pal.tree

Class ReadTree

java.lang.Object

pal.tree.SimpleTree

pal.tree.ReadTree

All Implemented Interfaces:

java.io.Serializable, IdGroup, Report, Units, UnitsProvider, Tree

public class ReadTree
extends SimpleTree

constructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted trees

Version:

$Id: ReadTree.java,v 1.10 2002/10/14 06:54:25 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.tree.Tree

Tree.TreeBase

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

Fields inherited from interface pal.misc.Units

DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS

Constructor Summary

Constructors

Constructor and Description
ReadTree(java.io.PushbackReader input) read tree from input stream
ReadTree(java.lang.String file) read tree from file

Method Summary

Methods inherited from class pal.tree.SimpleTree

createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setIdentifier, setRoot, setUnits, toString, whichIdNumber

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadTree

public ReadTree(java.io.PushbackReader input)
         throws TreeParseException

read tree from input stream

Parameters:

input - input stream

Throws:

TreeParseException

ReadTree

public ReadTree(java.lang.String file)
         throws TreeParseException,
                java.io.IOException

read tree from file

Parameters:

file - name of file

Throws:

TreeParseException

java.io.IOException