evaluator.h

#ifndef EVALUATOR_H
#define EVALUATOR_H

#include <stdio.h>
#include <stdlib.h>
#include <string>
#include "options.h"
#include "util.h"
#include "read.h"

using namespace std;

class Evaluator{
public:
    Evaluator(Options* opt);
    ~Evaluator();
    // evaluate how many reads are stored in the input file
    void evaluateReadNum(long& readNum);
    string evalAdapterAndReadNumDepreciated(long& readNum);
    string evalAdapterAndReadNum(long& readNum, bool isR2);
    bool isOneOrTwoColorSystem();
    void evaluateSeqLen();
    void evaluateOverRepSeqs();
    void computeOverRepSeq(string filename, map<string, long>& hotseqs, int seqLen);
    int computeSeqLen(string filename);

    static bool test();
    static string matchKnownAdapter(string seq);
private:
    Options* mOptions;
    string int2seq(unsigned int val, int seqlen);
    int seq2int(string* seq, int pos, int seqlen, int lastVal = -1);
    int seq2int(string& seq, int pos, int seqlen, int lastVal = -1);
    string getAdapterWithSeed(int seed, Read** loadedReads, long records, int keylen);
};


#endif