/**
* @param alphabet ownership of alphabet is with the newly produced
* sequence object if return value is non-NULL
*/
BWTSeq *
gt_newBWTSeq(EISeq *seqIdx, MRAEnc *alphabet,
const enum rangeSortMode *defaultRangeSort)
{
BWTSeq *bwtSeq;
GtUword *counts;
size_t countsOffset, rangeSortOffset, totalSize;
enum rangeSortMode *rangeSort;
unsigned alphabetSize;
gt_assert(seqIdx);
/* alphabetSize is increased by one to handle the flattened
* terminator symbol correctly */
alphabetSize = gt_MRAEncGetSize(alphabet) + 1;
countsOffset = offsetAlign(sizeof (struct BWTSeq), sizeof (GtUword));
rangeSortOffset = offsetAlign(countsOffset
+ sizeof (GtUword) * (alphabetSize + 1),
sizeof (enum rangeSortMode));
totalSize = rangeSortOffset + sizeof (enum rangeSortMode)
* MRAEncGetNumRanges(alphabet);
bwtSeq = gt_malloc(totalSize);
bwtSeq->pckbuckettable = NULL;
counts = (GtUword *)((char *)bwtSeq + countsOffset);
rangeSort = (enum rangeSortMode *)((char *)bwtSeq + rangeSortOffset);
if (!initBWTSeqFromEncSeqIdx(bwtSeq, seqIdx, alphabet, counts, rangeSort,
defaultRangeSort))
{
gt_free(bwtSeq);
bwtSeq = NULL;
}
return bwtSeq;
}
MRAEnc *
gt_newMultiRangeAlphabetEncodingUInt8(AlphabetRangeID numRanges,
const AlphabetRangeSize symbolsPerRange[],
const uint8_t *mappings)
{
MRAEncUInt8 *newAlpha = NULL;
size_t rEIOffset = offsetAlign(
sizeof (MRAEncUInt8),
sizeof (newAlpha->baseClass.rangeEndIndices[0]));
size_t sPROffset = offsetAlign(
rEIOffset + sizeof (newAlpha->baseClass.rangeEndIndices[0]) * numRanges,
sizeof (newAlpha->baseClass.symbolsPerRange[0]));
AlphabetRangeID i;
if ((newAlpha = gt_calloc(
sPROffset
+ sizeof (newAlpha->baseClass.symbolsPerRange[0]) * numRanges,
1)))
{
newAlpha->baseClass.rangeEndIndices
= (AlphabetRangeSize *)((char *)newAlpha + rEIOffset);
newAlpha->baseClass.symbolsPerRange
= (AlphabetRangeSize *)((char *)newAlpha + sPROffset);
newAlpha->baseClass.encType = sourceUInt8;
newAlpha->baseClass.numRanges = numRanges;
memset(newAlpha->mappings, UNDEF_UCHAR, UINT8_MAX+1);
memset(newAlpha->revMappings, UNDEF_UCHAR, UINT8_MAX+1);
newAlpha->baseClass.rangeEndIndices[0] =
newAlpha->baseClass.symbolsPerRange[0] = symbolsPerRange[0];
for (i = 1; i < numRanges; ++i)
{
newAlpha->baseClass.rangeEndIndices[i] =
newAlpha->baseClass.rangeEndIndices[i-1]
+ (newAlpha->baseClass.symbolsPerRange[i] = symbolsPerRange[i]);
}
for (i = 0; i <= UINT8_MAX; ++i)
{
newAlpha->mappings[i] = mappings[i];
newAlpha->revMappings[mappings[i]] = i;
}
}
else
{
if (newAlpha)
{
if (newAlpha->baseClass.symbolsPerRange)
gt_free(newAlpha->baseClass.symbolsPerRange);
if (newAlpha->baseClass.rangeEndIndices)
gt_free(newAlpha->baseClass.rangeEndIndices);
gt_free(newAlpha);
}
return NULL;
}
return &(newAlpha->baseClass);
}
