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#include "ClipMate.h"
#include "Parameters.h"
#include "SequenceFuns.h"
void ClipMate::initialize(uint32 Nin, const string &adSeqIn, uint32 NafterAdin, double adMMpIn)
{
N=Nin;
adSeq=adSeqIn;
if (adSeq=="-") {
adSeq="";
} else {
if ( adSeq=="polyA") {
adSeqNum.clear(); //it should be empty, but just in case...
adSeqNum.resize(DEF_readSeqLengthMax, 0); //fill with A=0
} else {
adSeqNum.resize(adSeq.size(),0);
convertNucleotidesToNumbers(adSeq.data(), adSeqNum.data(), adSeqNum.size());
};
};
if (N==0 && adSeq=="")
type=-1;
if (type==10)
cr4 = new ClipCR4;
NafterAd=NafterAdin;
adMMp=adMMpIn;
};
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