bpp::Newick Member List

This is the complete list of members for bpp::Newick, 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
allowComments_	bpp::Newick	protected
bootstrapPropertyName_	bpp::Newick	protected
disableExtendedBootstrapProperty()	bpp::Newick	inline
enableExtendedBootstrapProperty(const std::string &propertyName)	bpp::Newick	inline
getDataType() const	bpp::IOTree	inlinevirtual
getElement(const std::string &elt) const override	bpp::Newick	protectedvirtual
getFormatDescription() const override	bpp::Newick	virtual
getFormatName() const override	bpp::Newick	virtual
IMultiPhyloTree()	bpp::IMultiPhyloTree	inline
IMultiTree()	bpp::IMultiTree	inline
IOFormat()	bpp::IOFormat
IOTree()	bpp::IOTree	inline
IPhyloTree()	bpp::IPhyloTree	inline
ITree()	bpp::ITree	inline
Newick(bool allowComments=false, bool writeId=false, bool verbose=false)	bpp::Newick	inline
nodeToParenthesis(const PhyloTree &tree, std::shared_ptr< PhyloNode > node, bool writeId=false) const	bpp::Newick	protected
nodeToParenthesis(const PhyloTree &tree, std::shared_ptr< PhyloNode > node, bool bootstrap, const std::string &propertyName) const	bpp::Newick	protected
OMultiPhyloTree()	bpp::OMultiPhyloTree	inline
OMultiTree()	bpp::OMultiTree	inline
OPhyloTree()	bpp::OPhyloTree	inline
OTree()	bpp::OTree	inline
parenthesisToNode(PhyloTree &tree, std::shared_ptr< PhyloNode > father, const std::string &description, unsigned int &nodeCounter, bool bootstrap, const std::string &propertyName, bool withId, bool verbose) const	bpp::Newick	private
parenthesisToPhyloTree(const std::string &description, bool bootstrap=false, const std::string &propertyName="", bool withId=false, bool verbose=false) const	bpp::Newick
readPhyloTree(std::istream &in) const override	bpp::Newick	virtual
readPhyloTree(std::istream &in) const override=0	bpp::Newick
readPhyloTree(const std::string &path) const override	bpp::Newick	inline
bpp::AbstractIPhyloTree::readPhyloTree(const std::string &path) const override	bpp::AbstractIPhyloTree	inlinevirtual
readPhyloTrees(std::istream &in, std::vector< std::unique_ptr< PhyloTree >> &trees) const override	bpp::Newick	virtual
readPhyloTrees(std::istream &in, std::vector< std::unique_ptr< PhyloTree >> &trees) const override=0	bpp::Newick
readPhyloTrees(const std::string &path, std::vector< std::unique_ptr< PhyloTree >> &trees) const override	bpp::Newick	inline
bpp::AbstractIMultiPhyloTree::readPhyloTrees(const std::string &path, std::vector< std::unique_ptr< PhyloTree >> &trees) const override	bpp::AbstractIMultiPhyloTree	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::Newick	virtual
readTrees(std::istream &in, std::vector< std::unique_ptr< Tree >> &trees) const override=0	bpp::Newick
readTrees(const std::string &path, std::vector< std::unique_ptr< Tree >> &trees) const override	bpp::Newick	inline
bpp::AbstractIMultiTree::readTrees(const std::string &path, std::vector< std::unique_ptr< Tree >> &trees) const override	bpp::AbstractIMultiTree	inlinevirtual
readTreeTemplate(std::istream &in) const override	bpp::Newick	virtual
readTreeTemplate(std::istream &in) const=0	bpp::Newick
readTreeTemplate(const std::string &path) const	bpp::Newick	inline
bpp::AbstractITree::readTreeTemplate(const std::string &path) const	bpp::AbstractITree	inlinevirtual
treeToParenthesis(const PhyloTree &tree, bool writeId=false) const	bpp::Newick	protected
treeToParenthesis(const PhyloTree &tree, bool bootstrap, const std::string &propertyName) const	bpp::Newick	protected
useBootstrap_	bpp::Newick	protected
verbose_	bpp::Newick	protected
write_(const Tree &tree, std::ostream &out) const	bpp::Newick	protected
write_(const PhyloTree &tree, std::ostream &out) const	bpp::Newick	protected
write_(const TreeTemplate< N > &tree, std::ostream &out) const	bpp::Newick	protected
write_(const std::vector< const Tree * > &trees, std::ostream &out) const	bpp::Newick	protected
write_(const std::vector< const PhyloTree * > &trees, std::ostream &out) const	bpp::Newick	protected
write_(const std::vector< TreeTemplate< N > * > &trees, std::ostream &out) const	bpp::Newick	protected
writeId_	bpp::Newick	protected
writePhyloTree(const PhyloTree &tree, std::ostream &out) const override	bpp::Newick	inlinevirtual
writePhyloTree(const PhyloTree &tree, std::ostream &out) const=0	bpp::Newick
writePhyloTree(const PhyloTree &tree, const std::string &path, bool overwrite) const	bpp::Newick	inline
bpp::AbstractOPhyloTree::writePhyloTree(const PhyloTree &tree, const std::string &path, bool overwrite) const	bpp::AbstractOPhyloTree	inlinevirtual
writePhyloTrees(const std::vector< const PhyloTree * > &trees, std::ostream &out) const override	bpp::Newick	inlinevirtual
writePhyloTrees(const std::vector< const PhyloTree * > &trees, std::ostream &out) const=0	bpp::Newick
writePhyloTrees(const std::vector< const PhyloTree * > &trees, const std::string &path, bool overwrite) const	bpp::Newick	inline
bpp::AbstractOMultiPhyloTree::writePhyloTrees(const std::vector< const PhyloTree * > &trees, const std::string &path, bool overwrite) const	bpp::AbstractOMultiPhyloTree	inlinevirtual
writeTree(const Tree &tree, std::ostream &out) const override	bpp::Newick	inlinevirtual
writeTree(const Tree &tree, std::ostream &out) const=0	bpp::Newick
writeTree(const Tree &tree, const std::string &path, bool overwrite) const	bpp::Newick	inline
bpp::AbstractOTree::writeTree(const Tree &tree, const std::string &path, bool overwrite) const	bpp::AbstractOTree	inlinevirtual
writeTrees(const std::vector< const Tree * > &trees, std::ostream &out) const override	bpp::Newick	inlinevirtual
writeTrees(const std::vector< const Tree * > &trees, std::ostream &out) const=0	bpp::Newick
writeTrees(const std::vector< const Tree * > &trees, const std::string &path, bool overwrite) const	bpp::Newick	inline
bpp::AbstractOMultiTree::writeTrees(const std::vector< const Tree * > &trees, const std::string &path, bool overwrite) const	bpp::AbstractOMultiTree	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
~Newick()	bpp::Newick	inlinevirtual
~OMultiPhyloTree()	bpp::OMultiPhyloTree	inlinevirtual
~OMultiTree()	bpp::OMultiTree	inlinevirtual
~OPhyloTree()	bpp::OPhyloTree	inlinevirtual
~OTree()	bpp::OTree	inlinevirtual