--- /dev/null
+/* Generated automatically from squid.h.in by configure. */
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQUIDH_INCLUDED
+#define SQUIDH_INCLUDED
+
+/* squid.h
+ * Header file for my library of sequence functions.
+ *
+ * CVS $Id: squid.h.in,v 1.5 2002/10/09 14:26:09 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
+
+/* include clustal's config.h */
+#ifdef CLUSTALO
+#include "config.h"
+#define CLUSTALO 1
+#else
+#include "clustal-omega-config.h"
+#define CLUSTALO 1
+#endif
+
+#ifdef CLUSTALO
+/* we don't want squidconf.h but our own config header. but, there are
+ * some checks, espcially at the end of squidconf.h might be
+ * necessary for squid to work. They follow after the inclusion of
+ * config.h
+ */
+#undef DEBUG
+
+/* squidconf.h checks:
+ */
+#if defined HAVE_NTOHL && defined HAVE_NTOHS && defined HAVE_HTONS && defined HAVE_HTONL
+#define USE_HOST_BYTESWAP_FUNCTIONS 1
+#endif
+/* On 64-bit machines like Alphas, strtoull doesn't exist, strotul will work
+ */
+#if SIZEOF_UNSIGNED_LONG == 8 && defined HAVE_STRTOUL && ! defined HAVE_STRTOULL
+#define strtoull strtoul
+#endif
+
+#if defined HAVE_FTELLO && defined HAVE_FSEEKO && SIZEOF_OFF_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined HAVE_FTELLO64 && defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined HAVE_FTELL64 && defined HAVE_FSEEK64
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#else
+#undef HAS_64BIT_FILE_OFFSETS
+#endif
+
+/* The following check seems like nonsense to me (AW), therefore */
+#if 0
+/* Stuff to work around Tru64 not having strtoull() -
+ * on systems with 64-bit longs, we can use strtoul()
+ */
+#undef HAVE_STRTOULL
+#if ! defined HAVE_STRTOULL && SIZEOF_UNSIGNED_LONG == 8
+#define strtoull strtoul
+#endif
+#endif
+
+#else /* CLUSTALO */
+#include "squidconf.h" /* #define's generated by ./configure script */
+#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*/
+#ifdef CLUSTALO
+#define SQFILE_VIENNA 18 /* Vienna format: concatenated fasta */
+#endif
+#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
+#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 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 */
git://source.jalview.org / jabaws.git / blobdiff