/*====================================================================*

 -  Copyright (C) 2001 Leptonica.  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.

 -

 -  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 ANY

 -  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.

 *====================================================================*/

/*!

 * \file  bytearray.c

 * <pre>

 *

 *   Functions for handling byte arrays, in analogy with C++ 'strings'

 *

 *      Creation, copy, clone, destruction

 *           L_BYTEA      *l_byteaCreate()

 *           L_BYTEA      *l_byteaInitFromMem()

 *           L_BYTEA      *l_byteaInitFromFile()

 *           L_BYTEA      *l_byteaInitFromStream()

 *           L_BYTEA      *l_byteaCopy()

 *           void          l_byteaDestroy()

 *

 *      Accessors

 *           size_t        l_byteaGetSize()

 *           l_uint8      *l_byteaGetData()

 *           l_uint8      *l_byteaCopyData()

 *

 *      Appending

 *           l_int32       l_byteaAppendData()

 *           l_int32       l_byteaAppendString()

 *           static l_int32  l_byteaExtendArrayToSize()

 *

 *      Join/Split

 *           l_int32       l_byteaJoin()

 *           l_int32       l_byteaSplit()

 *

 *      Search

 *           l_int32       l_byteaFindEachSequence()

 *

 *      Output to file

 *           l_int32       l_byteaWrite()

 *           l_int32       l_byteaWriteStream()

 *

 *   The internal data array is always null-terminated, for ease of use

 *   in the event that it is an ascii string without null bytes.

 * </pre>

 */

#ifdef HAVE_CONFIG_H

#include <config_auto.h>

#endif  /* HAVE_CONFIG_H */

#include <string.h>

#include "allheaders.h"

#include "array_internal.h"

    /* Bounds on array size */

static const l_uint32  MaxArraySize = 1000000000;   /* 10^9 bytes */

static const l_int32   InitialArraySize = 200;      /*!< n'importe quoi */

    /* Static function */

static l_int32 l_byteaExtendArrayToSize(L_BYTEA *ba, size_t size);

/*---------------------------------------------------------------------*

 *                  Creation, copy, clone, destruction                 *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaCreate()

 *

 * \param[in]    nbytes    determines initial size of data array

 * \return  l_bytea, or NULL on error

 *

 * <pre>

 * Notes:

 *      (1) The allocated array is n + 1 bytes.  This allows room

 *          for null termination.

 * </pre>

 */

L_BYTEA *

l_byteaCreate(size_t  nbytes)

{

L_BYTEA  *ba;

    if (nbytes <= 0 || nbytes > MaxArraySize)

        nbytes = InitialArraySize;

    ba = (L_BYTEA *)LEPT_CALLOC(1, sizeof(L_BYTEA));

    if (!ba)

        return (L_BYTEA *)ERROR_PTR("bytea not made", __func__, NULL);

    ba->data = (l_uint8 *)LEPT_CALLOC(nbytes + 1, sizeof(l_uint8));

    if (!ba->data) {

        l_byteaDestroy(&ba);

        return (L_BYTEA *)ERROR_PTR("ba array not made", __func__, NULL);

    }

    ba->nalloc = nbytes + 1;

    ba->refcount = 1;

    return ba;

}

/*!

 * \brief   l_byteaInitFromMem()

 *

 * \param[in]    data    to be copied to the array

 * \param[in]    size    amount of data

 * \return  l_bytea, or NULL on error

 */

L_BYTEA *

l_byteaInitFromMem(const l_uint8  *data,

                   size_t          size)

{

L_BYTEA  *ba;

    if (!data)

        return (L_BYTEA *)ERROR_PTR("data not defined", __func__, NULL);

    if (size <= 0)

        return (L_BYTEA *)ERROR_PTR("no bytes to initialize", __func__, NULL);

    if (size > MaxArraySize)

        return (L_BYTEA *)ERROR_PTR("size is too big", __func__, NULL);

    if ((ba = l_byteaCreate(size)) == NULL)

        return (L_BYTEA *)ERROR_PTR("ba not made", __func__, NULL);

    memcpy(ba->data, data, size);

    ba->size = size;

    return ba;

}

/*!

