69 lines
2.3 KiB
C
69 lines
2.3 KiB
C
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/* ---------------------------------------------------------------- */
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/* Copyright (c) Atelier de BioInformatique */
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/* @file: libfasta.h */
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/* @desc: sequence IO in fasta format / include file */
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/* */
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/* @history: */
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/* @+ <Gloup> : Aug 92 : first version */
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/* @+ <Gloup> : Nov 95 : last revised version */
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/* ---------------------------------------------------------------- */
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#ifndef _H_libfasta
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#define _H_libfasta
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/* ==================================================== */
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/* Constantes */
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/* ==================================================== */
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#define FASTA_NAMLEN 64 /* max length of seq. name */
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#define FASTA_COMLEN 512 /* max length of seq. comment */
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#define FASTA_CHAR_PER_LINE 50 /* # of chars per line in output */
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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((unsigned)(dim) * sizeof(typ))
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#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (unsigned long)(dim) * sizeof(typ))
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#define FREE(ptr) free(ptr)
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#endif
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/* ==================================================== */
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/* Structures de donnees */
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/* ==================================================== */
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typedef struct { /* -- Sequence ---------------- */
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int ok; /* error flag */
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long length, /* longueur */
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offset, /* offset */
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bufsize; /* size of current seq buffer */
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char name[FASTA_NAMLEN], /* nom */
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comment[FASTA_COMLEN], /* commentaire */
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*seq; /* sequence */
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} FastaSequence, *FastaSequencePtr;
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/* ==================================================== */
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/* Prototypes (generated by mkproto) */
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/* ==================================================== */
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/* libfasta.c */
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char *GetFastaName ( char *buffer );
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char *GetFastaComment ( char *buffer );
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FastaSequencePtr NewFastaSequence ( void );
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FastaSequencePtr FreeFastaSequence ( FastaSequencePtr seq );
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int ReadFastaSequence ( FILE *streamin, FastaSequencePtr seq );
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int GetFastaSequence ( FILE *streamin, FastaSequencePtr seq );
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void WriteFastaSequence ( FILE *streamou, FastaSequencePtr seq,
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int char_per_line );
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void RewindFastaDB ( FILE *streamin );
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#endif
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