#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.

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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 )

◆ for() [1/2]

for ( )

◆ for() [2/2]

for ( len = 0;yy_str[len];++len )

◆ 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_bind_data(), _ct_handle_client_message(), _ct_handle_server_message(), hashtable< _Val, _Key, _HF, _ExK, _EqK, _All >::_M_copy_from(), _pcre2_check_escape(), _SQLFetch(), _SQLGetDiagField(), Messenger::AddHighlights(), CTL_Cmd::AssignCmdParam(), BLAST_LinkHsps(), BLAST_PreliminarySearchEngine(), BlastChooseNaExtend(), BlastNaWordFinder(), blk_bind(), buffer_add_row(), CPhyloTreePS::CalcForces(), CConnTest::CheckFWConnections(), CkSegmentSet(), 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(), decode_modifiers(), deflate_stored(), deflateInit2_(), deflateResetKeep(), detect_far_jump_type(), detect_jump_type(), AlignmentUtility::DoIBM(), DoSocketWait(), DP_GlobalBlockAlign(), DP_GlobalBlockAlignGeneric(), emit_non_commutative(), 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(), JumperNaWordFinder(), LookupTableOptionsNew(), CTable2AsnContext::MakeGenomeCenterId(), MD4Final(), MD4Update(), MD5Final(), 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(), odbc_tds2sql_col(), bm::bvector< Alloc >::optimize_gap_size(), parse_regex(), pcre2_compile(), pcre2_jit_compile(), pcre2_regexec(), process_pattern(), CTbl2AsnApp::ProcessTopEntry(), CBDB_Cache::Purge(), QSIndex(), python::RetrieveModuleFileName(), rtrim_bcpcol(), 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_type_bits(), CHistogramGlyph::SetAxisRange(), CBamCoverageGraphPanel::SetBamFiles(), bm::bvector< Alloc >::enumerator::skip(), SPHIPatternSearchBlkNew(), SQLGetData(), SQLGetTypeInfo(), tdefl_compress_normal(), tdefl_flush_block(), tds_datecrack(), tds_generic_get(), tds_money_to_string(), tds_msdatetime_put(), tds_mstabletype_put(), tds_numeric_put(), tds_process_login_tokens(), tds_process_loginack(), tds_put_char_param_as_string(), tds_put_param_as_string(), tds_row_free(), tds_sybbigtime_put(), tds_variant_get(), test(), CPhyloTreePS::Update(), updatewindow(), VDBSRC_GetSeq2na(), x_AddInfo(), CPhyloTreePS::x_ApplyRepulsiveForcesHashed(), CBlobCacher::x_CacheMapRecs(), CBlobCacher::x_CacheMetaRec(), x_DataToGiData(), x_Finalize(), 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.

◆ 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(), and s_DynamicSGenCodeNodeArray_BinSearch().

◆ yy_fatal_error() [1/2]

static void yy_fatal_error ( )

static

◆ yy_fatal_error() [2/2]

static void yy_fatal_error ( msg )

static

References msg().

◆ yy_flex_alloc() [1/2]

static void* yy_flex_alloc ( )

static

◆ yy_flex_alloc() [2/2]

static void* yy_flex_alloc ( size )

static

References malloc(), and 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

References free().

◆ 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.

◆ buf

buf[len]

Initial value:

{

YY_BUFFER_STATE b

b

Definition: lex.newick.cpp:1285

yy_buffer_state

Definition: lex.newick.cpp:163

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.

◆ file

FILE* file

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

◆ 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.

◆ len

int len

Definition at line 1450 of file lex.newick.cpp.

◆ n

n = len + 2

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

Definition at line 1455 of file lex.newick.cpp.

◆ newick_create_buffer

YY_BUFFER_STATE newick_create_buffer(file, size) FILE *file	(	file	,
		size
	)

◆ newick_scan_buffer

YY_BUFFER_STATE newick_scan_buffer(base, size) char *base	(	base	,
		size
	)

◆ newick_scan_bytes

YY_BUFFER_STATE newick_scan_bytes(bytes, len) char *bytes	(	bytes	,
		len
	)

◆ newick_scan_string

YY_BUFFER_STATE newick_scan_string(yy_str) char *yy_str ( yy_str )

◆ newickin

FILE * newickin = (FILE *) 0

Definition at line 286 of file lex.newick.cpp.

◆ newickleng

int newickleng

Definition at line 234 of file lex.newick.cpp.

◆ newickout

FILE * newickout = (FILE *) 0

Definition at line 120 of file lex.newick.cpp.

