libMems/LCB.h

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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif

#ifndef __LCB_h__
#define __LCB_h__

#include <vector>
#include <libGenome/gnDefs.h>

namespace mems {

class LCB{
public:
        LCB() : lcb_id(0), weight(0), to_be_deleted(false) {};
        std::vector< int64 > left_end;  
        std::vector< int64 > right_end;  
        std::vector< uint > left_adjacency;     
        std::vector< uint > right_adjacency;    
        int lcb_id;                     
        double weight;          
        bool to_be_deleted;     
};

class LCBLeftComparator {
public:
        LCBLeftComparator( uint seq ) : m_seq(seq){};
        bool operator()(const LCB& a, const LCB& b) const{
                
                int64 a_start = a.left_end[ m_seq ], b_start = b.left_end[ m_seq ];
                if( a_start == NO_MATCH || b_start == NO_MATCH ){
                        if( b_start != NO_MATCH )
                                return true;
                        return false;
                }
                if(a_start < 0)
                        a_start = -a_start;
                if(b_start < 0)
                        b_start = -b_start;

                int64 diff = a_start - b_start;
                return diff < 0;
        }
protected:
        uint m_seq;
private:
        LCBLeftComparator();
};

class LCBIDComparator {
public:
        bool operator()(const LCB& a, const LCB& b) const
        {
                return a.lcb_id < b.lcb_id;
        }
};


} // namespace mems


#endif  // __LCB_h__

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