This file is indexed.

/usr/include/rostlab/blast-parser-parser.h is in librostlab-blast0-dev 1.0.1-5.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
// A Bison parser, made by GNU Bison 3.0.2.

// Skeleton interface for Bison LALR(1) parsers in C++

// Copyright (C) 2002-2013 Free Software Foundation, Inc.

// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.

// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.

// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.

// As a special exception, you may create a larger work that contains
// part or all of the Bison parser skeleton and distribute that work
// under terms of your choice, so long as that work isn't itself a
// parser generator using the skeleton or a modified version thereof
// as a parser skeleton.  Alternatively, if you modify or redistribute
// the parser skeleton itself, you may (at your option) remove this
// special exception, which will cause the skeleton and the resulting
// Bison output files to be licensed under the GNU General Public
// License without this special exception.

// This special exception was added by the Free Software Foundation in
// version 2.2 of Bison.

/**
 ** \file y.tab.h
 ** Define the rostlab::blast::parser class.
 */

// C++ LALR(1) parser skeleton written by Akim Demaille.

#ifndef YY_YY_ROSTLAB_BLAST_PARSER_PARSER_H_INCLUDED
# define YY_YY_ROSTLAB_BLAST_PARSER_PARSER_H_INCLUDED
// //                    "%code requires" blocks.
#line 24 "blast-parser-parser.ypp" // lalr1.cc:372

#include <string>
#include "rostlab/blast-result.h"
namespace rostlab { namespace blast { class parser_driver; } }

#line 50 "rostlab/blast-parser-parser.h" // lalr1.cc:372


# include <vector>
# include <iostream>
# include <stdexcept>
# include <string>
# include "rostlab/blast-parser-stack.h"
# include "rostlab/blast-parser-location.h"


#ifndef YY_ATTRIBUTE
# if (defined __GNUC__                                               \
      && (2 < __GNUC__ || (__GNUC__ == 2 && 96 <= __GNUC_MINOR__)))  \
     || defined __SUNPRO_C && 0x5110 <= __SUNPRO_C
#  define YY_ATTRIBUTE(Spec) __attribute__(Spec)
# else
#  define YY_ATTRIBUTE(Spec) /* empty */
# endif
#endif

#ifndef YY_ATTRIBUTE_PURE
# define YY_ATTRIBUTE_PURE   YY_ATTRIBUTE ((__pure__))
#endif

#ifndef YY_ATTRIBUTE_UNUSED
# define YY_ATTRIBUTE_UNUSED YY_ATTRIBUTE ((__unused__))
#endif

#if !defined _Noreturn \
     && (!defined __STDC_VERSION__ || __STDC_VERSION__ < 201112)
# if defined _MSC_VER && 1200 <= _MSC_VER
#  define _Noreturn __declspec (noreturn)
# else
#  define _Noreturn YY_ATTRIBUTE ((__noreturn__))
# endif
#endif

/* Suppress unused-variable warnings by "using" E.  */
#if ! defined lint || defined __GNUC__
# define YYUSE(E) ((void) (E))
#else
# define YYUSE(E) /* empty */
#endif

#if defined __GNUC__ && 407 <= __GNUC__ * 100 + __GNUC_MINOR__
/* Suppress an incorrect diagnostic about yylval being uninitialized.  */
# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN \
    _Pragma ("GCC diagnostic push") \
    _Pragma ("GCC diagnostic ignored \"-Wuninitialized\"")\
    _Pragma ("GCC diagnostic ignored \"-Wmaybe-uninitialized\"")
# define YY_IGNORE_MAYBE_UNINITIALIZED_END \
    _Pragma ("GCC diagnostic pop")
#else
# define YY_INITIAL_VALUE(Value) Value
#endif
#ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
# define YY_IGNORE_MAYBE_UNINITIALIZED_END
#endif
#ifndef YY_INITIAL_VALUE
# define YY_INITIAL_VALUE(Value) /* Nothing. */
#endif

/* Debug traces.  */
#ifndef YYDEBUG
# define YYDEBUG 1
#endif

#line 22 "blast-parser-parser.ypp" // lalr1.cc:372
namespace rostlab { namespace blast {
#line 121 "rostlab/blast-parser-parser.h" // lalr1.cc:372





  /// A Bison parser.
  class parser
  {
  public:
#ifndef YYSTYPE
    /// Symbol semantic values.
    union semantic_type
    {
    #line 47 "/build/librostlab-blast-dkVTBJ/librostlab-blast-1.0.1/lib/blast-parser-parser.ypp" // lalr1.cc:372

  long int        ival;
  double          dval;
  std::string*    sval;

#line 141 "rostlab/blast-parser-parser.h" // lalr1.cc:372
    };
#else
    typedef YYSTYPE semantic_type;
#endif
    /// Symbol locations.
    typedef location location_type;

    /// Syntax errors thrown from user actions.
    struct syntax_error : std::runtime_error
    {
      syntax_error (const location_type& l, const std::string& m);
      location_type location;
    };

