jebl.evolution.io

Class NewickImporter

java.lang.Object

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

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
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.