jebl.evolution.io
Class NewickImporter

java.lang.Object
  extended by jebl.evolution.io.NewickImporter
All Implemented Interfaces:
java.lang.Iterable<Tree>, TreeImporter

public class NewickImporter
extends java.lang.Object
implements TreeImporter

Version:
$Id: NewickImporter.java 967 2009-01-07 19:37:06Z matt_kearse $
Author:
Andrew Rambaut, Alexei Drummond

Constructor Summary
NewickImporter(java.io.Reader reader, boolean unquotedLabels)
          Constructor
 
Method Summary
 boolean hasTree()
          This can be used to read one tree at a time in a loop: List trees = new ArrayList(); while (hasTree()) { trees.add(importNextTree()); } return whether another tree is available.
 Tree importNextTree()
          Import a single tree
 java.util.List<Tree> importTrees()
          Import all the trees
 java.util.Iterator<Tree> iterator()
          Returns an iterator over a set of elements of type T.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

NewickImporter

public NewickImporter(java.io.Reader reader,
                      boolean unquotedLabels)
Constructor

Parameters:
reader - tree text
unquotedLabels - if true, try to read unqouted lables containing spaces
Method Detail

iterator

public java.util.Iterator<Tree> iterator()
Returns an iterator over a set of elements of type T.

Specified by:
iterator in interface java.lang.Iterable<Tree>
Returns:
an Iterator.

hasTree

public boolean hasTree()
                throws java.io.IOException,
                       ImportException
Description copied from interface: TreeImporter
This can be used to read one tree at a time in a loop: List trees = new ArrayList(); while (hasTree()) { trees.add(importNextTree()); } return whether another tree is available.

Specified by:
hasTree in interface TreeImporter
Throws:
java.io.IOException
ImportException

importNextTree

public Tree importNextTree()
                    throws java.io.IOException,
                           ImportException
Description copied from interface: TreeImporter
Import a single tree

Specified by:
importNextTree in interface TreeImporter
Returns:
the tree
Throws:
java.io.IOException
ImportException

importTrees

public java.util.List<Tree> importTrees()
                                 throws java.io.IOException,
                                        ImportException
Description copied from interface: TreeImporter
Import all the trees

Specified by:
importTrees in interface TreeImporter
Returns:
the list of trees
Throws:
java.io.IOException
ImportException - Any type of tree is fine.


http://code.google.com/p/jebl2/