info.bioinfweb.treegraph.document.io.nexus
Class NexusDocument

java.lang.Object
  info.bioinfweb.treegraph.document.io.nexus.NexusDocument

public class NexusDocument
extends java.lang.Object

Field Summary

private java.util.List<java.lang.String>	names
private TranslTable	translTable
private java.util.List<java.lang.String>	trees

Constructor Summary

NexusDocument()

Method Summary

boolean	add(java.lang.String name, java.lang.String tree)
Tree[]	createTrees(NodeBranchDataAdapter internalAdapter, NodeBranchDataAdapter branchLengthsAdapter, boolean translateInternals) Creates a Tree object from each stored Newick string.
java.lang.String	getName(int pos)
TranslTable	getTranslTable()
java.lang.String	getTree(int pos)
java.lang.String[]	namesToArray()
int	size()
java.lang.String[]	treesToArray()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

translTable

private TranslTable translTable

names

private java.util.List<java.lang.String> names

trees

private java.util.List<java.lang.String> trees

Constructor Detail

NexusDocument

public NexusDocument()

Method Detail

getTranslTable

public TranslTable getTranslTable()

add

public boolean add(java.lang.String name,
                   java.lang.String tree)

getName

public java.lang.String getName(int pos)

getTree

public java.lang.String getTree(int pos)

namesToArray

public java.lang.String[] namesToArray()

treesToArray

public java.lang.String[] treesToArray()

size

public int size()

createTrees

public Tree[] createTrees(NodeBranchDataAdapter internalAdapter,
                          NodeBranchDataAdapter branchLengthsAdapter,
                          boolean translateInternals)

Creates a Tree object from each stored Newick string.

Parameters:

internalAdapter -

branchLengthsAdapter -

translateInternals -

Returns:

an array containing all Tree-objects