◆ newicktext

char * newicktext

Definition at line 392 of file lex.newick.cpp.

◆ size

yy_size_t size

Definition at line 1280 of file lex.newick.cpp.

Referenced by yy_flex_alloc(), and yy_flex_realloc().

◆ yy_accept

short int yy_accept[26]

static

Initial value:

=
    {   0,
        4,    4,    4,    4,    8,    3,    2,    2,    6,    6,
        5,    3,    3,    1,    3,    0,    4,    3,    1,    1,
        3,    0,    3,    1,    0
    }

Definition at line 308 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

◆ yy_at_bol

b yy_at_bol = 1

Definition at line 1381 of file lex.newick.cpp.

◆ yy_base

short int yy_base[28]

static

Initial value:

=
    {   0,
        0,    0,    5,    0,   29,    0,   30,   30,   24,   30,
       30,    7,   19,   16,    0,   21,   20,    0,    0,   13,
       10,   18,   13,    0,   30,   16,   18
    }

Definition at line 352 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

◆ yy_buf_pos

b yy_buf_pos = &b->yy_ch_buf[0]

Definition at line 1379 of file lex.newick.cpp.

◆ yy_buf_size

b yy_buf_size = size

Definition at line 1289 of file lex.newick.cpp.

◆ yy_buffer_status

b yy_buffer_status = 0

Definition at line 1382 of file lex.newick.cpp.

◆ yy_c

YY_CHAR yy_c = 1

Definition at line 1080 of file lex.newick.cpp.

Referenced by newicklex(), while(), and yy_get_previous_state().

◆ yy_c_buf_p

char* yy_c_buf_p = (char *) 0

static

Definition at line 237 of file lex.newick.cpp.

Referenced by if(), input(), newick_load_buffer_state(), newicklex(), yy_get_next_buffer(), and yy_get_previous_state().

◆ yy_ch_buf

b yy_ch_buf = (char *) yy_flex_alloc( b->yy_buf_size + 2 )

Definition at line 1294 of file lex.newick.cpp.

Referenced by input(), and newicklex().

◆ yy_chk

short int yy_chk[41]

static

Initial value:

=
    {   0,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        3,    3,    3,   12,   12,   21,   26,   21,   27,   27,
       23,   22,   20,   17,   16,   14,   13,    9,    5,   25,
       25,   25,   25,   25,   25,   25,   25,   25,   25,   25
    }

Definition at line 374 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

◆ yy_cp

char* yy_cp = yy_c_buf_p

Definition at line 1078 of file lex.newick.cpp.

Referenced by if(), newicklex(), and yy_get_previous_state().

◆ yy_current_buffer

yy_current_buffer = 0

static

Definition at line 219 of file lex.newick.cpp.

Referenced by if(), newick_load_buffer_state(), newick_switch_to_buffer(), newicklex(), newickrestart(), and yy_get_next_buffer().

◆ yy_current_state

yy_current_state = yy_nxt[yy_base[yy_current_state] + (unsigned int) yy_c]

Definition at line 1092 of file lex.newick.cpp.

Referenced by if(), newicklex(), while(), and yy_get_previous_state().

◆ yy_def

short int yy_def[28]

static

Initial value:

=
    {   0,
       25,    1,    1,    3,   25,   26,   25,   25,   27,   25,
       25,   26,   26,   12,   26,   27,   25,   13,   14,   13,
       13,   27,   13,   23,    0,   25,   25
    }

Definition at line 359 of file lex.newick.cpp.

Referenced by newicklex(), while(), and yy_get_previous_state().

◆ yy_did_buffer_switch_on_eof

yy_did_buffer_switch_on_eof = 1

static

Definition at line 244 of file lex.newick.cpp.

Referenced by input(), and newicklex().

◆ yy_ec

int yy_ec[256]

static

Definition at line 315 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

◆ yy_fill_buffer

b yy_fill_buffer = 1

Definition at line 1345 of file lex.newick.cpp.

◆ yy_hold_char

char yy_hold_char

static

Definition at line 229 of file lex.newick.cpp.

Referenced by if(), input(), newick_load_buffer_state(), and newicklex().

◆ yy_init

int yy_init = 1

static

Definition at line 238 of file lex.newick.cpp.

Referenced by newicklex().

◆ yy_input_file

b yy_input_file = file

Definition at line 1344 of file lex.newick.cpp.

◆ yy_is_interactive

b yy_is_interactive = 0

Definition at line 1351 of file lex.newick.cpp.

