This file is indexed.

/usr/include/biosquid/squid.h is in biosquid-dev 1.9g+cvs20050121-4.

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
/* squid.h.  Generated from squid.h.in by configure. */
/*****************************************************************
 * @LICENSE@
 *****************************************************************/

#ifndef SQUIDH_INCLUDED
#define SQUIDH_INCLUDED

/* squid.h
 * Header file for my library of sequence functions.
 *
 * CVS $Id: squid.h.in,v 1.6 2003/04/14 16:00:16 eddy Exp $
 */

#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include <unistd.h>		/* for sysconf() #define's       */


#if DEBUGLEVEL > 0
#include <assert.h>		/* for SQD_DASSERT1(), etc.      */
#endif

/*****************************************************************
 * Integers of guaranteed size. (used for instance in gsi.c, gsi2.c)
 * These are set by the ./configure script; if they show up as FIXME,
 * they must be manually edited to appropriate type definitions. You
 * do need 64-bit integers in the current code; email me if this
 * prevents you from compiling SQUID and tell me your system (I don't
 * know of any systems that don't have 64-bit integers these days).
 *****************************************************************/
typedef unsigned short     sqd_uint16;
typedef unsigned int       sqd_uint32;
typedef unsigned long      sqd_uint64;

#ifdef USE_HOST_BYTESWAP_FUNCTIONS
#include <sys/types.h>		/* only for ntohl() and friends. */
#include <netinet/in.h>		/* only for ntohl() and friends. */
#define sre_ntoh16(x) ntohs(x);
#define sre_ntoh32(x) ntohl(x);
#define sre_hton16(x) htons(x);
#define sre_hton32(x) htonl(x);
#endif /* USE_HOST_BYTESWAP_FUNCTIONS */

/* Library version info is made available as a global to
 * any interested program. These are defined in iupac.c
 * with the other globals.
 */
extern char squid_version[];	/* version number  */
extern char squid_date[];	/* date of release */
extern int  squid_errno;	/* error codes     */



/****************************************************
 * Error codes returned by squid library functions (squid_errno)
 ****************************************************/

#define SQERR_OK        0	/* no error                     */
#define SQERR_UNKNOWN   1       /* generic error, unidentified  */
#define SQERR_NODATA    2	/* unexpectedly NULL stream     */
#define SQERR_MEM       3	/* malloc or realloc failed     */
#define SQERR_NOFILE    4	/* file not found               */
#define SQERR_FORMAT    5	/* file format not recognized   */
#define SQERR_PARAMETER 6	/* bad parameter passed to func */
#define SQERR_DIVZERO   7	/* error in sre_math.c          */
#define SQERR_INCOMPAT  8	/* incompatible parameters      */
#define SQERR_EOD       9	/* end-of-data (often normal)   */

/****************************************************
 * Single sequence information
 ****************************************************/ 
#define SQINFO_NAMELEN 64
#define SQINFO_DESCLEN 128

struct seqinfo_s {
  int      flags;               /* what extra data are available         */
  char     name[SQINFO_NAMELEN];/* up to 63 characters of name           */
  char     id[SQINFO_NAMELEN];	/* up to 63 char of database identifier  */
  char     acc[SQINFO_NAMELEN]; /* up to 63 char of database accession # */
  char     desc[SQINFO_DESCLEN];/* up to 127 char of description         */
  int      len;                 /* length of this seq                    */
  int      start;		/* (1..len) start position on source seq */
  int      stop;                /* (1..len) end position on source seq   */
  int      olen;                /* original length of source seq         */
  int      type;                /* kRNA, kDNA, kAmino, or kOther         */
  char    *ss;                  /* 0..len-1 secondary structure string   */
  char    *sa;			/* 0..len-1 % side chain surface access. */
};
typedef struct seqinfo_s SQINFO;

#define SQINFO_NAME  (1 << 0)
#define SQINFO_ID    (1 << 1)
#define SQINFO_ACC   (1 << 2)
#define SQINFO_DESC  (1 << 3)
#define SQINFO_START (1 << 4)
#define SQINFO_STOP  (1 << 5)
#define SQINFO_LEN   (1 << 6)
#define SQINFO_TYPE  (1 << 7)
#define SQINFO_OLEN  (1 << 8)
#define SQINFO_SS    (1 << 9)
#define SQINFO_SA    (1 << 10)