 * \brief   l_byteaInitFromFile()

 *

 * \param[in]    fname

 * \return  l_bytea, or NULL on error

 */

L_BYTEA *

l_byteaInitFromFile(const char  *fname)

{

FILE     *fp;

L_BYTEA  *ba;

    if (!fname)

        return (L_BYTEA *)ERROR_PTR("fname not defined", __func__, NULL);

    if ((fp = fopenReadStream(fname)) == NULL)

        return (L_BYTEA *)ERROR_PTR_1("file stream not opened",

                                      fname, __func__, NULL);

    ba = l_byteaInitFromStream(fp);

    fclose(fp);

    if (!ba)

        return (L_BYTEA *)ERROR_PTR_1("ba not made", fname, __func__, NULL);

    return ba;

}

/*!

 * \brief   l_byteaInitFromStream()

 *

 * \param[in]    fp    file stream

 * \return  l_bytea, or NULL on error

 */

L_BYTEA *

l_byteaInitFromStream(FILE  *fp)

{

l_uint8  *data;

size_t    nbytes;

L_BYTEA  *ba;

    if (!fp)

        return (L_BYTEA *)ERROR_PTR("stream not defined", __func__, NULL);

    if ((data = l_binaryReadStream(fp, &nbytes)) == NULL)

        return (L_BYTEA *)ERROR_PTR("data not read", __func__, NULL);

    if ((ba = l_byteaCreate(nbytes)) == NULL) {

        LEPT_FREE(data);

        return (L_BYTEA *)ERROR_PTR("ba not made", __func__, NULL);

    }

    memcpy(ba->data, data, nbytes);

    ba->size = nbytes;

    LEPT_FREE(data);

    return ba;

}

/*!

 * \brief   l_byteaCopy()

 *

 * \param[in]    bas        source lba

 * \param[in]    copyflag   L_COPY, L_CLONE

 * \return  clone or copy of bas, or NULL on error

 *

 * <pre>

 * Notes:

 *      (1) If cloning, up the refcount and return a ptr to %bas.

 * </pre>

 */

L_BYTEA *

l_byteaCopy(L_BYTEA  *bas,

            l_int32   copyflag)

{

    if (!bas)

        return (L_BYTEA *)ERROR_PTR("bas not defined", __func__, NULL);

    if (copyflag == L_CLONE) {

        bas->refcount++;

        return bas;

    }

    return l_byteaInitFromMem(bas->data, bas->size);

}

/*!

 * \brief   l_byteaDestroy()

 *

 * \param[in,out]   pba    will be set to null before returning

 * \return  void

 *

 * <pre>

 * Notes:

 *      (1) Decrements the ref count and, if 0, destroys the lba.

 *      (2) Always nulls the input ptr.

 *      (3) If the data has been previously removed, the lba will

 *          have been nulled, so this will do nothing.

 * </pre>

 */

void

l_byteaDestroy(L_BYTEA  **pba)

{

L_BYTEA  *ba;

    if (pba == NULL) {

        L_WARNING("ptr address is null!\n", __func__);

        return;

    }

    if ((ba = *pba) == NULL)

        return;

        /* Decrement the ref count.  If it is 0, destroy the lba. */

    if (--ba->refcount == 0) {

        if (ba->data) LEPT_FREE(ba->data);

        LEPT_FREE(ba);

    }

    *pba = NULL;

}

/*---------------------------------------------------------------------*

 *                               Accessors                             *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaGetSize()

 *

 * \param[in]    ba

 * \return  size of stored byte array, or 0 on error

 */

size_t

l_byteaGetSize(L_BYTEA  *ba)

{

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 0);

    return ba->size;

}

/*!

 * \brief   l_byteaGetData()

 *

 * \param[in]    ba

 * \param[out]   psize     size of data in lba

 * \return  ptr to existing data array, or NULL on error

 *

 * <pre>

 * Notes:

 *      (1) The returned ptr is owned by %ba.  Do not free it!

 * </pre>

 */

l_uint8 *

l_byteaGetData(L_BYTEA  *ba,

               size_t   *psize)

{

    if (!ba)

        return (l_uint8 *)ERROR_PTR("ba not defined", __func__, NULL);

    if (!psize)

        return (l_uint8 *)ERROR_PTR("&size not defined", __func__, NULL);

    *psize = ba->size;

    return ba->data;

}

/*!

