org.biojavax.bio.phylo.io.nexus

Class NexusFile

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusFile

public class NexusFile
extends Object

Represents Nexus files.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Constructor Summary

Constructors

Constructor and Description
NexusFile()

Method Summary

Methods

Modifier and Type	Method and Description
void	addObject(NexusObject object) Appends an object to the end of the file.
Iterator	blockIterator() Iterate over all blocks in the file in order.
Iterator	commentIterator() Iterate over all comments in the file in order.
boolean	containsObject(NexusObject object) Checks to see if we contain an object.
void	insertObject(NexusObject object, int pos) Inserts an object at the given position.
Iterator	objectIterator() Iterate over all objects in the file in order.
void	removeObject(NexusObject object) Removes an object from the file.

Methods inherited from class java.lang.Object

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

Constructor Detail

NexusFile

public NexusFile()

Method Detail

addObject

public void addObject(NexusObject object)

Appends an object to the end of the file.

Parameters:

object - the NexusObject to append.

insertObject

public void insertObject(NexusObject object,
                int pos)

Inserts an object at the given position.

Parameters:

object - the NexusObject to insert.

pos - the position (0-indexed) to add it at.

removeObject

public void removeObject(NexusObject object)

Removes an object from the file.

Parameters:

object - the NexusObject to remove.

containsObject

public boolean containsObject(NexusObject object)

Checks to see if we contain an object.

Parameters:

object - the NexusObject to check.

Returns:

true if we contain it.

objectIterator

public Iterator objectIterator()

Iterate over all objects in the file in order.

Returns:

an iterator of NexusObjects.

commentIterator

public Iterator commentIterator()

Iterate over all comments in the file in order.

Returns:

an iterator of NexusComments.

blockIterator

public Iterator blockIterator()

Iterate over all blocks in the file in order.

Returns:

an iterator of NexusBlocks.