bpp::Nhx Member List

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

AbstractIMultiPhyloTree()	bpp::AbstractIMultiPhyloTree	inline
AbstractIMultiTree()	bpp::AbstractIMultiTree	inline
AbstractIPhyloTree()	bpp::AbstractIPhyloTree	inline
AbstractITree()	bpp::AbstractITree	inline
AbstractOMultiPhyloTree()	bpp::AbstractOMultiPhyloTree	inline
AbstractOMultiTree()	bpp::AbstractOMultiTree	inline
AbstractOPhyloTree()	bpp::AbstractOPhyloTree	inline
AbstractOTree()	bpp::AbstractOTree	inline
changeNamesToTags(Node &node) const	bpp::Nhx
changeNamesToTags(PhyloTree &tree, std::shared_ptr< PhyloNode > node) const	bpp::Nhx
changeTagsToNames(Node &node) const	bpp::Nhx
changeTagsToNames(PhyloTree &tree, std::shared_ptr< PhyloNode > node) const	bpp::Nhx
checkNodesId_(PhyloTree &tree) const	bpp::Nhx	protected
getDataType() const	bpp::IOTree	inlinevirtual
getElement(const std::string &elt) const override	bpp::Nhx	protectedvirtual
getFormatDescription() const override	bpp::Nhx	virtual
getFormatName() const override	bpp::Nhx	virtual
hasIds_	bpp::Nhx	mutableprivate
IMultiPhyloTree()	bpp::IMultiPhyloTree	inline
IMultiTree()	bpp::IMultiTree	inline
IOFormat()	bpp::IOFormat
IOTree()	bpp::IOTree	inline
IPhyloTree()	bpp::IPhyloTree	inline
ITree()	bpp::ITree	inline
Nhx(bool useTagsAsPptNames=true)	bpp::Nhx
nodeToParenthesis(const Node &node) const	bpp::Nhx	protected
nodeToParenthesis(const PhyloTree &tree, const std::shared_ptr< PhyloNode > node) const	bpp::Nhx	protected
OMultiPhyloTree()	bpp::OMultiPhyloTree	inline
OMultiTree()	bpp::OMultiTree	inline
OPhyloTree()	bpp::OPhyloTree	inline
OTree()	bpp::OTree	inline
parenthesisToNode(const std::string &description) const	bpp::Nhx	private
parenthesisToNode(PhyloTree &tree, std::shared_ptr< PhyloNode > father, const std::string &description) const	bpp::Nhx	private
parenthesisToPhyloTree(const std::string &description) const	bpp::Nhx
parenthesisToTree(const std::string &description) const	bpp::Nhx
propertiesToParenthesis(const Node &node) const	bpp::Nhx
propertiesToParenthesis(const PhyloTree &tree, const std::shared_ptr< PhyloNode > node) const	bpp::Nhx
propertyToString_(const Clonable *pptObject, short type)	bpp::Nhx	protectedstatic
readPhyloTree(std::istream &in) const override	bpp::Nhx	virtual
readPhyloTree(std::istream &in) const override=0	bpp::Nhx	virtual
readPhyloTree(const std::string &path) const override	bpp::Nhx	inlinevirtual
readPhyloTrees(std::istream &in, std::vector< std::unique_ptr< PhyloTree > > &trees) const override	bpp::Nhx	virtual
readPhyloTrees(std::istream &in, std::vector< std::unique_ptr< PhyloTree > > &trees) const override=0	bpp::Nhx	virtual
readPhyloTrees(const std::string &path, std::vector< std::unique_ptr< PhyloTree > > &trees) const override	bpp::Nhx	inlinevirtual
readTree(std::istream &in) const override	bpp::AbstractITree	inlinevirtual
readTree(const std::string &path) const override	bpp::AbstractITree	inlinevirtual
readTrees(std::istream &in, std::vector< std::unique_ptr< Tree > > &trees) const override	bpp::Nhx	virtual
readTrees(std::istream &in, std::vector< std::unique_ptr< Tree > > &trees) const override=0	bpp::Nhx	virtual
readTrees(const std::string &path, std::vector< std::unique_ptr< Tree > > &trees) const override	bpp::Nhx	inlinevirtual
readTreeTemplate(std::istream &in) const override	bpp::Nhx	virtual
readTreeTemplate(std::istream &in) const=0	bpp::Nhx	virtual
