libstaden-read-dev 1.13.5-1.1 / usr / include / io_lib / seqIOABI.h

/*
 * Copyright (c) 2003, 2005, 2007 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): Simon Dear, LaDeana Hillier, James Bonfield
 * 
 * Copyright (c) 1990-1995, 1998 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.
 */

/*
 * Copyright (c) Medical Research Council 1994. All rights reserved.
 *
 * Permission to use, copy, modify and distribute this software and its
 * documentation for any purpose is hereby granted without fee, provided that
 * this copyright and notice appears in all copies.
 *
 * This file was written by James Bonfield, Simon Dear, Rodger Staden,
 * as part of the Staden Package at the MRC Laboratory of Molecular
 * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
 *
 * MRC disclaims all warranties with regard to this software.
 */

#ifndef _seqIOABI_h_
#define _seqIOABI_h_

#include <sys/types.h> /* off_t */
#include "io_lib/os.h"

#ifdef __cplusplus
extern "C" {
#endif

/*
 * The ABI magic number - "ABIF"
 */
#define ABI_MAGIC	((int_4) ((((('A'<<8)+'B')<<8)+'I')<<8)+'F')

/*
 * The index is located towards the end of the ABI trace file.
 * It's location is given by a longword at a fixed place.
 */
#define IndexPO ((off_t)26)

#define IndexEntryLength 28

/*
 * Here are some labels we will be looking for, four chars packed
 * into an int_4
 */
#define LABEL(a) ((int_4) ((((((a)[0]<<8)+(a)[1])<<8)+(a)[2])<<8)+(a)[3])
#define DataEntryLabel    LABEL("DATA")
#define BaseEntryLabel    LABEL("PBAS")
#define BasePosEntryLabel LABEL("PLOC")
#define SpacingEntryLabel LABEL("SPAC")
#define SignalEntryLabel  LABEL("S/N%")
#define FWO_Label         LABEL("FWO_")
#define MCHNLabel         LABEL("MCHN")
#define PDMFLabel         LABEL("PDMF")
#define SMPLLabel         LABEL("SMPL")
#define PPOSLabel         LABEL("PPOS")
#define CMNTLabel         LABEL("CMNT")
#define GelNameLabel      LABEL("GELN")
#define LANELabel         LABEL("LANE")
#define RUNDLabel         LABEL("RUND")
#define RUNTLabel         LABEL("RUNT")
#define MTXFLabel         LABEL("MTXF")
#define SPACLabel         LABEL("SPAC")
#define SVERLabel         LABEL("SVER")
#define MODLLabel         LABEL("MODL")
#define BaseConfLabel	  LABEL("PCON")


/*
 * From the ABI results file connected to `fp' whose index starts
 * at byte offset `indexO', return in `val' the `lw'th long word
 * from the `count'th entry labelled `label'.
 * The result is 0 for failure, or index offset for success.
 */
int getABIIndexEntryLW(FILE *fp, off_t indexO,
		       uint_4 label, uint_4 count, int lw,
		       uint_4 *val);

/*
 * From the ABI results file connected to `fp' whose index starts
 * at byte offset `indexO', return in `val' the `sw'th short word
 * from the `count'th entry labelled `label'.
 * The result is 0 for failure, or index offset for success.
 */
int getABIIndexEntrySW(FILE *fp, off_t indexO,
		       uint_4 label, uint_4 count, int sw,
		       uint_2 *val);

/*
 * Gets the offset of the ABI index.
 * Returns -1 for failure, 0 for success.
 */
int getABIIndexOffset(FILE *fp, uint_4 *indexO);

/*
 * Get an "ABI String". These strings are either pointed to by the index
 * offset, or held in the offset itself when the string is <= 4 characters.
 * The first byte of the string determines its length.
 * 'string' is a buffer 256 characters long.
 *
 * Returns -1 for failure, string length for success.
 */
int getABIString(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
		 char *string);

/*
 * Get an "ABI Int_1". This is raw 1-byte integer data pointed to by the
 * offset, or held in the offset itself when the data is <= 4 characters.
 *
 * If indexO is 0 then we do not search for (or indeed use) label and count,
 * but simply assume that we are already at the correct offset and read from
 * here. (NB: This negates the length <= 4 check.)
 *
 * Returns -1 for failure, length desired for success (it'll only fill out
 * up to max_data_len elements, but it gives an indication of whether there
 * was more to come).
 */
int getABIint1(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
	       uint_1 *data, int max_data_len);

/*
 * Get an "ABI Int_2". This is raw 2-byte integer data pointed to by the
 * offset, or held in the offset itself when the data is <= 4 characters.
 *
 * Returns -1 for failure, length desired for success (it'll only fill out
 * up to max_data_len elements, but it gives an indication of whether there
 * was more to come).
 */
int getABIint2(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
	       uint_2 *data, int max_data_len);

/*
 * Get an "ABI Int_4". This is raw 4-byte integer data pointed to by the
 * offset, or held in the offset itself when the data is <= 4 characters.
 *
 * Returns -1 for failure, length desired for success (it'll only fill out
 * up to max_data_len elements, but it gives an indication of whether there
 * was more to come).
 */
int getABIint4(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
	       uint_4 *data, int max_data_len);

int dump_labels(FILE *fp, off_t indexO);

/*
 * Change the DATA counts for fetching traces
 */
void abi_set_data_counts(int f, int w, int o, int _);

/*
 * Put the DATA counts back to their defaults.
 */
void abi_reset_data_counts(void);

#ifdef __cplusplus
}
#endif

#endif /* _seqIOABI_h_ */