lex.newick.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: lex.newick.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 18:09:27  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

#include <ncbi_pch.hpp>

#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

#line 19 "lex.newick.cpp"
/* A lexical scanner generated by flex */

/* Scanner skeleton version:
 * $Header: /src/NCBI/vault.ncbi/production/c++/src/algo/phy_tree/lex.newick.cpp,v 1000.1 2004/06/01 18:09:27 gouriano Exp $
 */

#define FLEX_SCANNER
#define YY_FLEX_MAJOR_VERSION 2
#define YY_FLEX_MINOR_VERSION 5


#include <stdio.h>


/* cfront 1.2 defines "c_plusplus" instead of "__cplusplus" */
#ifdef c_plusplus
#ifndef __cplusplus
#define __cplusplus
#endif
#endif


#ifdef __cplusplus

#include <stdlib.h>

/* Use prototypes in function declarations. */
#define YY_USE_PROTOS

/* The "const" storage-class-modifier is valid. */
#define YY_USE_CONST

#else	/* ! __cplusplus */

#if __STDC__

#define YY_USE_PROTOS
#define YY_USE_CONST

#endif	/* __STDC__ */
#endif	/* ! __cplusplus */

#ifdef __TURBOC__
 #pragma warn -rch
 #pragma warn -use
#include <io.h>
#include <stdlib.h>
#define YY_USE_CONST
#define YY_USE_PROTOS
#endif

#ifdef YY_USE_CONST
#define yyconst const
#else
#define yyconst
#endif


#ifdef YY_USE_PROTOS
#define YY_PROTO(proto) proto
#else
#define YY_PROTO(proto) ()
#endif

/* Returned upon end-of-file. */
#define YY_NULL 0

/* Promotes a possibly negative, possibly signed char to an unsigned
 * integer for use as an array index.  If the signed char is negative,
 * we want to instead treat it as an 8-bit unsigned char, hence the
 * double cast.
 */
#define YY_SC_TO_UI(c) ((unsigned int) (unsigned char) c)

/* Enter a start condition.  This macro really ought to take a parameter,
 * but we do it the disgusting crufty way forced on us by the ()-less
 * definition of BEGIN.
 */
#define BEGIN yy_start = 1 + 2 *

/* Translate the current start state into a value that can be later handed
 * to BEGIN to return to the state.  The YYSTATE alias is for lex
 * compatibility.
 */
#define YY_START ((yy_start - 1) / 2)
#define YYSTATE YY_START

/* Action number for EOF rule of a given start state. */
#define YY_STATE_EOF(state) (YY_END_OF_BUFFER + state + 1)

/* Special action meaning "start processing a new file". */
#define YY_NEW_FILE yyrestart( yyin )

#define YY_END_OF_BUFFER_CHAR 0

/* Size of default input buffer. */
#define YY_BUF_SIZE 16384

typedef struct yy_buffer_state *YY_BUFFER_STATE;

extern int yyleng;
extern FILE *yyin, *yyout;

#define EOB_ACT_CONTINUE_SCAN 0
#define EOB_ACT_END_OF_FILE 1
#define EOB_ACT_LAST_MATCH 2

/* The funky do-while in the following #define is used to turn the definition
 * int a single C statement (which needs a semi-colon terminator).  This
 * avoids problems with code like:
 *
 * 	if ( condition_holds )
 *		yyless( 5 );
 *	else
 *		do_something_else();
 *
 * Prior to using the do-while the compiler would get upset at the
 * "else" because it interpreted the "if" statement as being all
 * done when it reached the ';' after the yyless() call.
 */

/* Return all but the first 'n' matched characters back to the input stream. */

#define yyless(n) \
	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 )

#define unput(c) yyunput( c, yytext_ptr )