 * \brief   l_byteaCopyData()

 *

 * \param[in]    ba

 * \param[out]   psize     size of data in lba

 * \return  copy of data in use in the data array, or NULL on error.

 *

 * <pre>

 * Notes:

 *      (1) The returned data is owned by the caller.  The input %ba

 *          still owns the original data array.

 * </pre>

 */

l_uint8 *

l_byteaCopyData(L_BYTEA  *ba,

                size_t   *psize)

{

l_uint8  *data;

    if (!psize)

        return (l_uint8 *)ERROR_PTR("&size not defined", __func__, NULL);

    *psize = 0;

    if (!ba)

        return (l_uint8 *)ERROR_PTR("ba not defined", __func__, NULL);

    data = l_byteaGetData(ba, psize);

    return l_binaryCopy(data, *psize);

}

/*---------------------------------------------------------------------*

 *                               Appending                             *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaAppendData()

 *

 * \param[in]    ba

 * \param[in]    newdata    byte array to be appended

 * \param[in]    newbytes   size of data array

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaAppendData(L_BYTEA        *ba,

                  const l_uint8  *newdata,

                  size_t          newbytes)

{

size_t  size, nalloc, reqsize;

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    if (!newdata)

        return ERROR_INT("newdata not defined", __func__, 1);

    size = l_byteaGetSize(ba);

    reqsize = size + newbytes + 1;

    nalloc = ba->nalloc;

    if (nalloc < reqsize) {

        if (l_byteaExtendArrayToSize(ba, 2 * reqsize))

            return ERROR_INT("extension failed", __func__, 1);

    }

    memcpy(ba->data + size, newdata, newbytes);

    ba->size += newbytes;

    return 0;

}

/*!

 * \brief   l_byteaAppendString()

 *

 * \param[in]    ba

 * \param[in]    str    null-terminated string to be appended

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaAppendString(L_BYTEA     *ba,

                    const char  *str)

{

size_t  size, len, nalloc, reqsize;

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    if (!str)

        return ERROR_INT("str not defined", __func__, 1);

    size = l_byteaGetSize(ba);

    len = strlen(str);

    reqsize = size + len + 1;

    nalloc = ba->nalloc;

    if (nalloc < reqsize) {

        if (l_byteaExtendArrayToSize(ba, 2 * reqsize))

            return ERROR_INT("extension failed", __func__, 1);

    }

    memcpy(ba->data + size, str, len);

    ba->size += len;

    return 0;

}

/*!

 * \brief   l_byteaExtendArrayToSize()

 *

 * \param[in]    ba

 * \param[in]    size    new size of lba data array

 * \return  0 if OK; 1 on error

 *

 * <pre>

 * Notes:

 *      (1) If necessary, reallocs the byte array to %size.

 *      (2) The max buffer size is 1 GB.

 * </pre>

 */

static l_int32

l_byteaExtendArrayToSize(L_BYTEA  *ba,

                         size_t    size)

{

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    if (ba->nalloc > MaxArraySize)  /* belt & suspenders */

        return ERROR_INT("ba has too many ptrs", __func__, 1);

    if (size > MaxArraySize)

        return ERROR_INT("size > 1 GB; too large", __func__, 1);

    if (size <= ba->nalloc) {

        L_INFO("size too small; no extension\n", __func__);

        return 0;

    }

    if ((ba->data =

        (l_uint8 *)reallocNew((void **)&ba->data, ba->nalloc, size)) == NULL)

        return ERROR_INT("new array not returned", __func__, 1);

    ba->nalloc = size;

    return 0;

}

/*---------------------------------------------------------------------*

 *                        String join/split                            *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaJoin()

 *

 * \param[in]       ba1

 * \param[in,out]   pba2    data array is added to the one in ba1;

 *                          then ba2 is destroyed and its pointer is nulled.

 * \return  0 if OK, 1 on error

 *

 * <pre>

 * Notes:

 *      (1) It is a no-op, not an error, for %ba2 to be null.

 * </pre>

 */

l_ok

l_byteaJoin(L_BYTEA   *ba1,

            L_BYTEA  **pba2)

{

l_uint8  *data2;

size_t    nbytes2;

L_BYTEA  *ba2;

    if (!ba1)

        return ERROR_INT("ba1 not defined", __func__, 1);

    if (!pba2)

        return ERROR_INT("&ba2 not defined", __func__, 1);

    if ((ba2 = *pba2) == NULL) return 0;

    data2 = l_byteaGetData(ba2, &nbytes2);

    l_byteaAppendData(ba1, data2, nbytes2);

    l_byteaDestroy(pba2);

    return 0;

}

/*!

