/usr/include/libMUSCLE-3.7/libMUSCLE/clustsetmsa.h is in libmuscle-3.7-dev 3.7+4565-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 | #ifndef ClustSetMSA_h
#define ClustSetMSA_h
#include "libMUSCLE/clustset.h"
#include "libMUSCLE/msadist.h"
namespace muscle {
class MSA;
class Clust;
// 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;
};
} // namespace muscle
#endif // ClustSetMSA_h
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