bpp::TreeTools Member List

This is the complete list of members for bpp::TreeTools, including all inherited members.

bestRootPosition_(Tree &tree, int nodeId1, int nodeId2, double length)	bpp::TreeTools	privatestatic
bipartitionOccurrences(const std::vector< Tree *> &vecTr, std::vector< size_t > &bipScore)	bpp::TreeTools	static
BOOTSTRAP	bpp::TreeTools	static
checkIds(const Tree &tree, bool throwException)	bpp::TreeTools	static
computeBootstrapValues(Tree &tree, const std::vector< Tree *> &vecTr, bool verbose=true, int format=0)	bpp::TreeTools	static
computeBranchLengthsGrafen(Tree &tree, double power=1, bool init=true)	bpp::TreeTools	static
computeBranchLengthsGrafen(Tree &tree, int nodeId, double power, double total, double &height, double &heightRaised)	bpp::TreeTools	privatestatic
constrainedMidPointRooting(Tree &tree)	bpp::TreeTools	static
convertToClockTree(Tree &tree, int nodeId, bool noneg=false)	bpp::TreeTools	static
convertToClockTree2(Tree &tree, int nodeId)	bpp::TreeTools	static
fullyResolvedConsensus(const std::vector< Tree *> &vecTr, bool checkNames=true)	bpp::TreeTools	static
getAncestors(const Tree &tree, int nodeId)	bpp::TreeTools	static
getBranchLengths(const Tree &tree, int nodeId)	bpp::TreeTools	static
getDepth(const Tree &tree, int nodeId)	bpp::TreeTools	static
getDepths(const Tree &tree, int nodeId, std::map< int, size_t > &depths)	bpp::TreeTools	static
getDistanceBetweenAnyTwoNodes(const Tree &tree, int nodeId1, int nodeId2)	bpp::TreeTools	static
getDistanceMatrix(const Tree &tree)	bpp::TreeTools	static
getHeight(const Tree &tree, int nodeId)	bpp::TreeTools	static
getHeights(const Tree &tree, int nodeId, std::map< int, double > &heights)	bpp::TreeTools	static
getLastCommonAncestor(const Tree &tree, const std::vector< int > &nodeIds)	bpp::TreeTools	static
getLeafId(const Tree &tree, int nodeId, const std::string &name)	bpp::TreeTools	static
getLeavesId(const Tree &tree, int nodeId)	bpp::TreeTools	static
getLeavesId(const Tree &tree, int nodeId, std::vector< int > &leaves)	bpp::TreeTools	static
getMaxId(const Tree &tree, int id)	bpp::TreeTools	static
getMPNUId(const Tree &tree, int id)	bpp::TreeTools	static
getNodesId(const Tree &tree, int nodeId)	bpp::TreeTools	static
getNodesId(const Tree &tree, int nodeId, std::vector< int > &nodes)	bpp::TreeTools	static
getNumberOfLeaves(const Tree &tree, int nodeId)	bpp::TreeTools	static
getPathBetweenAnyTwoNodes(const Tree &tree, int nodeId1, int nodeId2, bool includeAncestor=true)	bpp::TreeTools	static
getTotalLength(const Tree &tree, int nodeId, bool includeAncestor=true)	bpp::TreeTools	static
haveSameTopology(const Tree &tr1, const Tree &tr2)	bpp::TreeTools	static
initBranchLengthsGrafen(Tree &tree)	bpp::TreeTools	static
initBranchLengthsGrafen(Tree &tree, int nodeId)	bpp::TreeTools	privatestatic
majorityConsensus(const std::vector< Tree *> &vecTr, bool checkNames=true)	bpp::TreeTools	static
midpointRooting(Tree &tree)	bpp::TreeTools	static
MRP(const std::vector< Tree *> &vecTr)	bpp::TreeTools	static
MRPEncode(const std::vector< Tree *> &vecTr)	bpp::TreeTools	static
MRPEncodeMultilabel(const std::vector< Tree *> &vecTr)	bpp::TreeTools	static
MRPMultilabel(const std::vector< Tree *> &vecTr)	bpp::TreeTools	static
nodeToParenthesis(const Tree &tree, int nodeId, bool writeId=false)	bpp::TreeTools	static
nodeToParenthesis(const Tree &tree, int nodeId, bool bootstrap, const std::string &propertyName)	bpp::TreeTools	static
robinsonFouldsDistance(const Tree &tr1, const Tree &tr2, bool checkNames=true, int *missing_in_tr2=NULL, int *missing_in_tr1=NULL)	bpp::TreeTools	static
scaleTree(Tree &tree, int nodeId, double factor)	bpp::TreeTools	static
searchLeaf(const Tree &tree, int nodeId, const std::string &name, int *&id)	bpp::TreeTools	static
setBranchLengths(Tree &tree, int nodeId, double brLen)	bpp::TreeTools	static
setVoidBranchLengths(Tree &tree, int nodeId, double brLen)	bpp::TreeTools	static
statFromNode_(Tree &tree, int rootId)	bpp::TreeTools	privatestatic
strictConsensus(const std::vector< Tree *> &vecTr, bool checkNames=true)	bpp::TreeTools	static
thresholdConsensus(const std::vector< Tree *> &vecTr, double threshold, bool checkNames=true)	bpp::TreeTools	static
TreeTools()	bpp::TreeTools	inline
treeToParenthesis(const Tree &tree, bool writeId=false)	bpp::TreeTools	static
treeToParenthesis(const Tree &tree, bool bootstrap, const std::string &propertyName)	bpp::TreeTools	static
~TreeTools()	bpp::TreeTools	inlinevirtual