/*
 * Copyright (c) 2005-2008 Genome Research Ltd.
 * Author(s): James Bonfield
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *    1. Redistributions of source code must retain the above copyright notice,
 *       this list of conditions and the following disclaimer.
 * 
 *    2. Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials provided
 *       with the distribution.
 * 
 *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
 *    Institute nor the names of its contributors may be used to endorse
 *    or promote products derived from this software without specific
 *    prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
 * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
 * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

/*
 * Author(s): James Bonfield
 * 
 * Copyright (c) 2001 MEDICAL RESEARCH COUNCIL
 * All rights reserved
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *    1 Redistributions of source code must retain the above copyright notice, 
 *      this list of conditions and the following disclaimer.
 * 
 *    2 Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in
 *      the documentation and/or other materials provided with the
 *      distribution.
 * 
 *    3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
 *      MOLECULAR BIOLOGY nor the names of its contributors may be used
 *      to endorse or promote products derived from this software without
 *      specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 */

#ifndef _ZTR_H
#define _ZTR_H

#include "io_lib/Read.h"
#include "io_lib/deflate_interlaced.h"

#ifdef __cplusplus
extern "C" {
#endif

/* The header */
typedef struct {
    unsigned char  magic[8];	  /* 0xae5a54520d0a1a0a (be) */
    unsigned char  version_major; /* ZTR_VERSION_MAJOR */
    unsigned char  version_minor; /* ZTR_VERSION_MINOR */
} ztr_header_t;

/* The ZTR magic numbers */
#define ZTR_MAGIC   		"\256ZTR\r\n\032\n"
#define ZTR_VERSION_MAJOR	1
#define ZTR_VERSION_MINOR	2

/*
 * CHUNKS
 *
 * Chunks consist of a block length followed by the type, format and data.
 */

typedef struct {
    uint4 type;			/* chunk type (be) */
    uint4 mdlength;		/* length of meta data field (be) */
    char *mdata;		/* meta data */
    uint4 dlength;		/* length of data field (be) */
    char *data;			/* a format byte and the data itself */
    int   ztr_owns;		/* boolean: true if we can free (meta)data */
} ztr_chunk_t;

/* Format types */
#define ZTR_FORM_RAW		0
#define ZTR_FORM_RLE		1
#define ZTR_FORM_ZLIB		2
#define ZTR_FORM_XRLE		3
#define ZTR_FORM_XRLE2		4
#define ZTR_FORM_DELTA1		64
#define ZTR_FORM_DELTA2		65
#define ZTR_FORM_DELTA4		66
#define ZTR_FORM_DDELTA1	67
#define ZTR_FORM_DDELTA2	68
#define ZTR_FORM_DDELTA4	69
#define ZTR_FORM_16TO8		70
#define ZTR_FORM_32TO8		71
#define ZTR_FORM_FOLLOW1	72
#define ZTR_FORM_CHEB445	73
#define ZTR_FORM_ICHEB		74
#define ZTR_FORM_LOG2		75
#define ZTR_FORM_STHUFF	        77
#define ZTR_FORM_QSHIFT		79
#define ZTR_FORM_TSHIFT		80

/* Converts a C string to a big-endian 4-byte int */
#define ZTR_STR2BE(str) (((str)[0] << 24) + \
                         ((str)[1] << 16) + \
                         ((str)[2] <<  8) + \
                         ((str)[3] <<  0))

/* Converts a big-endian 4-byte int to a C string */
#define ZTR_BE2STR(i,str) (((str)[0]=((i)>>24)&0xff),\
                           ((str)[1]=((i)>>16)&0xff),\
                           ((str)[2]=((i)>> 8)&0xff),\
                           ((str)[3]=((i)>> 0)&0xff),\
			   (str)[4]='\0',str)\

#define ZTR_TYPE_HEADER	0xae5a5452 /* M-. Z T R */

#define ZTR_TYPE_SAMP	0x53414d50
#define ZTR_TYPE_SMP4	0x534d5034
#define ZTR_TYPE_BASE	0x42415345
#define ZTR_TYPE_BPOS	0x42504f53
#define ZTR_TYPE_CNF4	0x434e4634
#define ZTR_TYPE_CNF1	0x434e4631
#define ZTR_TYPE_CSID	0x43534944
#define ZTR_TYPE_TEXT	0x54455854
#define ZTR_TYPE_CLIP	0x434c4950
#define ZTR_TYPE_COMM	0x434f4d4d
#define ZTR_TYPE_CR32	0x43523332
#define ZTR_TYPE_FLWO	0x464c574f
#define ZTR_TYPE_FLWC	0x464c5743
#define ZTR_TYPE_HUFF   0x48554646
#define ZTR_TYPE_REGN   0x5245474e

/* A text segment consists of identifier and value */
typedef struct {
    char *ident; /* Pointer to identifier */
    char *value; /* Pointer to value */
} ztr_text_t;

typedef struct {
    int ztr_owns; /* true is ZTR is to free the data later */
    huffman_codeset_t *codes;
} ztr_hcode_t;

/* The main ZTR structure, which holds the entire file contents */
typedef struct {
    /* General bits to do with the ZTR file format */
    ztr_header_t header;	/* File Header */
    ztr_chunk_t *chunk;		/* Array of chunks */
    int nchunks;		/* Number of chunks */

    /* Specifics to do with the standard chunk types */
    ztr_text_t *text_segments;
    int ntext_segments;

    /* 'Hint' for delta of SAMP and SMP4 */
    int delta_level;

    /* Cached huffman encoding/decoding tables for STHUFF format */
    ztr_hcode_t *hcodes;
    int nhcodes;
    int hcodes_checked;
} ztr_t;

int ztr_read_header(mFILE *fp, ztr_header_t *h);
ztr_chunk_t *ztr_read_chunk_hdr(mFILE *fp);

int fwrite_ztr(FILE *fp, ztr_t *ztr);
int mfwrite_ztr(mFILE *fp, ztr_t *ztr);
ztr_t *fread_ztr(FILE *fp);
ztr_t *mfread_ztr(mFILE *fp);
Read *ztr2read(ztr_t *ztr);
ztr_t *read2ztr(Read *r);
int compress_ztr(ztr_t *ztr, int level);
int uncompress_ztr(ztr_t *ztr);
ztr_t *new_ztr(void);
void delete_ztr(ztr_t *ztr);
ztr_chunk_t **ztr_find_chunks(ztr_t *ztr, uint4 type, int *nchunks_p);
void ztr_process_text(ztr_t *ztr);
int compress_chunk(ztr_t *ztr, ztr_chunk_t *chunk, int format,
		   int option, int option2);
int uncompress_chunk(ztr_t *ztr, ztr_chunk_t *chunk);
ztr_hcode_t *ztr_add_hcode(ztr_t *ztr, huffman_codeset_t *codes, int ztr_owns);
int ztr_store_hcodes(ztr_t *ztr);
ztr_hcode_t *ztr_find_hcode(ztr_t *ztr, int code_set);
ztr_chunk_t *ztr_find_hcode_chunk(ztr_t *ztr, int code_set);
char *ztr_lookup_mdata_value(ztr_t *z, ztr_chunk_t *chunk, char *key);
ztr_chunk_t *ztr_new_chunk(ztr_t *ztr, uint4 type,
			   char *data,  uint4 dlength,
			   char *mdata, uint4 mdlength);
ztr_chunk_t *ztr_add_text(ztr_t *z, ztr_chunk_t *ch,
			  const char *key, const char *value);

#ifdef __cplusplus
}
#endif

#endif /* _ZTR_H */