#include "allheaders.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
*
*
* Notes:
* (1) The allocated array is n + 1 bytes. This allows room
* for null termination.
*
*/
L_BYTEA *
l_byteaCreate(size_t nbytes)
{
L_BYTEA *ba;
PROCNAME("l_byteaCreate");
if (nbytes <= 0 || nbytes > MaxArraySize)
nbytes = InitialArraySize;
ba = (L_BYTEA *)LEPT_CALLOC(1, sizeof(L_BYTEA));
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", procName, 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;
PROCNAME("l_byteaInitFromMem");
if (!data)
return (L_BYTEA *)ERROR_PTR("data not defined", procName, NULL);
if (size <= 0)
return (L_BYTEA *)ERROR_PTR("no bytes to initialize", procName, NULL);
if (size > MaxArraySize)
return (L_BYTEA *)ERROR_PTR("size is too big", procName, NULL);
if ((ba = l_byteaCreate(size)) == NULL)
return (L_BYTEA *)ERROR_PTR("ba not made", procName, 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;
PROCNAME("l_byteaInitFromFile");
if (!fname)
return (L_BYTEA *)ERROR_PTR("fname not defined", procName, NULL);
if ((fp = fopenReadStream(fname)) == NULL)
return (L_BYTEA *)ERROR_PTR("file stream not opened", procName, NULL);
ba = l_byteaInitFromStream(fp);
fclose(fp);
if (!ba)
return (L_BYTEA *)ERROR_PTR("ba not made", procName, 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;
PROCNAME("l_byteaInitFromStream");
if (!fp)
return (L_BYTEA *)ERROR_PTR("stream not defined", procName, NULL);
if ((data = l_binaryReadStream(fp, &nbytes)) == NULL)
return (L_BYTEA *)ERROR_PTR("data not read", procName, NULL);
if ((ba = l_byteaCreate(nbytes)) == NULL) {
LEPT_FREE(data);
return (L_BYTEA *)ERROR_PTR("ba not made", procName, 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
*
*
* Notes:
* (1) If cloning, up the refcount and return a ptr to %bas.
*
*/
L_BYTEA *
l_byteaCopy(L_BYTEA *bas,
l_int32 copyflag)
{
PROCNAME("l_byteaCopy");
if (!bas)
return (L_BYTEA *)ERROR_PTR("bas not defined", procName, 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
*
*
* 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.
*
*/
void
l_byteaDestroy(L_BYTEA **pba)
{
L_BYTEA *ba;
PROCNAME("l_byteaDestroy");
if (pba == NULL) {
L_WARNING("ptr address is null!\n", procName);
return;
}
if ((ba = *pba) == NULL)
return;
/* Decrement the ref count. If it is 0, destroy the lba. */
ba->refcount--;
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)
{
PROCNAME("l_byteaGetSize");
if (!ba)
return ERROR_INT("ba not defined", procName, 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
*
*
* Notes:
* (1) The returned ptr is owned by %ba. Do not free it!
*
*/
l_uint8 *
l_byteaGetData(L_BYTEA *ba,
size_t *psize)
{
PROCNAME("l_byteaGetData");
if (!ba)
return (l_uint8 *)ERROR_PTR("ba not defined", procName, NULL);
if (!psize)
return (l_uint8 *)ERROR_PTR("&size not defined", procName, 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.
*
*
* Notes:
* (1) The returned data is owned by the caller. The input %ba
* still owns the original data array.
*
*/
l_uint8 *
l_byteaCopyData(L_BYTEA *ba,
size_t *psize)
{
l_uint8 *data;
PROCNAME("l_byteaCopyData");
if (!psize)
return (l_uint8 *)ERROR_PTR("&size not defined", procName, NULL);
*psize = 0;
if (!ba)
return (l_uint8 *)ERROR_PTR("ba not defined", procName, 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;
PROCNAME("l_byteaAppendData");
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
if (!newdata)
return ERROR_INT("newdata not defined", procName, 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", procName, 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;
PROCNAME("l_byteaAppendString");
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
if (!str)
return ERROR_INT("str not defined", procName, 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", procName, 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
*
*
* Notes:
* (1) If necessary, reallocs the byte array to %size.
* (2) The max buffer size is 1 GB.
*
*/
static l_int32
l_byteaExtendArrayToSize(L_BYTEA *ba,
size_t size)
{
PROCNAME("l_byteaExtendArrayToSize");
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
if (ba->nalloc > MaxArraySize) /* belt & suspenders */
return ERROR_INT("ba has too many ptrs", procName, 1);
if (size > MaxArraySize)
return ERROR_INT("size > 1 GB; too large", procName, 1);
if (size <= ba->nalloc) {
L_INFO("size too small; no extension\n", procName);
return 0;
}
if ((ba->data =
(l_uint8 *)reallocNew((void **)&ba->data, ba->nalloc, size)) == NULL)
return ERROR_INT("new array not returned", procName, 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
*
*
* Notes:
* (1) It is a no-op, not an error, for %ba2 to be null.
*
*/
l_ok
l_byteaJoin(L_BYTEA *ba1,
L_BYTEA **pba2)
{
l_uint8 *data2;
size_t nbytes2;
L_BYTEA *ba2;
PROCNAME("l_byteaJoin");
if (!ba1)
return ERROR_INT("ba1 not defined", procName, 1);
if (!pba2)
return ERROR_INT("&ba2 not defined", procName, 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;
PROCNAME("l_byteaSplit");
if (!pba2)
return ERROR_INT("&ba2 not defined", procName, 1);
*pba2 = NULL;
if (!ba1)
return ERROR_INT("ba1 not defined", procName, 1);
data1 = l_byteaGetData(ba1, &nbytes1);
if (splitloc >= nbytes1)
return ERROR_INT("splitloc invalid", procName, 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;
PROCNAME("l_byteaFindEachSequence");
if (!pda)
return ERROR_INT("&da not defined", procName, 1);
*pda = NULL;
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
if (!sequence)
return ERROR_INT("sequence not defined", procName, 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;
PROCNAME("l_byteaWrite");
if (!fname)
return ERROR_INT("fname not defined", procName, 1);
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
if ((fp = fopenWriteStream(fname, "wb")) == NULL)
return ERROR_INT("stream not opened", procName, 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;
PROCNAME("l_byteaWriteStream");
if (!fp)
return ERROR_INT("stream not defined", procName, 1);
if (!ba)
return ERROR_INT("ba not defined", procName, 1);
data = l_byteaGetData(ba, &size);
if (startloc >= size)
return ERROR_INT("invalid startloc", procName, 1);
maxbytes = size - startloc;
nbytes = (nbytes == 0) ? maxbytes : L_MIN(nbytes, maxbytes);
fwrite(data + startloc, 1, nbytes, fp);
return 0;
}