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Classes | |
| class | CPhyNodeData |
| Data contained at each node of a phylogenetic tree. More... | |
Typedefs | |
| typedef CTreeNode< CPhyNodeData > | TPhyTreeNode |
Functions | |
| CNcbiOstream & | operator<< (CNcbiOstream &os, const TPhyTreeNode &tree) |
| Newick format output. More... | |
| void | WriteNexusTree (CNcbiOstream &os, const TPhyTreeNode &tree, const string &tree_name="the_tree") |
| Nexus format output (Newick with some stuff around it). More... | |
| void | PrintNode (CNcbiOstream &os, const TPhyTreeNode &node) |
| Newick but without the terminal ';'. More... | |
| TPhyTreeNode * | ReadNewickTree (CNcbiIstream &is) |
| Newick format input. More... | |
Typedef Documentation
◆ TPhyTreeNode
| typedef CTreeNode<CPhyNodeData> TPhyTreeNode |
Definition at line 81 of file phy_node.hpp.
Function Documentation
◆ operator<<()
| CNcbiOstream& operator<< | ( | CNcbiOstream & | os, |
| const TPhyTreeNode & | tree | ||
| ) |
◆ PrintNode()
| void PrintNode | ( | CNcbiOstream & | os, |
| const TPhyTreeNode & | node | ||
| ) |
Newick but without the terminal ';'.
Definition at line 43 of file phy_node.cpp.
References CTreeNode< TValue, TKeyGetterP >::GetValue(), CTreeNode< TValue, TKeyGetterP >::IsLeaf(), s_EncodeLabel(), CTreeNode< TValue, TKeyGetterP >::SubNodeBegin(), and CTreeNode< TValue, TKeyGetterP >::SubNodeEnd().
Referenced by operator<<().
◆ ReadNewickTree()
| TPhyTreeNode* ReadNewickTree | ( | CNcbiIstream & | is | ) |
Newick format input.
Uses flex/bison lexer/parser.
- Warning
- This function is not thread safe. The parser stores its state in global variables.
Definition at line 1386 of file newick.tab.cpp.
References g_NewickIstr, g_NodeList, g_Tree, newick_flex_reset(), yyerror, and yyparse.
Referenced by CPhyObjectLoader::Execute(), CPhyloPhylipReader::GetTree(), CMSAToolJob::x_AddTreeProjectItem(), and CMultiReaderApp::xProcessNewick().
◆ WriteNexusTree()
| void WriteNexusTree | ( | CNcbiOstream & | os, |
| const TPhyTreeNode & | tree, | ||
| const string & | tree_name = "the_tree" |
||
| ) |
Nexus format output (Newick with some stuff around it).
tree_name gets put in the file.
Definition at line 75 of file phy_node.cpp.
