pal.tree
Class ReadTree

java.lang.Object
  |
  +--pal.tree.SimpleTree
        |
        +--pal.tree.ReadTree
All Implemented Interfaces:
Report, java.io.Serializable, Tree, Units

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

See Also:
Serialized Form

Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, YEARS
 
Constructor Summary
ReadTree(java.io.PushbackReader input)
          read tree from input stream
ReadTree(java.lang.String file)
          read tree from file
 
Methods inherited from class pal.tree.SimpleTree
createNodeList, findNode, getAttribute, getExternalNode, getExternalNodeCount, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setRoot, setUnits, toString
 
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

ReadTree

public ReadTree(java.lang.String file)
         throws TreeParseException,
                java.io.IOException
read tree from file
Parameters:
file - name of file