/**
* Given the prepared context build the dictionary.
*/
private static nuint FASTCOVER_buildDictionary(FASTCOVER_ctx_t *ctx, uint *freqs, void *dictBuffer, nuint dictBufferCapacity, ZDICT_cover_params_t parameters, ushort *segmentFreqs)
{
byte *dict = (byte *)(dictBuffer);
nuint tail = dictBufferCapacity;
COVER_epoch_info_t epochs = COVER_computeEpochs((uint)(dictBufferCapacity), (uint)(ctx->nbDmers), parameters.k, 1);
nuint maxZeroScoreRun = 10;
nuint zeroScoreRun = 0;
nuint epoch;
for (epoch = 0; tail > 0; epoch = (nuint)((epoch + 1) % epochs.num))
{
uint epochBegin = (uint)(epoch * epochs.size);
uint epochEnd = epochBegin + epochs.size;
nuint segmentSize;
COVER_segment_t segment = FASTCOVER_selectSegment(ctx, freqs, epochBegin, epochEnd, parameters, segmentFreqs);
if (segment.score == 0)
{
if (++zeroScoreRun >= maxZeroScoreRun)
{
break;
}
continue;
}
zeroScoreRun = 0;
segmentSize = ((segment.end - segment.begin + parameters.d - 1) < (tail) ? (segment.end - segment.begin + parameters.d - 1) : (tail));
if (segmentSize < parameters.d)
{
break;
}
tail -= segmentSize;
memcpy((void *)(dict + tail), (void *)(ctx->samples + segment.begin), segmentSize);
}
return(tail);
}
/*-*************************************
* Helper functions
***************************************/
/**
* Selects the best segment in an epoch.
* Segments of are scored according to the function:
*
* Let F(d) be the frequency of all dmers with hash value d.
* Let S_i be hash value of the dmer at position i of segment S which has length k.
*
* Score(S) = F(S_1) + F(S_2) + ... + F(S_{k-d+1})
*
* Once the dmer with hash value d is in the dictionary we set F(d) = 0.
*/
private static COVER_segment_t FASTCOVER_selectSegment(FASTCOVER_ctx_t *ctx, uint *freqs, uint begin, uint end, ZDICT_cover_params_t parameters, ushort *segmentFreqs)
{
uint k = parameters.k;
uint d = parameters.d;
uint f = ctx->f;
uint dmersInK = k - d + 1;
COVER_segment_t bestSegment = new COVER_segment_t
{
begin = 0,
end = 0,
score = 0,
};
COVER_segment_t activeSegment;
activeSegment.begin = begin;
activeSegment.end = begin;
activeSegment.score = 0;
while (activeSegment.end < end)
{
nuint idx = FASTCOVER_hashPtrToIndex((void *)(ctx->samples + activeSegment.end), f, d);
if (segmentFreqs[idx] == 0)
{
activeSegment.score += freqs[idx];
}
activeSegment.end += 1;
segmentFreqs[idx] += 1;
if (activeSegment.end - activeSegment.begin == dmersInK + 1)
{
nuint delIndex = FASTCOVER_hashPtrToIndex((void *)(ctx->samples + activeSegment.begin), f, d);
segmentFreqs[delIndex] -= 1;
if (segmentFreqs[delIndex] == 0)
{
activeSegment.score -= freqs[delIndex];
}
activeSegment.begin += 1;
}
if (activeSegment.score > bestSegment.score)
{
bestSegment = activeSegment;
}
}
while (activeSegment.begin < end)
{
nuint delIndex = FASTCOVER_hashPtrToIndex((void *)(ctx->samples + activeSegment.begin), f, d);
segmentFreqs[delIndex] -= 1;
activeSegment.begin += 1;
}
{
uint pos;
for (pos = bestSegment.begin; pos != bestSegment.end; ++pos)
{
nuint i = FASTCOVER_hashPtrToIndex((void *)(ctx->samples + pos), f, d);
freqs[i] = 0;
}
}
return(bestSegment);
}