/* The following is because we cannot portably get our hands on size_t
 * (without autoconf's help, which isn't available because we want
 * flex-generated scanners to compile on their own).
 */
typedef unsigned int yy_size_t;


struct yy_buffer_state
	{
	FILE *yy_input_file;

	char *yy_ch_buf;		/* input buffer */
	char *yy_buf_pos;		/* current position in input buffer */

	/* Size of input buffer in bytes, not including room for EOB
	 * characters.
	 */
	yy_size_t yy_buf_size;

	/* Number of characters read into yy_ch_buf, not including EOB
	 * characters.
	 */
	int yy_n_chars;

	/* Whether we "own" the buffer - i.e., we know we created it,
	 * and can realloc() it to grow it, and should free() it to
	 * delete it.
	 */
	int yy_is_our_buffer;

	/* Whether this is an "interactive" input source; if so, and
	 * if we're using stdio for input, then we want to use getc()
	 * instead of fread(), to make sure we stop fetching input after
	 * each newline.
	 */
	int yy_is_interactive;

	/* Whether we're considered to be at the beginning of a line.
	 * If so, '^' rules will be active on the next match, otherwise
	 * not.
	 */
	int yy_at_bol;

	/* Whether to try to fill the input buffer when we reach the
	 * end of it.
	 */
	int yy_fill_buffer;

	int yy_buffer_status;
#define YY_BUFFER_NEW 0
#define YY_BUFFER_NORMAL 1
	/* When an EOF's been seen but there's still some text to process
	 * then we mark the buffer as YY_EOF_PENDING, to indicate that we
	 * shouldn't try reading from the input source any more.  We might
	 * still have a bunch of tokens to match, though, because of
	 * possible backing-up.
	 *
	 * When we actually see the EOF, we change the status to "new"
	 * (via yyrestart()), so that the user can continue scanning by
	 * just pointing yyin at a new input file.
	 */
#define YY_BUFFER_EOF_PENDING 2
	};

static YY_BUFFER_STATE yy_current_buffer = 0;

/* We provide macros for accessing buffer states in case in the
 * future we want to put the buffer states in a more general
 * "scanner state".
 */
#define YY_CURRENT_BUFFER yy_current_buffer


/* yy_hold_char holds the character lost when yytext is formed. */
static char yy_hold_char;

static int yy_n_chars;		/* number of characters read into yy_ch_buf */


int yyleng;

/* Points to current character in buffer. */
static char *yy_c_buf_p = (char *) 0;
static int yy_init = 1;		/* whether we need to initialize */
static int yy_start = 0;	/* start state number */

/* Flag which is used to allow yywrap()'s to do buffer switches
 * instead of setting up a fresh yyin.  A bit of a hack ...
 */
static int yy_did_buffer_switch_on_eof;

void yyrestart YY_PROTO(( FILE *input_file ));

void yy_switch_to_buffer YY_PROTO(( YY_BUFFER_STATE new_buffer ));
void yy_load_buffer_state YY_PROTO(( void ));
YY_BUFFER_STATE yy_create_buffer YY_PROTO(( FILE *file, int size ));
void yy_delete_buffer YY_PROTO(( YY_BUFFER_STATE b ));
void yy_init_buffer YY_PROTO(( YY_BUFFER_STATE b, FILE *file ));
void yy_flush_buffer YY_PROTO(( YY_BUFFER_STATE b ));
#define YY_FLUSH_BUFFER yy_flush_buffer( yy_current_buffer )

YY_BUFFER_STATE yy_scan_buffer YY_PROTO(( char *base, yy_size_t size ));
YY_BUFFER_STATE yy_scan_string YY_PROTO(( yyconst char *yy_str ));
YY_BUFFER_STATE yy_scan_bytes YY_PROTO(( yyconst char *bytes, int len ));

static void *yy_flex_alloc YY_PROTO(( yy_size_t ));
static void *yy_flex_realloc YY_PROTO(( void *, yy_size_t ));
static void yy_flex_free YY_PROTO(( void * ));

