source: branches/lib/GDE/MUSCLE/src/clustsetmsa.h

#ifndef ClustSetMSA_h
#define ClustSetMSA_h

class MSA;
class Clust;

#include "clustset.h"
#include "msadist.h"

// Distance matrix based set.
// Computes distances between leaves, never between
// joined clusters (leaves this to distance matrix method).
class ClustSetMSA : public ClustSet
        {
public:
        ClustSetMSA(const MSA &msa, MSADist &MD) :
                m_ptrMSA(&msa),
                m_ptrMSADist(&MD)
                {
                }

public:
        virtual unsigned GetLeafCount()
                {
                return m_ptrMSA->GetSeqCount();
                }
        virtual const char *GetLeafName(unsigned uNodeIndex)
                {
                return m_ptrMSA->GetSeqName(uNodeIndex);
                }
        virtual unsigned GetLeafId(unsigned uNodeIndex)
                {
                return m_ptrMSA->GetSeqId(uNodeIndex);
                }
        virtual void JoinNodes(const Clust &C, unsigned uLeftNodeIndex,
          unsigned uRightNodeIndex, unsigned uJoinedNodeIndex,
          double *ptrdLeftLength, double *ptrdRightLength)
                {
                Quit("ClustSetMSA::JoinNodes, should never be called");
                }
        virtual double ComputeDist(const Clust &C, unsigned uNodeIndex1,
          unsigned uNodeIndex2)
                {
                return m_ptrMSADist->ComputeDist(*m_ptrMSA, uNodeIndex1, uNodeIndex2);
                }

public:
        const MSA &GetMSA();

private:
        const MSA *m_ptrMSA;
        MSADist *m_ptrMSADist;
        };

#endif  // ClustSetMSA_h