ChainAvgrange.h

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#ifndef CHAINAVGRANGE_H
#define CHAINAVGRANGE_H

#include "alnrange.h"
#include <vector>
#include <iostream>

/*
 * To buiild a chain of average ranges for chimera detection
 */

using namespace std;

class ChainAvgrange {
        public:
                ChainAvgrange(const string &id, int len) 
                        : seqid(id), seqlen(len), chain() {}
      /* this object will deallocate the memory given by the
       * addRange method
       */
                ~ChainAvgrange();

                /* either r merge with one of the chain element
                 * or create a new avgrange object out of r
                 */
                void addRange(const alnrange* r);
                int size() const { return chain.size(); }

                /* fill the list with rows of db formated
                 * quoted string values.
                 */
                void dbrows(list<string>& rows, const char dlm[]=",") const;
                /* tab-dlimited output, good for database loading */
                friend ostream& operator<<(ostream &ous, const ChainAvgrange &ar);
                bool isChimera() const { return chain.size()>1; }

                /* Accumulate results to the tablerows, also output the
                 * result in tab-delimited format to the output stream
                 */
                int checkSplits(list<string> &tablerows, ostream &ous) const;
                typedef vector<avgrange*>::iterator chain_iterator;

        private:
                string seqid;
                int seqlen;
                vector<avgrange*> chain;
};

#endif