#define yy_new_buffer yy_create_buffer

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

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

#define YY_AT_BOL() (yy_current_buffer->yy_at_bol)


#define yywrap() 1
#define YY_SKIP_YYWRAP
typedef unsigned char YY_CHAR;
FILE *yyin = (FILE *) 0, *yyout = (FILE *) 0;
typedef int yy_state_type;
extern char *yytext;
#define yytext_ptr yytext

static yy_state_type yy_get_previous_state YY_PROTO(( void ));
static yy_state_type yy_try_NUL_trans YY_PROTO(( yy_state_type current_state ));
static int yy_get_next_buffer YY_PROTO(( void ));
static void yy_fatal_error YY_PROTO(( yyconst char msg[] ));

/* Done after the current pattern has been matched and before the
 * corresponding action - sets up yytext.
 */
#define YY_DO_BEFORE_ACTION \
	yytext_ptr = yy_bp; \
	yyleng = (int) (yy_cp - yy_bp); \
	yy_hold_char = *yy_cp; \
	*yy_cp = '\0'; \
	yy_c_buf_p = yy_cp;

#define YY_NUM_RULES 7
#define YY_END_OF_BUFFER 8
static yyconst short int yy_accept[26] =
    {   0,
        4,    4,    4,    4,    8,    3,    2,    2,    6,    6,
        5,    3,    3,    1,    3,    0,    4,    3,    1,    1,
        0,    3,    3,    1,    0
    } ;

static yyconst int yy_ec[256] =
    {   0,
        1,    1,    1,    1,    1,    1,    1,    1,    2,    3,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    2,    1,    1,    1,    1,    1,    1,    4,    5,
        5,    1,    6,    5,    6,    7,    1,    8,    8,    8,
        8,    8,    8,    8,    8,    8,    8,    9,    5,    1,
        1,    1,    1,    1,    1,    1,    1,    1,   10,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        5,    1,    5,    1,    1,    1,    1,    1,    1,    1,

       10,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,

        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        1,    1,    1,    1,    1
    } ;

static yyconst int yy_meta[11] =
    {   0,
        1,    2,    2,    2,    2,    1,    1,    1,    2,    1
    } ;

static yyconst short int yy_base[28] =
    {   0,
        0,    0,    5,    0,   28,    0,   29,   29,   23,   29,
       29,    7,   18,    0,    0,   21,   20,    0,    0,   13,
       18,   10,   13,    0,   29,   16,   18
    } ;

static yyconst short int yy_def[28] =
    {   0,
       25,    1,    1,    3,   25,   26,   25,   25,   27,   25,
       25,   26,   26,   12,   26,   27,   25,   13,   12,   13,
       27,   13,   13,   23,    0,   25,   25
    } ;

static yyconst short int yy_nxt[40] =
    {   0,
        6,    7,    8,    9,   10,    6,    6,    6,   11,    6,
       12,   13,   14,   18,   19,   23,   15,   24,   16,   16,
       24,   17,   22,   21,   17,   20,   17,   25,    5,   25,
       25,   25,   25,   25,   25,   25,   25,   25,   25
    } ;

static yyconst short int yy_chk[40] =
    {   0,
        1,    1,    1,    1,    1,    1,    1,    1,    1,    1,
        3,    3,    3,   12,   12,   22,   26,   22,   27,   27,
       23,   21,   20,   17,   16,   13,    9,    5,   25,   25,
       25,   25,   25,   25,   25,   25,   25,   25,   25
    } ;

static yy_state_type yy_last_accepting_state;
static char *yy_last_accepting_cpos;