    /// Tokens.
    struct token
    {
      enum yytokentype
      {
        END = 0,
        BLAST_VERSION = 258,
        REFERENCE = 259,
        STRING = 260,
        INT = 261,
        DBL = 262,
        SEARCHING = 263,
        NOHITS = 264,
        ONELINE_DESC_HEADER = 265,
        SEQ_FOUND_AGAIN = 266,
        SEQ_FOUND_NEW = 267,
        CONVERGED = 268,
        TAIL = 269,
        QUERYEQ = 270,
        DATABASECOLON = 271,
        RESFROMROUND = 272,
        SCOREEQ = 273,
        EXPECTEQ = 274,
        METHODCOLON = 275,
        IDENTITIESEQ = 276,
        POSITIVESEQ = 277,
        GAPSEQ = 278,
        STRANDEQ = 279,
        FRAMEEQ = 280,
        QUERYCOLON = 281,
        SBJCTCOLON = 282
      };
    };

    /// (External) token type, as returned by yylex.
    typedef token::yytokentype token_type;

    /// Internal symbol number.
    typedef int symbol_number_type;

    /// Internal symbol number for tokens (subsumed by symbol_number_type).
    typedef unsigned char token_number_type;

    /// A complete symbol.
    ///
    /// Expects its Base type to provide access to the symbol type
    /// via type_get().
    ///
    /// Provide access to semantic value and location.
    template <typename Base>
    struct basic_symbol : Base
    {
      /// Alias to Base.
      typedef Base super_type;

      /// Default constructor.
      basic_symbol ();

      /// Copy constructor.
      basic_symbol (const basic_symbol& other);

      /// Constructor for valueless symbols.
      basic_symbol (typename Base::kind_type t,
                    const location_type& l);

      /// Constructor for symbols with semantic value.
      basic_symbol (typename Base::kind_type t,
                    const semantic_type& v,
                    const location_type& l);

      ~basic_symbol ();

      /// Destructive move, \a s is emptied into this.
      void move (basic_symbol& s);

      /// The semantic value.
      semantic_type value;

      /// The location.
      location_type location;

    private:
      /// Assignment operator.
      basic_symbol& operator= (const basic_symbol& other);
    };

    /// Type access provider for token (enum) based symbols.
    struct by_type
    {
      /// Default constructor.
      by_type ();

      /// Copy constructor.
      by_type (const by_type& other);

      /// The symbol type as needed by the constructor.
      typedef token_type kind_type;

      /// Constructor from (external) token numbers.
      by_type (kind_type t);

      /// Steal the symbol type from \a that.
      void move (by_type& that);

      /// The (internal) type number (corresponding to \a type).
      /// -1 when this symbol is empty.
      symbol_number_type type_get () const;

      /// The token.
      token_type token () const;

      enum { empty = 0 };

      /// The symbol type.
      /// -1 when this symbol is empty.
      token_number_type type;
    };

    /// "External" symbols: returned by the scanner.
    typedef basic_symbol<by_type> symbol_type;


    /// Build a parser object.
    parser (rostlab::blast::parser_driver& drv_yyarg, void* yyscanner_yyarg);
    virtual ~parser ();

    /// Parse.
    /// \returns  0 iff parsing succeeded.
    virtual int parse ();

#if YYDEBUG
    /// The current debugging stream.
    std::ostream& debug_stream () const YY_ATTRIBUTE_PURE;
    /// Set the current debugging stream.
    void set_debug_stream (std::ostream &);

    /// Type for debugging levels.
    typedef int debug_level_type;
    /// The current debugging level.
    debug_level_type debug_level () const YY_ATTRIBUTE_PURE;
    /// Set the current debugging level.
    void set_debug_level (debug_level_type l);
#endif

    /// Report a syntax error.
    /// \param loc    where the syntax error is found.
    /// \param msg    a description of the syntax error.
    virtual void error (const location_type& loc, const std::string& msg);

    /// Report a syntax error.
    void error (const syntax_error& err);

  private:
    /// This class is not copyable.
    parser (const parser&);
    parser& operator= (const parser&);

    /// State numbers.
    typedef int state_type;

    /// Generate an error message.
    /// \param yystate   the state where the error occurred.
    /// \param yytoken   the lookahead token type, or yyempty_.
    virtual std::string yysyntax_error_ (state_type yystate,
                                         symbol_number_type yytoken) const;

    /// Compute post-reduction state.
    /// \param yystate   the current state
    /// \param yysym     the nonterminal to push on the stack
    state_type yy_lr_goto_state_ (state_type yystate, int yysym);

    /// Whether the given \c yypact_ value indicates a defaulted state.
    /// \param yyvalue   the value to check
    static bool yy_pact_value_is_default_ (int yyvalue);

    /// Whether the given \c yytable_ value indicates a syntax error.
    /// \param yyvalue   the value to check
    static bool yy_table_value_is_error_ (int yyvalue);

    static const signed char yypact_ninf_;
    static const signed char yytable_ninf_;

    /// Convert a scanner token number \a t to a symbol number.
    static token_number_type yytranslate_ (int t);

