squid.h.in

hmmer源程序

  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
#ifdef  _SC_NPROCESSORS_ONLN    /* Sun Solaris, Digital UNIX */
#define SQD_NPROC  sysconf(_SC_NPROCESSORS_ONLN)
#else
#ifdef _SC_NPROC_ONLN		/* Silicon Graphics IRIX */
#define SQD_NPROC  sysconf(_SC_NPROC_ONLN)
#else   /* FreeBSD, Linux don't support getting ncpu via sysconf() */
#define SQD_NPROC  -1
#endif
#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 CHOOSE(a)     ((int) (sre_random() * (a)))
				/* 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 */
#endif /* SQUIDH_INCLUDED */