/*===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 */
#include <vdb/extern.h>

#include <klib/defs.h>
#include <klib/rc.h>
#include <vdb/table.h>
#include <vdb/xform.h>
#include <vdb/schema.h>
#include <vdb/cursor.h>
#include <vdb/manager.h>
#include <kdb/meta.h>
#include <klib/data-buffer.h>
#include <insdc/insdc.h>
#include <align/refseq-mgr.h>
#include <bitstr.h>
#include <sysalloc.h>
#include <stdint.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#include <stdio.h>

typedef struct RestoreRead RestoreRead;
struct RestoreRead
{
    const RefSeqMgr* rmgr;
};

static
void CC RestoreReadWhack ( void *obj )
{
    RestoreRead * self = obj;
    if( self != NULL ) {
        rc_t rc;
        rc = RefSeqMgr_Release(self->rmgr);
        assert(rc == 0);
        free(self);
    }
}

static
rc_t RestoreReadMake ( RestoreRead **objp, const VDBManager *mgr )
{
	rc_t rc = 0;
	RestoreRead *obj;

	assert(objp != NULL);
    assert(mgr != NULL);

    obj = calloc(1, sizeof(*obj));
    if( obj == NULL ) {
		rc = RC(rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted);
    } else {
        if( (rc = RefSeqMgr_Make(&obj->rmgr, mgr, errefseq_4NA, 1024 * 1024 * 1024, 30)) == 0 ) {
		    *objp = obj;
        } else {
            *objp = NULL;
            RestoreReadWhack(obj);
        }
	}
	return rc;
}

static
rc_t CC ref_restore_read_impl ( void *data, const VXformInfo *info, int64_t row_id,
                               VRowResult *rslt, uint32_t argc, const VRowData argv [] )
{
    rc_t rc;
    RestoreRead* self = data;
    uint8_t* dst;
    uint32_t read_len     = argv[0].u.data.elem_count;
    const uint8_t *read   = argv[0].u.data.base;
    uint32_t seqid_len    = argv[1].u.data.elem_count;
    const char* seqid     = argv[1].u.data.base;
    INSDC_coord_one   seq_start;
    INSDC_coord_len   seq_len;

    assert(argv[0].u.data.elem_bits == 8);
    assert(argv[1].u.data.elem_bits == 8);
    assert(argv[2].u.data.elem_bits == sizeof(INSDC_coord_one)*8);
    assert(argv[3].u.data.elem_bits == sizeof(INSDC_coord_len)*8);
    assert(argv[2].u.data.elem_count == 1);
    assert(argv[3].u.data.elem_count == 1);

    read   += argv [ 0 ] . u . data . first_elem;
    seqid  += argv [ 1 ] . u . data . first_elem;
    seq_start = ((INSDC_coord_one*)argv[2].u.data.base)[argv[2].u.data.first_elem];
    seq_len   = ((INSDC_coord_len*)argv[3].u.data.base)[argv[3].u.data.first_elem];

    if(seq_len < read_len) {
        rc = RC(rcXF, rcFunction, rcExecuting, rcData, rcInvalid );
    } else {
        /* resize output row for the total number of reads */    
        rslt->data->elem_bits = 8;
        rc = KDataBufferResize(rslt->data, seq_len);
        if ( rc == 0 ) {
            rslt->elem_count = seq_len;
            dst = rslt->data->base;

            if(seq_len > 0) {
                if(read_len > 0) {
                    memcpy(dst, read, read_len);
                    if(read_len < seq_len) {
                        memset(dst + read_len, 15, seq_len - read_len); /* pad with 'N' */
                    }
                } else if(seq_start == 0) {
                    memset(dst, 15, seq_len); /* fill with 'N' */
                } else {
                    INSDC_coord_len read = 0;
                    if( (rc = RefSeqMgr_Read(self->rmgr, seqid, seqid_len, seq_start - 1, seq_len, dst, &read)) == 0 ) {
                        if( read != seq_len) {
                            rc = RC(rcXF, rcFunction, rcExecuting, rcData, read < seq_len ? rcTooShort : rcTooLong);
                        }
                    }
                }
            }
        }
    }
    return rc;
}

/* 
 * function
 * INSDC:4na:bin ALIGN:ref_restore_read #1 (  INSDC:4na:bin rd , ascii seq_id , INSDC:coord:one seq_start, INSDC:coord:len seq_len);
 */
VTRANSFACT_IMPL ( ALIGN_ref_restore_read, 1, 0, 0 ) ( const void *Self, const VXfactInfo *info,
                                                     VFuncDesc *rslt, const VFactoryParams *cp, const VFunctionParams *dp )
{
    RestoreRead *fself;
    rc_t rc = RestoreReadMake ( & fself, info -> mgr);
    if(rc == 0 ) {
        rslt->self = fself;
        rslt->u.ndf = ref_restore_read_impl;
        rslt->variant = vftRow;
        rslt -> whack = RestoreReadWhack;
    }
    return rc;
}