/* The intent behind this definition is that it'll catch
 * any uses of REJECT which flex missed.
 */
#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
char *yytext;
#line 1 "newick.lpp"
#define INITIAL 0
/*  $Id: lex.newick.cpp,v 1000.1 2004/06/01 18:09:27 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Josh Cherry
 *
 * File Description:  flex lexer for Newick format phylogenetic trees
 *
 */
/*
 * Meant to be used in conjunction with bison parser defined
 * by newick.ypp.  Generate code using (essentially)
 *   flex -olex.newick.cpp newick.lpp
 *   bison -d -p newick newick.ypp
 * The line '#include <unistd.h>' must be removed from the flex-generated
 * code for it to compile on some platforms.
 */
#line 44 "newick.lpp"
#include <string.h>
#include <util/stream_utils.hpp>
#include <algo/phy_tree/phy_node.hpp>

USING_SCOPE(ncbi);

#include "newick.tab.hpp"

static string g_Buffer;

// input from a stream
extern CNcbiIstream *g_NewickIstr;
#define YY_INPUT(buf, result, max_size) \
{ \
    result = CStreamUtils::Readsome(*g_NewickIstr, buf, max_size); \
    if (result == 0 && !*g_NewickIstr) { \
        result = YY_NULL; \
    } \
}

#define YY_NEVER_INTERACTIVE 1
#define EXPECT_NUM 1

#line 458 "lex.newick.cpp"

/* Macros after this point can all be overridden by user definitions in
 * section 1.
 */

#ifndef YY_SKIP_YYWRAP
#ifdef __cplusplus
extern "C" int yywrap YY_PROTO(( void ));
#else
extern int yywrap YY_PROTO(( void ));
#endif
#endif

#ifndef YY_NO_UNPUT
static void yyunput YY_PROTO(( int c, char *buf_ptr ));
#endif

#ifndef yytext_ptr
static void yy_flex_strncpy YY_PROTO(( char *, yyconst char *, int ));
#endif

#ifdef YY_NEED_STRLEN
static int yy_flex_strlen YY_PROTO(( yyconst char * ));
#endif

#ifndef YY_NO_INPUT
#ifdef __cplusplus
static int yyinput YY_PROTO(( void ));
#else
static int input YY_PROTO(( void ));
#endif
#endif

#if YY_STACK_USED
static int yy_start_stack_ptr = 0;
static int yy_start_stack_depth = 0;
static int *yy_start_stack = 0;
#ifndef YY_NO_PUSH_STATE
static void yy_push_state YY_PROTO(( int new_state ));
#endif
#ifndef YY_NO_POP_STATE
static void yy_pop_state YY_PROTO(( void ));
#endif
#ifndef YY_NO_TOP_STATE
static int yy_top_state YY_PROTO(( void ));
#endif

#else
#define YY_NO_PUSH_STATE 1
#define YY_NO_POP_STATE 1
#define YY_NO_TOP_STATE 1
#endif

#ifdef YY_MALLOC_DECL
YY_MALLOC_DECL
#else
#if __STDC__
#ifndef __cplusplus
#include <stdlib.h>
#endif
#else
/* Just try to get by without declaring the routines.  This will fail
 * miserably on non-ANSI systems for which sizeof(size_t) != sizeof(int)
 * or sizeof(void*) != sizeof(int).
 */
#endif
#endif

/* Amount of stuff to slurp up with each read. */
#ifndef YY_READ_BUF_SIZE
#define YY_READ_BUF_SIZE 8192
#endif

/* Copy whatever the last rule matched to the standard output. */

#ifndef ECHO
/* This used to be an fputs(), but since the string might contain NUL's,
 * we now use fwrite().
 */
#define ECHO (void) fwrite( yytext, yyleng, 1, yyout )
#endif

/* Gets input and stuffs it into "buf".  number of characters read, or YY_NULL,
 * is returned in "result".
 */
#ifndef YY_INPUT
#define YY_INPUT(buf,result,max_size) \
	if ( yy_current_buffer->yy_is_interactive ) \
		{ \
		int c = '*', n; \
		for ( n = 0; n < max_size && \
			     (c = getc( yyin )) != EOF && c != '\n'; ++n ) \