/****************************************************
 * Sequence alphabet: see also iupac.c
 ****************************************************/
				/* IUPAC symbols defined globally in iupac.c */
struct iupactype {
  char       sym;		/* character representation */
  char       symcomp;           /* complement (regular char */
  char       code;		/* my binary rep */
  char       comp;              /* binary encoded complement */
};
extern struct iupactype iupac[];
#define IUPACSYMNUM 17

extern char    *stdcode1[];	/* 1-letter amino acid translation code */
extern char    *stdcode3[];	/* 3-letter amino acid translation code */
extern float    dnafq[];        /* nucleotide occurrence frequencies    */
extern float    aafq[];		/* amino acid occurrence frequencies    */
extern char     aa_alphabet[];  /* amino acid alphabet                  */
extern int      aa_index[];     /* convert 0..19 indices to 0..26       */

				/* valid symbols in IUPAC code */
#define NUCLEOTIDES    "ACGTUNRYMKSWHBVDacgtunrymkswhbvd"
#define AMINO_ALPHABET "ACDEFGHIKLMNPQRSTVWY"
#define DNA_ALPHABET   "ACGT"
#define RNA_ALPHABET   "ACGU"
#define WHITESPACE     " \t\n"

#define isgap(c) ((c) == ' ' || (c) == '.' || (c) == '_' || (c) == '-' || (c) == '~')


/****************************************************
 * Sequence i/o: originally from Don Gilbert's readseq 
 ****************************************************/
#include "msa.h"		/* for multiple sequence alignment support   */

	/* buffer size for reading in lines from sequence files*/
#define LINEBUFLEN  4096

/* sequence types parsed by Seqtype()                          */
/* note that these must match hmmAMINO and hmmNUCLEIC in HMMER */
#define kOtherSeq   0		/* hmmNOTSETYET */
#define kDNA        1
#define kRNA        2		/* hmmNUCLEIC   */
#define kAmino      3		/* hmmAMINO     */

/* Unaligned sequence file formats recognized 
 * Coexists with definitions of multiple alignment formats in msa.h:
 *   >100 reserved for alignment formats
 *   <100 reserved for unaligned formats
 *   0 reserved for unknown
 *   
 * Some "legacy" formats are supported only when explicitly 
 * requested; not autodetected by SeqfileFormat().
 * 
 * DON'T REASSIGN THESE CODES. They're written into
 * GSI index files. You can use new ones, but reassigning
 * the sense of old ones will break GSI indices.
 * Alignment format codes were reassigned with the creation
 * of msa.c, but before Stockholm format, there were no
 * indexed alignment databases. 
 */
#define SQFILE_UNKNOWN  0	/* unknown format                  */
#define SQFILE_IG       1	/* Intelligenetics (!)             */
#define SQFILE_GENBANK  2	/* GenBank flatfile                */
				/* 3 was A2M. Now an alignment format  */
#define SQFILE_EMBL     4	/* EMBL or Swissprot flatfile      */
#define SQFILE_GCG      5	/* GCG single sequence files       */
#define SQFILE_STRIDER  6	/* MacStrider (!!)                 */
#define SQFILE_FASTA    7	/* FASTA format: default           */
#define SQFILE_ZUKER    8	/* Zuker MFOLD format (legacy)     */
#define SQFILE_IDRAW    9	/* Idraw-style PostScript (legacy) */
				/* 10 was SELEX. Now alignment format  */
				/* 11 was MSF. Now alignment format    */
#define SQFILE_PIR      12	/* PIR format                      */
#define SQFILE_RAW      13	/* raw sequence                    */
#define SQFILE_SQUID    14	/* my obsolete squid format        */
				/* 15 was kXPearson, extended FASTA; withdrawn */
#define SQFILE_GCGDATA  16	/* GCG data library file           */
				/* 17 was Clustal. Now alignment format*/

#define IsUnalignedFormat(fmt)  ((fmt) && (fmt) < 100)

#include "ssi.h"

struct ReadSeqVars {
  FILE   *f;                    /* open file pointer                  */
  char   *fname;                /* name of file; used for diagnostics */
  int     linenumber;           /* what line are we on in the file    */

  char   *buf;                  /* dynamically allocated sre_fgets() buffer */
  int     buflen;               /* allocation length for buf                */
  
  int       ssimode;		/* SSI_OFFSET_I32 or SSI_OFFSET_I64        */
  SSIOFFSET ssioffset;		/* disk offset to last line read into buf  */
  SSIOFFSET r_off;		/* offset to start of record               */
  SSIOFFSET d_off;		/* offset to start of sequence data        */

  int     rpl;			/* residues per data line for this file; -1 if unset, 0 if invalid */
  int     lastrpl;		/* rpl on last line seen */
  int     maxrpl;		/* max rpl on any line of the file */
  int     bpl;			/* bytes per data line; -1 if unset, 0 if invalid */
  int     lastbpl;		/* bpl on last line seen */
  int     maxbpl;		/* max bpl on any line of the file */

  char   *seq;                  /* growing sequence during parse */
  SQINFO *sqinfo;	        /* name, id, etc, gathered during parse */
  char   *sp;
  int     seqlen;		/* current sequence length */
  int     maxseq;		/* current allocation length for seq */

  int     format;		/* format of seqfile we're reading. */
  int     do_gzip;		/* TRUE if f is a pipe from gzip -dc */
  int     do_stdin;		/* TRUE if f is stdin */