    // Tables.
  // YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
  // STATE-NUM.
  static const signed char yypact_[];

  // YYDEFACT[STATE-NUM] -- Default reduction number in state STATE-NUM.
  // Performed when YYTABLE does not specify something else to do.  Zero
  // means the default is an error.
  static const unsigned char yydefact_[];

  // YYPGOTO[NTERM-NUM].
  static const signed char yypgoto_[];

  // YYDEFGOTO[NTERM-NUM].
  static const signed char yydefgoto_[];

  // YYTABLE[YYPACT[STATE-NUM]] -- What to do in state STATE-NUM.  If
  // positive, shift that token.  If negative, reduce the rule whose
  // number is the opposite.  If YYTABLE_NINF, syntax error.
  static const unsigned char yytable_[];

  static const unsigned char yycheck_[];

  // YYSTOS[STATE-NUM] -- The (internal number of the) accessing
  // symbol of state STATE-NUM.
  static const unsigned char yystos_[];

  // YYR1[YYN] -- Symbol number of symbol that rule YYN derives.
  static const unsigned char yyr1_[];

  // YYR2[YYN] -- Number of symbols on the right hand side of rule YYN.
  static const unsigned char yyr2_[];


    /// Convert the symbol name \a n to a form suitable for a diagnostic.
    static std::string yytnamerr_ (const char *n);


    /// For a symbol, its name in clear.
    static const char* const yytname_[];
#if YYDEBUG
  // YYRLINE[YYN] -- Source line where rule number YYN was defined.
  static const unsigned char yyrline_[];
    /// Report on the debug stream that the rule \a r is going to be reduced.
    virtual void yy_reduce_print_ (int r);
    /// Print the state stack on the debug stream.
    virtual void yystack_print_ ();

    // Debugging.
    int yydebug_;
    std::ostream* yycdebug_;

    /// \brief Display a symbol type, value and location.
    /// \param yyo    The output stream.
    /// \param yysym  The symbol.
    template <typename Base>
    void yy_print_ (std::ostream& yyo, const basic_symbol<Base>& yysym) const;
#endif

    /// \brief Reclaim the memory associated to a symbol.
    /// \param yymsg     Why this token is reclaimed.
    ///                  If null, print nothing.
    /// \param yysym     The symbol.
    template <typename Base>
    void yy_destroy_ (const char* yymsg, basic_symbol<Base>& yysym) const;

  private:
    /// Type access provider for state based symbols.
    struct by_state
    {
      /// Default constructor.
      by_state ();

      /// The symbol type as needed by the constructor.
      typedef state_type kind_type;

      /// Constructor.
      by_state (kind_type s);

      /// Copy constructor.
      by_state (const by_state& other);

      /// Steal the symbol type from \a that.
      void move (by_state& that);

      /// The (internal) type number (corresponding to \a state).
      /// "empty" when empty.
      symbol_number_type type_get () const;

      enum { empty = 0 };

      /// The state.
      state_type state;
    };

    /// "Internal" symbol: element of the stack.
    struct stack_symbol_type : basic_symbol<by_state>
    {
      /// Superclass.
      typedef basic_symbol<by_state> super_type;
      /// Construct an empty symbol.
      stack_symbol_type ();
      /// Steal the contents from \a sym to build this.
      stack_symbol_type (state_type s, symbol_type& sym);
      /// Assignment, needed by push_back.
      stack_symbol_type& operator= (const stack_symbol_type& that);
    };

    /// Stack type.
    typedef stack<stack_symbol_type> stack_type;

    /// The stack.
    stack_type yystack_;

    /// Push a new state on the stack.
    /// \param m    a debug message to display
    ///             if null, no trace is output.
    /// \param s    the symbol
    /// \warning the contents of \a s.value is stolen.
    void yypush_ (const char* m, stack_symbol_type& s);

    /// Push a new look ahead token on the state on the stack.
    /// \param m    a debug message to display
    ///             if null, no trace is output.
    /// \param s    the state
    /// \param sym  the symbol (for its value and location).
    /// \warning the contents of \a s.value is stolen.
    void yypush_ (const char* m, state_type s, symbol_type& sym);

    /// Pop \a n symbols the three stacks.
    void yypop_ (unsigned int n = 1);

    // Constants.
    enum
    {
      yyeof_ = 0,
      yylast_ = 81,     ///< Last index in yytable_.
      yynnts_ = 24,  ///< Number of nonterminal symbols.
      yyempty_ = -2,
      yyfinal_ = 6, ///< Termination state number.
      yyterror_ = 1,
      yyerrcode_ = 256,
      yyntokens_ = 31  ///< Number of tokens.
    };


    // User arguments.
    rostlab::blast::parser_driver& drv;
    void* yyscanner;
  };


#line 22 "blast-parser-parser.ypp" // lalr1.cc:372
} } // rostlab::blast
#line 495 "rostlab/blast-parser-parser.h" // lalr1.cc:372




#endif // !YY_YY_ROSTLAB_BLAST_PARSER_PARSER_H_INCLUDED