/*
 *   segemehl - a read aligner
 *   Copyright (C) 2008-2017  Steve Hoffmann and Christian Otto
 *
 *   This program is free software: you can redistribute it and/or modify
 *   it under the terms of the GNU General Public License as published by
 *   the Free Software Foundation, either version 3 of the License, or
 *   (at your option) any later version.
 *
 *   This program is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *   GNU General Public License for more details.
 *
 *   You should have received a copy of the GNU General Public License
 *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef _BIOFILES_
#define _BIOFILES_

/*
 *
 *	biofiles.h
 *  declarations
 * 
 *  @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
 *  @company Bioinformatics, University of Leipzig 
 *  @date 07/10/2007 02:32:29 PM CEST  
 *
 *  SVN
 *  Revision of last commit: $Rev: 19 $
 *  Author: $Author: steve $
 *  Date: $Date: 2008-05-14 15:43:29 +0200 (Wed, 14 May 2008) $
 *
 *  Id: $Id: biofiles.h 19 2008-05-14 13:43:29Z steve $
 *  Url: $URL: file:///homes/bierdepot/steve/svn/segemehl/trunk/libs/biofiles.h $
 */

#include <stdio.h>
#include <stdlib.h>
#include "stringutils.h"
#include "basic-types.h"
#include "charsequence.h"
#include "gzidx.h"
#include "annotation.h"

#define ID 1
#define IDEND 2
#define SEQEND 3
#define QUALIDEND 4
#define END 5

#define GFFITEM 0
#define BEDITEM 1
#define SNPITEM 2

typedef struct seqaccesspoint_s {
  off_t offset;
  Uint fileid;
  Uint noofseqs;
  Uint cumnoofseqs;
} seqaccesspoint_t;


typedef struct fastxseqindex_s {
  seqaccesspoint_t *ap;
  Uint size;
  Uint allocated;
} fastxseqindex_t;


typedef struct fastxfileindex_s {
  seqaccesspoint_t *ap;
  Uint size;
  Uint allocated;
} fastxfileindex_t;


typedef struct fasta_s {

  CharSequence** seqs;
  CharSequence** quals;

  Uint *matestart;
  Uint noofseqs;
  Uint active_noofseqs;
  Uint active_noofmates;
  Uint minlen;
  Uint maxlen;
  char minqual;
  char maxqual;
  Uint curchunk;
  Uint offset;

  unsigned char lower;
  unsigned char upper;
  unsigned char gzip;
  unsigned char hasMates;
  unsigned char hasIndex;
  unsigned char chunkIsActive;
  unsigned char checkid;
 
  Uint nooffiles;
  Uint *filetotal; 
  char **filenames;
  char **matefilenames;  

  fastxseqindex_t *chunkindex;
  fastxseqindex_t *matechunkindex;

  fastxfileindex_t **findex;
  fastxfileindex_t **matefindex;
  
  struct access **gzindex;
  struct access **mategzindex;

  Uint nextindex;

} fasta_t;


typedef struct {
  Uint start;
  Uint end;
} cds_t;

typedef struct {
  Uint start;
  Uint end;
  char *refchr;
  char strand;
  Uint noofcds;
  cds_t *cds;
} exon_t;

typedef struct {
  char *id;
  char direction;
  Uint noofexons;
  exon_t *exons;
  Uint startcodon;
  Uint stopcodon;
} gene_t;


typedef struct {
  Uint noofgenes;
  gene_t *genes;
} geneset_t;