 * \brief   l_byteaSplit()

 *

 * \param[in]    ba1       lba to split; array bytes nulled beyond the split loc

 * \param[in]    splitloc  location in ba1 to split; ba2 begins there

 * \param[out]   pba2      with data starting at splitloc

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaSplit(L_BYTEA   *ba1,

             size_t     splitloc,

             L_BYTEA  **pba2)

{

l_uint8  *data1;

size_t    nbytes1, nbytes2;

    if (!pba2)

        return ERROR_INT("&ba2 not defined", __func__, 1);

    *pba2 = NULL;

    if (!ba1)

        return ERROR_INT("ba1 not defined", __func__, 1);

    data1 = l_byteaGetData(ba1, &nbytes1);

    if (splitloc >= nbytes1)

        return ERROR_INT("splitloc invalid", __func__, 1);

    nbytes2 = nbytes1 - splitloc;

        /* Make the new lba */

    *pba2 = l_byteaInitFromMem(data1 + splitloc, nbytes2);

        /* Null the removed bytes in the input lba */

    memset(data1 + splitloc, 0, nbytes2);

    ba1->size = splitloc;

    return 0;

}

/*---------------------------------------------------------------------*

 *                                Search                               *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaFindEachSequence()

 *

 * \param[in]    ba

 * \param[in]    sequence   subarray of bytes to find in data

 * \param[in]    seqlen     length of sequence, in bytes

 * \param[out]   pda        byte positions of each occurrence of %sequence

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaFindEachSequence(L_BYTEA        *ba,

                        const l_uint8  *sequence,

                        size_t          seqlen,

                        L_DNA         **pda)

{

l_uint8  *data;

size_t    size;

    if (!pda)

        return ERROR_INT("&da not defined", __func__, 1);

    *pda = NULL;

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    if (!sequence)

        return ERROR_INT("sequence not defined", __func__, 1);

    data = l_byteaGetData(ba, &size);

    *pda = arrayFindEachSequence(data, size, sequence, seqlen);

    return 0;

}

/*---------------------------------------------------------------------*

 *                              Output to file                         *

 *---------------------------------------------------------------------*/

/*!

 * \brief   l_byteaWrite()

 *

 * \param[in]    fname      output file

 * \param[in]    ba

 * \param[in]    startloc   first byte to output

 * \param[in]    nbytes     number of bytes to write; use 0 to write to

 *                          the end of the data array

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaWrite(const char  *fname,

             L_BYTEA     *ba,

             size_t       startloc,

             size_t       nbytes)

{

l_int32  ret;

FILE    *fp;

    if (!fname)

        return ERROR_INT("fname not defined", __func__, 1);

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    if ((fp = fopenWriteStream(fname, "wb")) == NULL)

        return ERROR_INT_1("stream not opened", fname, __func__, 1);

    ret = l_byteaWriteStream(fp, ba, startloc, nbytes);

    fclose(fp);

    return ret;

}

/*!

 * \brief   l_byteaWriteStream()

 *

 * \param[in]    fp         file stream opened for binary write

 * \param[in]    ba

 * \param[in]    startloc   first byte to output

 * \param[in]    nbytes     number of bytes to write; use 0 to write to

 *                          the end of the data array

 * \return  0 if OK, 1 on error

 */

l_ok

l_byteaWriteStream(FILE     *fp,

                   L_BYTEA  *ba,

                   size_t    startloc,

                   size_t    nbytes)

{

l_uint8  *data;

size_t    size, maxbytes;

    if (!fp)

        return ERROR_INT("stream not defined", __func__, 1);

    if (!ba)

        return ERROR_INT("ba not defined", __func__, 1);

    data = l_byteaGetData(ba, &size);

    if (startloc >= size)

        return ERROR_INT("invalid startloc", __func__, 1);

    maxbytes = size - startloc;

    nbytes = (nbytes == 0) ? maxbytes : L_MIN(nbytes, maxbytes);

    fwrite(data + startloc, 1, nbytes, fp);

    return 0;

}