70 lines
2.4 KiB
C
70 lines
2.4 KiB
C
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/* ---------------------------------------------------------------- */
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/* Copyright (c) Atelier de BioInformatique */
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/* @file: libbio.h */
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/* @desc: bioseq & strings generic library / include file */
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/* */
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/* @history: */
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/* @+ <Gloup> : Jan 96 : first draft for PWG */
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/* ---------------------------------------------------------------- */
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#ifndef _H_libbio
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#define _H_libbio
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/* ==================================================== */
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/* Constants */
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/* ==================================================== */
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#define DNA_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz"
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#define C_DNA_ALPHA "TVGHEFCDIJMLKNOPQYSAABWXRZtvghefcdijmlknopqysaabwxrz"
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#ifndef TICKS_PER_SEC
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#define TICKS_PER_SEC 60
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#endif
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#define PWG_TIME_NO_RESET TIME_NO_RESET
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#define PWG_TIME_RESET TIME_RESET
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/* ==================================================== */
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/* Macros standards */
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/* ==================================================== */
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#ifndef NEW
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#define NEW(typ) (typ*)malloc(sizeof(typ))
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#define NEWN(typ, dim) (typ*)malloc((size_t)(dim) * sizeof(typ))
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#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (size_t)(dim) * sizeof(typ))
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#define FREE(ptr) free((Ptr) ptr)
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#endif
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#define PWG_STRDUP(s) pwg_dup_string((s), 0)
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/* ==================================================== */
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/* Prototypes of library functions */
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/* ==================================================== */
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/* string.c */
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char *str_dup_string ( char *str, int extra );
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char *str_erase_char ( char *str, int c );
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char *str_replace_char ( char *str, int cfrom, int cto );
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char *str_trim_trailing ( char *str );
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char *str_trim_leading ( char *str );
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char *str_pad_right ( char *str, long size, int padchar );
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char *str_pad_left ( char *str, long size, int padchar );
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char *str_drop_string ( char *str, long start, long nchars );
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char *str_insert_string ( char *dst, char *src, long pos );
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char *str_extract_string ( char *dst, char *src, long from, long to );
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char *str_extract_to_mark ( char *dst, char *src, long start, int markchar );
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char *str_reverse_string ( char *str );
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char *str_upper_string ( char *str );
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char *str_lower_string ( char *str );
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/* bioseq.c */
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int bio_base_complement ( int c );
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char *bio_seq_complement ( char *str );
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int bio_codon_translate ( char *codon, int codid);
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char *bio_seq_translate ( char *seq, int codid);
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#endif
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