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#ifndef CODE_ClipCR4
#define CODE_ClipCR4
#include "IncludeDefine.h"
#include "opal/opal.h"
class ClipCR4
{
public:
int dbN;//number of sequence in the opal "database"
vector<uint8*> storeClip;
// Results for each sequence in database
vector<OpalSearchResult> opalRes;
OpalSearchResult** opalResP;
//constructor
ClipCR4();
void opalFillOneSeq(uint32 idb, char *seq, uint32 seqL);
void opalAlign(uint8 *query, uint32 queryLen, int dbN1);
uint32 polyTail3p(char *seq, uint32 seqLen);
private:
uint32 readLen; //sequence length to align against
int alphabetLength;
int gapOpen;
int gapExt;
vector<int> scoreMatrix;
// Database
uint8_t* dbSeqArr;
uint8_t** dbSeqs;
int* dbSeqsLen;
};
#endif
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