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

java.lang.Object
  extended by org.biojavax.bio.phylo.io.nexus.NexusFile

public class NexusFile
extends java.lang.Object

Represents Nexus files.

Since:
1.6
Author:
Richard Holland, Tobias Thierer, Jim Balhoff

Constructor Summary
NexusFile()
           
 
Method Summary
 void addObject(NexusObject object)
          Appends an object to the end of the file.
 java.util.Iterator blockIterator()
          Iterate over all blocks in the file in order.
 java.util.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.
 java.util.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 java.util.Iterator objectIterator()
Iterate over all objects in the file in order.

Returns:
an iterator of NexusObjects.

commentIterator

public java.util.Iterator commentIterator()
Iterate over all comments in the file in order.

Returns:
an iterator of NexusComments.

blockIterator

public java.util.Iterator blockIterator()
Iterate over all blocks in the file in order.

Returns:
an iterator of NexusBlocks.