NCBI C++ ToolKit
Classes | Typedefs | Functions
phy_node.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_tree.hpp>
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class  CPhyNodeData
 Data contained at each node of a phylogenetic tree. More...


typedef CTreeNode< CPhyNodeDataTPhyTreeNode


CNcbiOstreamoperator<< (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...
TPhyTreeNodeReadNewickTree (CNcbiIstream &is)
 Newick format input. More...

Typedef Documentation

◆ TPhyTreeNode

Definition at line 81 of file phy_node.hpp.

Function Documentation

◆ operator<<()

CNcbiOstream& operator<< ( CNcbiOstream os,
const TPhyTreeNode tree 

Newick format output.

Definition at line 67 of file phy_node.cpp.

References PrintNode().

◆ PrintNode()

void PrintNode ( CNcbiOstream os,
const TPhyTreeNode node 

◆ ReadNewickTree()

TPhyTreeNode* ReadNewickTree ( CNcbiIstream is)

Newick format input.

Uses flex/bison lexer/parser.

This function is not thread safe. The parser stores its state in global variables.

Definition at line 1386 of file

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.

Modified on Wed Nov 29 02:19:08 2023 by rev. 669887