pal.tree
Class ReadTree

java.lang.Object
  extended by pal.tree.SimpleTree
      extended by 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
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