sequencer.h

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/* =============================================================================
 *
 * sequencer.h
 *
 * =============================================================================
 *
 * Copyright (C) Stanford University, 2006.  All Rights Reserved.
 * Author: Chi Cao Minh
 *
 * =============================================================================
 *
 * For the license of bayes/sort.h and bayes/sort.c, please see the header
 * of the files.
 * 
 * ------------------------------------------------------------------------
 * 
 * For the license of kmeans, please see kmeans/LICENSE.kmeans
 * 
 * ------------------------------------------------------------------------
 * 
 * For the license of ssca2, please see ssca2/COPYRIGHT
 * 
 * ------------------------------------------------------------------------
 * 
 * For the license of lib/mt19937ar.c and lib/mt19937ar.h, please see the
 * header of the files.
 * 
 * ------------------------------------------------------------------------
 * 
 * For the license of lib/rbtree.h and lib/rbtree.c, please see
 * lib/LEGALNOTICE.rbtree and lib/LICENSE.rbtree
 * 
 * ------------------------------------------------------------------------
 * 
 * Unless otherwise noted, the following license applies to STAMP files:
 * 
 * Copyright (c) 2007, Stanford University
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met:
 * 
 *     * Redistributions of source code must retain the above copyright
 *       notice, this list of conditions and the following disclaimer.
 * 
 *     * 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.
 * 
 *     * Neither the name of Stanford University 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 STANFORD UNIVERSITY ``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 STANFORD UNIVERSITY 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 SEQUENCER_H
#define SEQUENCER_H 1


#include "hashtable.h"
#include "segments.h"
#include "table.h"
#include "tm.h"


typedef struct endInfoEntry endInfoEntry_t;
typedef struct constructEntry constructEntry_t;


typedef struct sequencer {

/* public: */

    char* sequence;

/* private: */

    segments_t* segmentsPtr;

    /* For removing duplicate segments */
    hashtable_t* uniqueSegmentsPtr;

    /* For matching segments */
    endInfoEntry_t* endInfoEntries;
    table_t** startHashToConstructEntryTables;

    /* For constructing sequence */
    constructEntry_t* constructEntries;
    table_t* hashToConstructEntryTable;

    /* For deallocation */
    long segmentLength;

} sequencer_t;


typedef struct sequencer_run_arg {
    sequencer_t* sequencerPtr;
    segments_t* segmentsPtr;
    long preAllocLength;
    char* returnSequence; /* variable stores return value */
} sequencer_run_arg_t;


/* =============================================================================
 * sequencer_alloc
 * -- Returns NULL on failure
 * =============================================================================
 */
sequencer_t*
sequencer_alloc (long geneLength, long segmentLength, segments_t* segmentsPtr);


/* =============================================================================
 * sequencer_run
 * =============================================================================
 */

void
sequencer_run (void* argPtr);


/* =============================================================================
 * sequencer_free
 * =============================================================================
 */
void
sequencer_free (sequencer_t* sequencerPtr);


#endif /* SEQUENCER_H */


/* =============================================================================
 *
 * End of sequencer.h
 *
 * =============================================================================
 */