  /* An (important) hack for sequential access of multiple alignment files: 
   * we read the whole alignment in,
   * and then copy it one sequence at a time into seq and sqinfo.
   * It is active if msa is non NULL. 
   * msa->lastidx is reused/overloaded: used to keep track of what 
   * seq we'll return next.
   * afp->format is the real format, while SQFILE->format is kMSA.
   * Because we keep it in the SQFILE structure,
   * ReadSeq() and friends are always reentrant for multiple seqfiles.
   */
  MSA      *msa;
  MSAFILE  *afp;
};
typedef struct ReadSeqVars SQFILE;


/****************************************************
 * Cluster analysis and phylogenetic tree support
 ****************************************************/ 

/* struct phylo_s - a phylogenetic tree
 *                     
 * For N sequences, there will generally be an array of 0..N-2
 * phylo_s structures representing the nodes of a tree.
 * [0] is the root. The indexes of left and
 * right children are somewhat confusing so be careful. The
 * indexes can have values of 0..2N-2. If they are 0..N-1, they 
 * represent pointers to individual sequences. If they are
 * >= N, they represent pointers to a phylo_s structure
 * at (index - N).
 */
struct phylo_s {
  int    parent;                /* index of parent, N..2N-2, or -1 for root */
  int    left;			/* index of one of the branches, 0..2N-2 */
  int    right;			/* index of other branch, 0..2N-2        */
  float  diff;			/* difference score between seqs         */
  float  lblen;      		/* left branch length                    */
  float  rblen;                 /* right branch length                   */
  char  *is_in;                 /* 0..N-1 flag array, 1 if seq included  */
  int    incnum;                /* number of seqs included at this node  */
};


/* Strategies for cluster analysis; cluster by mean distance,
 * minimum distance, or maximum distance.
 */
enum clust_strategy { CLUSTER_MEAN, CLUSTER_MAX, CLUSTER_MIN };

/****************************************************
 * Generic data structure support
 ****************************************************/

/* a struct intstack_s implements a pushdown stack for storing
 * single integers.
 */
struct intstack_s {
  int                data;
  struct intstack_s *nxt;
};

/****************************************************
 * Binary nucleotide alphabet support
 ****************************************************/

/* Binary encoding of the IUPAC code for nucleotides
 * 
 *    four-bit "word", permitting rapid degenerate matching
 *         A  C  G  T/U
 *         0  0  1  0
 */
#define NTA 8
#define NTC 4
#define NTG 2
#define NTT 1
#define NTU 1
#define NTN 15			/* A|C|G|T */
#define NTR 10			/* A|G */
#define NTY 5			/* C|T */
#define NTM 12			/* A|C */
#define NTK 3			/* G|T */
#define NTS 6			/* C|G */
#define NTW 9			/* A|T */
#define NTH 13			/* A|C|T */
#define NTB 7			/* C|G|T */
#define NTV 14			/* A|C|G */
#define NTD 11			/* A|G|T */
#define NTGAP 16		/* GAP */
#define NTEND 0			/* null string terminator */

/* ntmatch(): bitwise comparison of two nuc's 
 * note that it's sensitive to the order;
 * probe may be degenerate but target should not be 
 */
#define ntmatch(probe, target)  ((probe & target) == target)

/****************************************************
 * Support for a portable, flexible Getopt()
 ****************************************************/

/* Structure: opt_s
 * 
 * Structure for declaring options to a main().
 */
struct opt_s {
  char *name;			/* name of option, e.g. "--option1" or "-o" */
  int   single;			/* TRUE if a single letter option           */
  int   argtype;		/* for typechecking, e.g. sqdARG_INT        */
};
				/* acceptable argtype's...           */
#define sqdARG_NONE   0		/* no argument                       */
#define sqdARG_INT    1		/* something that atoi() can grok    */
#define sqdARG_FLOAT  2		/* something that atof() can grok    */
#define sqdARG_CHAR   3		/* require single character or digit */
#define sqdARG_STRING 4		/* anything goes                     */

/****************************************************
 * Support for convenient Perl-y regexp matching
 * See hsregexp.c for copyright notice: this code is derived
 * from Henry Spencer's freely distributed regexp library.
 ****************************************************/

