- Generated on Fri Jul 19 2024 11:49:29 for bpp-phyl3 by
1.9.1
|
bpp-phyl3
3.0.0
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This is the complete list of members for bpp::TreeTemplateTools, including all inherited members.
| buildFromPhyloTree(const PhyloTree &treetemp) | bpp::TreeTemplateTools | static |
| cloneSubtree(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| cloneSubtree(const Tree &tree, int nodeId) | bpp::TreeTemplateTools | inlinestatic |
| deleteBranchLengths(Node &node) | bpp::TreeTemplateTools | static |
| deleteBranchProperties(Node &node, const std::vector< std::string > &propertyNames) | bpp::TreeTemplateTools | static |
| deleteNodeProperties(Node &node, const std::vector< std::string > &propertyNames) | bpp::TreeTemplateTools | static |
| deleteSubtree(N *node) | bpp::TreeTemplateTools | inlinestatic |
| dropLeaf(TreeTemplate< N > &tree, const std::string &leafName) | bpp::TreeTemplateTools | inlinestatic |
| dropSubtree(TreeTemplate< N > &tree, Node *subtree) | bpp::TreeTemplateTools | inlinestatic |
| getAncestorsId(const Node &node) | bpp::TreeTemplateTools | static |
| getBestRootInSubtree_(bpp::TreeTemplate< bpp::Node > &tree, short criterion, bpp::Node *node, std::pair< bpp::Node *, std::map< std::string, double >> &bestRoot) | bpp::TreeTemplateTools | privatestatic |
| getBranchLengths(const Node &node) | bpp::TreeTemplateTools | static |
| getBranchProperties(const Node &node, const std::string &propertyName, std::map< int, const Clonable * > &properties) | bpp::TreeTemplateTools | static |
| getBranchProperties(Node &node, const std::string &propertyName, std::map< int, Clonable * > &properties) | bpp::TreeTemplateTools | static |
| getBranchPropertyNames(const Node &node, std::vector< std::string > &propertyNames) | bpp::TreeTemplateTools | static |
| getDepth(const Node &node) | bpp::TreeTemplateTools | static |
| getDepths(const Node &node, std::map< const Node *, unsigned int > &depths) | bpp::TreeTemplateTools | static |
| getDistanceBetweenAnyTwoNodes(const Node &node1, const Node &node2) | bpp::TreeTemplateTools | static |
| getDistanceMatrix(const TreeTemplate< Node > &tree) | bpp::TreeTemplateTools | static |
| getElement(const std::string &elt) | bpp::TreeTemplateTools | static |
| getHeight(const Node &node) | bpp::TreeTemplateTools | static |
| getHeights(const Node &node, std::map< const Node *, double > &heights) | bpp::TreeTemplateTools | static |
| getInnerNodes(N &node) | bpp::TreeTemplateTools | inlinestatic |
| getInnerNodes(N &node, std::vector< N * > &nodes) | bpp::TreeTemplateTools | inlinestatic |
| getInnerNodesId(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| getInnerNodesId(const Node &node, std::vector< int > &ids) | bpp::TreeTemplateTools | inlinestatic |
| getLeafId(const Node &node, const std::string &name) | bpp::TreeTemplateTools | inlinestatic |
| getLeaves(N &node) | bpp::TreeTemplateTools | inlinestatic |
| getLeaves(N &node, std::vector< N * > &leaves) | bpp::TreeTemplateTools | inlinestatic |
| getLeavesId(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| getLeavesId(const Node &node, std::vector< int > &ids) | bpp::TreeTemplateTools | static |
| getLeavesNames(const Node &node) | bpp::TreeTemplateTools | static |
| getNodeProperties(const Node &node, const std::string &propertyName, std::map< int, const Clonable * > &properties) | bpp::TreeTemplateTools | static |
| getNodeProperties(Node &node, const std::string &propertyName, std::map< int, Clonable * > &properties) | bpp::TreeTemplateTools | static |
| getNodePropertyNames(const Node &node, std::vector< std::string > &propertyNames) | bpp::TreeTemplateTools | static |
| getNodes(N &node) | bpp::TreeTemplateTools | inlinestatic |
| getNodes(N &node, std::vector< N * > &nodes) | bpp::TreeTemplateTools | inlinestatic |
| getNodesId(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| getNodesId(const Node &node, std::vector< int > &ids) | bpp::TreeTemplateTools | inlinestatic |
| getNumberOfBranches(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| getNumberOfLeaves(const Node &node) | bpp::TreeTemplateTools | static |
