44 #include "../TreeTemplate.h" 105 Newick(
bool allowComments =
false,
bool writeId =
false):
153 void write(
const Tree& tree,
const std::string& path,
bool overwrite =
true)
const throw (Exception)
158 void write(
const Tree& tree, std::ostream& out)
const throw (Exception)
169 void read(
const std::string& path, std::vector<Tree*>& trees)
const throw (Exception)
173 void read(std::istream& in, std::vector<Tree*>& trees)
const throw (Exception);
181 void write(
const std::vector<Tree*>& trees,
const std::string& path,
bool overwrite =
true)
const throw (Exception)
185 void write(
const std::vector<Tree*>& trees, std::ostream& out)
const throw (Exception)
192 void write_(
const Tree& tree, std::ostream& out)
const throw (Exception);
197 void write_(
const std::vector<Tree*>& trees, std::ostream& out)
const throw (Exception);
void write(const std::vector< Tree *> &trees, std::ostream &out) const =0
Write trees to a stream.
const std::string getFormatName() const
void write(const Tree &tree, std::ostream &out) const =0
Write a tree to a stream.
Partial implementation of the ITree interface.
void write(const std::vector< Tree *> &trees, const std::string &path, bool overwrite=true) const
Write trees to a file.
The phylogenetic tree class.
Interface for phylogenetic tree objects.
void write(const Tree &tree, std::ostream &out) const
Write a tree to a stream.
const std::string getFormatDescription() const
TreeTemplate< Node > * read(const std::string &path) const
Read a tree from a file.
The so-called 'newick' parenthetic format.
virtual Tree * read(std::istream &in) const =0
Read a tree from a stream.
void read(const std::string &path, std::vector< Tree *> &trees) const
Read trees from a file.
void write(const Tree &tree, const std::string &path, bool overwrite=true) const
Write a tree to a file.
virtual void read(std::istream &in, std::vector< Tree *> &trees) const =0
Read trees from a stream.
void write_(const Tree &tree, std::ostream &out) const
void write(const std::vector< Tree *> &trees, std::ostream &out) const
Write trees to a stream.
std::string bootstrapPropertyName_
Partial implementation of the OTree interface.
void disableExtendedBootstrapProperty()
Partial implementation of the OTree interface.
Partial implementation of the IMultiTree interface.
void enableExtendedBootstrapProperty(const std::string &propertyName)
Newick(bool allowComments=false, bool writeId=false)
Build a new Newick reader/writer.