◆ yy_is_jam

return yy_is_jam = (yy_current_state == 25)

Definition at line 1093 of file lex.newick.cpp.

Referenced by yy_try_NUL_trans().

◆ yy_is_our_buffer

b yy_is_our_buffer = 1

Definition at line 1298 of file lex.newick.cpp.

◆ yy_last_accepting_cpos

char* yy_last_accepting_cpos

static

Definition at line 383 of file lex.newick.cpp.

Referenced by if(), newicklex(), and yy_get_previous_state().

◆ yy_last_accepting_state

yy_state_type yy_last_accepting_state

static

Definition at line 382 of file lex.newick.cpp.

Referenced by if(), newicklex(), and yy_get_previous_state().

◆ yy_meta

int yy_meta[11]

static

Initial value:

=
    {   0,
        1,    2,    2,    2,    2,    1,    1,    1,    2,    1
    }

Definition at line 347 of file lex.newick.cpp.

Referenced by newicklex(), while(), and yy_get_previous_state().

◆ yy_n_chars

b yy_n_chars = 0

static

Definition at line 231 of file lex.newick.cpp.

Referenced by if(), input(), newick_load_buffer_state(), newicklex(), and yy_get_next_buffer().

◆ yy_nxt

short int yy_nxt[41]

static

Initial value:

=
    {   0,
        6,    7,    8,    9,   10,    6,    6,    6,   11,    6,
       12,   13,   14,   18,   19,   23,   15,   24,   16,   16,
       24,   17,   21,   22,   17,   21,   20,   17,   25,    5,
       25,   25,   25,   25,   25,   25,   25,   25,   25,   25
    }

Definition at line 366 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

◆ yy_start

int yy_start = 0

static

Definition at line 239 of file lex.newick.cpp.

Referenced by newicklex(), and yy_get_previous_state().

Classes

Macros

Typedefs

Functions

Variables

Macro Definition Documentation

◆ BEGIN

◆ ECHO

◆ EOB_ACT_CONTINUE_SCAN

◆ EOB_ACT_END_OF_FILE

◆ EOB_ACT_LAST_MATCH

◆ EXPECT_NUM

◆ FLEX_SCANNER

◆ INITIAL

◆ REJECT

◆ unput

◆ YY_AT_BOL

◆ YY_BREAK

◆ YY_BUF_SIZE

◆ YY_BUFFER_EOF_PENDING

◆ YY_BUFFER_NEW

◆ YY_BUFFER_NORMAL

◆ yy_create_buffer

◆ YY_CURRENT_BUFFER

◆ YY_DECL

◆ yy_delete_buffer

◆ YY_DO_BEFORE_ACTION

◆ YY_END_OF_BUFFER

◆ YY_END_OF_BUFFER_CHAR

◆ YY_EXIT_FAILURE

◆ YY_FATAL_ERROR

◆ yy_flex_debug

◆ YY_FLEX_MAJOR_VERSION

◆ YY_FLEX_MINOR_VERSION

◆ yy_flush_buffer

◆ YY_FLUSH_BUFFER

◆ yy_init_buffer

◆ YY_INPUT

◆ yy_load_buffer_state

◆ YY_MORE_ADJ

◆ YY_NEVER_INTERACTIVE

◆ yy_new_buffer

◆ YY_NEW_FILE

◆ YY_NO_POP_STATE

◆ YY_NO_PUSH_STATE

◆ YY_NO_TOP_STATE

◆ YY_NO_UNPUT

◆ YY_NULL

◆ YY_NUM_RULES

◆ YY_PROTO

◆ YY_READ_BUF_SIZE

◆ YY_RESTORE_YY_MORE_OFFSET

◆ YY_RULE_SETUP

◆ YY_SC_TO_UI

◆ yy_scan_buffer

◆ yy_scan_bytes

◆ yy_scan_string

◆ yy_set_bol

◆ yy_set_interactive

◆ YY_SKIP_YYWRAP

◆ YY_START

◆ YY_START_STACK_INCR

◆ YY_STATE_EOF

◆ yy_switch_to_buffer

◆ YY_USER_ACTION

◆ yyconst

◆ yyin

◆ yyleng

◆ yyless [1/2]

◆ yyless [2/2]

◆ yylex

◆ yymore

◆ yyout

◆ yyrestart

◆ YYSTATE

◆ yyterminate

◆ yytext

◆ yytext_ptr

◆ yywrap

Typedef Documentation