readTreeTemplate(const std::string &path) const	bpp::Nhx	inlinevirtual
registerProperty(const Property &property)	bpp::Nhx	inline
setNodeProperties(Node &node, const std::string properties) const	bpp::Nhx	protected
setNodeProperties(PhyloTree &tree, std::shared_ptr< PhyloNode > node, const std::string properties) const	bpp::Nhx	protected
stringToProperty_(const std::string &pptDesc, short type)	bpp::Nhx	protectedstatic
supportedProperties_	bpp::Nhx	private
treeToParenthesis(const TreeTemplate< Node > &tree) const	bpp::Nhx
treeToParenthesis(const PhyloTree &tree) const	bpp::Nhx
useTagsAsPropertyNames(bool yn)	bpp::Nhx	inline
useTagsAsPropertyNames() const	bpp::Nhx	inline
useTagsAsPropertyNames_	bpp::Nhx	private
write_(const Tree &tree, std::ostream &out) const	bpp::Nhx	protected
write_(const PhyloTree &tree, std::ostream &out) const	bpp::Nhx	protected
write_(const TreeTemplate< N > &tree, std::ostream &out) const	bpp::Nhx	protected
write_(const std::vector< const Tree * > &trees, std::ostream &out) const	bpp::Nhx	protected
write_(const std::vector< const PhyloTree * > &trees, std::ostream &out) const	bpp::Nhx	protected
write_(const std::vector< TreeTemplate< N > * > &trees, std::ostream &out) const	bpp::Nhx	protected
writePhyloTree(const PhyloTree &tree, std::ostream &out) const override	bpp::Nhx	inlinevirtual
writePhyloTree(const PhyloTree &tree, std::ostream &out) const=0	bpp::Nhx	virtual
writePhyloTree(const PhyloTree &tree, const std::string &path, bool overwrite) const	bpp::Nhx	inlinevirtual
writePhyloTrees(const std::vector< const PhyloTree * > &trees, std::ostream &out) const override	bpp::Nhx	inlinevirtual
writePhyloTrees(const std::vector< const PhyloTree * > &trees, std::ostream &out) const=0	bpp::Nhx	virtual
writePhyloTrees(const std::vector< const PhyloTree * > &trees, const std::string &path, bool overwrite) const	bpp::Nhx	inlinevirtual
writeTree(const Tree &tree, std::ostream &out) const override	bpp::Nhx	inlinevirtual
writeTree(const Tree &tree, std::ostream &out) const=0	bpp::Nhx	virtual
writeTree(const Tree &tree, const std::string &path, bool overwrite) const	bpp::Nhx	inlinevirtual
writeTrees(const std::vector< const Tree * > &trees, std::ostream &out) const override	bpp::Nhx	inlinevirtual
writeTrees(const std::vector< const Tree * > &trees, std::ostream &out) const=0	bpp::Nhx	virtual
writeTrees(const std::vector< const Tree * > &trees, const std::string &path, bool overwrite) const	bpp::Nhx	inlinevirtual
~AbstractIMultiPhyloTree()	bpp::AbstractIMultiPhyloTree	inlinevirtual
~AbstractIMultiTree()	bpp::AbstractIMultiTree	inlinevirtual
~AbstractIPhyloTree()	bpp::AbstractIPhyloTree	inlinevirtual
~AbstractITree()	bpp::AbstractITree	inlinevirtual
~AbstractOMultiPhyloTree()	bpp::AbstractOMultiPhyloTree	inlinevirtual
~AbstractOMultiTree()	bpp::AbstractOMultiTree	inlinevirtual
~AbstractOPhyloTree()	bpp::AbstractOPhyloTree	inlinevirtual
~AbstractOTree()	bpp::AbstractOTree	inlinevirtual
~IMultiPhyloTree()	bpp::IMultiPhyloTree	inlinevirtual
~IMultiTree()	bpp::IMultiTree	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IOTree()	bpp::IOTree	inlinevirtual
~IPhyloTree()	bpp::IPhyloTree	inlinevirtual
~ITree()	bpp::ITree	inlinevirtual
~Nhx()	bpp::Nhx	inlinevirtual
~OMultiPhyloTree()	bpp::OMultiPhyloTree	inlinevirtual
~OMultiTree()	bpp::OMultiTree	inlinevirtual
~OPhyloTree()	bpp::OPhyloTree	inlinevirtual
~OTree()	bpp::OTree	inlinevirtual