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//
// C++ Interface: phylotree.h
//
// Description:
//
//
// Copyright: See COPYING file that comes with this distribution
//
//
#ifndef CONSTRAINTTREE_H
#define CONSTRAINTTREE_H
#include "mtree.h"
#include "alignment.h"
struct NNIMove;
/**
ConstraintTree used to guide tree search.
Note that constraint tree may contain only a subset of taxa from a full tree.
*/
class ConstraintTree : public MTree, public SplitIntMap {
public:
ConstraintTree();
/**
initialize constraint tree
@param constraint_file the name of the constraint tree file
@param fulltaxname the full list of all taxa names
*/
void initConstraint(const char *constraint_file, StrVector &fulltaxname);
/**
check if a "partial" split defined by two taxa name sets is compatible with the constraint tree.
The union of 2 taxa set do not need to comprise all taxa in the constraint tree.
@param[in] tax1 names of taxa in one side of split
@param[in] tax2 names of taxa in other side of split
@return true if the split is compatible with all splits in the constraint tree, false otherwise.
*/
bool isCompatible(StrVector &tax1, StrVector &tax2);
/**
check if a branch defined by two nodes in any tree is compatible or not
@param node1 one end node of the branch
@param node2 the other end node of the same branch
@return TRUE if the branch is compatible, FALSE otherwise
*/
bool isCompatible(Node *node1, Node *node2);
/**
@param tree input tree
@return TRUE if input tree is compatible with constraint, FALSE otherwise
*/
bool isCompatible (MTree *tree);
/**
check if an NNI is compatible with the constraint tree or not
@param nni an NNIMove
@return TRUE if the NNI is compatible, FALSE otherwise
*/
bool isCompatible(NNIMove &nni);
/**
@param taxname taxon name to search for
@return TRUE if constraint tree has a taxon, FALSE otherwise
*/
bool hasTaxon(string &taxname) {
return taxname_index.find(taxname) != taxname_index.end();
}
protected:
/* map from taxon name to its index, used for quick taxon name search */
StringIntMap taxname_index;
};
#endif
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