| getNumberOfNodes(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| getPathBetweenAnyTwoNodes(Node &node1, Node &node2, bool includeAncestor=true, bool includeAncestorAtEndOfPath=true) | bpp::TreeTemplateTools | static |
| getPathBetweenAnyTwoNodes(const Node &node1, const Node &node2, bool includeAncestor=true, bool includeAncestorAtEndOfPath=true) | bpp::TreeTemplateTools | static |
| getRadius(TreeTemplate< Node > &tree) | bpp::TreeTemplateTools | static |
| getRandomTree(std::vector< std::string > &leavesNames, bool rooted=true) | bpp::TreeTemplateTools | static |
| getRemainingNeighbors(const Node *node1, const Node *node2, const Node *node3) | bpp::TreeTemplateTools | static |
| getSubtreeMoments_(const Node *node) | bpp::TreeTemplateTools | privatestatic |
| getTotalLength(const Node &node, bool includeAncestor=true) | bpp::TreeTemplateTools | static |
| hasNodeWithId(const N &node, int id) | bpp::TreeTemplateTools | inlinestatic |
| hasNodeWithName(const N &node, const std::string &name) | bpp::TreeTemplateTools | inlinestatic |
| haveSameOrderedTopology(const Node &n1, const Node &n2) | bpp::TreeTemplateTools | static |
| incrementAllIds(Node *node, int increment) | bpp::TreeTemplateTools | static |
| isMultifurcating(const Node &node) | bpp::TreeTemplateTools | static |
| isRoot(const Node &node) | bpp::TreeTemplateTools | inlinestatic |
| midRoot(TreeTemplate< Node > &tree, short criterion, bool forceBranchRoot) | bpp::TreeTemplateTools | static |
| MIDROOT_SUM_OF_SQUARES | bpp::TreeTemplateTools | static |
| MIDROOT_VARIANCE | bpp::TreeTemplateTools | static |
| nodeToParenthesis(const Node &node, bool writeId=false) | bpp::TreeTemplateTools | static |
| nodeToParenthesis(const Node &node, bool bootstrap, const std::string &propertyName) | bpp::TreeTemplateTools | static |
| orderTree(Node &node, bool downward=true, bool orderLeaves=false) | bpp::TreeTemplateTools | inlinestatic |
| orderTree_(Node &node, bool downward, bool orderLeaves) | bpp::TreeTemplateTools | privatestatic |
| parenthesisToNode(const std::string &description, unsigned int &nodeCounter, bool bootstrap=true, const std::string &propertyName=TreeTools::BOOTSTRAP, bool withId=false, bool verbose=true) | bpp::TreeTemplateTools | static |
| parenthesisToTree(const std::string &description, bool bootstrap=true, const std::string &propertyName=TreeTools::BOOTSTRAP, bool withId=false, bool verbose=true) | bpp::TreeTemplateTools | static |
| processDistsInSubtree_(const Node *node, DistanceMatrix &matrix, std::vector< std::pair< std::string, double >> &distsToNodeFather) | bpp::TreeTemplateTools | privatestatic |
| sampleSubtree(TreeTemplate< N > &tree, const std::vector< std::string > &leaves, size_t size) | bpp::TreeTemplateTools | inlinestatic |
| scaleTree(Node &node, double factor) | bpp::TreeTemplateTools | static |
| searchFirstNodeWithId(Node &node, int id) | bpp::TreeTemplateTools | inlinestatic |
| searchFirstNodeWithId(const Node &node, int id) | bpp::TreeTemplateTools | inlinestatic |
| searchLeaf(const Node &node, const std::string &name, int *&id) | bpp::TreeTemplateTools | static |
| searchNodeWithId(N &node, int id) | bpp::TreeTemplateTools | inlinestatic |
| searchNodeWithId(N &node, int id, std::vector< N * > &nodes) | bpp::TreeTemplateTools | inlinestatic |
| searchNodeWithName(N &node, const std::string &name) | bpp::TreeTemplateTools | inlinestatic |
| searchNodeWithName(N &node, const std::string &name, std::vector< N * > &nodes) | bpp::TreeTemplateTools | inlinestatic |
| setBranchLengths(Node &node, double brLen) | bpp::TreeTemplateTools | static |
| setVoidBranchLengths(Node &node, double brLen) | bpp::TreeTemplateTools | static |
| TreeTemplateTools() | bpp::TreeTemplateTools | inline |
| treeToParenthesis(const TreeTemplate< Node > &tree, bool writeId=false) | bpp::TreeTemplateTools | static |
| treeToParenthesis(const TreeTemplate< Node > &tree, bool bootstrap, const std::string &propertyName) | bpp::TreeTemplateTools | static |
| unresolveUncertainNodes(Node &subtree, double threshold, const std::string &property=TreeTools::BOOTSTRAP) | bpp::TreeTemplateTools | static |
| ~TreeTemplateTools() | bpp::TreeTemplateTools | inlinevirtual |
1.9.1