fasta_t**
bl_fastxChopIndex(void *space, fasta_t *f, Uint pieces);
void bl_fastaGetClipPos (fasta_t *f, Uint elem, Uint *p5, Uint *p3);
void bl_fastaGetMateClipPos (fasta_t *f, Uint elem, Uint *p5, Uint *p3); 
Uint bl_fastaSoftClip (void *space, fasta_t *f, Uint elem, 
    char *p5, Uint p5len, Uint p5scr, char *p3, Uint p3len, Uint p3scr, Uint pAlen);
Uint bl_fastaMateSoftClip (void *space, fasta_t *f, Uint elem, 
    char *p5, Uint p5len, Uint p5scr, char *p3, Uint p3len, Uint p3scr, Uint pAlen);
Uint bl_fastaHardClip (void *space, fasta_t *f, Uint elem, 
    Uint p5, Uint p3);
Uint bl_fastaMateHardClip (void *space, fasta_t *f, Uint elem, 
    Uint p5, Uint p3);
void bl_fastaDestruct(void *space, fasta_t* f);
void bl_fastxDestructSequence(void *space, fasta_t* f);
int bl_fastxGetChunk (fasta_t *fasta, Uint k);
fasta_t** bl_fastaChop(void *space, fasta_t* f, Uint pieces);
Uint bl_fastaGetMateDescriptionLength(fasta_t *f, Uint elem);
char* bl_fastaGetMateDescription(fasta_t *f, Uint elem);
unsigned char bl_fastaHasQuality(fasta_t *f);
fasta_t* bl_fastaInit(void *);
void bl_fastaAdd(void *space, fasta_t*, char *desc, Uint, 
    char* sequence, Uint, Uint);
fasta_t* bl_fastaRead(void *space, fasta_t*, char* filename, 
    unsigned char upper, unsigned char lower, unsigned int n, 
    void (*handler) (void *, fasta_t*, char*, Uint, char*, Uint, Uint));
fasta_t* bl_fastxGetSet(void *space, char **filenames, unsigned int nooffiles,
    unsigned char upper, unsigned char lower, unsigned char index, Uint pieces);
fasta_t* bl_fastaGetSet(void *space, char **filenames, unsigned int nooffiles,
    unsigned char upper, unsigned char lower);
Uint bl_fastaGetMateStart(fasta_t *f, Uint elem);
void bl_fastxDestructChunkIndex (void *space, fasta_t *);
fasta_t* bl_fastxGetMateSet(void *space, fasta_t* set, char** filenames, 
    unsigned int nooffiles, unsigned char upper, unsigned lower, 
    unsigned char index, Uint pieces);
void bl_fastxDestructSequence(void *space, fasta_t* f);
fasta_t* bl_fastxgzRead (void *space, fasta_t *fasta, char *filename, struct access *idx,
    unsigned char upper, unsigned char lower, off_t offset, Uint startseq, Uint lastseq,
    void (*handler)(void *, fasta_t*, char *, Uint, char *, char *, Uint, Uint));
fasta_t* bl_fastxRead(void *space, fasta_t* fasta, char* filename, 
    unsigned char upper, unsigned char lower, off_t offset, Uint startseq, Uint lastseq, 
    void (*handler) (void *, fasta_t*, char *, Uint, char *, char *, Uint, Uint));
void bl_fastxAdd(void *space, fasta_t *f, char *desc, Uint descrlen,
    char *sequence, char *quality, Uint seqlen, Uint sNo);
void bl_fastxAddMate(void *space, fasta_t *f, char *desc, Uint desclen,
    char *sequence, char *quality, Uint seqlen, Uint sNo);
void bl_fastxDump( void *space, fasta_t *fasta, char *desc, Uint desclen, 
    char *sequence, char *quality, Uint quallen, Uint sNo);
Uint bl_fastxGetChunkElem (void *space, fasta_t *f, Uint k);
fasta_t* bl_fastxIndex(void *space, fasta_t *f, char **filenames, Uint nooffiles, 
    unsigned char isMate, unsigned char gzip, Uint pieces);
Uint bl_fastaGetDescriptionLength(fasta_t *f, Uint elem);
char* bl_fastaGetDescription(fasta_t *f, Uint elem);
Uint bl_fastaGetSequenceLength(fasta_t *f, Uint elem);
char* bl_fastaGetSequence(fasta_t *f, Uint elem);
char* bl_fastaGetQuality(fasta_t* f, Uint elem);
#ifdef HASHING
Uint bl_fastaGetQuantity(fasta_t* f, Uint elem);
void bl_fastaSetQuantity(fasta_t* f, Uint elem, Uint quantity);
#endif
unsigned char bl_fastaHasMate(fasta_t *f);
Uint bl_fastaGetMateLength(fasta_t *f, Uint elem);
char* bl_fastaGetMate(fasta_t *f, Uint elem);
char* bl_fastaGetMateQuality(fasta_t *f, Uint elem);
fasta_t* bl_fastxgzIndex(void *space, char *gzfilename);
fastxseqindex_t* bl_fastxChunkIndex (void *space, char **filenames, struct access **gzindex, 
    fastxfileindex_t **findex, Uint *n, Uint nooffiles, Uint total, Uint k);
void bl_fastaSetMateClip (fasta_t *f, Uint elem, Uint p5, Uint p3);
void bl_fastaSetClip (fasta_t *f, Uint elem, Uint p5, Uint p3);
int bl_rm(void *space, char *filename);
Uint bl_fastxFindIDIdx (char *id, fasta_t *set);

annotationtrack_t* bl_GFFread (void *space, char *filename);
Uint bl_annotationitem_cmp_track (Uint item, void *track, void *elem, void *nfo);
int bl_fastxIDcmp (char *a, char *b);
void bl_GFFAddAttribute (void *space, annotationitem_t *item, char *attr, Uint len);
void bl_GFFwrite(char *filename, annotationtrack_t *set);

char* bl_fastaGetLeftClip(fasta_t *f, Uint elem) ;
char* bl_fastaGetRightClip(fasta_t *f, Uint elem) ;
char* bl_fastaGetLeftClipQual(fasta_t *f, Uint elem) ;
char* bl_fastaGetRightClipQual(fasta_t *f, Uint elem) ;
char* bl_fastaGetMateLeftClip(fasta_t *f, Uint elem) ;
char* bl_fastaGetMateRightClip(fasta_t *f, Uint elem) ;
char* bl_fastaGetMateLeftClipQual(fasta_t *f, Uint elem) ;
char* bl_fastaGetMateRightClipQual(fasta_t *f, Uint elem) ;
char* bl_fastaGetMateNoClip(fasta_t *f, Uint elem);
char* bl_fastaGetSequenceNoClip(fasta_t *f, Uint elem);
char* bl_fastaGetQualityNoClip(fasta_t* f, Uint elem);
char* bl_fastaGetMateQualityNoClip(fasta_t *f, Uint elem);
void bl_addExon (gene_t *gene, Uint start, Uint end, char strand, char *refchr);
void bl_dumpGene(gene_t *gene);
gene_t* bl_initGene (char *identifier, char strand);
char bl_isExon(gene_t *gene, Uint pos);
void bl_wrapGene(gene_t *gene);
Uint bl_getExonNumber (gene_t *model);
Uint bl_getExonStart (gene_t *model, Uint id);
Uint bl_getExonEnd (gene_t *model, Uint id);
fasta_t* bl_fastxCopyIndex (void *space, fasta_t *f, Uint offset, Uint size);
fasta_t* bl_fastxCopy (void *space, fasta_t *f, Uint offset, Uint size);
annotationtrack_t* bl_annotationRead (void *space, char *fn) ;
#endif