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#if UCHIMES
#include "myutils.h"
#include "seqdb.h"
#include "seq.h"
#include "alpha.h"
void SortDescending(const vector<float> &Values, vector<unsigned> &Order);
static byte *g_QueryHasWord;
static unsigned g_WordCount;
unsigned GetWord(const byte *Seq)
{
unsigned Word = 0;
const byte *Front = Seq;
for (unsigned i = 0; i < opt_w; ++i)
{
unsigned Letter = g_CharToLetterNucleo[*Front++];
Word = (Word*4) + Letter;
}
return Word;
}
static void SetQuery(const SeqData &Query)
{
if (g_QueryHasWord == 0)
{
g_WordCount = 4;
for (unsigned i = 1; i < opt_w; ++i)
g_WordCount *= 4;
g_QueryHasWord = myalloc(byte, g_WordCount);
}
memset(g_QueryHasWord, 0, g_WordCount);
if (Query.L <= opt_w)
return;
const unsigned L = Query.L - opt_w + 1;
const byte *Seq = Query.Seq;
for (unsigned i = 0; i < L; ++i)
{
unsigned Word = GetWord(Seq++);
g_QueryHasWord[Word] = 1;
}
}
static unsigned GetUniqueWordsInCommon(const SeqData &Target)
{
if (Target.L <= opt_w)
return 0;
unsigned Count = 0;
const unsigned L = Target.L - opt_w + 1;
const byte *Seq = Target.Seq;
for (unsigned i = 0; i < L; ++i)
{
unsigned Word = GetWord(Seq++);
if (g_QueryHasWord[Word])
++Count;
}
return Count;
}
void USort(const SeqData &Query, const SeqDB &DB, vector<float> &WordCounts,
vector<unsigned> &Order)
{
WordCounts.clear();
Order.clear();
SetQuery(Query);
const unsigned SeqCount = DB.GetSeqCount();
for (unsigned SeqIndex = 0; SeqIndex < SeqCount; ++SeqIndex)
{
SeqData Target;
DB.GetSeqData(SeqIndex, Target);
float WordCount = (float) GetUniqueWordsInCommon(Target);
WordCounts.push_back(WordCount);
}
SortDescending(WordCounts, Order);
}
#endif // UCHIMES
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