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Former-commit-id: 202296404e6a70f8ae96db99faffb456104c57e9
Former-commit-id: 118417735d2055683607df9809c9b721cc1b1bab
This commit is contained in:
Eric Coissac
2015-10-02 21:12:35 +02:00
parent f44f0d8179
commit d298385685
316 changed files with 122579 additions and 0 deletions
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src/sequtils/lxpack/include/libbio.h Normal file
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/* ---------------------------------------------------------------- */
/* Copyright (c) Atelier de BioInformatique */
/* @file: libbio.h */
/* @desc: bioseq & strings generic library / include file */
/* */
/* @history: */
/* @+ <Gloup> : Jan 96 : first draft for PWG */
/* ---------------------------------------------------------------- */
#ifndef _H_libbio
#define _H_libbio
/* ==================================================== */
/* Constants */
/* ==================================================== */
#define DNA_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"
#define C_DNA_ALPHA "TVGHEFCDIJMLKNOPQYSAABWXRZtvghefcdijmlknopqysaabwxrz"
#ifndef TICKS_PER_SEC
#define TICKS_PER_SEC 60
#endif
#define PWG_TIME_NO_RESET TIME_NO_RESET
#define PWG_TIME_RESET TIME_RESET
/* ==================================================== */
/* Macros standards */
/* ==================================================== */
#ifndef NEW
#define NEW(typ) (typ*)malloc(sizeof(typ))
#define NEWN(typ, dim) (typ*)malloc((size_t)(dim) * sizeof(typ))
#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (size_t)(dim) * sizeof(typ))
#define FREE(ptr) free((Ptr) ptr)
#endif
#define PWG_STRDUP(s) pwg_dup_string((s), 0)
/* ==================================================== */
/* Prototypes of library functions */
/* ==================================================== */
/* string.c */
char *str_dup_string ( char *str, int extra );
char *str_erase_char ( char *str, int c );
char *str_replace_char ( char *str, int cfrom, int cto );
char *str_trim_trailing ( char *str );
char *str_trim_leading ( char *str );
char *str_pad_right ( char *str, long size, int padchar );
char *str_pad_left ( char *str, long size, int padchar );
char *str_drop_string ( char *str, long start, long nchars );
char *str_insert_string ( char *dst, char *src, long pos );
char *str_extract_string ( char *dst, char *src, long from, long to );
char *str_extract_to_mark ( char *dst, char *src, long start, int markchar );
char *str_reverse_string ( char *str );
char *str_upper_string ( char *str );
char *str_lower_string ( char *str );
/* bioseq.c */
int bio_base_complement ( int c );
char *bio_seq_complement ( char *str );
int bio_codon_translate ( char *codon, int codid);
char *bio_seq_translate ( char *seq, int codid);
#endif