComplement(), CRgbaColor::CRgbaColor(), cs_locale(), CSearch_Base< LEGACY, NHITS, derived_t >::CSearch_Base(), CDbIndex::CSearchResults::CSearchResults(), CSearchResultSet::CSearchResultSet(), CSelection::CSelection(), CSeqDBLMDBEntry::CSeqDBLMDBEntry(), CSeqDBLMDBSet::CSeqDBLMDBSet(), CSeqDBVolSet::CSeqDBVolSet(), CSeqDictionaryBuilder< Alphabet >::CSeqDictionaryBuilder(), CSeqFormatter::CSeqFormatter(), CSeqMaskerIstatAscii::CSeqMaskerIstatAscii(), CSeqMaskerIstatOAscii::CSeqMaskerIstatOAscii(), CSeqScores::CSeqScores(), CSeqTextFontList::CSeqTextFontList(), CSimpleBlobStore::CSimpleBlobStore(), CSimpleGiList::CSimpleGiList(), CSnpBitfield2::CSnpBitfield2(), CSNPDb_Impl::CSNPDb_Impl(), CSortedSeq_ids::CSortedSeq_ids(), CSubjectMap::CSubjectMap(), CSubstMatrix::CSubstMatrix(), CSymDustMasker::CSymDustMasker(), ct_compute_info(), ct_options(), ct_param(), ct_res_info(), CTaxNRCriteria::CTaxNRCriteria(), CTL_RowResult::CTL_RowResult(), ctr_drbg_update_internal(), CTrackingEnvHolder::CTrackingEnvHolder(), CTranslationTable::CTranslationTable(), CTreeWMClient::CTreeWMClient(), pythonpp::CTuple::CTuple(), Splines::cubicRoots(), CGeneModel::CutExons(), CPaintSequence::CutSelection(), CVdbFastaExtractor::CVdbFastaExtractor(), CSeqportUtil_implementation::CWrapper_2D< T >::CWrapper_2D(), CWriteDB_CreateAliasFile(), CWriteDB_CreateOidMaskDB(), CwxGridTableAdapter::CwxGridTableAdapter(), cxei(), CTextPanel::DataLoaded(), CItemsInfo::DataSpec(), CTime::DayOfWeekNameToNum(), dbacolptr(), dbbylist(), dbclose(), dbcolinfo(), dbconvert_ps(), dbexit(), DBLB_GetServer(), DBLB_StatusStr(), dblib_add_connection(), dblib_del_connection(), dbnextrow_pivoted(), dbnumalts(), dbperror(), dbpivot(), dbprhead(), dbprrow(), dbsafestr(), dbsetmaxprocs(), dbsetopt(), dbsettime(), dbspr1row(), dbsprhead(), dbsprline(), dbstring_getchar(), AMatrix_base::DeAllocate(), NtlookupTestFixture::debruijnInit(), debug_print_pk(), CBlastQueryInfo::DebugDump(), CBlastEffectiveLengthsOptions::DebugDump(), CSeqDBAliasFile::DebugDump(), bm::rsc_sparse_vector< Val, SV >::decode(), bm::deserializer< BV, DEC >::decode_arr_sblock(), bm::rsc_sparse_vector< Val, SV >::decode_buf(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::decode_substr(), decodeNewickSubtree(), CGlFeedbackFont::DecodeText(), DecodeXml(), bm::rank_compressor< BV >::decompress(), CScriptPanel::DecreaseFont(), mu::ParserBase::DefineOprt(), CHTML_area::DefinePolygon(), BlockModelPair::degap(), ConsensusMaker::degapAlignment(), CMakeDbPosMatrix::Delete(), alp_data::delete_memory_for_matrix(), CHMMParameters::SDetails::DeleteAllCreatedModels(), DeleteElements(), DeleteFields(), CNetBLASTUIDataSource::DeleteJobDescriptors(), UngappedAlignedBlock::DeleteRow(), UnalignedBlock::DeleteRow(), CLocationListCtrl::DeleteRow(), CScriptPanel::DeleteSelected(), CNCMMSizePool_Getter::DeleteTlsObject(), CSearch< LEGACY, NHITS >::DeleteVariableOverlap(), DelSegnum(), bm::blocks_manager< Alloc >::deoptimize_block(), bm::blocks_manager< Alloc >::deoptimize_block_no_check(), CDockLayoutTree::CNode::DepthFirstForEach(), CDockLayoutTree::CNode::DepthFirstSearch(), des3_set2key(), des3_set3key(), desc_alloc_records(), desc_copy(), desc_free_records(), DescribeSAMOutputFormatSpecifiers(), DescribeTabularOutputFormatSpecifiers(), TaxTreeData::deselectAllTaxNodes(), bm::compressed_collection_deserializer< CBC >::deserialize(), CBDB_ExtBlobMap::Deserialize(), CBDB_BlobMetaContainer::Deserialize(), CSegmentSmearGlyph::CSegMap::Deserialize(), bm::sparse_vector_deserializer< SV >::deserialize_planes(), bm::sparse_vector_deserializer< SV >::deserialize_structure(), DesrializationTest2(), CAlignRowGraphCont::Destroy(), bm::blocks_manager< Alloc >::destroy_tree(), DetailedCheckCompressedDecode(), DetailedCheckVectors(), CCigar::DetailedCigarString(), DetailedCompareSparseVectors(), CDataLoader::DetailsToChoice(), CWGSDb_Impl::DetermineFeatLocIdType(), CSeqAnnotFromFasta::DetermineMasterIndex(), CNcbiMatrix< T >::Diagonal(), CDiffText::Diff(), rapidjson::internal::BigInteger::Difference(), DirectCompareFunction(), CSeqMaskerIstatFactory::DiscoverStatType(), OpenGLRenderer::Display(), CAdjustFeaturesForGaps::DisplayGappedFeatures(), CTaxFormat::DisplayLineageReport(), CTaxFormat::DisplayOrgReport(), CDisplaySeqalign::DisplaySeqalign(), CTaxFormat::DisplayTaxonomyReport(), CCigar::Distance(), bm::distance_and_operation(), bm::distance_operation(), bm::distance_operation_any(), HitDistributor::distribute(), bm::dm_control(), DNACompressionTest(), CSampleJob::Do(), CStrTokenize< TStr, TV, TP, TCount, TReserve >::Do(), CDbIndex_Factory::do_create_1_2(), DoAnchoredScan(), COpenViewManager::DoAsyncConversion(), SAppProjectT::DoCreate(), SLibProjectT::DoCreate(), Does3primerAbutGap(), Does5primerAbutGap(), DoesPatternMatchHighlightedResidues(), CSeqMaskerOstatAscii::doFinalize(), CSeqMaskerOstatBin::doFinalize(), CSeqMaskerOstatOpt::doFinalize(), DoHighlightMotif(), CEJournalSearch::DoJournalSearch(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), CLockVectorGuard< TLockVect >::DoLock(), CSeqMasker::DoMask(), CSeqScores::DonorScore(), CEJournalSearch::DoOneESummary(), DoSocketWait(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), DoTest(), CSampleTest::DoTest(), CSuspectProductRulesEditor::DoubleClick(), DP_CreateBlockInfo(), DP_DestroyMultipleAlignmentResults(), DP_GlobalBlockAlign(), DP_GlobalBlockAlignGeneric(), dpScoreFunction(), SequenceDisplay::DraggedCell(), Residue::Draw(), CStrWithURLRenderer::Draw(), CRenderingContext::Draw3DQuad_HorzLines(), StructureBase::DrawAll(), CPaintAlignment::DrawFeatureLabels(), CPaintSequence::DrawFeatureLabels(), CPaintAlignment::DrawFeatures(), CPaintSequence::DrawFeatures(), OpenGLRenderer::DrawHalfWorm(), SequenceViewerWidget_SequenceArea::DrawLine(), CPaintSequence::DrawMismatch(), CPaintSequence::DrawOnTheFly(), OpenGLRenderer::DrawStrand(), CRenderingContext::DrawStrandIndicators(), CPaintSequence::DrawTextLine(), CPaintAlignment::DrawTextLine(), CPaintSequence::DrawTripletMismatch(), CChainer::DropAlignmentInfo(), CScriptPanel::DropMacro(), DSNDlgProc(), DTDFileNameBase(), DTDPublicModuleName(), DualResiduals(), CRCache::dump(), CBDB_FileDumper::Dump(), CSeq_id_Mapper::Dump(), CLDS2_Database::Dump(), HitDistributor::dump(), CBlastDB_SeqFormatter::DumpAll(), CBlastDB_FastaFormatter::DumpAll(), CBlastDB_BioseqFormatter::DumpAll(), CSeqFormatter::DumpAll(), CNCMMReserve::DumpChunks(), AlignmentDisplay::DumpCondensed(), IPhyloTreeRender::CExtentDimension::DumpExtent(), dumpit(), CConvGraph::DumpPath(), CGlUtils::DumpState(), CPackString::DumpStatistics(), CDumpSysInfo::DumpSystemInfo(), DumpText(), CAnnotCompareDS::DumpTextReport(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::CChainerImpl::DuplicateNotOriented(), CBDB_BufferManager::DuplicateStructureFrom(), CChainer::CChainerImpl::DuplicateUTRs(), bm::dynamic_range_clip_high(), bm::dynamic_range_clip_low(), DynamicMatrixTest(), DynamicSGenCodeNodeArrayFree(), DynamicUint4Array_AreEqual(), DynamicUint4Array_Copy(), ecp_comb_recode_core(), ecp_mod_koblitz(), ecp_mod_p255(), ecp_mod_p448(), ecp_mod_p521(), ecp_mul_comb(), ecp_mul_comb_core(), ecp_mul_mxz(), ecp_normalize_jac_many(), ecp_precompute_comb(), ecp_select_comb(), EditDistance(), CAlignMap::EditedSequence(), ElementsSum(), WSDLParser::EmbeddedElement(), EmblAscii(), EmblGetDivisionNewID(), EmblIndex(), EmblSegment(), SequenceDisplay::Empty(), CCacheDemoApp::EmptyOnOverflowDemo(), ViewerWindowBase::EnableBaseEditorMenuItems(), CExtraEncoder::Encode(), CIDs::Encode(), bm::serializer< BV >::encode_bit_interval(), CGlFeedbackFont::EncodeText(), EndAdded(), rapidjson::internal::Hasher< Encoding, Allocator >::EndArray(), COpenViewDlg::EndModal(), rapidjson::internal::Hasher< Encoding, Allocator >::EndObject(), CIndexedDb_New::EndSearchIndication(), rapidjson::internal::Schema< SchemaDocumentType >::EndValue(), CDockLayoutTree::CNode::EnforceChildOrder(), DistanceMatrix::EnforceSymmetry(), CRCache::CDataPool::ensure(), CFormatGuess::EnsureSplitLines(), CFormatGuess::EnsureStats(), Entropy(), entropy_gather_internal(), DTDParser::EnumeratedBlock(), EnumeratorTest(), CEnumParser< TEnum, TParam >::EnumToString(), mu::Test::ParserTester::EqnTest(), CDataFrame< MAX_SIZE >::Equal(), bm::compressed_collection< Value, BV >::equal(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::equal_sz(), CNamespace::EqualLevels(), CClassTypeInfo::Equals(), bm::bvector< Alloc >::erase(), bm::basic_bmatrix< BV >::erase_column(), eraseChar(), eraseInitialChar(), eraseInitialWhiteSpace(), CCdCore::EraseSequence(), CCdCore::EraseSequences(), CCdCore::EraseTheseRows(), CCdCore::EraseUID(), eraseWhiteSpace(), ErrSetLog(), jetbrains::teamcity::TeamcityMessages::escape(), SBamIndexRefIndex::EstimateDataSizeByAlnStartPos(), CScannerFunctorAND::Eval(), CScannerFunctorOR::Eval(), CTreeQueryExec::EvalNext(), rapidjson::internal::GenericRegex< Encoding, Allocator >::EvalQuantifier(), CSGQueryFunctionCompare::Evaluate(), CQueryFuncFunction::Evaluate(), CQueryFuncPromoteAndOr::Evaluate(), CQueryFuncPromoteIn::Evaluate(), CQueryFunction_BV_In_Or< BV >::Evaluate(), CBDB_Cache::EvaluateTimeLine(), ex_display_header(), ex_display_results(), SAnnotSelector::ExcludeAnnotType(), ExcludeBadExons(), SAnnotSelector::ExcludeFeatType(), CCodeGenerator::ExcludeTypes(), CMacroEngineParallel::Exec(), CCassandraFullscanRunner::Execute(), CDownwardTreeFiller::Execute(), CEventHandler::CPostQueue::ExecuteFirstRequest(), CStatement::ExecuteLast(), CMMFlusher::ExecuteSlice(), CStatRotator::ExecuteSlice(), CWriteBackControl::ExecuteSlice(), CNewFileCreator::ExecuteSlice(), CSrvListener::ExecuteSlice(), CTDQueryDataSource::ExecuteStringQuery(), CSeqDBAliasStack::Exists(), CFeaturesGroup::ExpandAll(), CSequenceGroup::ExpandAll(), CPatternStats::ExpandPattern(), bm::export_array(), ExportPNG(), CSequenceEditingEventHandler::ExportStructuredCommentsTable(), CwxTableListCtrl::ExportTableControlToCSV(), CTableImportDataSource::ExportTableParms(), CGeneModel::Extend(), CDiscrepancyContext::Extend(), ExtendCDSToStopCodon(), CSearch_Base< LEGACY, NHITS, derived_t >::ExtendLeft(), BlockExtender::extendOnePair(), CSearch_Base< LEGACY, NHITS, derived_t >::ExtendRight(), DeBruijn::CDBGraphDigger::ExtendToRightMT(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CFileSet::ExternalResolve(), bm::sparse_vector< Val, BV >::extract(), extract_error(), bm::sparse_vector< Val, BV >::extract_planes(), CIgBlastArgs::ExtractAlgorithmOptions(), CExonSelectorApplication::ExtractExonsFromSAM(), CDFamily::extractFamily(), CTableImportDataSource::ExtractFixedFields(), CIDs::ExtractID(), ExtractMetaDataStr(), ExtractObjectLocation(), CTimeLine< BV >::ExtractObjects(), BlockMultipleAlignment::ExtractRows(), CObjMgr_QueryFactory::ExtractScopes(), CAlignFormatUtil::ExtractSeqAlignForSeqList(), ExtractStatAlgoVersion(), CObjMgr_QueryFactory::ExtractUserSpecifiedMasks(), CGlTextureFont::FaceFromString(), FactorReNewtonSystem(), fallbackSimpleSort(), fallbackSort(), CDistMethods::FastMeTree(), CField_type::FeatureFieldFromCDSGeneProtField(), CTL_CursorResultExpl::Fetch(), CEFetch_Request::FetchIdList(), python::CCursor::fetchmany(), FieldIndex(), FileGetsBuf(), FileReadBuf(), bm::bvector< Alloc >::fill_alloc_digest(), bm::bv_ref_vector< BV >::fill_alloc_digest(), fill_orgref(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CRgbaGradColorTable::FillGradient(), CMSSpectrumMatch::FillMatchedPeaks(), Sequence::FillOutSeqId(), CSeqMaskerScoreMean::FillScores(), FillSets(), FillSetsIntervals(), FillSetsRandom(), FillSetsRegular(), fillSfp(), FillSparseIntervals(), FillTestBuffer(), Filter(), CAlignCollapser::FilterAlignments(), CSeqAlignFilter::FilterByAccessionType(), CEntrez2Client::FilterIds(), CChainer::CChainerImpl::FilterOutChimeras(), COrg_ref::FilterOutParts(), CChainer::CChainerImpl::FilterOutTandemOverlap(), FilterQueriesForMapping(), FilterTokenRanges(), CTrackListCtrl::FilterValues(), bm::iterator_deserializer< BV, SerialIterator >::finalize_target_vector(), CTempString::find(), CItemsInfo::Find(), TypeStringAssociator< StyleSettings::eLabelType >::Find(), CWinMaskUtil::CIdSet_TextMatch::find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), bm::bvector< Alloc >::find(), bm::rs_index< BVAlloc >::find(), bm::bv_ref_vector< BV >::find(), CMSSpectrumMatch::Find(), bm::serializer< BV >::find_bit_best_encoding(), bm::serializer< BV >::find_bit_best_encoding_l5(), bm::bv_ref_vector< BV >::find_bv(), bm::find_effective_columns(), bm::aggregator< BV >::find_effective_sub_block_size(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_eq_with_nulls_horizontal(), bm::aggregator< BV >::find_first_and_sub(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_first_eq(), bm::bvector< Alloc >::find_first_mismatch(), bm::find_first_nz(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_gt_horizontal(), bm::find_interval_end(), bm::find_interval_start(), bm::find_max_nz(), bm::blocks_manager< Alloc >::find_max_top_blocks(), bm::blocks_manager< Alloc >::find_next_nz_block(), bm::sparse_vector_scanner< SV, S_FACTOR >::find_nonzero(), bm::find_ptr(), bm::blocks_manager< Alloc >::find_real_top_blocks(), bm::bvector< Alloc >::find_reverse(), bm::rs_index< BVAlloc >::find_super_block(), alp_reg::find_tetta_general(), FindAllStops(), CChainer::CChainerImpl::FindAltsForGeneSeeds(), CSeqMaskerOstatOpt::findBestRoff(), CDllResolver::FindCandidates(), CClusterer::CSingleCluster::FindCenterElement(), CSplitter::FindChild(), CDFamily::findChildren(), CRgbaGradColorTable::FindClosestColor(), CRgbaGradColorTable::FindColor(), CWriteDB_Impl::FindColumn(), BlockExtender::findCommonExtension(), FindCompartments(), CCdCore::FindConsensusInSequenceList(), CChainer::CChainerImpl::FindContainedAlignments(), FindContentType(), CObjectIStreamJson::FindDeep(), CObjectIStreamXml::FindDeep(), CDFamily::findFamily(), FindFGapIntronNog(), CCleave::findfirst(), FindForwardOrfs(), FindGeneticCode(), CGlModel2D::FindGeomNode(), CGlModel2D::FindGeomObject(), FindGoodParts(), findHighestScoringRowByPssm(), MoleculeIdentifier::FindIdentifier(), FindIGapIntrons(), BlockModel::findIntersectingBlocks(), BlockFormater::findIntersectingBlocks(), CStreamPathHookBase::FindItem(), CAttribMenu::FindItem(), CNetBLASTUIDataSource::FindJobDescriptor(), CSeqMatch::FindMatches(), SequenceSet::FindMatchingSequence(), CContigAssembly::FindMaxRange(), CEnumeratedTypeValues::FindName(), FindNewLocations(), CSplitCDSwithTooManyXs::FindNewLocations(), CItemsInfo::FindNextMandatory(), CPssmInputTestData::FindNonIdenticalHighScoringResidue(), FindNotNullPtrTest(), CFindPattern::FindNucNmerRepeats(), CChainer::CChainerImpl::FindOptimalChainForProtein(), impl::CCachedRowInfo::FindParamPosInternal(), CResultSetMetaData::FindParamPosInternal(), CDFamily::findParent(), MultipleAlignment::findParentalCastible(), MultipleAlignment::findParentalEquivalent(), FindPartialyCoveredQueries(), CEditSeqEndsWithAlign::FindPosition(), SeqSwapper::findReplacements(), CFeaturePropagator::FindRow(), CDUpdater::findRowsWithOldSeq(), CValidError_align::FindSegmentGaps(), CDUpdater::findSeq(), CDataSource::FindSeq_feat_Lock(), AlignmentCollection::FindSeqInterval(), SequenceTable::findSequence(), NAdapterSearch::CSimpleUngappedAligner::FindSingleBest(), variation::FindSSRLoc(), FindStartsStops(), SeqSwapper::findStructuralPendings(), DeBruijn::FindValleyAndPeak(), CEnumeratedTypeValues::FindValue(), CSimpleBlobStore::Fini(), FireAllTimers(), FixCapitalizationInElement(), CFixProductNames::FixCaps(), CSubSource::FixDateFormat(), ctll::fixed_string< N >::fixed_string(), DTDParser::FixEmbeddedNames(), FixFeatureIdsForUpdates(), COrgMod::FixHostCapitalization(), CPCRPrimerSeq::Fixi(), CSubSource::FixIsolationSourceCapitalization(), FixMixLoc(), SeqTree::fixRowNumber(), CSubSource::FixSexQualifierValue(), CSubSource::FixTissueTypeCapitalization(), FixupMouseStrain(), CObjectIStreamAsnBinary::FixVisibleChars(), FixWindowForNonAsciiText(), fkm(), fkm_output(), TestUtil::FlattenSeqAlignSet(), CImageUtil::FlipX(), AbstractLexer::FlushCommentsTo(), FNV_hash(), bm::for_each_bit(), bm::for_each_bit_block_range(), bm::for_each_block(), bm::for_each_gap_dbit(), bm::for_each_nzblock(), bm::for_each_nzblock2(), bm::for_each_nzblock_if(), bm::for_each_nzblock_range(), SAnnotSelector::ForceAnnotType(), CReadObjectList::ForgetObjects(), CWriteObjectList::ForgetObjects(), CTabularFormatter::Format(), CFlatSubmitterSeqidQVal::Format(), CFlatSubSourcePrimer::Format(), CFlatModelEvQVal::Format(), CwxIntWithFlagsFormat::Format(), FormatAsAsn(), BlockFormater::formatBlocksForQualifiedRows(), CSeqMaskerOstat::FormatMetaData(), CExonSelectorApplication::FormatPaired(), CExonSelectorApplication::FormatSingle(), FrAlign(), FrAlignFNog1(), CGeneModel::FrameShifts(), FrBackAlign(), DynProgProb::free(), Matrix< T >::free(), bm::xor_scanner< BV >::free_blocks(), bm::basic_bmatrix< BV >::free_rows(), bm::base_sparse_vector< Val, BV, 1 >::free_slice(), CBucketPool< Value, Lock, RPool >::FreeAllPools(), FreeFldMtf(), freeMatrix(), FreeRcxPtl(), FreeSeqMtf(), FreeThdTbl(), CIdDeMux< TBV, TBVFact >::FreeUnusedMem(), FreezeBlocks(), FreezeIsolatedBlocks(), FreezeTest(), FromArrayString(), CNWFormatter::SSegment::FromBuffer(), CRegistryFile::FromConfigFile(), CDistanceMatrix::FromMatrix(), CAgpRow::FromString(), CGlTextureFont::FromString(), CDockLayoutTree::CNode::FromUserObject(), CAlignMap::FShiftedLen(), fta_check_multiple_locus_tag(), fta_check_non_tpa_tsa_tls_locations(), fta_check_old_locus_tags(), fta_check_satellite(), fta_cmp_gene_syns(), fta_create_wgs_seqid(), fta_fix_last_initials(), fta_fix_seq_id(), fta_fix_seq_loc_id(), fta_get_dblink_user_object(), fta_get_gi_for_seq_id(), fta_get_orgref_byid(), fta_get_part_sup(), fta_get_project_user_object(), fta_if_wgs_acc(), fta_number_is_huge(), fta_parse_structured_comment(), fta_process_con_slice(), fta_remark_is_er(), fta_replace_org(), fta_sort_features(), fta_sort_quals(), fta_StringMatch(), fta_tls_keywords_check(), fta_tpa_keywords_check(), fta_tsa_keywords_check(), CSeqMaskerCacheBoost::full_check(), CCustomTree::FullHeight(), SPSG_StatsCounters::SReport::Func(), alp_reg::function_for_robust_regression_sum_with_cut_LSM(), alp_reg::function_for_robust_regression_sum_with_cut_LSM_beta1_is_defined(), g(), g0(), bm::serializer< BV >::gamma_gap_array(), GammaEncoderTest(), bm::gap_bit_count_unr(), bm::gap_convert_to_arr(), bm::gap_insert(), bm::operation_functions< T >::gap_op_to_bit(), bm::operation_functions< T >::gap_operation(), bm::gap_set_array(), bm::gap_shift_l1(), bm::gap_shift_r1(), GAPCheck(), GapEditScriptCombine(), CSeq_align::GapLengthRange(), GapsToDelta(), GAPTestStress(), CAgpRow::GapTypeToString(), bm::rsc_sparse_vector< Val, SV >::gather(), bm::sparse_vector< Val, BV >::gather(), GBQualSplit(), gcm_gen_table(), gcm_mult(), gen_random(), GenBankAscii(), GenBankAsciiOrig(), GenBankIndex(), generate_bvector(), generate_inter_test(), alp_sim::generate_random_permulation(), generate_serialization_test_set(), generate_sparse_bv(), generate_sparse_bvector(), generate_vect48_range(), CRegExFSA::GenerateArrayMapData(), CClassTypeStrings::GenerateClassCode(), CChoicePtrTypeStrings::GenerateClassCode(), CChoiceTypeStrings::GenerateClassCode(), CWsdlTypeStrings::GenerateClassCode(), CFileCode::GenerateCode(), CCodeGenerator::GenerateCombiningFile(), GenerateCompressedBufferCollection(), CFileCode::GenerateCPP(), CCodeGenerator::GenerateCvsignore(), DTDParser::GenerateDataTree(), CDeflineGenerator::GenerateDefline(), CCodeGenerator::GenerateDoxygenGroupDescription(), CCodeGenerator::GenerateFileList(), CFileCode::GenerateHPP(), CNcbiEncryptApp::GenerateKey(), CProjBulderApp::GenerateMsvcProjects(), generateMTFValues(), GeneratePipelineTestData(), GenerateRandomKleenVect(), GenerateShiftTestCollection(), GenerateSV(), GenerateTestCollection(), GenerateTestStrCollection(), CWsdlTypeStrings::GenerateTypeCode(), CEnumTypeStrings::GenerateTypeCode(), CProjBulderApp::GenerateUnixProjects(), CFileCode::GenerateUserCPPCode(), CFileCode::GenerateUserHPPCode(), CClassTypeStrings::GenerateUserHPPCode(), CNewCleanup_imp::GenerefBC(), rapidjson::GenericValue< rapidjson::Encoding, rapidjson::Allocator >::GenericValue(), CBlobStoreBase::GenReadQuery(), CScore_CdsInternalStops::Get(), CScore_SegPct::Get(), std::get(), CNcbiEnvironment::Get(), bm::bit_trans_grabber< T, BPC, BPS >::get(), SNgHttp2_Header< NGHTTP2_NV_FLAG_NO_COPY_NAME >::Get(), bm::sparse_vector< Val, BV >::get(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::get(), CAlignmentCollectionScore::Get(), CGlVboNode::Get2DVertexBuffer(), bm::decoder_little_endian::get_32_AND(), bm::decoder::get_32_AND(), bm::decoder_little_endian::get_32_OR(), bm::decoder::get_32_OR(), alp_sim::get_and_allocate_alp_distribution(), bm::aggregator< BV >::get_arg_block(), get_art(), get_attr_stmt(), get_auth_from_toks(), bm::bvector< Alloc >::get_bit(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_AND(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_ASSIGN(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_A(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_AND(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_OR(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_SUB_AB(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_SUB_BA(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_COUNT_XOR(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_OR(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_SUB(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::get_bit_block_XOR(), bm::blocks_manager< Alloc >::get_block(), bm::basic_bmatrix< BV >::get_block(), bm::get_block_coord(), bm::blocks_manager< Alloc >::get_block_ptr(), bm::get_block_start(), bm::random_subset< BV >::get_block_subset(), get_book(), SBaseStats::get_bytes(), SBamAlignInfo::get_cigar(), get_coll_md5(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_create_slice(), bm::rsc_sparse_vector< Val, SV >::get_create_slice(), get_date(), get_embl_pmid(), bm::bvector_mini< A >::get_first(), bm::decoder_base::get_h64(), bm::basic_bmatrix< BV >::get_half_octet(), SBaseStats::get_ints(), get_LSH_hashes2(), get_LSH_match_from_hash(), alp_data::get_memory_for_matrix(), SBaseStats::get_min_max(), alp_sim::get_minimal_simulation(), get_muid(), bm::bvector_mini< A >::get_next(), bm::sparse_vector< Val, BV >::get_no_check(), get_one_and_zeros_padding(), pvalues::get_P_error_using_splitting_method(), get_pkcs_padding(), bm::sparse_vector_serial_layout< SV >::get_plane(), bm::random_subset< BV >::get_random_array(), bm::xor_scanner< bvector_type >::get_ref_block(), alp_sim::get_root(), bm::basic_bmatrix< BV >::get_row(), bm::base_sparse_vector< Val, BV, 1 >::get_slice(), bm::rsc_sparse_vector< Val, SV >::get_slice(), bm::base_sparse_vector< Val, BV, MAX_SIZE >::get_slice_mask(), get_stacktrace(), bm::rs_index< BVAlloc >::get_super_block_count(), bm::rs_index< BVAlloc >::get_super_block_rcount(), bm::get_super_block_start(), bm::blocks_manager< Alloc >::get_topblock(), get_ucpname(), bm::sparse_vector< Val, BV >::get_unsigned(), get_zeros_and_len_padding(), get_zeros_padding(), CWGSDb_Impl::SProtAccInfo::GetAcc(), CCdCore::GetAccession(), GetAccession(), CDataLoader::GetAccVers(), CDataSource::GetAccVers(), CGBDataLoader_Native::GetAccVers(), CScope_Impl::GetAccVers(), CPSGDataLoader_Impl::GetAccVersOnce(), CSeqDBGiMask::GetAlgorithmId(), CSeqDBAliasFile::GetAliasFileValues(), GetAlignColl(), CSeq_align::GetAlignedBases(), ResidueMatrix::getAlignedPair(), GetAlignedPositions(), GetAlignedResidueIndexes(), AlignmentCollection::GetAlignedResiduesForAll(), CAlignFormatUtil::GetAlignLengths(), CAlignCommon::GetAlignment(), CCdCore::GetAlignmentAnnotationDescription(), GetAlignmentColumnsForCD(), AlignmentManager::GetAlignmentSetDependentSequences(), GetAlignParts(), CSparseMultiDataSource::GetAlignType(), CDockContainer::GetAllClients(), CPhyloTree::GetAllCollapsed(), CGlTextureFont::GetAllFaces(), CStructCommentSubpanel::GetAllLabels(), CTaxon1::GetAllNames(), CTaxon1::GetAllNamesEx(), CNAUtils::GetAllNAMetaData(), CCdCore::GetAllRowIndicesForSeqId(), AlignmentCollection::getAllRowsForCD(), AlignmentCollection::GetAllSequences(), CTaxon1::GetAllTaxIdByName(), SBamIndexRefIndex::GetAlnOverStarts(), CCSraRefSeqIterator::GetAlnOverStarts(), CAlnVec::GetAlnSeqString(), Molecule::GetAlphaCoords(), CAmbigDataBuilder::GetAmbig(), SSeqTableContent::GetAnnot(), IBISAnnotateDialog::GetAnnotIbisOverlaps(), CSeq_annot_Info::GetAnnotObjectKey(), SSeqTableConverter::GetAnnots(), CJniUtil::GetArgsFromNcbiApp(), CScannerFunctorArgN::GetArguments(), CAlignFormatUtil::GetAsciiProteinMatrix(), CGencollSvc::GetAssmAccs(), StructureSet::GetAtomFromName(), CCgiSession_NetCache::GetAttribute(), CCgiSession_NetCache::GetAttrIStream(), CApplyEditconvertPanel::GetAutopopulateValue(), CSeqDBGiMask::GetAvailableMaskAlgorithms(), CMinHashFile::GetBadMers(), CSeqTableGridPanel::GetBestTableWidth(), SRequestBuilder::SReader< CArgs >::GetBioIds(), CCdCore::GetBioseqForIndex(), CAlnVec::GetBioseqHandle(), GetBioseqWithFootprintForNRows(), CAlignFormatUtil::GetBlastDbInfo(), GroupUpdater::getBlastHits(), CBlastQueryVector::GetBlastSearchQuery(), CBlastQuerySourceOM::GetBlastSequence(), CAsnCacheStoreMany::GetBlob(), SCacheInfo::GetBlob_idsSubkey(), CWGSClient::GetBlobId(), CBDB_ExtBlobMap::GetBlobIdRange(), CBDB_ExtBlobMap::GetBlobLoc(), CRemoteBlastDbDataLoader::GetBlobs(), BlockModel::getBlockNumber(), GetBlockNumberForResidue(), CSeqAnnotFromFasta::GetBlocksFromCounts(), CReadBlastApp::getBounds(), CCompartmentAccessor< THit >::GetBox(), CBroadcastVRChangeDialog::GetBroadcastFlag(), CScope_Impl::GetCDDAnnots(), CDataLoader::GetCDDAnnots(), CPSGDataLoader_Impl::GetCDDAnnotsOnce(), ASNDataManager::GetCDDNotes(), GetCdRegionCB(), GroupUpdater::getCds(), CHMMParameters::SDetails::GetCGList(), CNCMMReserve::GetChain(), CLayoutGroup::GetChild(), CTaxon1::GetChildren(), CMolInfoTableCommandConverter::GetChoices(), CGenomeTableCommandConverter::GetChoices(), CFeatureTableCommandConverter::GetChoices(), CPubFieldType::GetChoicesForField(), CSNPDbSeqIterator::GetChunkForVersion(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CNCMMReserve::GetChunks(), CFileCode::GetClasses(), CClassTypeInfoBase::GetClassInfoById(), CClassTypeInfoBase::GetClassInfoByName(), CFileCode::GetClassNamespace(), CClusterer::GetClusterDistMatrix(), CCassConnection::GetClusteringKeyColumnNames(), CPhyloSelectionSetMgr::GetClusterToSelectionMap(), GetCmdlineArgs(), CNCStat::GetCntRunningCmds(), GetCntRunningThreads(), CAlignCollapser::GetCollapsedAlgnments(), CResultSet::GetColNum(), GetColor(), CRgbaGradColorTable::GetColor(), CFillerPointVboGeomBase::GetColorBufferUC(), CTraceGraph::GetColorByValue(), CTraceGlyph::GetColorByValue(), CColorTableMethod::GetColorForScore(), CGlVboNode::GetColors(), CApplyEditconvertPanel::GetColumn(), CUnculTaxTool::GetColumn(), CSubpanel::GetColumn2(), CTableDataSeq_table::GetColumnCommonStrings(), CSeqDBVol::GetColumnId(), CwxTableListCtrl::GetColumnIndexByName(), CAlnMultiRenderer::GetColumnIndexByType(), CCassConnection::GetColumnNames(), CTableImportListCtrl::GetColumnsCombinedCharWidth(), CwxTableListCtrl::GetColumnsOrder(), CAddFeatureBetweenDlg::GetCommand(), CAddGlobalCodeBreak::GetCommand(), CAddSecondary::GetCommand(), CCdsFromGeneMrnaExon::GetCommand(), CCorrectRNAStrandDlg::GetCommand(), CEditHistory::GetCommand(), CEditSequenceEnds::GetCommand(), CExtendCDSToStop::GetCommand(), CFarPointerSeq::GetCommand(), CFuseFeaturesDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CReorderSequencesDlg::GetCommand(), CRevCompSequencesDlg::GetCommand(), CSegregateSets::GetCommand(), CtRNAFromGene::GetCommand(), CWithdrawSequences::GetCommand(), CAlignCDSAddPanel::GetCommand(), CAlignRNAAddPanel::GetCommand(), CAlignOtherAddPanel::GetCommand(), CCrossRefFeatsDlg::GetCommand(), CUnculTaxTool::GetCommandFromValuesTable(), CStructuredCommentCommandConverter::GetCommandFromValuesTable(), variation::GetCommonPrefixLen(), variation::GetCommonSuffixLen(), GetCommonTax(), CBlastSeqVectorFromCSeq_data::GetCompressedPlusStrand(), ResidueProfiles::getConsensus(), CStringConstraintSelect::GetConstrainedColumn(), CMacroCompoundConstraintPanel::GetConstraints(), GetContacts(), CTreeIteratorTmpl< CTreeLevelIterator >::GetContext(), CTreeIteratorTmpl< CTreeLevelIterator >::GetContextData(), CSplitQueryBlk::GetContextOffsets(), CBDB_BlobDeMux::GetCoordinates(), CIdDeMux< TBV, TBVFact >::GetCoordinatesFast(), CScriptPanel::GetCount(), CCompartmentAccessor< THit >::GetCounts(), CCSraRefSeqIterator::GetCoverageGraph(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CJson_WalkHandler::GetCurrentJPath(), CJson_WalkHandler::GetCurrentJPointer(), CUpdateSeqPanel::GetData(), CBroadcastDialog::GetData(), CGBProject::GetData(), CBedCoverageGraph::GetData(), CWigGraph::GetData(), CDDTypedAnnotDialog::GetData(), CGlBuffer20< T >::GetData(), CBlastServices::GetDatabaseInfoLegacy(), CTableImportColumn::GetDataTypeFromString(), CSeqDBImpl::GetDate(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::GetDb(), CSeqDBLMDBSet::GetDBTaxIds(), CBlastFormat::GetDbTotalLength(), CRealDataType::GetDefaultString(), CStringDataType::GetDefaultString(), CFileCode::GetDefineBase(), CCdCore::GetDefline(), CShowBlastDeflineTest::GetDeflineInfo(), CCharHistogram::GetDelimiterProbablities(), CDFamily::getDescendants(), GetDescrEmblBlock(), CMacroCompoundConstraintPanel::GetDescription(), GetDescrSPBlock(), CIdDeMux< TBV, TBVFact >::GetDimVector(), GetDiscrepancyCaseName(), CEnumeratedTypeValues::GetDisplayName(), GetDNAConv(), CIgAnnotationInfo::GetDomainInfo(), CSGDataSourceContext::GetDS(), GetDTDModuleName(), CEditObjectSeq_feat::GetEditCommand(), CDictionaryUtil::GetEditDistance(), CTypedArrayAdapter< Type, TBase >::GetElem(), PeriodicTableClass::GetElement(), GetEmblInst(), GetEmblInstContig(), GetEmblMolInfo(), CAsnCacheStoreMany::GetEntry(), CSNPDbSeqIterator::GetEntry(), CNetBlastSubmittingJob::GetErrors(), CRemoteBlast::GetErrors(), CBedCoverageGraph::GetEstimatedFeatureCount(), CFeatureGenerator::SImplementation::GetExonStructure(), CPaintAlignment::GetExportCont(), CPaintAlignment::GetExportInter(), GetExtensionAsInterface(), GetExtraAccession(), CDocsumTableModel::GetExtraValueAt(), AMatrix_base::GetExtremalEntries(), CPaintSequence::GetFeatsWithExons(), CPaintAlignment::GetFeatsWithExons(), CBioseqEditor::GetFeatTypeFromCmdID(), CPaintSequence::GetFeaturesInRow(), CPaintAlignment::GetFeaturesInRow(), CPaintSequence::GetFeatureStart(), CPaintSequence::GetFeatureStop(), CPaintAlignment::GetFeatWholeRange(), CPaintSequence::GetFeatWholeRange(), CBDB_BufferManager::GetFieldIndex(), CMolInfoFieldType::GetFieldNames(), CMolInfoFieldType::GetFieldType(), CFieldChoicePanel::GetFieldTypes(), CWGSDataLoader_Impl::GetFileInfoByAcc(), CMultiFileInput::GetFilenames(), CAutoCompleteCombo::GetFilteredItems(), GetFirstItemOffset(), GetFlatBiomol(), CNCBlobStorage::GetFullBlobsList(), CChoiceDataType::GetFullCType(), CApplyAuthorsTreeItemData::GetFunction(), CApplyStructCommentTreeItemData::GetFunction(), CSegmentSmearGlyph::CSegMap::GetGaps(), GetGBBlock(), CTaxon1::GetGCName(), GetGenBankInstContig(), CParse::GetGenes(), CBlastQuerySourceOM::GetGeneticCodeId(), GetGenomeInfo(), CDiscrepancyContext::GetGenomeName(), CDUpdater::getGi(), CSeqDBImpl::GetGiBounds(), CCdCore::GetGIFromSequenceList(), CDataLoader::GetGis(), CDataSource::GetGis(), CGBDataLoader_Native::GetGis(), CScope_Impl::GetGis(), CPSGDataLoader_Impl::GetGisOnce(), CSeqUtils::GetGIString(), CDensityMapDS::GetGraphTypes(), CDbvarValidationSorter::GetGroupIdx(), CGroupMapWidget::GetGroupLabels(), CCharHistogram::GetGroupOccuranceAverage(), CGuidGenerator::GetGuidUser(), CMD5::GetHexSum(), CHitMatrixDataSource::GetHitSeqIdsForParams(), CSplign::SAlignedCompartment::GetIdentity(), CLocationListCtrl::GetIdFromForm(), CAsnCacheStoreMany::GetIdInfo(), CSeqidlistRead::GetIds(), GetIdxVolNumOIDs(), SRequestBuilder::SImpl< TRequest >::GetIncludeInfo(), CCigar::GetInDels(), CGeneModel::GetInDels(), CScriptPanel::GetIndex(), CLayoutGroup::GetIndex(), CIndexedStrings::GetIndex(), CIndexedOctetStrings::GetIndex(), CAsnCacheStoreMany::GetIndexEntry(), BlockIntersector::getIntersectedAlignment(), pythonpp::CSequnceHelper< T >::GetItem(), CMapControl::GetItemIndex(), CItemsInfo::GetItemsByName(), CItemsInfo::GetItemsByOffset(), CItemsInfo::GetItemsByTagInfo(), PT::GetItemTypes(), CNetBLASTUIDataSource::GetJobDescriptors(), CNetScheduleGetJobImpl< CMainLoopThread::CImpl >::GetJobImmediately(), CSchedulerEngine::GetJobState(), SAnnotObjectsIndex::GetKey(), GetKeyFromCmdID(), CComment_rule::GetKeywordList(), COrf::GetKozakIdentity(), GetKValues(), CPub_equiv::GetLabel(), CDataLoader::GetLabels(), CDataSource::GetLabels(), CGBDataLoader_Native::GetLabels(), CScope_Impl::GetLabels(), CStructCommentSubpanel::GetLabelsFromSeq(), CSearch< LEGACY, NHITS >::GetLadderCalc(), CQueryDataPerChunk::GetLastChunk(), CRna_qual::GetLegalQual(), GetLength(), CBlastQuerySourceOM::GetLength(), CPacked_seqint::GetLength(), CTableSortMultiChoice::GetLevels(), MultiTextDialog::GetLine(), GetLineOSorOC(), MultiTextDialog::GetLines(), CGuiObjectInfoComponent::GetLinks(), CGuiObjectInfoSeq_feat::GetLinks(), CGuiObjectInfoVariant::GetLinks(), CSeqDBLMDBSet::GetLMDBFileNames(), CRegexp_loc::GetLoc(), DTDParser::GetLocation(), CCdCore::GetLongDescription(), UnalignedSegReader::getLongUnalignedSegs(), CCdCore::GetLowerBound(), GetLowestEvalue(), CMolInfoFieldType::GetMacroFieldNames(), CScriptPanel::GetMacros(), BlockMultipleAlignment::GetMarkedBlockNumbers(), CPhyloNodeData::GetMarkerColorsAsString(), CBlastQuerySourceOM::GetMask(), CBlastQuerySourceOM::GetMaskedRegions(), CBlastQueryVector::GetMaskedRegions(), CBlastQueryVector::GetMasks(), CBamAlignIterator::GetMatchAlign(), CCSraAlignIterator::GetMatchAlign(), CSnpTrackFactory::GetMatchedAnnots(), CVcfTrackFactory::GetMatchedAnnots(), CObjectIndex::GetMatches(), CSeq_id_Mapper::GetMatchingHandles(), CCSraShortReadIterator::GetMateCount(), CMSSpectrumMatch::GetMaxDelta(), CMSPeak::GetMaxI(), AlignedDM::GetMaxScore(), AlignedDM::GetMaxScoreForAligned(), GetMD5Digest(), CMSSpectrumMatch::GetMeanDelta(), CGlTextureFont::GetMetric(), CGlBitmapFont::GetMetric(), GetMinimumLoopLengths(), GetMiscTableFromSeqEntry(), GetMismatches(), CSparseGraph::GetMissingRegions(), CCdCore::GetMmdbId(), CwxTableListCtrl::GetModelIndexByName(), CObjectOStreamXml::GetModuleName(), CFileCode::GetModuleNames(), ColumnResidueProfile::getMostFrequentResidue(), CAsnCacheStoreMany::GetMultipleBlobs(), CAsnCacheStoreMany::GetMultipleEntries(), CAsnCacheStoreMany::GetMultipleIndexEntries(), CAsnCacheStoreMany::GetMultipleRaw(), CHttpRequest::GetMultipleValuesParam(), CWithdrawSequences::GetNames(), CNamespace::GetNamespaceRef(), CObjectPool< C >::GetNewChunk(), CSeqEntrySource::GetNext(), CRawSeqDBSource::GetNext(), CClusterDBSource::GetNext(), GetNextTest(), AlignmentCollection::getNormalRowsNotInChild(), CWGSDb_Impl::GetNucGiRanges(), GetNumAlignedResidues(), CPileUpGraph::GetNumberOfReads(), NJ_TreeAlgorithm::GetNumLoopsForTreeCalc(), SLC_TreeAlgorithm::GetNumLoopsForTreeCalc(), AlignmentCollection::GetNumPendingRows(), CCdCore::GetNumRowsWithSequences(), CTableDataGCAssembly::GetObjectValue(), DTDElement::GetOccurrence(), CSeqDBLMDB::GetOids(), CSeqDBLMDB::GetOidsForTaxIds(), CVDBBlastUtil::GetOidsFromSeqIds_WGS(), CAlignCollapser::GetOnlyOtherAlignments(), COrgrefProp::GetOrgrefProp(), COrgrefProp::GetOrgrefPropBool(), COrgrefProp::GetOrgrefPropInt(), BlockFormater::getOverlappingPercentages(), CSeq_id_PDB_Info::GetPackedSeqId(), getParam(), CHttpRequest::GetParam(), CHMMParameters::SDetails::GetParameter(), CObjectIStream::GetParentObjectPtr(), CCassConnection::GetPartitionKeyColumnNames(), CFindEditSequence::GetPattern(), CMsvcMetaMakefile::GetPchInfo(), StructureObject::GetPDBID(), GetPendingSeqId(), CNucProp::GetPercentGC(), DM_Identities::GetPercentIdentities(), FlexiDm::GetPercentIdentities(), CTriPerimeter::GetPerimiter(), CSeqDBImpl::GetPigBounds(), CPMCIDConverterServer::GetPmids(), CGlCurve< Curve >::GetPoint(), CGlTube< Curve >::GetPoint(), CCurveBezier::GetPoint(), CCurveCubic::GetPoint(), CTaxon1::GetPopsetJoin(), CPosToIndex::GetPositionForIndex(), Sequence::GetPreferredIdentifier(), CInferencePrefixList::GetPrefixAndRemainder(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), CBasicRelation::GetProperty(), CTaxon2_data::GetProperty(), CWGSDb_Impl::GetProtAccRanges(), GetProteinConv(), CEditSequence::GetProteinFeatures(), CProtProp::GetProteinPI(), CPaintSequence::GetProtFeatureStart(), CPaintSequence::GetProtFeatureStop(), PssmMaker::getPssmColumnResidues(), CDoiLookup::GetPubFromCrossRef(), GetPublicModuleName(), SrcEditDialog::GetQualChoices(), CCSraAlignIterator::GetQualityGraph(), CConvertFeatDlg::GetQualList(), CSplitQueryBlk::GetQueryContexts(), CSplitQueryBlk::GetQueryIndices(), CBlastQueryVector::GetQuerySeqLoc(), LocalMaxStatMatrix::getR(), GetRandomNumbers(), CAsnCacheStoreMany::GetRaw(), GetRawSequenceString(), CSUCRefreshCntrl::GetRefreshedText(), CClassTypeInfoBase::GetRegisteredClassNames(), CPhyloTreeWidget::GetRenderersNames(), GetReplacementSeqIds(), GetReportableSeqIdForAlignment(), GetReportFromMailReportTable(), CCgiRequest::GetRequestMethod(), GetResidue(), AlignedDM::GetResidueListsWithShifts(), CIndexedDb_Old::GetResults(), CMultiAligner::GetResults(), CSeq_id_Mapper::GetReverseMatchingHandles(), CRna_feat_type::GetRnaRefType(), CRNAFieldNamePanel::GetRnaTypeOnly(), CDualRNAFieldNamePanel::GetRnaTypeOnly(), CVcfTableSelection::GetRows(), CCdCore::GetRowsWithConsensus(), AlignmentCollection::GetRowsWithSameSeqID(), AlignmentCollection::GetRowsWithSeqID(), NWinHook::CKernell32::GetRVAFromExportSection(), CBlastQueryVector::GetScope(), CCodingPropensity::GetScore(), CGnomonEngine::GetScore(), ScoreMatrix::GetScore(), DM_AlignedScore::GetScore(), CEditScript::GetScore(), CGeneralScoreMatrix::GetScore(), CScriptPanel::GetScript(), CSeqTextPane::GetScrollAdjustmentForLastLineVariations(), OpenGLRenderer::GetSelected(), CwxHistogramDlg::GetSelected(), CwxCSVExportDlg::GetSelectedColumns(), CCSVSelectionExportDlg::GetSelectedColumns(), CSelectionControl::GetSelectedIndex(), CSelectionControl::GetSelectedIndexes(), CConversionResultPanel::GetSelectedIndices(), CGridWidget::GetSelectedObjectsOrdered(), CBamRefSequencesPanel::GetSelectedReferenceSeqIds(), CGridWidget::GetSelectedRows(), CStringConstraintSelect::GetSelectedRows(), CApplyEditconvertPanel::GetSelectedRows(), CCompareWithBiosample::GetSelectedRows(), CVcfSampleSelectionPanel::GetSelectedSamples(), CVcfTableSelection::GetSelection(), CAlnTableWidget::GetSelection(), CFeatTableWidget::GetSelection(), CConversionResultPanel::GetSelection(), CObjectListWidget::GetSelection(), CAlnSpanWidget::GetSelection(), TaxTreeData::getSelections(), CPhyloSelectionSetMgr::GetSelectionSet(), CSNPDbFeatIterator::GetSeq_feat(), CWGSScaffoldIterator::GetSeq_inst(), CLocationListCtrl::GetSeq_loc(), CCdCore::GetSeqAligns(), AalookupTestFixture::GetSeqBlk(), CSeqDBVol::GetSeqData(), CAlnReader::GetSeqEntry(), CRemoveSequencesDlg::GetSeqEntry(), CSegregateSetsBase::GetSeqEntry(), CCdCore::GetSeqEntryForIndex(), GetSeqID(), CBlastQuerySourceOM::GetSeqId(), CCdCore::GetSeqIDForIndex(), CCdCore::GetSeqIDForRow(), GetSeqIdProblems(), CAsnCacheStoreMany::GetSeqIds(), CCdCore::GetSeqIDs(), CCdCore::GetSeqIndex(), CWGSScaffoldIterator::GetSeqLength(), CBlastQuerySourceOM::GetSeqLoc(), CSeqMap::GetSeqMapForSeq_loc(), CSeq_align::GetSeqRange(), CStd_seg::GetSeqRange(), CStd_seg::GetSeqStart(), CStd_seg::GetSeqStop(), GetSeqTableForSrcQualFromSeqEntry(), CSeqDictionary< Alphabet >::GetSequence(), CRemoteBlastDbAdapter::GetSequenceBatch(), SeqTree::getSequenceComposition(), CDataLoader::GetSequenceHashes(), CGBDataLoader_Native::GetSequenceHashes(), CScope_Impl::GetSequenceHashes(), CDataLoader::GetSequenceLengths(), CDataSource::GetSequenceLengths(), CBlastDbDataLoader::GetSequenceLengths(), CGBDataLoader_Native::GetSequenceLengths(), CScope_Impl::GetSequenceLengths(), CPSGDataLoader_Impl::GetSequenceLengthsOnce(), GetSequenceProtein(), GetSequenceSingleNucleotideStrand(), CDataLoader::GetSequenceStates(), CDataSource::GetSequenceStates(), CGBDataLoader_Native::GetSequenceStates(), CScope_Impl::GetSequenceStates(), CDataLoader::GetSequenceTypes(), CDataSource::GetSequenceTypes(), CGBDataLoader_Native::GetSequenceTypes(), CScope_Impl::GetSequenceTypes(), CPSGDataLoader_Impl::GetSequenceTypesOnce(), CNCDistributionConf::GetServersForSlot(), SNetStorageRPC::GetServiceIfLocator(), CElementaryMatching::CBoolVector::GetSetCount(), GetSetOfSpecies(), ShowHideManager::GetShowHideInfo(), pythonpp::CTuple::GetSlice(), pythonpp::CList::GetSlice(), CSortedSeq_ids::GetSortedIds(), GetSPDescrComment(), GetSplicePriority(), CAdvancedAlignCleanup::GetSplignCompartments(), CSNPDbSeqIterator::GetSplitInfoAndVersion(), CSraRun::GetSpotEntry(), CCSraDb_Impl::GetSpotGroups(), GetSPSitesMod(), CNCDistributionConf::GetSrvIdByIP(), CObjectStack::GetStackPath(), CObjectStack::GetStackTraceASN(), GetStandardProbability(), CNetBlastJobDescriptor::GetStateLabel(), CPosToIndex::GetStatistics(), CCompartmentAccessor< THit >::GetStatus(), GetStatusByMessage(), CPubFieldType::GetStatusFromString(), CMSSpectrumMatch::GetStdDevDelta(), GetStdPath(), CBlastQuerySourceOM::GetStrand(), CCompartmentAccessor< THit >::GetStrand(), CPacked_seqint::GetStrand(), CLocationListCtrl::GetStrandFromForm(), CPtbRegistry::GetString(), CSeqDBImpl::GetStringBounds(), CCommentItem::GetStringForRefTrack(), CCommentItem::GetStringForTPA(), CTableDataGCAssembly::GetStringValue(), CImage::GetSubImage(), CPssmCddInputTest::GetSubjectMsaIndex(), CNetICacheClient::GetSubkeyList(), NSearchFeatPanel::GetSubtypesForType(), CSUCDataGenerator::GetSUCResults(), ILocalQueryData::GetSumOfSequenceLengths(), CTableDataBase::GetTableTypeId(), CItemsInfo::GetTagAndClass(), GetTargetAcc(), GetTargetedLocusNameConsensus(), CNetBLASTUILoadManager::GetTask(), COrg_ref::GetTaxId(), CDataLoader::GetTaxIds(), CDataSource::GetTaxIds(), CBlastDbDataLoader::GetTaxIds(), CGBDataLoader_Native::GetTaxIds(), CScope_Impl::GetTaxIds(), CSeqDBLMDB::GetTaxIdsForOids(), CSeqDBLMDBEntry::GetTaxIdsForOids(), CSeqDBLMDBSet::GetTaxIdsForOids(), CSeqDBImpl::GetTaxIdsForSeqId(), CPSGDataLoader_Impl::GetTaxIdsOnce(), TaxonomyTree::GetTaxInfoForTaxID(), CSUCResults::GetText(), CCompositeTextItem::GetText(), CBlastQuerySourceOM::GetTitle(), CGuiObjectInfoSeq_align::GetToolTip(), CPhyloTreeLabel::GetToolTipForNode(), BlockModel::getTotalBlockLength(), ISequenceSource::GetTotalLength(), CNWAligner::GetTranscriptString(), CUnicodeToAsciiTranslation::GetTranslation(), GetTreeNeighborhood(), CObjMgr_QueryFactory::GetTSeqLocVector(), CResolvedTypeSet::GetType(), CPubFieldType::GetTypeForLabel(), CDBLinkFieldType::GetTypeForLabel(), CDBLinkField::GetTypeForLabel(), CGBBlockField::GetTypeForLabel(), CImageIO::GetTypeFromFileName(), CImageIO::GetTypeFromMagic(), CTaxon1::GetTypeMaterial(), CCompressionUtil::GetUI4(), CUIDataSourceService::GetUIDataSourceByLabel(), CUIDataSourceService::GetUIDataSourceTypeByLabel(), CCdCore::GetUpdateDate(), CCdCore::GetUpperBound(), CRichTextCtrl::GetUtf8(), GetValidCountryCode(), CRptTypePanel::GetValue(), impl::CDBBindedParams::GetValue(), CSimpleMakeFileContents::GetValue(), CEditingActionFeatCodonsRecognized::GetValue(), CEnumeratedTypeValues::GetValueFlags(), CUnculTaxTool::GetValuesTableFromSeqEntry(), CFeatureTableCommandConverter::GetValuesTableFromSeqEntry(), CApplyAuthorsTreeItemData::GetVariables(), CMacroCompoundConstraintPanel::GetVariables(), CMultAlign::GetVariationAlignList(), UpdateViewer::GetVASTAlignments(), GetVDBScope(), CTreeNodeVboBase::GetVertexBuffer2D(), CFillerPointVboGeomBase::GetVertexBuffer2D(), GetVideoId(), GetVirtualCoordinates(), CFlatFileViewContext::GetVisibleObjects(), CSeqDBVolSet::GetVol(), CSeqDBVolSet::GetVolEntry(), CSeqDBVolSet::GetVolNonConst(), CSeqDBVolSet::GetVolOIDStart(), CSeqDBLMDB::GetVolumesInfo(), CRemoteBlast::GetWarnings(), CAlnVec::GetWholeAlnSeqString(), GetWizardNameList(), CTextUtil::GetWordFrequencies(), CReadDispatcher::GetWriter(), CEnumDataType::GetXMLContents(), CDataValueTmpl< Type >::GetXmlString(), CSeqDBImpl::GiToOid(), CSeqDBImpl::GiToOidwFilterCheck(), GlbAlign(), bm::bvector< Alloc >::enumerator::go_first(), bm::bvector< Alloc >::enumerator::go_to(), bm::interval_enumerator< BV >::go_to_impl(), CChainer::CChainerImpl::GoodCDNAScore(), GoodSupportForIntrons(), bm::greedy_refine_match_vector(), CDistMethods::GrishinDist(), CDistMethods::GrishinGeneralDist(), CAlignGroup::GroupByStrand(), GroupUpdater::GroupUpdater(), CTableColumnTypeGuesser::GuessColumns(), CSubPrep_panel::GuessWizardTypefromSeqEntry(), rapidjson::GenericSchemaDocument< ValueT, Allocator >::HandleRefSchema(), Has4Numbers(), CObjectIStreamXml::HasAnyContent(), HasBadWord(), CBDB_ExtBlobMap::HasBlob(), GroupUpdater::hasCd(), IResultSetMetaData::HasColumn(), CCdCore::HasConsensusSequence(), CSubSource::HasCultureNotes(), CTableQueryExec::HasIdentifier(), IBISAnnotateDialog::HasInteractionData(), CObjectIndex::HasMatches(), CQueryImpl::HasMoreResultSets(), CDockContainer::HasNoWMClients(), CBDB_BufferManager::HasNull(), COrgrefProp::HasOrgrefProp(), CChain::HasTrustedEvidence(), CSeqTable_sparse_index::HasValueAt(), CMacroCompoundConstraintPanel::HasVariables(), CModelCompare::HaveCommonExonOrIntron(), CSeq_id_Mapper::HaveMatchingHandles(), CSeq_id_Mapper::HaveReverseMatch(), bm::heap_vector< const bm::word_t *, allocator_type, true >::heap_vector(), CCacheDemoApp::HeapCacheDemo(), heapify(), CPsgCgiApp::Help(), BlockMultipleAlignment::HighlightAlignedColumnsOfMasterRange(), Sequence::HighlightPattern(), HighlightResidues(), DeBruijn::HistogramRange(), CLadder::HitCount(), hmac_md5(), CAlignFormatUtil::HspListToHitMap(), CRgbaColor::HsvToRgb(), CHTMLHelper::HTMLDecode(), huft_build(), hunt(), Identifier(), CTableQueryExec::IdentifierType(), CSeq_id::IdentifyAccession(), CMsvc7RegSettings::IdentifyPlatform(), CNcbiMatrix< T >::Identity(), IfOnlyStopCodon(), bm::sparse_vector< Val, BV >::import(), bm::sparse_vector< Val, BV >::import_back(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::import_no_check(), bm::bvector< Alloc >::import_sorted(), bm::sparse_vector< Val, BV >::import_u_nocheck(), CCdFromFasta::ImportAlignmentData(), importance_sampling::importance_sampling(), UpdateViewer::ImportStructure(), CTableImportDataSource::ImportTableParms(), bm::improve_gap_levels(), CRegExFSA::In(), Matrix< T >::in(), Vector< T >::in(), bm::sparse_vector< Val, BV >::inc_no_null(), SAnnotSelector::IncludeAnnotType(), SAnnotSelector::IncludedAnnotType(), SAnnotSelector::IncludedFeatType(), SAnnotSelector::IncludeFeatType(), CScriptPanel::IncreaseFont(), array_positive< T >::increment_array(), array< T >::increment_array_on_the_left(), array< T >::increment_array_on_the_rigth(), alp::increment_H_matrix(), alp::increment_H_weights(), alp::increment_H_weights_with_sentinels(), alp::increment_sequences(), alp::increment_W_matrix(), alp::increment_W_weights(), ind_subdbp(), CSequenceEditingEventHandler::IndexerTypeSelection(), IndexerTypeToName(), CGen_code_table::IndexToCodon(), NAdapterSearch::CPairedEndAdapterDetector::CConsensusPattern::InferConsensus(), inflate_dynamic(), inflate_fixed(), CSplitCacheApp::Info(), CSeqMaskerScoreMeanGlob::Init(), CSubPrep_panel::Init(), CSubmissionPrepMainPanel::Init(), CBlastDBAliasApp::Init(), CBlastVdbCmdApp::Init(), CResultSet::Init(), CTableDataBioTreeContainer::Init(), CSeqEditPackage::Init(), CScoreMethodsDlg::Init(), CSeqportUtil_implementation::Init(), NAdapterSearch::CSimpleUngappedAligner::Init(), CMassArray::Init(), CFastIScore::Init(), CLorentz::Init(), CMarkovChain< 0 >::Init(), CMarkovChain< order >::Init(), CSparseAlignment::Init(), CGroupMapWidget::Init(), CSeqScores::Init(), CNSeq::Init(), CAlnMultiDSBuilder::Init(), DynProgProb::init(), Matrix< T >::init(), CObjectList::Init(), CPdfFontHandler::Init(), CDustMaskApplication::Init(), SegMaskerApplication::Init(), Init(), init_basic_converters(), init_dboptions(), init_project_converters(), Init_wxControl(), CSeqportUtil_implementation::InitAmbigIupacnaNcbi2na(), InitClientMessages(), CSeqportUtil_implementation::InitCodes(), CBoyerMooreMatcher::InitCommonDelimiters(), CAlignCollapser::InitContig(), CObject::InitCounter(), SBamRangeBlock::InitData(), COpenDlg::InitDialog(), CIdDeMux< TBV, TBVFact >::InitDim(), COrgRefCache::InitDomain(), initDoubleMatrix(), CFlatFileViewContext::InitDrawStream(), CSeqportUtil_implementation::InitFastNcbi2naNcbi4na(), CSeqportUtil_implementation::InitFastNcbi4naIupacna(), CPhyloNodeData::InitFeatures(), CPhyloSelectionSetMgr::InitFromUserObject(), CPhyloSelectionSet::InitFromUserObject(), SBDB_CacheUnitStatistics::InitHistorgam(), InitialEntry(), CNCBlobStorage::Initialize(), C5ColImportData::Initialize(), CBedImportData::Initialize(), CNCMMChunksPool_Getter::Initialize(), CNCMMChainsPool_Getter::Initialize(), CNCMMReserve::Initialize(), CNCMMStats_Getter::Initialize(), CNCStat::Initialize(), CNCPeriodicSync::Initialize(), NJ_TreeAlgorithm::initializeNodes(), SLC_TreeAlgorithm::initializeNodes(), CSeqportUtil_implementation::InitIndexCodeName(), CSeqportUtil_implementation::InitIupacnaComplement(), CSearch< LEGACY, NHITS >::InitLadders(), CSeqTableGridPanel::InitMapRowLabelToIndex(), CSeqportUtil_implementation::InitMasks(), CSearch< LEGACY, NHITS >::InitModIndex(), COrgRefCache::InitNameClasses(), CTrackContainer::InitNATracks(), CSeqportUtil_implementation::InitNcbi2naComplement(), CSeqportUtil_implementation::InitNcbi2naRev(), CSeqportUtil_implementation::InitNcbi4naComplement(), CSeqportUtil_implementation::InitNcbi4naRev(), initPerm(), CSparseKmerCounts::InitPosBits(), CFIntron::InitRowScores(), CMarkovChainArray< order >::InitScore(), CDataMiningService::InitService(), InitSpellChecker(), SMMStat::InitStartState(), CNcbiTestApplication::InitTestFramework(), InitThreadsMan(), CFileLoadManager::InitUI(), CMPCrossAlignView::InitView(), SRemoteCgi::Input(), CVectorSet< CSupportInfo >::insert(), CLayoutGroup::Insert(), pythonpp::CList::Insert(), CRawScoreVector< Key, Score >::insert(), bm::bvector< Alloc >::insert(), bm::basic_bmatrix< BV >::insert_column(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::insert_value_no_null(), bm::sparse_vector< Val, BV >::insert_value_no_null(), CSeqTableGrid::InsertCols(), CAlnMultiRenderer::InsertColumn(), CMultAlign::InsertDashesInBase(), CSequence::InsertGaps(), AlignmentDisplay::InsertGaps(), CSelListModelImpl< Item >::InsertItems(), TaxTreeData::insertLineage(), CScriptPanel::InsertMacro(), CWriteDB_LMDB::InsertVolumesInfo(), InspectSeqFeat(), CCpuFeatures::InstructionSet::InstructionSet(), rapidjson::internal::Schema< SchemaDocumentType >::Int(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::Int(), rapidjson::PrettyWriter< OutputStream, SourceEncoding, TargetEncoding, StackAllocator, writeFlags >::Int(), rapidjson::internal::Hasher< Encoding, Allocator >::Int(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::Int(), rapidjson::Writer< OutputStream, UTF8<>, UTF8<>, CrtAllocator, kWriteDefaultFlags >::Int(), CNucProp::Int2Nmer(), rapidjson::internal::Schema< SchemaDocumentType >::Int64(), rapidjson::GenericDocument< Encoding, Allocator, StackAllocator >::Int64(), rapidjson::internal::Hasher< Encoding, Allocator >::Int64(), rapidjson::GenericSchemaValidator< SchemaDocumentType, OutputHandler, StateAllocator >::Int64(), integerPositivePower(), integerPower(), internal_dfa_exec(), InterpolativeCodingTest(), BlockModel::intersect(), IntersectByMaster(), CPrecalcGapInfo< CBlastTabular >::IntersectsNonBridgeableGap(), CSeqDB_BitSet::IntersectWith(), IntervalEnumeratorTest(), Intervals_RangesTest(), intPower(), intSortRowsFunction(), CNormalizer::IntToReal(), CNormalizer::IntToSize(), bm::bvector< Alloc >::invert(), InvertCase(), InvertInto(), ir_fp_entry_create(), bm::bvector< Alloc >::is_all_one_range(), ctll::fixed_string< N >::is_same_as(), bm::blocks_manager< Alloc >::is_sparse_sblock(), CSeqScores::isAG(), IsAllOneRangeTest(), CGene::IsAllowedAlternative(), CProjBulderApp::IsAllowedProjectTag(), IsAllPunctuation(), CGene::IsAlternative(), CFormatGuess::IsAsciiText(), ILocalQueryData::IsAtLeastOneQueryValid(), mu::ParserInt::IsBinVal(), CBDB_FieldLString::IsBlank(), MultipleAlignment::isBlockAligned(), mu::ParserTokenReader::IsBuiltIn(), IsCapNameCorrect(), CPaintSequence::IsClipboard(), CObjectStack::IsCompressed(), CSeqScores::isConsensusIntron(), IsConversionPossible(), CDFamily::isDup(), CPaintSequence::IsExonPresent(), CPaintAlignment::IsExonPresent(), IsExtendableLeft(), IsExtendableRight(), CSeqScores::isGT(), CRepeatMaskerReader::IsHeaderLine(), CGb_qual::IsIllegalQualName(), AlignmentManager::IsInAlignment(), CFormatGuess::IsInputRepeatMaskerWithHeader(), CAttribTableColumnIdPanel::IsInputValid(), CObjectStack::IsKnownElement(), IsKnownField(), CGb_qual::IsLegalInferenceDatabase(), CFindITSParser::IsLengthTooLarge(), CMsvcSite::IsLibOk(), CFormatGuess::IsLineFlatFileSequence(), CFormatGuess::IsLineGlimmer3(), CNWFormatter::SSegment::IsLowComplexityExon(), NStr::IsLower(), NWinHook::CHookedFunction::IsMandatory(), CGeneModel::isNMD(), CObjectStack::IsNsQualified(), CPager::IsPagerCommand(), CSplign::IsPolyA(), IsPositionAligned(), CDataType::IsPrimitive(), isProbDist(), CNCBlobAccessor::IsPurged(), CSeqScores::isReadingFrameLeftEnd(), CSeqScores::isReadingFrameRightEnd(), isReplicate(), RowSourceTable::isRowInCD(), isScoreIncreasing(), CCdCore::IsSeqAligns(), CPacked_seqint::IsSetStrand(), CUnculTaxTool::IsSpeciesSpecific(), CSeqScores::isStart(), CDataType::IsStdType(), CSeqScores::isStop(), IsStopCodon(), COrgMod::IsStrainValid(), CGeneModel::IsSubAlignOf(), CFormatGuess::IsSupportedFormat(), Matrix< T >::isSymmetric(), IsTPAAccPrefix(), IsUnexpectedViralOrgModQualifier(), COrgMod::IsUnexpectedViralOrgModQualifier(), IsUnexpectedViralSubSourceQualifier(), NStr::IsUpper(), BlockModel::isValid(), IsValidAccessPrefix(), CSmallDNS::IsValidIP(), ILocalQueryData::IsValidQuery(), IsValidStateAbbreviation(), COrgMod::IsValidTypeMaterial(), ShowHideDomain::IsVisible(), CVDBBlastUtil::IsWGS(), IsWGSAccession(), CAlignFormatUtil::IsWGSPattern(), CwxGridTableAdapter::IterateSelection(), CSeqMatch::IupacToNcbi8na(), Java_org_ncbi_toolkit_NcbiToolkit_init0(), CTextJoiner< num_prealloc, TIn, TOut >::Join(), CDistMethods::JukesCantorDist(), JumperEditsBlockCombine(), JumperExtendLeft(), JumperExtendLeftCompressed(), JumperExtendLeftCompressedWithTraceback(), JumperExtendLeftCompressedWithTracebackOptimal(), JumperExtendRight(), JumperExtendRightCompressed(), JumperExtendRightCompressedWithTraceback(), JumperExtendRightCompressedWithTracebackOptimal(), JumperExtendRightWithTraceback(), JumperFindEdits(), JumperGappedAlignmentCompressedWithTraceback(), JumperNaWordFinder(), JumperPrelimEditBlockToGapEditScript(), rapidjson::internal::Schema< SchemaDocumentType >::Key(), key_cpy(), key_equal(), CComment_rule::KeywordForPrefix(), alp_sim::kill(), alp::kill_upto_level(), CPoolOfThreads_ForServer::KillAllThreads(), CStdPoolOfThreads::KillAllThreads(), CDistMethods::KimuraDist(), KleeneLogicAndStressTest(), KleeneLogicOrStressTest(), KleeneLogicTest(), importance_sampling::lambda_equation(), DeBruijn::LargeInt< precision >::LargeInt(), CThreadPool_Impl::LaunchThreads(), LaunchWebPage(), CGraphContainer::Layout(), CStatusBar::Layout(), CMinPanelContainer::Layout(), C2DLayoutEngine::Layout(), LB_Select(), LBSM_Shmem_Create(), LBSM_Shmem_Destroy(), LBSM_Shmem_Update(), LclAlign(), CChainer::CChainerImpl::LeftRight(), AMatrix_base::LinearTransform(), CFeatureTypePanel::ListPresentFeaturesFirst(), CBDB_BlobDeMuxPersistent::Load(), CMatrixScoringMethod::Load(), CProfileData::Load(), CSubjectMap::Load(), ASNDataManager::Load(), bm::rsc_sparse_vector< Val, SV >::load_from(), bm::iterator_deserializer< BV, SerialIterator >::load_id_list(), bm::sparse_vector_deserializer< SV >::load_null_plane(), bm::sparse_vector_deserializer< SV >::load_planes_off_table(), bm::rsc_sparse_vector< Val, SV >::load_to(), CCacheReader::LoadAccVers(), CId2ReaderBase::LoadAccVers(), CReader::LoadAccVers(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CTableDelimiterRules::LoadAsn(), CCompoundRWRegistry::LoadBaseRegistries(), CTraceDataProxy::LoadData(), CSGTraceGraphDS::LoadData(), CProjBulderApp::LoadDepGraph(), LoadEntry(), LoadEntryGenbank(), LoadFeat(), CFileLoadWizard::LoadFormats(), CFastaObjectLoader::LoadFromStream(), CTextAlignObjectLoader::LoadFromStream(), CFileLoadMRUList::LoadFromStrings(), CCacheReader::LoadGis(), CId2ReaderBase::LoadGis(), CReader::LoadGis(), CId2ReaderBase::LoadHashes(), CReader::LoadHashes(), CCacheReader::LoadLabels(), CId2ReaderBase::LoadLabels(), CReader::LoadLabels(), CId2ReaderBase::LoadLengths(), CReader::LoadLengths(), loadMatrix(), loadMatrixOLD(), loadNewickTree(), CBamRefSeqInfo::LoadPileupChunk(), CRedoAlignmentTestFixture::loadPssmFromFile(), CCSRARefSeqInfo::LoadRefSeqMainEntry(), CFileLoadManager::LoadRegisteredManagers(), CCacheReader::LoadSeq_idBlob_ids(), LoadSequencesToScope(), CProjectService::LoadSettings(), CFileLoadManager::LoadSettings(), CAECRFrame::LoadSettings(), CBulkEditFeatDlg::LoadSettings(), CEditPubDlg::LoadSettings(), CFindASN1Dlg::LoadSettings(), CParseTextDlg::LoadSettings(), CSUCRefreshCntrl::LoadSettings(), CValidateFrame::LoadSettings(), CQueryParsePanel::LoadSettings(), CEditSequence::LoadSettings(), CwxGridTableAdapter::LoadSettings(), CFileLoadWizard::LoadSettings(), COpenObjectsPanel::LoadSettings(), CWidgetDisplayStyle::LoadSettings(), CTrackListCtrl::LoadSettings(), CGenBankLoadOptionPanel::LoadSettings(), CSequenceEditingEventHandler::LoadSettings(), CEditingBtnsPanel::LoadSettings(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CBDB_SplitTest::LoadSplitStore(), CId2ReaderBase::LoadStates(), CReader::LoadStates(), CTaxon1::LoadSubtreeEx(), CTestApplication::LoadTable(), CCacheReader::LoadTaxIds(), CId2ReaderBase::LoadTaxIds(), CReader::LoadTaxIds(), CRgbaGradColorTable::LoadTexture(), CId2ReaderBase::LoadTypes(), CReader::LoadTypes(), LoadVectors(), MultipleAlignment::locateChildRow(), CIndexedDb_Old::LocateIndex(), Log2Test(), CBlastFormat::LogBlastSearchInfo(), CTableImportDataSource::LogColumnInfo(), CTableDelimiterRules::LogDelims(), CTableImportDataSource::LogFixedFieldWidths(), CDockLayoutTree::LogPost(), CEJournalSearch::LooksLikeISSN(), lookup_attr(), lookup_canonic(), COrgRefCache::LookupAndAdd(), LookupNCBIStdaaNumberFromCharacter(), CUnculTaxTool::LookupSuggestions(), LookupThreaderResidueNumberFromCharacterAbbrev(), bm::sparse_vector_scanner< SV, S_FACTOR >::lower_bound_str(), SPhyloCSFCompactScore::LowerBound(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), LZCNTTest(), CLocalAdapterThread::Main(), main(), CPrefetchThreadOld::Main(), CDLTestThread::Main(), CDLTest2Thread::Main(), CSeqDBTestThread::Main(), CSeqDBTest2Thread::Main(), CSeqDBTest3Thread::Main(), CTestThread::Main(), CAsyncDiagThread::Main(), CMTTestThread::Main(), CTotalRangeThread::Main(), CChain::MainPeaks(), mainSimpleSort(), mainSort(), PssmMaker::make(), value_slice::CMakeObject< CP, vector< T >, CDB_Result >::Make(), value_slice::CMakeObject< CP, stack< T >, CDB_Result >::Make(), value_slice::CMakeObject< CP, deque< T >, CDB_Result >::Make(), value_slice::CMakeObject< CP, set< T >, CDB_Result >::Make(), value_slice::CMakeObject< SRunTimeCP, map< K, V >, CDB_Result >::Make(), value_slice::CMakeObject< SSafeCP, map< K, V >, CDB_Result >::Make(), CQueryFunctionBase::MakeArgVector(), CSeqAnnotFromFasta::MakeAsIsSeqAnnot(), MultipleAlignment::makeBlockTable(), CHitList::MakeCanonical(), CChainer::CChainerImpl::MakeChains(), SeqSwapper::makeClusters(), CSeqTableGridPanel::MakeColumnReadOnly(), MakeCompartments(), CGlState::MakeCurrent(), PssmMaker::makeDefaultPssm(), CEditScript::MakeEditScript(), CBamIndex::MakeEstimatedCoverageAnnot(), MakeFileName(), CCSraAlignIterator::MakeFullMismatch(), CWig2tableApplication::MakeGraph(), CSeqAnnotFromFasta::MakeIBMSeqAnnot(), CBlobSplitterImpl::MakeID2Chunk(), MakeMailReportPostReport(), makeMaps_d(), makeMaps_e(), CSearch< LEGACY, NHITS >::MakeModString(), CMSHits::MakeModString(), TMultiSourceFileSet< _enum, _options... >::MakeNewFileset(), makeNewNode(), CNWAligner::MakePattern(), CMSHits::MakePepString(), CFeatureTableCommandConverter::MakeProblemsColumn(), CRebase::MakeRSpec(), MakeSeqLong(), ViewerWindowBase::MakeSequenceVisible(), MakeSplicedSeg(), MakeSubjectScores(), makeThreshHeap(), python::MakeTupleFromResult(), CUniqueLabelGenerator::MakeUniqueLabel(), CSeqMaskerWindowPattern::MakeUnit(), CAutoDefOptions::MakeUserObject(), MapBlockFromConsensusToMaster(), MapDependentToMaster(), CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), CSeqportUtil_implementation::MapIupacnaToNcbi2na(), CGnomonAnnotator_Base::MapModelsToOrigContig(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), MapperWordHitsNew(), MapPosition(), AlignmentCollection::mapRow(), CHTMLBasicPage::MapTag(), SChainMember::MarkIncludedForChain(), SChainMember::MarkPostponedForChain(), SChainMember::MarkUnwantedCopiesForChain(), MarkUnwantedLowSupportIntrons(), BlockModel::mask(), BlockModelPair::mask(), MasterDependentAlignment::MasterDependentAlignment(), MasterSlaveAlignment::MasterSlaveAlignment(), CSeqMatch::Match(), match(), match_patterns(), MatchArrayIString(), MatchArrayISubString(), MatchArrayString(), MatchArraySubString(), CProteinAlignText::MatchChar(), CCigar::Matches(), Sequence::MatchesSeqId(), MoleculeIdentifier::MatchesSeqId(), MatchExceptSpaceColon(), CSelectionEvent::MatchIdWithId(), CHitList::MatchOverlappingSubHits(), CObjectTypeInfo::MatchPattern(), CProteinAlignText::MatchText(), Matrix< T >::matrix(), Matrix< T >::Matrix(), mu::Parser::Max(), mu::ParserInt::Max(), bm::aggregator< BV >::max_top_blocks(), maximum(), MaxSTest(), mbedtls_aes_crypt_cbc_ncbicxx_2_28_3(), mbedtls_aes_crypt_ctr_ncbicxx_2_28_3(), mbedtls_aes_crypt_xts_ncbicxx_2_28_3(), mbedtls_aes_setkey_dec_ncbicxx_2_28_3(), mbedtls_aes_setkey_enc_ncbicxx_2_28_3(), mbedtls_arc4_crypt_ncbicxx_2_28_3(), mbedtls_arc4_setup_ncbicxx_2_28_3(), mbedtls_base64_decode_ncbicxx_2_28_3(), mbedtls_base64_encode_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_cbc_ncbicxx_2_28_3(), mbedtls_blowfish_crypt_ctr_ncbicxx_2_28_3(), mbedtls_blowfish_setkey_ncbicxx_2_28_3(), mbedtls_camellia_crypt_cbc_ncbicxx_2_28_3(), mbedtls_camellia_crypt_ctr_ncbicxx_2_28_3(), mbedtls_camellia_setkey_dec_ncbicxx_2_28_3(), mbedtls_camellia_setkey_enc_ncbicxx_2_28_3(), mbedtls_ccm_star_auth_decrypt_ncbicxx_2_28_3(), mbedtls_chacha20_update_ncbicxx_2_28_3(), mbedtls_chachapoly_auth_decrypt_ncbicxx_2_28_3(), mbedtls_ct_mem_move_to_left(), mbedtls_ct_memcmp_ncbicxx_2_28_3(), mbedtls_ct_memcpy_if_eq_ncbicxx_2_28_3(), mbedtls_ct_mpi_uint_cond_assign_ncbicxx_2_28_3(), mbedtls_ct_rsaes_pkcs1_v15_unpadding_ncbicxx_2_28_3(), mbedtls_ctr_drbg_random_with_add_ncbicxx_2_28_3(), mbedtls_debug_print_buf_ncbicxx_2_28_3(), mbedtls_debug_print_crt_ncbicxx_2_28_3(), mbedtls_des3_crypt_cbc_ncbicxx_2_28_3(), mbedtls_des3_crypt_ecb_ncbicxx_2_28_3(), mbedtls_des_crypt_cbc_ncbicxx_2_28_3(), mbedtls_des_crypt_ecb_ncbicxx_2_28_3(), mbedtls_des_key_check_key_parity_ncbicxx_2_28_3(), mbedtls_des_key_check_weak_ncbicxx_2_28_3(), mbedtls_des_key_set_parity_ncbicxx_2_28_3(), mbedtls_des_setkey_dec_ncbicxx_2_28_3(), mbedtls_des_setkey_ncbicxx_2_28_3(), mbedtls_ecp_fix_negative(), mbedtls_ecp_group_free_ncbicxx_2_28_3(), mbedtls_ecp_grp_id_list_ncbicxx_2_28_3(), mbedtls_entropy_func_ncbicxx_2_28_3(), mbedtls_gcm_auth_decrypt_ncbicxx_2_28_3(), mbedtls_gcm_finish_ncbicxx_2_28_3(), mbedtls_gcm_starts_ncbicxx_2_28_3(), mbedtls_gcm_update_ncbicxx_2_28_3(), mbedtls_hkdf_expand_ncbicxx_2_28_3(), mbedtls_internal_aes_decrypt_ncbicxx_2_28_3(), mbedtls_internal_aes_encrypt_ncbicxx_2_28_3(), mbedtls_internal_sha256_process_ncbicxx_2_28_3(), mbedtls_internal_sha512_process_ncbicxx_2_28_3(), mbedtls_md_hmac_starts_ncbicxx_2_28_3(), mbedtls_mpi_add_abs_ncbicxx_2_28_3(), mbedtls_mpi_bitlen_ncbicxx_2_28_3(), mbedtls_mpi_cmp_abs_ncbicxx_2_28_3(), mbedtls_mpi_cmp_mpi_ncbicxx_2_28_3(), mbedtls_mpi_copy_ncbicxx_2_28_3(), mbedtls_mpi_div_mpi_ncbicxx_2_28_3(), mbedtls_mpi_exp_mod_ncbicxx_2_28_3(), mbedtls_mpi_lsb_ncbicxx_2_28_3(), mbedtls_mpi_lt_mpi_ct_ncbicxx_2_28_3(), mbedtls_mpi_mod_int_ncbicxx_2_28_3(), mbedtls_mpi_mul_mpi_ncbicxx_2_28_3(), mbedtls_mpi_read_binary_le_ncbicxx_2_28_3(), mbedtls_mpi_read_string_ncbicxx_2_28_3(), mbedtls_mpi_safe_cond_assign_ncbicxx_2_28_3(), mbedtls_mpi_safe_cond_swap_ncbicxx_2_28_3(), mbedtls_mpi_shift_l_ncbicxx_2_28_3(), mbedtls_mpi_shift_r_ncbicxx_2_28_3(), mbedtls_mpi_shrink_ncbicxx_2_28_3(), mbedtls_mpi_write_binary_le_ncbicxx_2_28_3(), mbedtls_mpi_write_binary_ncbicxx_2_28_3(), mbedtls_mpi_write_string_ncbicxx_2_28_3(), mbedtls_oid_get_numeric_string_ncbicxx_2_28_3(), mbedtls_pkcs12_derivation_ncbicxx_2_28_3(), mbedtls_pkcs5_pbkdf2_hmac_ncbicxx_2_28_3(), mbedtls_psa_safer_memcmp(), mbedtls_rsa_rsaes_oaep_decrypt_ncbicxx_2_28_3(), mbedtls_ssl_encrypt_buf_ncbicxx_2_28_3(), mbedtls_ssl_write_finished_ncbicxx_2_28_3(), mbedtls_ssl_write_record_ncbicxx_2_28_3(), mbedtls_x509_dn_gets_ncbicxx_2_28_3(), mbedtls_x509_serial_gets_ncbicxx_2_28_3(), mbedtls_xtea_crypt_cbc_ncbicxx_2_28_3(), mbedtls_xtea_crypt_ecb_ncbicxx_2_28_3(), mbedtls_xtea_setup_ncbicxx_2_28_3(), mdb_cursor_copy(), mdb_cursor_put(), mdb_cursor_set(), mdb_cursor_shadow(), mdb_cursors_close(), mdb_dbi_open(), mdb_dbis_update(), mdb_dlist_free(), mdb_drop0(), mdb_env_close1(), mdb_env_cwalk(), mdb_env_open2(), mdb_env_read_header(), mdb_find_oldest(), mdb_freelist_save(), mdb_mid2l_insert(), mdb_midl_sort(), mdb_midl_xmerge(), mdb_node_add(), mdb_node_del(), mdb_node_search(), mdb_node_shrink(), mdb_ovpage_free(), mdb_page_alloc(), mdb_page_flush(), mdb_page_merge(), mdb_page_search_root(), mdb_page_spill(), mdb_page_split(), mdb_pages_xkeep(), mdb_reader_check0(), mdb_reader_list(), mdb_rebalance(), mdb_strerror(), mdb_txn_begin(), mdb_txn_commit(), mdb_txn_renew0(), mdb_update_key(), alp_reg::median(), memcchr(), CCacheDemoApp::MemoryCacheDemo(), bm::bvector< Alloc >::merge(), BlockMultipleAlignment::MergeAlignment(), gfx::TimSort< RandomAccessIterator, LessFunction >::mergeAt(), DTDElement::MergeAttributes(), BlockMultipleAlignment::MergeBlocks(), CTableImportDataSource::MergeColumns(), CCdsToMatPeptide::MergeConvert(), CCpGIslands::MergeIslesWithin(), CDUpdater::mergePending(), CGlState::MergeStates(), AlignmentManager::MergeUpdates(), MessWithSegGenes(), meSwap(), NDirectNetStorageImpl::CObj::Meta(), mgf_mask(), MIME_ParseContentTypeEx(), mu::Parser::Min(), mu::ParserInt::Min(), bm::min_delta_apply(), bm::min_delta_u32(), minhash_query(), minhash_query2(), minimum(), MiniSetTest(), DeBruijn::CDBGraphDigger::SContig::MinKmerPosition(), minusOnePower(), mod(), ProteinWithBigHole::model_predicate(), HasShortIntron::model_predicate(), HasLongIntron::model_predicate(), ModelMethod(), CDirEntry::ModeToString(), CRemoveSeqFromAlignDlg::ModifyAlign(), Molecule::Molecule(), CTime::MonthNameToNum(), CPaintSequence::MouseToFeature(), SequenceViewerWidget_SequenceArea::MoveRubberband(), CNetScheduleGetJobImpl< TImpl >::MoveToImmediateActions(), mpi_check_small_factors(), mpi_miller_rabin(), mpi_montg_init(), mpi_montmul(), mpi_mul_hlp(), mpi_select(), mpi_sub_hlp(), mpi_uint_bigendian_to_host_c(), MSerial_None(), mu(), fix_pub::MULooksLikeISSN(), MultiplyByA(), MultiplyByAtranspose(), MutationOperationsTest(), MutationTest(), OpenGLRenderer::MyGluCylinder(), OpenGLRenderer::MyGluDisk(), OpenGLRenderer::MyGluSphere(), mz_adler32(), mz_zip_reader_locate_header_sig(), mz_zip_reader_read_central_dir(), mz_zip_string_equal(), mz_zip_validate_archive(), n_meanPowerAssoc(), n_totalProbAssoc(), NaHashLookupThreadDataFree(), NaHashLookupThreadDataNew(), CEnumeratedTypeValues::NameToValue(), NCBI_memcchr(), NCBI_memrchr(), NCBI_PARAM_DEF_EX(), NcbiBlowfishInit(), NcbiCrypt(), NcbiDecrypt(), variation::Ncbieaa2HgvsAA(), NcbiGetCgiClientIPv6Ex(), NcbiLog_AppRun(), NCBISM_Unpack(), CSeqDBLMDB::NegativeSeqIdsToOids(), CSeqDBLMDBSet::NegativeSeqIdsToOids(), CSeqDBLMDB::NegativeTaxIdsToOids(), CSeqDBLMDBSet::NegativeTaxIdsToOids(), neighbor_query(), AlignmentManager::NewAlignments(), CRCache::CRVPool::newBlock(), NewFldMtf(), newicklex(), NewickPrintTreeString(), AlignmentManager::NewMultipleWithRows(), NewQrySeq(), NewRcxPtl(), NewSeqMtf(), NewThdTbl(), CSequenceIStreamBlastDB::next(), CResultSet::Next(), CScanner::Next(), CScanner::NextASNSelector(), CNetScheduleGetJobImpl< TImpl >::NextDiscoveryIteration(), CScanner::NextNamedAnnot(), CDistMethods::NjTree(), Nlm_AddVectors(), Nlm_DenseMatrixNew(), Nlm_EuclideanNorm(), Nlm_FactorLtriangPosDef(), Nlm_FindSubString(), Nlm_Int4MatrixNew(), Nlm_LtriangMatrixNew(), Nlm_MemSearch(), Nlm_rule_line(), Nlm_SearchSubString(), Nlm_SolveLtriangPosDef(), Nlm_StepBound(), NlmKarlinLambdaNR(), CNucProp::Nmer2Int(), NNI(), impl::CDriverContext::NofConnections(), normal_inserts(), pvalues::normal_probability(), normal_select(), CSeq_id_PDB_Info::Normalize(), notAStandardFile(), CActiveObject::Notify(), NotName(), CDemoApplication::NumAdderHook(), numeric_to_longlong(), CBaseClusterer::NumItems(), DeBruijn::LargeInt< precision >::oahash(), odbc_c2string(), odbc_cursor_execute(), odbc_db_is_microsoft(), odbc_driver_is_freetds(), odbc_errs_reset(), odbc_find_last_socket(), odbc_from_sqlwchar(), odbc_mark_sockets_opened(), odbc_populate_ird(), odbc_set_return_params(), odbc_sql2tds(), odbc_stat_execute(), odbc_tds2sql(), odbc_to_sqlwchar(), odbc_wchar2hex(), OffsetArrayToContextOffsets(), CSubPrep_panel::OkToBulkEditSeqTech(), CUnculTaxTool::OkToTaxFix(), CSegregateSets::OnAccept(), CSequesterSets::OnAccept(), CEditSequence::OnAccept(), CProjectTreePanel::OnActivateClients(), CAlignmentAssistant::OnAddAlignCDS(), CAlignmentAssistant::OnAddAlignOther(), CAlignmentAssistant::OnAddAlignRNA(), CUnculTaxTool::OnAddBacterium(), CPhyloSaveSelectiondlg::OnAddCurrentSelBtnClick(), CUnculTaxTool::OnAddSp(), CCompareWithBiosample::OnAddToSample(), CCompareWithBiosample::OnAddToSource(), CFeatureGraph::OnAJNotification(), StructureWindow::OnAlignStructures(), CMacroFlowEditor::OnAppendClick(), CStringConstraintSelect::OnApply(), CColorTableScoringPanel::OnApply(), CMatchFeatureTableDlg::OnAutomatchTableIdClick(), CMultiFileInput::OnBrowseBtn(), CTableSortMultiChoice::OnBrowseBtn(), CDDRefDialog::OnButton(), PNGOptionsDialog::OnButton(), ShowHideDialog::OnButton(), CReorderSequencesDlg::OnButtonDown(), CRemoveSequencesDlg::OnButtonMoveLeft(), CRBSubpanel::OnButtonMoveLeft(), CRemoveSequencesDlg::OnButtonMoveRight(), CRBSubpanel::OnButtonMoveRight(), CReorderSequencesDlg::OnButtonUp(), CEditingBtnsPanel::OnCancelFindButton(), StructureWindow::OnCDD(), CSeqTableGridPanel::OnCellDoubleLeftClick(), CSeqTableGridPanel::OnCellLeftClick(), CFarPointerSeq::OnCheck(), CCustomTree::OnClick(), CMacroFlowEditor::OnClose(), CWindowsDlg::OnCloseClick(), CFrameworkDemoGUI::OnCloseClientsRequest(), CProjectTreePanel::OnCloseView(), CFlatFileViewContext::OnCollapseSequences(), CDataMiningPanel::OnContextMenu(), CProjectTreePanel::OnContextMenu(), CTextItemPanel::OnContextMenu(), CCompareWithBiosample::OnCopyToSampleButtonClick(), CCompareWithBiosample::OnCopyToSourceButtonClick(), CwxMainFrame::OnCreateMapControlItems(), CProjectTreeViewDropTarget::OnData(), CMultiFileInput::CDropTarget::OnData(), CFrameworkDemoGUIDropTarget::OnData(), CSrcModListPanel::OnDelete(), CSeqTableGridPanel::OnDeleteColumn(), CMacroFlowEditor::OnDeleteFromLibrary(), CSuspectProductRulesEditor::OnDeleteRules(), CBamRefSequencesPanel::OnDeselectAllBtnClick(), CVcfRefSequencesPanel::OnDeselectAllBtnClick(), CCSVSelectionExportDlg::OnDeselectAllBtnClick(), CwxCSVExportDlg::OnDeselectAllBtnClick(), CVcfSampleSelectionPanel::OnDeselectallSamplesClick(), CFilterColumnsDlg::OnDeselectBtnClick(), CSuspectProductRulesEditor::OnDisplay(), StructureWindow::OnEditFavorite(), CAppJobDispatcher::OnEngineJobStateChanged(), DeBruijn::CDBGraphDigger::OneStepBranchExtend(), CBioSourcePanel::OnEvtText(), CFarPointerSeq::OnExport(), CMacroFlowEditor::OnExportMenuClick(), CMacroFlowEditor::OnExportStepsClick(), CGridWidget::OnExportToCSV(), CSuspectProductRulesEditor::OnFileAdd(), CSuspectProductRulesEditor::OnFileLoad(), CSuspectProductRulesEditor::OnFileSave(), CSuspectProductRulesEditor::OnFileSaveAs(), CEditingBtnsPanel::OnFindButton(), CMacroFlowEditor::OnFindClick(), CDiscrepancyPanel::OnFindNext(), ViewerWindowBase::OnFindPattern(), CDiscrepancyPanel::OnFindPrev(), CDiscrepancyPanel::OnFindText(), CWindowsDlg::OnFloatClick(), CAgpValidateReader::OnGapOrComponent(), CTableImportListCtrl::OnGetItemText(), CGridWidget::OnGridCellRightClick(), CGrid::OnGridLabelLeftClick(), CAlignTabExportPage2::OnIdle(), COrganismInfoPanel::OnImportSrcTable(), CSaveDlg::OnInitDialog(), CMacroFlowEditor::OnInputFile(), CISOJTALookupDlg::OnIsoJtaReportBtnClick(), CGridCgiSampleApplication::OnJobDone(), ViewerWindowBase::OnJustification(), CAttribTableDelimitersPanel::OnListctrlColLeftClick(), CSuspectProductRulesEditor::OnListMatches(), CAdjustFeaturesForGaps::OnMakeReport(), CDataMiningPanel::OnMenuEvent(), CAttribTableColumnIdPanel::OnMergeIDColsClick(), CWindowsDlg::OnMinimizeClick(), CBarcodePanel::OnMouseClick(), CPaintSequence::OnMouseClick(), CGlPreviewSetupWidget::OnMouseDoubleClick(), CGlPreviewSetupWidget::OnMouseDown(), ViewerWindowBase::OnMouseMode(), CMapControl::OnMouseWheel(), CDockManager::OnMove(), CAgpValidateReader::OnObjectChange(), CDiscrepancyConf::OnOk(), CAlnPropertiesDlg::OnOkClick(), CwxTableListCtrl::OnPaint(), CBarcodePanel::OnPaint(), CGradientColorPanel::OnPaint(), CGradientPanel::OnPaint(), CMinPanelContainer::OnPaint(), CPaintSequence::OnPaste(), CMacroFlowEditor::OnPasteClick(), CwxMainFrame::OnPostEventsClick(), CQueryParsePanel::OnQuerySel(), SPSG_IoImpl::OnQueue(), SequenceViewerWindow::OnRealign(), CWindowsDlg::OnRecoverClick(), CMacroWordSubstitutionDlg::OnRemove(), CWordSubstitutionDlg::OnRemove(), CCompoundConstraintPanel::OnRemoveConstraint(), CSuspectCompoundConstraintPanel::OnRemoveConstraint(), CMacroCompoundConstraintPanel::OnRemoveConstraint(), CBarcodeTool::OnRemoveKeyword(), CAlignmentAssistant::OnRemoveSeqFromAlign(), CWindowsDlg::OnRestoreClick(), CCDSTranslationPanel::OnRetranslateLinkHyperlinkClicked(), CQueryParsePanel::OnSearchctrlTextEnter(), CSeqTableGridPanel::OnSearchTable(), CBarcodeTool::OnSelect(), CRemoveSequencesDlg::OnSelect(), CRevCompSequencesDlg::OnSelect(), StructureWindow::OnSelect(), CBarcodeTool::OnSelectAll(), CEditSequenceEnds::OnSelectAll(), CRemoveSequencesDlg::OnSelectAll(), CFilterColumnsDlg::OnSelectAllBtnClick(), CBamRefSequencesPanel::OnSelectAllBtnClick(), CVcfRefSequencesPanel::OnSelectAllBtnClick(), CCSVSelectionExportDlg::OnSelectAllBtnClick(), CwxCSVExportDlg::OnSelectAllBtnClick(), CSaveDlg::OnSelectAllClick(), CVcfSampleSelectionPanel::OnSelectallSamplesClick(), CFilterColumnsDlg::OnSelectBtnClick(), CLengthSubpanel::OnSelectButton(), CIDSubpanel::OnSelectButton(), CTextSubpanel::OnSelectButton(), CNumSubpanel::OnSelectButton(), CFileSubpanel::OnSelectButton(), CFieldSubpanel::OnSelectButton(), CFeatureTypeSubpanel::OnSelectButton(), CDescTypeSubpanel::OnSelectButton(), CMolInfoSubpanel::OnSelectButton(), CStructCommentSubpanel::OnSelectButton(), CSaveDlg::OnSelectChangedClick(), StructureWindow::OnSelectFavorite(), ShowHideDialog::OnSelection(), CSequesterSets::OnSequester(), CAlnMultiWidget::OnSettings(), CHitMatrixWidget::OnSetupGraphs(), CPhyloTreeWidget::OnShowAll(), CSuspectProductRulesEditor::OnShowDiffs(), StructureWindow::OnShowHide(), SequenceViewerWindow::OnShowHideRows(), CAttribTableColumnIdPanel::OnSplitFirstColClick(), CQueryParsePanel::OnStringMatchTypeBtn(), CTaxTreeTestDlg::OnSubmitClick(), CCompareWithBiosample::OnSyncButtonClick(), CAlignmentAssistant::OnTarget(), CBioSourcePanel::OnTaxonomyLookup(), CColorPanel::OnTextCtrlUpdated(), CMacroPanelLoader::OnToggleButtonClicked(), CApplyEditconvertPanel::OnUndoButtonClick(), CEditSequenceEnds::OnUnselectAll(), CPhyloTreeWidget::OnUpdateCollapseSelected(), CProjectTreePanel::OnUpdateEnableDisable(), CDockContainer::OnUpdateTabOrder(), CBamRawDb::Open(), CPipeHandle::Open(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::OpenProjections(), CMacroFlowEditor::OpenScript(), CAppDialogs::OpenViewlDialog(), DeBruijn::LargeInt< precision >::operator!=(), DeBruijn::LargeInt< precision >::operator%(), DeBruijn::LargeInt< precision >::operator&(), DeBruijn::LargeInt< precision >::operator&=(), CSeqMaskerScoreMin::operator()(), CWinMaskCountsConverter::operator()(), CWinMaskCountsGenerator::operator()(), CSearch_Base< LEGACY, NHITS, derived_t >::operator()(), CCassandraFullscanWorker::operator()(), compile_time_bits::ct_crc32< poly >::MakeCRC32Table::operator()(), MultiExonsCompare::operator()(), CAlnSeqIdsExtract< TAlnSeqId, TIdConverter >::operator()(), CCompareByFind::operator()(), CCompareByCat::operator()(), SCompareDirEntries::operator()(), PEqualNocase::operator()(), IsStandard::operator()(), CAlignSort::SSortKey_Less::operator()(), CPhyTreeCalc::CDistMatrix::operator()(), CMatrix3< double >::operator()(), CMatrix4< float >::operator()(), CNcbiMatrix< T >::operator()(), DeBruijn::CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >::extract_uniq::operator()(), CReverseAndComplement< T >::operator()(), CSequenceDataTester::operator()(), bm::gamma_decoder< T, TBitIO >::operator()(), DeBruijn::CReadHolder::string_iterator::operator*(), operator*(), CMatrix3< T >::operator*=(), CMatrix4< T >::operator*=(), rapidjson::internal::BigInteger::operator*=(), DeBruijn::LargeInt< precision >::operator+(), CRevComp_It< Iterator >::operator+(), CJson_ConstArray::const_iterator::operator+(), CJson_ConstArray::iterator::operator+(), CMatrix3< T >::operator+=(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::operator+=(), CRevComp_It< Iterator >::operator+=(), CJson_ConstArray::const_iterator::operator+=(), CMatrix4< T >::operator+=(), rapidjson::internal::BigInteger::operator+=(), BlockModel::operator-(), DeBruijn::LargeInt< precision >::operator-(), CRevComp_It< Iterator >::operator-(), CJson_ConstArray::const_iterator::operator-(), CJson_ConstArray::iterator::operator-(), CMatrix3< T >::operator-=(), compile_time_bits::const_bitset< static_cast< size_t >(eTestNames::max_test_names), eTestNames >::operator-=(), CRevComp_It< Iterator >::operator-=(), CJson_ConstArray::const_iterator::operator-=(), CMatrix4< T >::operator-=(), DeBruijn::LargeInt< precision >::operator/(), CMatrix3< T >::operator/=(), CMatrix4< T >::operator/=(), CSortableSeq_id::operator<(), DeBruijn::LargeInt< precision >::operator<(), SIntron::operator<(), operator<<(), DeBruijn::LargeInt< precision >::operator<<(), CSrvStrStream::operator<<(), rapidjson::internal::BigInteger::operator<<=(), CMSHit::operator=(), CRowReader< TTraits >::CRowIterator::operator=(), CDB_Double::operator=(), CDB_Float::operator=(), bm::heap_vector< const bm::word_t *, allocator_type, true >::operator=(), CDB_Bit::operator=(), CDB_SmallInt::operator=(), CDB_Int::operator=(), CDB_BigInt::operator=(), Matrix< T >::operator=(), bm::similarity_descriptor< SO, DMD_SZ, IDX_VALUE, SValue, SFunc >::operator=(), CDB_TinyInt::operator=(), bm::block_match_chain< BLOCK_IDX >::operator==(), BlockModel::operator==(), operator==(), CPhyloSelectionSetMgr::operator==(), CRowReader< TTraits >::CRowIterator::operator==(), CVectorSet< CSupportInfo >::operator==(), DeBruijn::LargeInt< precision >::operator==(), operator>>(), DeBruijn::LargeInt< precision >::operator>>(), CSQLITE3_Statement::operator>>(), dup_lookup_table::operator[](), CRgbaGradColorTable::operator[](), CQuat< float >::operator[](), pythonpp::CSequnceHelper< T >::iterator::operator[](), CMatrix3< double >::operator[](), CMatrix4< float >::operator[](), CVect2< size_t >::operator[](), CVect3< size_t >::operator[](), pythonpp::CSequnceHelper< T >::const_iterator::operator[](), CNWAligner::CBacktraceMatrix4::operator[](), CVect4< TPoint >::operator[](), CSraValueFor< V >::operator[](), CVDBValueFor< char >::operator[](), CNcbiMatrix< T >::operator[](), ctll::fixed_string< N >::operator[](), CSearchResultSet::operator[](), CBlastKmerResultsSet::operator[](), CSeqDB::TSequenceRanges::operator[](), CBlastQueryVector::operator[](), CSimpleBufferT< char >::operator[](), CAlnMap::CAlnChunkVec::operator[](), CSRSearch::CMismatchResultsInfo::operator[](), Vector< T >::operator[](), Matrix< T >::operator[](), DeBruijn::LargeInt< precision >::operator^(), DeBruijn::LargeInt< precision >::operator^=(), DeBruijn::LargeInt< precision >::operator|(), DeBruijn::LargeInt< precision >::operator|=(), DeBruijn::LargeInt< precision >::operator~(), bm::blocks_manager< Alloc >::opt_copy_bit_block(), SSparseIndex::Optimize(), bm::blocks_manager< Alloc >::optimize_bit_block(), bm::basic_bmatrix< BV >::optimize_block(), bm::blocks_manager< Alloc >::optimize_block(), optimize_fill(), bm::blocks_manager< Alloc >::optimize_tree(), CSeqDBVolSet::OptimizeGiLists(), CLadder::Or(), CDense_seg::OrderAdjacentGaps(), CCompartmentFinder< THit >::OrderCompartments(), OrderQual(), OrderThdTbl(), OrOperationsTest(), Matrix< T >::out(), Vector< T >::out(), CProSplignText::Output(), PSSMWrapper::OutputPSSM(), CDUpdater::overlapWithCDRow(), CBDB_BufferManager::Pack(), pack(), CSeqConvert_imp::CPacker::Pack(), Pack(), pad(), CCustomTree::Paint(), param_info_alloc(), paraminfoalloc(), CSeq_id_General_Str_Info::Parse(), rapidjson::GenericPointer< ValueType, Allocator >::Parse(), rapidjson::internal::GenericRegex< Encoding, Allocator >::Parse(), parse_args(), CSeq_id_Textseq_Info::ParseAcc(), CTrackMgrClient::ParseAlignId(), mu::ParserBase::ParseCmdCode(), ParseDegenerateCodons(), JSDParser::ParseDependencies(), SDiagMessage::ParseDiagStream(), CGb_qual::ParseExperiment(), ParseFeatureBlock(), CNetStorageObjectLoc::ParseFileTrackSite(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseHex4(), CGb_qual::ParseInferenceString(), rapidjson::GenericReader< SourceEncoding, TargetEncoding, StackAllocator >::ParseNumber(), JSDParser::ParseOneOf(), mu::ParserErrorMsg::ParserErrorMsg(), SSNP_Info::ParseSeq_feat(), ParseSourceFeat(), ParseSpComment(), ParseSPFeat(), CWGSResolver_Ids::ParseWGSAcc(), CWGSResolver_Ids::ParseWGSPrefix(), ParseYear(), alp::partially_release_memory(), CUsageReportSampleApp::Pattern_3_StatusControl(), Splines::pchip(), pcre_compile2(), pcre_get_substring_list(), pcre_maketables(), pcre_memmove(), pcre_printint(), pcre_study(), pcregrep(), CSpectrumSet::Peaks2Spectrum(), CChain::PeaksAndLimits(), pearson_hash(), rapidjson::BasicIStreamWrapper< StreamType >::Peek4(), CObjectIStreamAsnBinary::PeekAnyTagFirstByte(), CObjectIStreamAsnBinary::PeekClassTag(), CObjectIStreamAsnBinary::PeekLongTag(), pem_get_iv(), SPSG_BlobReader::PendingCount(), CProcessing::Performance(), perminit_fp(), perminit_ip(), permInverse(), PHIGetPatternOccurrences(), CPhyloSelectionSetMgr::PickBestColor(), CDUpdater::pickBioseq(), CSeqDBImpl::PigToOid(), PiiOk(), pkcs12_pbe_derive_key_iv(), CEditingBtnsPanel::PlaceButtons(), IPhyloTreeRender::PointToNode(), CDistMethods::PoissonDist(), CSocketAPI::Poll(), CPdfObject::Poly(), poly1305_process(), DeBruijn::LargeInt< precision >::polynom(), LargeInt< 1 >::polynom(), pool_allocate(), pool_allocate2(), pool_free(), popHeap(), CTripleConstraintPanel< T >::PopulateFeatureListbox(), NWinHook::CPsapiHandler::PopulateModules(), CWithdrawSequences::PopulateSet(), CReorderSequencesDlg::PopulateSet(), CSegregateSetsBase::PopulateSet(), CWordPairIndexer::PopulateWordPairIndex(), CSeqMaskerScoreMeanGlob::PostAdvance(), CPaintSequence::PosToSegment(), CAbstractProjectItem::PostRead(), variation_ref::CVariationUtil::PrecursorToProt(), CGnomonAnnotator::Predict(), CGraphContainer::PreferredSize(), CWigGraph::Prefetch(), CComment_rule::PrefixForKeyword(), CUnculTaxTool::PreloadCache(), bm::sparse_vector_scanner< SV, S_FACTOR >::prepare_and_sub_aggregator(), prepare_new_block(), bm::aggregator< BV >::prepare_shift_right_and(), CReorderSequencesDlg::PrepareList(), CQueryFuncPromoteBase::PreProcess(), CLocalVDBBlast::PreprocessDBs(), rapidjson::internal::Prettify(), CAttribTableDelimitersPanel::PreviewData(), CMacroRep::Print(), SGFFrec::print(), CTabularFormatter_AllSeqIds::Print(), CTabularFormatter_MismatchPositions::Print(), CTabularFormatter_BestPlacementGroup::Print(), CTabularFormatter_AssemblyInfo::Print(), CComments::Print(), CNCBINode::Print(), Print(), SInteractiveNewRequestStart::SExtra::Print(), CNCMMStats::Print(), CMaskWriterFasta::Print(), CMaskWriterTabular::Print(), CDiagFilter::Print(), bm::print_bc(), bm::print_blocks_count(), print_char(), print_gap(), print_mv(), bm::print_stat(), bm::print_str_svector_stat(), bm::print_svector_stat(), CNCBlobStorage::PrintablePassword(), PssmMaker::printAlignment(), PssmMaker::printAlignmentByColumn(), CAgpErrEx::PrintAllMessages(), CArgDescriptions::CPrintUsageXml::PrintArguments(), CBlastFormatUtil::PrintAsciiPssm(), CDataTypeModule::PrintASN(), CFileSet::PrintASN(), CDataMemberContainerType::PrintASN(), CChoiceDataType::PrintASN(), CEnumDataType::PrintASN(), CBlockDataValue::PrintASN(), CDataValueTmpl< Type >::PrintASN(), CFileModules::PrintASNRefInfo(), CHTML_table::PrintBegin(), bm::PrintBinary(), PrintBLOB_Table(), CNCBINode::PrintChildren(), PrintCompartments(), PrintCorDef(), CAlignFormatUtil::PrintDbReport(), PrintDemoDB(), bm::PrintDGap(), bm::PrintDGapGamma(), bm::PrintDistanceMatrix(), printDoubleTable(), CDataTypeModule::PrintDTD(), CFileSet::PrintDTD(), CDataTypeModule::PrintDTDModular(), CFileSet::PrintDTDModular(), CQueryTreePrintFunc::PrintElement(), CPrintTaxFields::PrintEntry(), COMSSABase::PrintEnzymes(), PrintFldMtf(), CNamespace::PrintFullName(), bm::PrintGammaCode(), bm::PrintGap(), PrintGapLevels(), printGFF3(), CBDB_FileDumper::PrintHeader(), CIgBlastTabularInfo::PrintHtmlSummary(), CParse::PrintInfo(), COMSSABase::PrintIons(), CDataTypeModule::PrintJSONSchema(), CFileSet::PrintJSONSchema(), CDataMemberContainerType::PrintJSONSchema(), CChoiceDataType::PrintJSONSchema(), CEnumDataType::PrintJSONSchema(), CTreePrintFunc< TTreeNode, TConverter >::PrintLevelMargin(), CQueryTreePrintFunc::PrintLevelMargin(), CPdf::PrintLineBuffer(), CMaskWriterInt::PrintMasks(), CIgBlastTabularInfo::PrintMasterAlign(), CAgpErrEx::PrintMessageCounts(), CPdf::PrintModel(), COMSSABase::PrintMods(), printMsa(), CBlastFormat::PrintOneResultSet(), CHttpRequest::PrintParams(), CPdf::PrintPointBuffer(), PrintQrySeq(), CPdf::PrintQuadBuffer(), PrintResults(), PrintSAM(), CFileSet::PrintSampleDEF(), CBlastSeqidlistFile::PrintSeqidlistInfo(), PrintSeqMtf(), TestUtil::PrintSequence(), CDataTypeModule::PrintSpecDump(), CFileSet::PrintSpecDump(), CDataMemberContainerType::PrintSpecDumpExtra(), CEnumDataType::PrintSpecDumpExtra(), SMMStat::PrintState(), CNCPeerControl::PrintSyncStat(), PrintTabular(), PrintThdTbl(), bm::PrintTMatrix(), CBBox< 3 >::PrintTo(), CNcbiApplogApp::PrintTokenInformation(), CNCStat::PrintToSocket(), CTree::PrintTree(), CArgDependencyGroup::PrintUsage(), CArgDependencyGroup::PrintUsageXml(), CFileModules::PrintXMLRefInfo(), CDataTypeModule::PrintXMLSchema(), CFileSet::PrintXMLSchema(), CDataMemberContainerType::PrintXMLSchema(), CUniSequenceDataType::PrintXMLSchema(), CDataTypeModule::PrintXMLSchemaModular(), CFileSet::PrintXMLSchemaModular(), CdPssmInput::Process(), CSeqEntryPresenter::Process(), CWinMaskCountsGenerator::process(), bm::aggregator< BV >::process_bit_blocks_or(), bm::iterator_deserializer< BV, SerialIterator >::process_id_list(), CQueryFunction_BV_Base< BV >::ProcessArgVector(), SBamIndexRefIndex::ProcessBin(), GroupUpdater::processBlastHits(), CdBlaster::processBlastHits(), CProjectTreeBuilder::ProcessDir(), WSDLParser::ProcessEndpointTypes(), ProcessForTrimAndSplitUpdates(), CCgiRequestProcessor::ProcessHelpRequest(), CESearchParser< T >::ProcessMessages(), XSDParser::ProcessNamedTypes(), CDUpdater::processPendingToNormal(), CCgiRedirectApplication::ProcessRequest(), ProcessSAM(), ProcessStream(), ProductNamesAreSimilar(), CApplyRNAITSDlg::Propagate_RNAITSList(), CSequence::PropagateGaps(), Prosite2Regex(), PrositePatternLength(), CAutoCompleteCombo::ProvideItems(), SequenceDisplay::ProximitySort(), PSSMWrapper::PSSMWrapper(), CNCBlobAccessor::Purge(), CNWAligner::CBacktraceMatrix4::Purge(), CBDB_Cache::Purge(), CHitList::PurgeAllHits(), PurgeConsensusSequences(), CSeqAnnotFromFasta::PurgeNonAlphaFromCachedSequences(), AlignmentManager::PurgeSequence(), CHitList::PurgeUnwantedHits(), CRegExFSA::Push(), CVariantDescriptors::PushBack(), DeBruijn::CReadHolder::PushBack(), DTDParser::PushEntityLexer(), CObjectStack::PushFrameLong(), pushHeap(), bm::encoder::put_h64(), CIdDeMux< TBV, TBVFact >::PutDimVector(), CErrorLogger::PutError(), COStreamBuffer::PutInt4(), COStreamBuffer::PutInt8(), CPriorityTaxNodes::putIntoMap(), rapidjson::PutN(), COStreamBuffer::PutUint4(), COStreamBuffer::PutUint8(), QSbuf_ReadLine(), QSCmp(), QSIndex(), query_test(), SequenceViewerWindow::QueryShowAllRows(), CBLASTToolManager::QuickLaunch(), QuoteDot(), alp_sim::randomize_realizations_ind(), RangeCopyTest(), RangeForEachTest(), CModelCompare::RangeNestedInIntron(), CMSPeakList::Rank(), bm::bvector< Alloc >::rank_corrected(), RankFindTest(), RankRangeSplitTest(), bm::rs_index< BVAlloc >::rcount(), SBamIndexRefIndex::Read(), CBioTreeAttrReader::Read(), CSeq_annot_SNP_Info_Reader::Read(), CAlnAsnReader::Read(), SBamIndexBinInfo::Read(), CBamIndex::Read(), CMSPeak::Read(), CDistanceMatrix::Read(), CPhrapReader::Read(), bm::deseriaizer_base< DEC, BLOCK_IDX >::read_gap_block(), alp_data::read_RR(), alp_data::read_smatr(), CPhrap_Contig::ReadBaseQualities(), CObjectIStreamAsn::ReadBitString(), CObjectIStreamAsnBinary::ReadBitString(), readBlob(), readBlobAsChar(), ReadCassandraMessages(), ReadCassandraSatInfo(), CObjectIStreamAsn::ReadChars(), CReadSeqSetHook::ReadClassMember(), CAsnvalThreadState::ReadClassMember(), CBiosampleChkApp::ReadClassMember(), CReadSetHook::ReadClassMember(), ReadCol(), readGFF3(), readhdr(), ReadId(), CImageIORaw::ReadImage(), CResultZBtSrcX::ReadLength(), ReadMap(), CObjectIStreamAsn::ReadMemberId(), CObjectIStreamXml::ReadName(), CObjectIStreamAsn::ReadNumber(), CReadEntryHook::ReadObject(), CSoapReadHook::ReadObject(), ReadProject(), ReadSecureSatUsers(), CCacheReader::ReadSeq_ids(), CFastaReader::ReadSet(), CObjectIStreamAsn::ReadStringValue(), ReadTabDelimitedTable(), ReadTestData(), CObjectIStreamAsn::ReadTypeId(), Threader::Realign(), AlignmentManager::RealignAllDependentStructures(), StructureObject::RealignStructure(), CReferenceItem::Rearrange(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::recalc_remap_matrix2(), COSGConnection::ReceiveReply(), CTableImportDataSource::RecomputeFields(), CTableImportDataSource::RecomputeHeaders(), CMSHit::RecordMatchesScan(), CMSHit::RecordModInfo(), dtl::Diff< elem, vector< elem >, Compare< elem > >::recordSequence(), CSequesterSets::RecursivePropagateDown(), CSequesterSets::RecursivePropagateUp(), CNcbiApplogApp::Redirect(), SequenceDisplay::RedrawAlignedMolecules(), CDRefresher::refresh(), regexec(), bm::rs_index< BVAlloc >::register_super_block(), CBioseqEditorFactory::RegisterCommands(), CClassTypeInfo::RegisterSubClasses(), RegisterTooManyVariantsOfSameMaskingAlgorithm(), regression_tests(), reHeapElement(), reinit_results(), Matrix< T >::relApprox(), variation_ref::CVariationUtil::Remap(), variation::CVariationUtil::Remap(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::remap(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_from_impl(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_fromsv(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_n_tosv_2way(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::remap_tosv(), CCgiRedirectApplication::RemapEntries(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::remapz(), ReMasterCdWithoutUnifiedBlocks(), RemasterWithStructure(), CPointerPot::Remove(), remove_comments(), CSplitter::RemoveAll(), CdBlaster::RemoveAllDataLoaders(), CSimpleB2SWrapper::RemoveAllDataLoaders(), CProjectService::RemoveAllProjectViews(), CCgiSession_NetCache::RemoveAttribute(), CEditingBtnsPanel::RemoveButton(), CCdCore::RemoveCddDescrsOfType(), CSubSource::RemoveCultureNotes(), CSimpleMakeFileContents::RemoveDefinition(), CExportTableDlg::RemoveEmptyColsAndRows(), RowSourceTable::removeEntriesForCD(), CChain::RemoveFshiftsFromUTRs(), CGene::RemoveGeneFromOtherGenesSets(), Messenger::RemoveHighlights(), CBioSource::RemoveLineageSourceNotes(), COrgName::RemoveModBySubtype(), COrgrefProp::RemoveOrgrefProp(), CGBDocument::RemoveProjectItems(), CProjectTask::RemoveProjects(), CDense_seg::RemovePureGapSegs(), SequenceViewerWidget_SequenceArea::RemoveRubberband(), CPhyloTreeDataSource::RemoveSelected(), CGeneModel::RemoveShortHolesAndRescore(), CEditingBtnsPanel::RemoveStaticButtons(), CWindowManagerService::RemoveToolBarContext(), UpdaterInterface::removeUpdaters(), RemoveWhitespace_CJL(), CWriteDB_File::RenameFileIndex(), CGlModel2D::Render(), CAlnMultiHeader::Render(), CAlignedFeatureGraph::Render(), CTreeGraphicsModel::Render(), CHitGlyph::Render(), CAlignRowGraphCont::Render(), CPieGraph::Render(), CScatterGraph::Render(), IBoundaryShape::Render(), CTreeGraphicsModel::RenderPDF(), CTreeBoundaryNode::RenderPdf(), CPhyloNodeData::RenderRotated(), OpenGLRenderer::RenderTransparentSpheres(), CAsnOctetStringBlock::RenderValue(), IBoundaryShape::RenderVbo(), Reorder(), CReorderSequencesDlg::ReorderById(), ReorderStructureAlignments(), CLayoutGroup::Replace(), NWinHook::CHookedFunction::ReplaceInAllModules(), CFindASN1Dlg::ReplaceLinebreaks(), CRegexpUtil::ReplaceRange(), CSuspectProductRulesEditor::ReplaceRule(), CTableImportDataSource::ReplaceSpaces(), ReplaceStateAbbreviation(), DistanceMatrix::ReplaceZeroWithTinyValue(), bm::dynamic_heap_matrix< unsigned, bv_allocator_type >::replicate_triange(), CChainer::CChainerImpl::ReplicatePStops(), SPSG_StatsAvgTime::Report(), CODBC_Reporter::ReportErrors(), CDB_MultiEx::ReportErrorStack(), ReportMailReportLine(), CValidError_imp::ReportMissingBiosource(), CSubmissionWizard::ReportMissingFields(), COrganismInfoPanel::ReportMissingFields(), CGenomeInfoPanel::ReportMissingFields(), CReferencePanel::ReportMissingFields(), CSubMolinfoPanel::ReportMissingFields(), CSubmitterPanel::ReportMissingFields(), CReadBlastApp::reportProblems(), CCdregionValidator::ReportShortIntrons(), ColumnarVcfCache::ReportSyntaxErrors(), CPhyloTreeDataSource::ReRootMidpoint(), DynProgProb::reserve(), DynProgProbLim::reserve(), bm::blocks_manager< Alloc >::reserve_top_blocks(), bm::bv_statistics::reset(), CAgpValidateReader::Reset(), CSparseKmerCounts::Reset(), CBinaryKmerCounts::Reset(), CSequence::Reset(), CNcbiArguments::Reset(), SCompoundIDImpl::Reset(), CRandom::Reset(), CFIntronDon::Reset(), bm::serializer< BV >::reset_compression_stats(), ResetCapitalization(), CScriptPanel::ResetCounters(), AnnotateDialog::ResetListBoxes(), CMenuService::ResetMenuBar(), CTaxon2_data::ResetProperty(), CGnomonEngine::ResetRange(), SrcEditDialog::ResetSubPanels(), CEditingBtnsPanel::ResetTabs(), ResidualsLinearConstraints(), Residue::Residue(), CNcbiMatrix< T >::Resize(), bm::heap_vector< const bm::word_t *, allocator_type, true >::resize(), CSRSearch::CMismatchResultsInfo::resize(), CSRSearch::CResCache::resize(), UnalignedBlock::Resize(), bm::aggregator< BV >::resize_target(), CDataTypeModule::Resolve(), CWGSClient::ResolveBlobId(), CCodeGenerator::ResolveFileName(), CCodeGenerator::ResolveImportRefs(), CFileModules::ResolveInAnyModule(), CFileSet::ResolveInAnyModule(), CSysPath::ResolvePathExisting(), CHit::ResolveSubHitConflicts(), CWGSClient::ResolveWGSAcc(), CCassQuery::Restart(), alp::restore_state(), CProSplignTrimmer::RestoreFivePrime(), CSortedSeq_ids::RestoreOrder(), CChain::RestoreReasonableConfirmedStart(), CProSplignTrimmer::RestoreThreePrime(), CCDSTranslationPanel::Retranslate(), CDUpdater::retrieveAllSequences(), CDbapiSimpleApp::RetrieveData(), RetrievePartsOfLargeChromosome(), CAlnVec::RetrieveSegmentSequences(), CNetScheduleGetJobImpl< TImpl >::ReturnNotFullyCheckedServers(), DeBruijn::revcomp(), CDense_seg::Reverse(), CSeqMaskerUtil::reverse_complement(), ReverseAlignmentStrand(), ReverseAndComplement(), ReverseComplement(), CEditScript::ReverseEditScript(), CFarPointerSeq::ReverseRow(), ColumnResidueProfile::reweightColumnByRowWeights(), CTempString::rfind(), CChainer::CChainerImpl::RightLeft(), RigidBodyFit(), CExplodeRNAFeats::RNAWordsFromString(), alp_reg::robust_sum(), CAsnViewContext::RootInitialized(), CFlatFileViewContext::RootInitialized(), alp_sim::round_doulbe(), CMatrix3< T >::Row(), CMatrix4< T >::Row(), bm::basic_bmatrix< BV >::row(), SequenceDisplay::RowsRemoved(), RPSFillScores(), RPSLookupTableDestruct(), RPSLookupTableNew(), RSIndexTest(), rsmp(), CDeltaBlast::Run(), CLocalBlast::Run(), CBlastPrelimSearch::Run(), CBlastTracebackSearch::Run(), CBlastKmer::Run(), CLocalVDBBlast::Run(), CMergeVolumes::Run(), mu::Test::ParserTester::Run(), CForceJob::Run(), CPrimeNumbersJob::Run(), CMergeyApp::Run(), CBlastDBCmdApp::Run(), CGridCommandLineInterfaceApp::Run(), CComponentIDToolApp::Run(), CMagicBlastApp::Run(), CSplignApp::Run(), CAttachProjectItemsJob::Run(), CSeqDescrRetrievalJob::Run(), CFeatCompareJob_Align::Run(), CFeatureRetrievalJob::Run(), CTrackInitializationJob::Run(), CAnnotMetaDataJob::Run(), CSeqDBDemo_GetSequence::Run(), CDbapiTest::Run(), CSdbapiTest::Run(), CCompartmentFinder< THit >::Run(), CSeedTop::Run(), CSampleIdleTask::Run(), CSeqAlignCmp::Run(), CSplign::Run(), bm::thread_pool_executor< TPool >::run(), CScorePValuesCalc::Run(), CThreadedApp::Run(), CAVApp::Run(), CTestCompartApplication::Run(), CBlastKmerApplication::Run(), CMultiApplication::Run(), CLocalFinderApp::Run(), CCpGDemoApp::Run(), SUApp::Run(), CWinMaskDemoApplication::Run(), CAgpValidateApplication::Run(), CAsn2Asn::Run(), CTest::Run(), CPrimeCacheApplication::Run(), CId2FetchApp::Run(), CMultipatternApp::Run(), CDemoApp::Run(), CWinMaskApplication::Run(), CMysqlDemoApp::Run(), CAppJobTestApplication::Run(), CAlnTestApp::Run(), CSampleAlnmgrApplication::Run(), CBlastDemoApplication::Run(), CGridClientSampleApp::Run(), CSampleNetScheduleClient::Run(), CRemoteAppClientSampleApp::Run(), CSampleSoapClientApplication::Run(), bm::aggregator< BV >::run_step(), bm::run_task_batch(), CAsn2Asn::RunAsn2Asn(), RunNIterationsWithoutConverging(), CPSG_EventLoop::RunOnce(), CDbapiCursorApp::RunOneSample(), CDbapiBcpApp::RunSample(), CConnectPolicyApp::RunSample(), CDbapiTestSpeedApp::RunSample(), CMacroFlowEditor::RunScript(), CMacroFlowEditor::RunScriptStandalone(), COMSSABase::RunSearch(), CVDBThread::RunTandemSearches(), CTestProtProd_EntrezNeighbors::RunTest(), CTestSingleAln_All::RunTest(), RunTests(), CAppDialogs::RunToolDialog(), s_AA20alphaStd(), s_AddCoalescedLocations(), s_AddMask(), s_AddNeighboringWords(), s_AddOneDataFile(), s_AddPrimers(), s_AddProjItemToDll(), s_AddPSSMNeighboringWords(), s_AddPSSMWordHits(), s_AddPSSMWordHitsCore(), s_AddTimerTicket(), s_AddToLog(), s_AddToRPSBucket(), s_AddWordHit(), s_AddWordHits(), s_AddWordHitsCore(), s_AdjustGapParametersByGcd(), s_AdjustSubjectForSraSearch(), s_AdjustSubjectForTranslatedSraSearch(), s_AdjustToAnnotatedCDS(), s_Align(), s_AlignToSeqRanges(), s_AllLowerCase(), s_AllocNewPage(), s_AmbiguousMatch(), s_AnalyzeLibraryOrder(), CIgBlast::s_AppendResults(), s_AppStart(), s_AreSequencesEqual(), s_ArrayToString(), NAdapterSearch::s_AsIUPAC(), s_AssignBufferToSeqData(), s_BandedAlign(), s_BitmapFrom7x4(), s_Blast_HSPGetNumIdentitiesAndPositives(), s_Blast_HSPGetOOFNumIdentitiesAndPositives(), s_BLAST_OneSubjectResults2CSeqAlign(), s_BlastAaExtendLeft(), s_BlastAaExtendOneHit(), s_BlastAaExtendRight(), s_BlastAaExtendTwoHit(), s_BlastAaScanSubject(), s_BlastAaWordFinder_OneHit(), s_BlastAaWordFinder_TwoHit(), s_BlastAlignPackedNucl(), s_BlastCompressedAaScanSubject(), s_BlastDiagClear(), s_BlastEvenGapLinkHSPs(), s_BlastFindSmallestLambda(), s_BlastFindValidKarlinBlk(), s_BlastGapAlignStruct_Copy(), s_BlastGreedyAlignMemAlloc(), s_BlastHSP2SeqAlign(), s_BlastHSPBestHitInit(), s_BlastHSPBestHitRun(), s_BlastHSPBestHitRun_RPS(), s_BlastHSPCullingRun(), s_BlastHSPListRPSUpdate(), s_BlastHSPMapperSplicedPairedRun(), s_BlastHSPStreamCountNumOids(), s_BlastHSPStreamResultsBatchArrayReset(), s_BlastKmerVerifyVolume(), s_BlastLookupRetrieve(), s_BlastMBLookupRetrieve(), s_BlastMBLookupRetrieve2(), s_BlastNaHashLookupFinalize(), s_BlastNaHashLookupRetieveHits(), s_BlastNaLookupFinalize(), s_BlastOOFTracebackToGapEditScript(), s_BlastPSSMExtendLeft(), s_BlastPSSMExtendRight(), s_BlastResults2SeqAlignSequenceCmp_OMF(), s_BlastRPSWordFinder_OneHit(), s_BlastRPSWordFinder_TwoHit(), s_BlastScoreBlk_Copy(), s_BlastSearchEngineCore(), s_BlastSeqLocListToArrayOfPointers(), s_BlastSmallAaScanSubject(), s_BlastSmallNaLookupFinalize(), s_BlastSumP(), s_BreakSeq_loc(), s_BufHash(), s_BuildCompressedScoreMatrix(), s_BuildCompressedTranslation(), s_BuildNa4ToNa2Table(), s_BuildResultsRemote(), s_BuiltInSM(), s_CalcLambda(), s_CalculateIdentity(), s_CalculateMaxLength(), s_CanLoadUnloadProjects(), s_CArgs_ReadFromConsole(), s_CheckAccessStat(), s_CheckDefClientConfig(), s_CheckDuplicateVols(), s_CheckEndlessRecursion(), s_CheckErrorsVersusExpected(), s_CheckFiles(), s_CheckPValues(), s_CheckTraceMateAlign(), s_CleanCDDFeature(), s_CleanUpConstraints(), s_CloneBlastQueryVector(), s_CodonToAA(), variation_ref::CVariationUtil::s_CollapseAmbiguities(), variation::CVariationUtil::s_CollapseAmbiguities(), s_CollectBestOverlaps(), s_CollectClientConfigKeys(), s_CollectRelPathes(), s_ColorDifferentBases(), s_CombineSearchSets(), s_CompareProtProdToTrans(), s_CompoHeapifyDown(), s_CompoHeapifyUp(), s_CompoHeapIsValid(), s_CompressDiscToDenseq(), s_CompressedAddNeighboringWords(), s_CompressedAddWordHits(), s_CompressedAddWordHitsCore(), s_CompressedLookupFinalize(), s_ComputeAlignmentScore(), s_ComputeBtopAndIdentity(), s_ComputeCompressedIndex(), s_ComputeExtensionScore(), s_ComputeNumIdentities(), s_ComputeTraceback(), s_ConstBioseqSetToSeqLocs(), s_ConvertBlastnMasks(), s_ConvertMetaData(), s_ConvertToBlastQueries(), s_ConvertToHeap(), s_ConvertToHexString(), s_CountGaps(), s_CountHspListsPerQuery(), variation_ref::CVariationUtil::s_CountMatches(), variation::CVariationUtil::s_CountMatches(), s_Create_Args_L(), s_Create_Args_V(), s_Create_Env(), s_CreateAlign(), s_CreateBioseq(), s_CreateHeap(), s_CreateHSPForWordHit(), s_CreateObjList(), s_CreateRotatedFont(), s_CreateStdSegs(), s_CreateTable(), s_CreateWordArray(), s_DeleteOldestSockets(), s_DeleteRow(), s_DescriptorPropagateDown(), s_DistinctAlignmentsSort(), s_DivideDBsForThread(), s_DoNWalign(), s_DupSequencesTest(), s_effectiveObservations(), CAscii85::s_Encode(), s_EncodeLabel(), s_Entropy(), s_EscapeCommaAndPipe(), s_ExonToDenseg(), s_ExpandPattern(), s_ExpandThisQual(), s_ExtendAlignment(), s_ExtractKey(), s_FillBlastOutput(), s_FillCdsStartPosition(), python::s_FillDescription(), s_FillFromFreePages(), s_FillModuleListPSAPI(), s_FillSearchSpace(), s_FindAdapterInSequence(), s_FindBestPairs(), s_FindBestPath(), s_FindColumn(), s_FindDimerEntropy(), s_FindEntryName(), s_FindFirstVowel(), s_FindHigh(), s_FindHitsLong(), s_FindHitsShortDNA(), s_FindInArray(), variation::CVariationUtil::s_FindLocationProperties(), s_FindLow(), s_FindOrfs(), s_FindPolyAInSequence(), s_FindPrefixAndSuffixPos(), s_FindRebalanceTasks(), s_FindSpliceJunctionsForGap(), s_FindSpliceJunctionsForOverlaps(), s_FixNumIdent(), s_FlushPoolSet(), s_FormatRegularSequencePiece(), s_FormatResults(), s_FreeBlastCompo_QueryInfoArray(), s_GappingParamsNew(), s_GeneralLnGamma(), s_GenerateCollapsedNode(), s_Get_LSH_index_hashes2(), s_GetAaAsChar(), s_GetAlignmentLength(), s_GetAlignmentLengths(), s_GetAlignmentTooltip(), s_GetAttrByTag(), s_GetAttrByType(), s_GetBioseq_setType(), s_GetBitScores(), s_GetBlastNameColor(), s_GetCandidate(), s_GetChunksForThread(), s_GetCigarString(), s_GetCleanMenuText(), s_GetCmdlineArgs(), s_GetCompressedProbs(), s_GetConcatenatedExon(), s_GetCountByPct(), s_GetCountIdentityMismatch(), s_GetCSRADBs(), s_GetEnd(), s_GetFileSystemInfo(), s_GetFilteredOidRange(), s_GetFinalTranslatedString(), s_GetFullLinkoutUrl(), s_GetGapCount(), s_GetGermlineTranslation(), s_GetHSPList(), CAdapterSearchApplication::s_GetIdentity(), s_GetIndels(), s_GetInfoContent(), s_GetLabel(), s_GetLine(), s_GetMaxRows(), s_GetMenuName(), CSrcModPanel::s_GetModifierList(), s_GetNextInfo(), s_GetNextSubjectChunk(), s_GetNucIdentityMismatch(), s_GetOverlapCost(), s_GetPosBasedStartFreqRatios(), s_GetPrimerInfo(), s_GetQueryInfo(), s_GetRandomNumbers(), s_GetSeq4na(), s_GetSeq4naChunkSeq(), s_GetSeq4naChunkSeq_PartialFetching(), s_GetSplicedSegIdentityMismatch(), s_GetStartFreqRatios(), s_GetStrand(), s_GetTaxIDList(), s_GetTraceback(), NAdapterSearch::s_GetWordComplexity(), s_HashHashQuery(), s_HasSubSourceNote(), s_Heapify(), s_HexDumpText(), s_HighPairFrequencies(), s_HSPNodeArrayCopy(), s_InframeUpstreamStart(), s_InframeUpstreamStop(), s_InitAlignHitLineage(), s_InitDataFlags(), s_InitializeInstitutionCollectionCodeMaps(), s_InitializeOrgRefMap(), s_InitializeStructuredCommentRules(), s_InitPoolsSet(), CSeqFeatData::s_InitSubtypesTable(), s_InsertGap(), s_InsertSpacesBetweenTokens(), s_InsureOrder(), s_InvalidateQueryContexts(), s_Is_ISO_8859_1(), s_IsAllowedPrefix(), s_IsAssemblyMethodValid(), s_IsBadMethod(), s_IsExtendedNAA(), s_IsIdentity(), s_IsNAA(), s_IsNumeric(), s_IsOidInFilteredVol(), s_IsSuccessor(), s_IsTokenPosInt(), s_IsUpdateNeeded(), s_ItemsToViews(), s_Join(), s_JoinAllThreads(), s_LnAss(), s_LnPerm(), INonAsnDataSource::s_LoadBlob(), s_loadSortedMatrix(), s_LocalQueryData2Packed_seqint(), s_LocateFrequencyData(), s_LogDerivative(), s_LogHitID(), s_LogSubHitID(), s_LowLevelInit(), s_MakeDegenerateBase(), s_MakeDomainString(), s_MakeEmptyResults(), s_MakeRandomDeflineSet(), s_MakeScore(), s_MakeStep(), s_MakeUniquenessVal(), s_Match_id(), s_MatchTitle(), s_MatrixMultiply(), s_MatrixSquare(), s_MBCountWordsInSubject_16_1(), s_MinhashSequences(), s_MinhashSequences2(), s_MoveDataToGarbage(), s_MTDataLoaderTest(), s_MTDataLoaderTest2(), s_MTSeqDBTest(), s_MTSeqDBTest2(), s_MTSeqDBTest3(), s_MultiplyByte(), s_NaHashLookupCountWordsInSubject_16_1(), s_NaHashLookupRemovePolyAWords(), s_NaHashLookupScanSubjectForWordCounts(), s_NaLookup(), s_Ncbi4naToNcbi2na(), s_NextClauseStop(), s_NextRow(), s_NextTokenStart(), s_NextTokenStop(), s_NodeToDistMat(), s_NormalizeTokens(), s_NuclSmithWaterman(), s_NuclUngappedExtend(), s_OctalToNum(), s_OpenIndexDB(), s_OrfExtension(), s_OutOfFrameAlignWithTraceback(), s_OutOfFrameGappedAlign(), s_OutputFeature(), s_PackLongPattern(), s_PackPattern(), s_ParseCaseVariant(), s_ParseNumber(), s_ParseResponse(), s_ParseTime(), CGenusSpeciesFixup::s_PermuteTaxname(), s_PHIGetExtraLongPattern(), s_PHIGetLongPattern(), s_PHIGetShortPattern(), s_PreFetchSeqs(), s_PrematureStopCodon(), s_PrevRow(), s_PrintBlocksState(), s_PrintTable(), s_PrintVector(), s_ProcessForStandby(), s_ProcessInstitutionCollectionCodeLine(), s_ProcessParameters(), s_ProcessSeqIdFilters(), s_ProcessSeqIDsForV5(), s_ProcessTaxIdFilters(), s_ProcessWBAddDel(), s_ProjectFolderClone(), s_PruneChains(), s_PSIDiscardIfUnused(), s_PSIPurgeNearIdenticalAlignments(), s_QueryVectorToBioseqSet(), s_QueryVectorToTSeqLocs(), s_ReadDistMatrix(), s_ReadPerClientConfig(), s_ReadRandParams(), s_RebuildEditScript(), s_RecordInitialSearch(), s_ReduceGaps(), s_ReleaseToFreePages(), s_RemoveAliasComponents(), s_RemoveFiles(), s_RemoveNonCSRAEntry(), s_RemovePolyAWords(), s_RemoveSpacesWithinNumbers(), s_ReplaceGIs(), s_ReplaceNonAlphaNum(), s_ReportDependenciesStatus(), s_RescaleSearch(), s_Reset(), s_ResLenNew(), s_ResLenOld(), s_ResPosNew(), s_ResPosOld(), s_RestoreCaseVariant(), s_RestoreSearch(), s_RestrictedGappedAlign(), s_ResVal(), CHitFilter< THit >::s_RunGreedy(), s_RunOfStars(), s_SavedParametersFree(), s_SavedParametersNew(), s_SaveSubjectOverhangs(), s_ScaleSquareMatrix(), s_ScoresStdAlphabet(), s_SearchPending(), s_SegSeq(), s_Select(), CMacroFunction_AutodefId::s_SelectModifiersforAutodefID(), s_SelectStallsafe(), s_Seq_align_Seq_loc(), s_SeqAlignSetToXMLHsps(), s_SeqDB_FindOffsets(), s_SeqDB_ReadLine(), s_SeqDbGetSequence(), s_SeqDBMapNA2ToNA4(), s_SeqDBMapNA2ToNA8Setup(), s_SeqDBMapNcbiNA8ToBlastNA8(), s_SeqDBMaskSequence(), s_SeqDBRebuildDNA_NA4(), s_SeqDBRebuildDNA_NA8(), s_SeqDbSetRanges(), s_SeqDBWriteSeqDataNucl(), s_SeqDBWriteSeqDataProt(), s_SeqEntropy(), s_SeqIntRevCmp(), s_SeqToProfilePosition(), s_SequenceGetProteinRange(), s_SerFlags(), s_SetAirrAlignmentInfo(), s_SetBSFromOS(), s_SetCloneInfo(), s_SetInitialMatrix(), s_SetOSFromBS(), s_SetPrimerNames(), s_SetPrimerSeqs(), s_SetTrnaProduct(), s_SetupHSPListBlastn(), s_SetupHSPListTransl(), s_SetupQueryInfoForReevaluateTest(), s_SetXUOScores(), s_ShiftGaps(), s_ShiftGapsRight(), s_ShiftTimers(), s_SmithWatermanScoreOnly(), s_SortChains(), s_SplitAccIndex(), s_SplitCommandLine(), s_StartAllThreads(), s_StartListening(), s_SThreadLocalDataArraySetGapXDropoffFinal(), s_StoreStartupParams(), s_StringToInt(), s_SwapRows(), s_TarChecksum(), s_TestAlignmentFromMSAs(), s_TestCalc(), s_TestClustersAndTrees(), s_TestClusterTree(), s_TestCreatePssmFromFreqs(), s_TestHSPRanges(), s_TestMaskingLimits(), s_TestNode(), s_TestPartialAmbig(), CSplign::s_TestPolyA(), s_TestQueriesAsBioseqs(), s_TestQueriesAsSeq_locs(), s_TestReadPDBAsn1(), s_TestResultAlignment(), s_TestToApplyREAdjustmentConditional(), s_ToIupacaa(), s_Tokenize(), s_TraceParams(), NAdapterSearch::s_Translate(), s_TranslateAndExpand(), s_Trim(), s_TrimHSP(), s_TrimResults(), s_Uint8ToString(), s_UpdateAdler32(), s_UpdateSeqAlnWithFilteredSeqIDs(), s_UpdateUpCoords(), s_UpdateVolumesInAliasFile(), s_UseSets(), s_ValidateCustomDelim(), s_ValidateMatrix(), CBlastSetupTestFixture::s_ValidateProtein130912(), s_ValidCodon(), s_ValToString(), s_VerbosityText(), s_WarnAboutIgnoredResidues(), s_Win_GetHandleTimes(), s_WrapOutputLine(), s_WriteComment(), s_WriteLine(), s_WriteToNamedPipe(), CBamDb::SAADBImpl::SAADBImpl(), sAbbreviate(), SAccGuide::SAccGuide(), sal0(), compile_time_bits::ct_crc32< poly >::SaltedHash(), CWGSDb_Impl::SAmbiguityInfo::SAmbiguityInfo(), impl::CDriverContext::SatisfyPoolMinimum(), CBDB_BlobDeMuxPersistent::Save(), alp::save_state(), SequenceViewer::SaveAlignment(), CTableDelimiterRules::SaveAsn(), SMMStat::SaveEndState(), CDbIndex_Factory::SaveHeader(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::SaveIdDeMux(), CDockManager::SaveLayout(), CMacroFlowEditor::SaveScript(), CFileLoadManager::SaveSettings(), CSequencingTechnologyPanel::SaveSettings(), CwxGridTableAdapter::SaveSettings(), CFileLoadWizard::SaveSettings(), COpenObjectsPanel::SaveSettings(), CTrackListCtrl::SaveSettings(), CWidgetDisplayStyle::SaveSettings(), CEditingBtnsPanel::SaveSettings(), CTextPanel::SaveState(), SrcEditDialog::SaveTableFile(), SaveTableFile(), SaveTableRowAsListFile(), CPhyloSelectionSetMgr::SaveToUserObject(), SBamRangeBlock::SBamRangeBlock(), SBaseStat::SBaseStat(), CImageUtil::Scale(), ScaledSymmetricProductA(), ScaleThdTbl(), TestFixture::ScanCheckHitsCore(), CObjectIStreamAsn::ScanEndOfId(), ScanForCpGs(), TestFixture::ScanOffsetTestCore(), SchedCheckOverloads(), SchedIsAllIdle(), rapidjson::internal::Schema< SchemaDocumentType >::Schema(), CWAM_Donor< order >::Score(), CWAM_Acceptor< order >::Score(), CWMM_Start::Score(), CWAM_Stop::Score(), CMC_NonCodingRegion< order >::Score(), CMC3_CodingRegion< order >::Score(), CCigar::Score(), CMarkovChainArray< order >::Score(), SPhyloCSFCompactScore::Score(), BlockExtender::scoreBlockPair(), ScoreByBlosum62(), ScoreByPSSM(), CChainer::CChainerImpl::ScoreCdnas(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), AlignmentUtility::ScoreRowByPSSM(), CCoiledCoil::ScoreToProb(), sDeleteIds(), CSeqSearch::Search(), CSRSearch_Impl< index_t >::search(), bm::xor_scanner< BV >::search_best_xor_mask(), bm::bvector< Alloc >::enumerator::search_in_blocks(), CSRSearch_Impl< index_t >::searchExact(), CSRSearch_Impl< index_t >::searchOneMismatch(), ResidueProfiles::segsToSet(), CAlnMultiWidget::Select(), bm::bvector< Alloc >::select(), select_rows(), CwxTableListCtrl::SelectAll(), CRegularGridGen::SelectBaseStep(), CGnomonEngine::SelectBestReadingFrame(), SeqTree::selectByGI(), CPhyloTree::SelectByRect(), SeqTree::selectByTax(), SequenceDisplay::SelectedRectangle(), CTableDataBioTreeContainer::SelectFeatures(), CFileLoadOptionPanel::SelectFormat(), CFileLoadPanel::SelectFormat(), ShowHideManager::SelectionChangedCallback(), CScriptPanel::SelectItem(), CScriptPanel::SelectMacros(), CCompareSeqRegions::SelectMatches(), CTreeCollisionModel2D::SelectNodes(), COpenDlg::SelectOptionByLabel(), CTableDataBioTreeContainer::SelectSeqIds(), CBDB_BlobDeMuxSplit::SelectSplit(), CTableDataBioTreeContainer::SelectTaxIds(), TaxTreeData::selectTaxNode(), SelectTest(), CDataMiningPanel::SelectToolByName(), CTL_BCPInCmd::Send(), CODBC_BCPInCmd::Send(), sendMTFValues(), CBrowserUtils::SendToBrowser(), SeqDB_CombineAndQuote(), SeqDB_ConvertOSPath(), SeqDB_SplitQuoted(), SeqDB_SplitString(), SeqDB_UnpackAmbiguities(), SeqDB_VectorAssign(), CDUpdater::SeqEntryHasSeqId(), SeqFeatPub(), CFeatureEdit::SeqIdEdited(), CRemoteBlastDbAdapter::SeqidToOidBatch(), CSeqDBImpl::SeqidToOids(), CSeqScores::SeqPtr(), variation::SeqsMatch(), SeqToDelta(), SeqTreeAPI::SeqTreeAPI(), Sequence::Sequence(), CTextPanel::SequenceListLoaded(), CFormatGuess::SequenceType(), Serial_GetAssignedMembers(), Serial_ResetMembers(), bm::serial_stream_iterator< DEC, BLOCK_IDX >::serial_stream_iterator(), SerializationCompressionLevelsTest(), SerializationTest(), CBDB_ExtBlobMap::Serialize(), CBDB_BlobMetaContainer::Serialize(), bm::serializer< BV >::serialize(), bm::compressed_collection_serializer< CBC >::serialize(), bm::sparse_vector_serializer< SV >::serialize(), SERV_Close(), SERV_Print(), SERV_ReadInfoEx(), CNamespace::Set(), CSDB_ConnectionParam::Set(), CNcbiEnvironment::Set(), CAlignmentCollectionScore::Set(), bm::blocks_manager< Alloc >::set_all_set(), bm::blocks_manager< Alloc >::set_all_zero(), bm::basic_bmatrix< BV >::set_allocator_pool(), bm::blocks_manager< Alloc >::set_block(), bm::blocks_manager< Alloc >::set_block_all_set(), bm::blocks_manager< Alloc >::set_block_all_set_no_check(), bm::blocks_manager< Alloc >::set_block_all_set_ptr(), bm::set_block_bits_u64(), bm::blocks_manager< Alloc >::set_block_ptr(), bm::rs_index< BVAlloc >::set_full_super_block(), bm::similarity_descriptor< SO, DMD_SZ, IDX_VALUE, SValue, SFunc >::set_metric(), bm::rs_index< BVAlloc >::set_null_super_block(), bm::sparse_vector_serial_layout< SV >::set_plane(), bm::bvector< Alloc >::set_range_no_check(), bm::rs_index< BVAlloc >::set_super_block(), bm::str_sparse_vector< CharType, BV, STR_SIZE >::set_value_no_null(), CCdCore::SetAccession(), CIgBlastTabularInfo::SetAirrFormatData(), SetAlignedResiduesForCD(), SetAlignedResiduesOnSequence(), MultipleAlignment::setAlignment(), BlockExtender::setAlignments(), CBDB_BufferManager::SetAllNull(), CAlnSpanWidget::SetAlnModel(), CAlnMap::SetAnchor(), CBlastDatabaseArgs::SetArgumentDescriptions(), CNWAligner::CBacktraceMatrix4::SetAt(), CPhyloTreeCalculator::SetAttrTable(), CReadDispatcher::SetBlobState(), CBroadcastVRChangeDialog::SetBroadcastFlag(), ASNDataManager::SetCDDNotes(), StructureSet::SetCenter(), CStringConstraintPanel::SetChoices(), CMacroAdvStringConstraintPanel< T >::SetChoices(), CLengthSubpanel::SetClusters(), CIDSubpanel::SetClusters(), CTextSubpanel::SetClusters(), CFileSubpanel::SetClusters(), CFieldSubpanel::SetClusters(), CFeatureTypeSubpanel::SetClusters(), CDescTypeSubpanel::SetClusters(), CMolInfoSubpanel::SetClusters(), CStructCommentSubpanel::SetClusters(), CUICommand::SetCmdID(), CPhyloTreeDataSource::SetCollapsedLabels(), CwxTableListCtrl::SetColumnOrder(), CApplyEditconvertPanel::SetColumns(), CAlnMultiRenderer::SetColumnsByStyle(), CSeqTableGridPanel::SetColumnSizesAndChoices(), CCSVSelectionExportDlg::SetColumnsList(), CwxCSVExportDlg::SetColumnsList(), CAlnMultiRenderer::SetColumnVisible(), CCdCore::SetComment(), CMSPeak::SetComputedCharge(), CChain::SetConfirmedEnds(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), CChain::SetConsistentCoverage(), CDemoApp::SetContainer(), SetConvertedSequencesForCD(), CIdDeMux< TBV, TBVFact >::SetCoordinatesFast(), CMacroPanelLoader::SetCtrlValue(), CBroadcastDialog::SetData(), CAppExplorerDataObject::SetData(), CwxTableListCtrl::SetDataRowsSelected(), CTableImportListCtrl::SetDataSource(), CQueryParsePanel::SetDataSource(), CClassTypeInfo::SetDefault(), SetErrorsAccessions(), COpenViewDlg::SetFactories(), CGeneFieldPanel::SetFieldName(), CMiscFieldPanel::SetFieldName(), CProteinFieldPanel::SetFieldName(), CCDSGeneProtFieldNamePanel::SetFieldName(), CFieldHandlerNamePanel::SetFieldName(), CRNAFieldNamePanel::SetFieldName(), CDualRNAFieldNamePanel::SetFieldName(), CTripleConstraintPanel< T >::SetFieldName(), CDualRNAFieldNamePanel::SetFieldName2(), CTripleConstraintPanel< T >::SetFieldNames(), CBlastTabularInfo::SetFields(), CStatusBar::SetFieldsCount(), CBamLoadOptionPanel::SetFilenames(), CSearchResultSet::SetFilteredQueryRegions(), CChainer::CChainerImpl::SetFlagsForChains(), CSeqTextFontList::SetFontSize(), CFileAutoLoader::SetFormatManager(), CFileLoadOptionPanel::SetFormats(), CRNAPanel::SetGBQualPanel(), CtRNASubPanel::SetGBQualPanel(), CChainer::CChainerImpl::SetGenomicRange(), CClassTypeInfo::SetGlobalHook(), CChoiceTypeInfo::SetGlobalHook(), CSplitter::SetHeights(), CGeneModel::SetIdent(), CIgBlastTabularInfo::SetIgAnnotation(), CMultiAligner::SetInputMSAs(), CSearch< LEGACY, NHITS >::SetIons(), pythonpp::CSequnceHelper< T >::SetItem(), CSelListModelImpl< Item >::SetItems(), CGrowableListCtrl::SetItems(), CwxScoreDlg::SetItems(), CSearch< LEGACY, NHITS >::SetLadderCalc(), CBamIndex::SetLengthFromHeader(), CPdfObject::SetLineDashStyle(), CDataSource::SetLoginTimeout(), CMacroParamsPanel::SetMacro(), CDesktopCanvas::SetMainItem(), CFileLoadPanel::SetManager(), COpenObjectsPanel::SetManagers(), COpenDlg::SetManagers(), CWriteDB_Impl::SetMaskedLetters(), CBlastQueryVector::SetMaskedRegions(), CSearch< LEGACY, NHITS >::SetMassAndMask(), CTimeMRUList< T >::SetMaxSize(), CFileLoadWizard::SetNextPage(), COrgName::SetNomenclature(), CTextTableModel::SetNumRows(), CStatement::SetParam(), CBuildOptionsDlg::SetParams(), CDB_Exception::SetParams(), CAlnPropertiesDlg::SetParams(), CAutodefOrgPanel::SetParams(), CFileLoadWizard::SetParentWindow(), CNWAligner::SetPattern(), variation::CVariationUtil::SetPlacementProperties(), CGlCurve< Curve >::SetPoint(), CGlTube< Curve >::SetPoint(), CCurveBezier::SetPoint(), CCurveCubic::SetPoint(), CChoicePointerTypeInfo::SetPointerType(), CMacroEditor::SetPositionAndSize(), CMacroFlowEditor::SetPositionAndSize(), CFileLoadWizard::SetPrevPage(), CIdDeMux< TBV, TBVFact >::SetProjection(), CTaxon2_data::SetProperty(), CMultiAligner::SetQueries(), CPhyTreeCalc::SetQuery(), CSegmentSmearGlyph::CSegMap::SetRange(), COpenDlg::SetRegistryPath(), COpenViewDlg::SetRegistryPath(), CRunToolDlg::SetRegistryPath(), CFileLoadManager::SetRegistryPath(), CFileLoadWizard::SetRegistryPath(), CSRSearch_Impl< index_t >::setResults4Idx(), CNetBlastLoadingJob::SetRIDs(), CRNAFieldNamePanel::SetRnaType(), CDualRNAFieldNamePanel::SetRnaType(), CAlnMultiModel::SetRowOrder(), CPSSMAligner::SetScoreMatrix(), CRandom::SetSeed(), CGridWidget::SetSelectAll(), CGridWidget::SetSelection(), TaxTreeData::setSelections(), CPhyloSaveSelectiondlg::SetSelections(), CPhyloSelectionSetMgr::SetSelectionSetProperty(), CIntronParameters::SetSeqLen(), CPSSMAligner::SetSequences(), CQualPanel< T1 >::SetShowLegalOnly(), pythonpp::CList::SetSlice(), CGeneModel::SetSplices(), CStatusBar::SetStatusWidths(), CMacroAddConstraint::SetStringSelection(), CTableDataSeq_table::SetStringValue(), CRBSubpanel::SetSubsets(), CBlobStoreBase::SetTableDescr(), COrg_ref::SetTaxId(), SetTest(), MultiTextDialog::SetToInitialText(), CValidError_imp::Setup(), CPssmInputTestData::SetupDuplicateHit(), NuclWordFinderTextFixture::setupExtendWord(), StructureWindow::SetupFavoritesMenu(), IBISAnnotateDialog::SetupGUIControls(), CPssmInputTestData::SetupHenikoffsPositionBasedSequenceWeights(), CRedoAlignmentTestFixture::setUpHSPList(), CPssmInputTestData::SetupMsaHasUnalignedRegion(), CPssmInputTestData::SetupNearIdenticalHits(), python::CCursor::SetupParameters(), SetupQueries_OMF(), CPssmInputTestData::SetupQueryAlignedWithInternalGaps(), SetupQueryInfo_OMF(), setupQueryInfoForOffsetTranslation(), CPssmInputTestData::SetupSelfHit(), SetupSubjects_OMF(), CMultipleAssemblyProgramPanel::SetValue(), CInferencePanel::SetValue(), CRptTypePanel::SetValue(), DynProgProb::setValueBegin(), DynProgProbLim::setValueBegin(), CwxGridTableAdapter::SetView(), CMergeVolumes::SetVolumes(), CSplitter::SetWidths(), CBoyerMooreMatcher::SetWordDelimiters(), CFileLoadWizard::SetWorkDir(), sFindBrackets(), sGenerateFields(), sgoi(), ShiftRotateTest(), BlockMultipleAlignment::ShiftRow(), ShortAndEscapedString(), CBioSource::ShouldIgnoreConflict(), CAttribTableDelimitersPanel::Show(), CTableDelimitersPanel::Show(), ShowHideDomain::Show(), BlockMultipleAlignment::ShowGeometryViolations(), AlignmentManager::ShowHideCallbackFunction(), ShowHideManager::ShowHideCallbackFunction(), ShowHideDialog::ShowHideDialog(), StructureSet::ShowRejects(), CBarcodeTool::ShowReport(), SequenceViewerWidget_TitleArea::ShowTitles(), AMatrix_base::Shrink(), CViewManagerService::ShutDownService(), bm::similarity_descriptor< SO, DMD_SZ, IDX_VALUE, SValue, SFunc >::similarity_descriptor(), CCacheDemoApp::SimpleCacheDemo(), SimpleGapFillSets(), SimpleRandomFillTest(), tree< T, tree_node_allocator >::size(), CArrayString< PREFIX >::Size(), CRangeMapBase< CRangeMultimapTraits< int, Mapped > >::size(), CGlBitmapFont::SizeFromInt(), CQueryParserEnv::Skip(), CDemoHook::SkipChoiceVariant(), CDemoHook::SkipClassMember(), TestFixture::SkipMaskedRangesCore(), SkipMixedContent(), CAgpErrEx::SkipMsg(), CBlastDbBlob::SkipPadBytes(), CObjectIStreamAsn::SkipSNumber(), CObjectIStreamXml::SkipSNumber(), CObjectIStreamAsn::SkipString(), CObjectIStreamAsn::SkipUNumber(), CObjectIStreamXml::SkipUNumber(), SkipWeasel(), bm::base_sparse_vector< Val, BV, 1 >::slice(), CSelListModelImpl< Item >::SLM_GetSelectedIndices(), CSelListModelImpl< Item >::SLM_GetSelectedItems(), CSelListModelImpl< Item >::SLM_SelectAll(), CSelListModelImpl< Item >::SLM_SelectItems(), CSelListModelImpl< Item >::SLM_SelectSingleItem(), CSelListModelImpl< Item >::SLM_SelectTo(), slo0(), SLoadTokens::SLoadTokens(), slor(), slou(), AMatrix_base::SlowCopy(), CFeatureGenerator::SImplementation::SMapper::SMapper(), SMatrix::SMatrix(), SmithWatermanScoreWithTraceback(), SNCChunkMaps::SNCChunkMaps(), SOCK_Poll(), SOCK_ReadLine(), SOCK_StringToHostPortEx(), SolveReNewtonSystem(), xml::node::sort(), xml::node::sort_fo(), bm::aggregator< BV >::sort_input_blocks_and(), bm::aggregator< BV >::sort_input_blocks_or(), CAlnMultiModel::SortByColumn(), CwxGridTableAdapter::SortByColumn(), UpdateViewer::SortByPSSM(), UpdateViewer::SortUpdates(), SourceFeatStructFillIn(), sp_who(), bm::sparse_vector_find_first_mismatch(), bm::sparse_vector_find_mismatch(), SparseSerializationTest(), CPoolOfThreads_ForServer::Spawn(), CPoolOfThreads< TRequest >::Spawn(), spci(), spea(), special_select(), SpecificHostCleanupCommand(), spel(), SpFeatKeyNameValid(), spinit(), CBlobSplitterImpl::Split(), CSplitter::Split(), CCustomTree::Split(), Split_Qscore_SeqGraph_By_DeltaSeq(), CBlobSplitterImpl::SplitBioseq(), CTableImportDataSource::SplitColumn(), CBlobSplitterImpl::SplitPieces(), SplitQueryBlkFree(), SplitQueryBlkNew(), SplitString(), AlignmentDisplay::SplitUnaligned(), spni(), sPrepareSeqAlign(), CWGSDb_Impl::SProtAccInfo::SProtAccInfo(), SprotAscii(), SprotIndex(), SPSG_IoCoordinator::SPSG_IoCoordinator(), sql_cmd(), SQLDisconnect(), SQLGetFunctions(), SrchCdRegion(), SrchKeyword(), sReadAA_M(), bm::sse2_bit_block_xor(), bm::sse2_gap_sum_arr(), bm::sse42_bit_block_xor(), bm::sse42_shift_r1_and(), SSeqTableContent::SSeqTableContent(), ssl_bitmask_check(), ssl_build_record_nonce(), ssl_parse_client_hello(), ssl_parse_encrypted_pms(), ssl_parse_server_hello(), ssl_prepare_record_content(), ssl_ticket_select_key(), ssl_write_client_hello(), CAlnStatGlyph::SStatStruct::SStatStruct(), CTcpWorkersList::Start(), bm::thread_pool< QValue, Lock >::start(), start_query(), CTestThread::StartCascadingThreads(), CSchedulerEngine::StartJob(), CPrimeNumberClient::StartJobs(), CNetBLASTUIDataSource::StartRetrievingTask(), CSeqScores::StartScore(), CConnTest::StatefulOkay(), CSeqTextPane::STG_SetSubtypesForFeature(), CTextSelHandler::STGH_GetMouseOverFeatureSubtypes(), CTextSelHandler::STGH_GetSelectedFeatureSubtypes(), SThreadLocalDataArrayConsolidateResults(), SThreadLocalDataArrayFree(), SThreadLocalDataArrayNew(), SThreadLocalDataArraySetup(), SThreadLocalDataArrayTrim(), CFeatureGenerator::SImplementation::StitchSmallHoles(), CSeqScores::StopScore(), CHMMParameters::SDetails::StoreParam(), mu::ParserByteCode::StorePtr(), CCompressionUtil::StoreUI4(), SBDB_BvStore_Id< TBV >::StoreVectorList(), str_icmp(), StressTest(), StressTestAggregatorAND(), StressTestAggregatorAND_SUB(), StressTestAggregatorOR(), StressTestAggregatorShiftAND(), StressTestStrSparseVector(), string_to_datetime(), string_to_numeric(), StringFrom2na(), StringFrom4na(), StringFromStdaa(), StringMatchIcase(), StringRStr(), StringToAscii(), CEnumParser< TEnum, TParam >::StringToEnum(), CDirEntry::StringToMode(), NStr::StringToNonNegativeInt(), CSeqUtils::StringToRange(), StringToVector(), CHTMLHelper::StripSpecialChars(), CSymResolver::StripSuffix(), rapidjson::internal::StrtodDiyFp(), StrToLower(), StructureObject::StructureObject(), SU_PSSMInput::SU_PSSMInput(), bm::rs_index< BVAlloc >::sub_count(), CMarkovChain< order >::SubChain(), CMarkovChain< 0 >::SubChain(), SubjectIndexFree(), SubjectIndexNew(), GroupUpdater::submitBlast(), CNetScheduleSubmitter::SubmitJobBatch(), SubOperationsTest(), substituteChar(), CCgiEntry::substr(), mu::Parser::Sum(), mu::ParserInt::Sum(), mu::Test::ParserTester::Sum(), bm::svector_check(), bm::blocks_manager< Alloc >::swap(), bm::bvmini< N >::swap(), bm::basic_bmatrix< BV >::swap_columns(), swap_numeric_endian(), CColorPanel::SwapColors(), CNcbiMatrix< T >::SwapRows(), CDense_seg::SwapRows(), SeqSwapper::swapSequences(), sx_AllDigits(), sx_Find_4na_Ambiguity(), sx_FindFirstNonZeroBit(), sx_FindNextNonZeroBit(), CSeqVectorTypes::sx_GetConvertTable(), sx_HasNonZero(), sx_IsNA(), sx_NewStringToNonNegativeInt(), CCompartmentFinder< THit >::sx_XFilter(), CBDB_BlobSplitStore< TBV, TObjDeMux, TL >::Sync(), CPhyloNodeData::Sync(), bm::xor_scanner< BV >::sync_nb_vect(), CTreeGraphicsModel::SyncBuffers(), CTableImportListCtrl::SynchDataSourceColumnWidths(), CAttribStringsMenuItem::SynchToUserValue(), CEditingBtnsPanel::TableReader(), CSequenceEditingEventHandler::TableReader(), CSequenceEditingEventHandler::TableReaderClipboard(), CEditingBtnsPanel::TableReaderFromClipboard(), CPriorityTaxNodes::TaxIdsToCddOrgRefSet(), CSeqDBImpl::TaxIdsToOids(), CSeqDBLMDBSet::TaxIdsToOids(), TaxonomyLookupCommand(), tdefl_flush_block(), tdefl_huffman_enforce_max_code_size(), tdefl_optimize_huffman_table(), tdefl_radix_sort_syms(), tdefl_start_dynamic_block(), tdefl_start_static_block(), tdefl_write_image_to_png_file_in_memory_ex(), tds5_fix_dot_query(), tds71_do_login(), tds71_read_table_names(), tds71_submit_prepexec(), tds7_bcp_send_colmetadata(), tds7_build_param_def_from_params(), tds7_build_param_def_from_query(), tds7_crypt_pass(), tds7_get_instance_ports(), tds7_put_query_params(), tds7_send_execute(), tds_alloc_row(), tds_answer_challenge(), tds_bcp_add_fixed_columns(), tds_bcp_add_variable_columns(), tds_bcp_init(), tds_bcp_send_record(), tds_bcp_start_copy_in(), tds_bcp_start_insert_stmt(), tds_char2hex(), tds_connect(), tds_convert_char(), tds_convert_numeric(), tds_cursor_open(), tds_datecrack(), tds_des_set_key(), tds_des_set_odd_parity(), tds_find(), tds_free_compute_results(), tds_free_results(), tds_get_dynid(), tds_getmac(), tds_iconv_alloc(), tds_iconv_close(), tds_iconv_free(), tds_iconv_get_info(), tds_iconv_init(), tds_msdatetime_get(), tds_numeric_change_prec_scale(), tds_numeric_to_string(), tds_packet_check_overflow(), tds_process_compute(), tds_process_compute_result(), tds_process_nbcrow(), tds_process_params_result_token(), tds_process_row(), tds_process_tabname(), tds_put_int(), tds_put_int8(), tds_put_param_as_string(), tds_put_params(), tds_quote_and_put(), tds_quote_id(), tds_random_buffer(), tds_read_conf_section(), tds_row_free(), tds_send_emulated_execute(), tds_send_emulated_rpc(), tds_set_iconv_name(), tds_set_server(), tds_submit_execdirect(), tds_submit_query_params(), tds_submit_rpc(), tds_sys_iconv_open(), tds_vstrbuild(), tdsdump_do_dump_buf(), test(), Test(), test0(), Test0(), test_file(), bm::aggregator< BV >::test_gap_blocks_and(), bm::aggregator< BV >::test_gap_blocks_sub(), CThreadedApp::TestApp_GlobalSyncPoint(), TestArraysAndBuffers(), TestBlockAND(), TestBlockCountChange(), TestBlockCountXORChange(), TestBlockDigest(), TestBlockLast(), TestBlockOR(), TestBlockSUB(), TestBlockToGAP(), TestBlockZero(), TestCompressedCollection(), TestCompressedSparseVectorAlgo(), TestCompressedSparseVectorScan(), TestCompressedSparseVectorScanGT(), TestCompressSparseGather(), TestCompressSparseSignedVector(), TestCompressSparseVector(), TestCompressSparseVectorSerial(), TestEqualSparseVectors(), TestFindBlockDiff(), TestFindFirst(), CFormatGuess::TestFormatBinaryAsn(), CFormatGuess::TestFormatDistanceMatrix(), CFormatGuess::TestFormatFlatFileEna(), CFormatGuess::TestFormatFlatFileUniProt(), CFormatGuess::TestFormatNewick(), CFormatGuess::TestFormatXml(), CTreeCollisionModel2D::TestForNode(), TestHasZeroByte(), TestHeapVector(), CTableViewFactory::TestInputObjects(), CProjectTableViewFactory::TestInputObjects(), CAlignSpanViewFactory::TestInputObjects(), CAlnSummaryViewFactory::TestInputObjects(), CAnnotCompareViewFactory::TestInputObjects(), CCrossAlignViewFactory::TestInputObjects(), CDotMatrixViewFactory::TestInputObjects(), CMPCrossAlignViewFactory::TestInputObjects(), CPhyTreeViewFactory::TestInputObjects(), CSeqTextViewFactory::TestInputObjects(), CVcfTableViewFactory::TestInputObjects(), CFeatTableViewFactory::TestInputObjects(), CViewGraphicFactory::TestInputObjects(), CSequinDesktopViewFactory::TestInputObjects(), CTextViewFactory::TestInputObjects(), TestMapping_ThroughAlignments(), TestMTWriter(),