jebl.evolution.io
Class NewickImporter

java.lang.Object
  jebl.evolution.io.NewickImporter

All Implemented Interfaces:

Iterable<Tree>, TreeImporter

public class NewickImporter
extends Object
implements TreeImporter

Author:

Andrew Rambaut, Alexei Drummond

Constructor Summary

NewickImporter(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
List<Tree>	importTrees() Import all the trees
Iterator<Tree>	iterator() Returns an iterator over a set of elements of type T.

Methods inherited from class java.lang.Object

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

Constructor Detail

NewickImporter

public NewickImporter(Reader reader,
                      boolean unquotedLabels)

Constructor

Parameters:

reader - tree text

unquotedLabels - if true, try to read unqouted lables containing spaces

Method Detail

iterator

public Iterator<Tree> iterator()

Returns an iterator over a set of elements of type T.

Specified by:

iterator in interface Iterable<Tree>

Returns:

an Iterator.

hasTree

public boolean hasTree()
                throws 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:

IOException

ImportException

importNextTree

public Tree importNextTree()
                    throws IOException,
                           ImportException

Description copied from interface: TreeImporter

Import a single tree

Specified by:

importNextTree in interface TreeImporter

Returns:

the tree

Throws:

IOException

ImportException

importTrees

public List<Tree> importTrees()
                       throws IOException,
                              ImportException

Description copied from interface: TreeImporter

Import all the trees

Specified by:

importTrees in interface TreeImporter

Returns:

the list of trees

Throws:

IOException

ImportException - Any type of tree is fine.