#define NSUBEXP  10
typedef struct sqd_regexp {
	char *startp[NSUBEXP];
	char *endp[NSUBEXP];
	char regstart;		/* Internal use only. */
	char reganch;		/* Internal use only. */
	char *regmust;		/* Internal use only. */
	int regmlen;		/* Internal use only. */
	char program[1];	/* Unwarranted chumminess with compiler. */
} sqd_regexp;

/* Strparse() defines and manages these. 
 * sqd_parse[0] contains the substring that matched the pattern.
 * sqd_parse[1-9] contain substrings matched with ()'s.
 */
extern char *sqd_parse[10];

/****************************************************
 * Portable detection of multiprocessor # of CPUs.
 *      #include <unistd.h>
 *      long foo = SQD_NPROC;
 *      returns the number of available processors.
 *      if foo == -1, we failed.
 ****************************************************/

/* Our problem here is that POSIX apparently doesn't specify
 * a standard for how to get sysconf() to report the number of
 * processors on-line. _SC_NPROCESSORS_ONLN is specified
 * by SVR4.0MP. Thanks to W. Gish for help here.
 */
#undef SQD_NPROC
#if   defined(_SC_NPROCESSORS_ONLN)    /* Sun Solaris, Digital UNIX */
  #define SQD_NPROC  sysconf(_SC_NPROCESSORS_ONLN)
#elif defined(_SC_NPROC_ONLN)          /* Silicon Graphics IRIX */
  #define SQD_NPROC  sysconf(_SC_NPROC_ONLN)
#elif defined(_SC_NPROCESSORS_CONF)    /* _ONLN is favored over _CONF */
  #define SQD_NPROC  sysconf(_SC_NPROCESSORS_CONF)
#else   /* some systems don't support getting ncpu via sysconf() */
  #define SQD_NPROC  -1
#endif

/****************************************************
 * Three levels of debugging printf's and assert's
 *      level 1: little impact on verbosity or performance
 *      level 2: moderate impact
 *      level 3: high impact
 * Example:
 *    SQD_DPRINTF3(("Matrix row %d col %d = %f\n", i, j, val));
 * Note the double parentheses; these are important.
 ****************************************************/

#ifndef DEBUGLEVEL
#define DEBUGLEVEL 0
#endif

#if (DEBUGLEVEL >= 1)
#define SQD_DPRINTF1(x)  printf x
#define SQD_DASSERT1(x)  assert x
#else
#define SQD_DPRINTF1(x)  
#define SQD_DASSERT1(x)
#endif
#if (DEBUGLEVEL >= 2)
#define SQD_DPRINTF2(x)  printf x
#define SQD_DASSERT2(x)  assert x
#else
#define SQD_DPRINTF2(x)  
#define SQD_DASSERT2(x)
#endif
#if (DEBUGLEVEL >= 3)
#define SQD_DPRINTF3(x)  printf x
#define SQD_DASSERT3(x)  assert x
#else
#define SQD_DPRINTF3(x)  
#define SQD_DASSERT3(x)
#endif

/* PANIC is called for failures of Std C/POSIX functions,
 * instead of my own functions. Panic() calls perror() and exits
 * abnormally.
 */
#define PANIC   Panic(__FILE__, __LINE__)

/* Malloc/realloc calls are wrapped
 */
#define MallocOrDie(x)     sre_malloc(__FILE__, __LINE__, (x))
#define ReallocOrDie(x,y)  sre_realloc(__FILE__, __LINE__, (x), (y))

/****************************************************
 * Miscellaneous macros and defines
 ****************************************************/

#define SQDCONST_E    2.71828182845904523536028747135
#define SQDCONST_PI   3.14159265358979323846264338328

				/* must declare swapfoo to use SWAP() */
#define SWAP(a,b) {swapfoo = b; b = a; a = swapfoo;}
#define ScalarsEqual(a,b) (fabs((a)-(b)) < 1e-7)

#ifndef MIN
#define MIN(a,b)         (((a)<(b))?(a):(b))
#endif
#ifndef MAX
#define MAX(a,b)         (((a)>(b))?(a):(b))
#endif

/* For convenience and (one hopes) clarity in boolean tests:
 */
#ifndef TRUE
#define TRUE 1
#endif
#ifndef FALSE 
#define FALSE 0
#endif

/* Somewhere, there is a universe in which Unix vendors comply
 * with the ANSI C standard. Unfortunately, it is not ours:
 */
#ifndef EXIT_SUCCESS
#define EXIT_SUCCESS 0
#endif
#ifndef EXIT_FAILURE
#define EXIT_FAILURE 1
#endif

#include "sqfuncs.h"		/* squid function declarations */
#include "sre_random.h"         /* random number generator and samplers */
#include "vectorops.h"          /* vector operations  */
#endif /* SQUIDH_INCLUDED */