Package org.biojavax.bio.phylo.io.nexus

Class TreesBlockBuilder

java.lang.Object

org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract

org.biojavax.bio.phylo.io.nexus.TreesBlockBuilder

All Implemented Interfaces:

NexusBlockBuilder, NexusBlockListener, TreesBlockListener

public class TreesBlockBuilder
extends NexusBlockBuilder.Abstract
implements TreesBlockListener

Builds Nexus taxa blocks.

Since:

1.6

Author:

Richard Holland, Tobias Thierer, Jim Balhoff

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder

NexusBlockBuilder.Abstract

Constructor Summary

Constructors

Constructor	Description
TreesBlockBuilder()

Method Summary

Modifier and Type	Method	Description
protected void	addComment(NexusComment comment)	Tell the builder to add the given comment at the current location.
void	addTranslation(String label, String taxa)	Add a translation.
void	addTree(String label, TreesBlock.NewickTreeString tree)	Adds a tree.
void	endBlock()	Notifies the parser that a block is ending.
void	endTokenGroup()	Closing a line (semi-colon encountered).
protected NexusBlock	startBlockObject()	Tell the builder to start a new block object.

Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlockBuilder.Abstract

beginComment, commentText, endComment, getBlockName, getNexusBlock, startBlock

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlockListener

beginComment, commentText, endComment, startBlock

Constructor Detail

TreesBlockBuilder

public TreesBlockBuilder()

Method Detail

addComment

protected void addComment(NexusComment comment)

Description copied from class: NexusBlockBuilder.Abstract

Tell the builder to add the given comment at the current location.

Specified by:

addComment in class NexusBlockBuilder.Abstract

Parameters:

comment - the comment to add.

startBlockObject

protected NexusBlock startBlockObject()

Description copied from class: NexusBlockBuilder.Abstract

Tell the builder to start a new block object.

Specified by:

startBlockObject in class NexusBlockBuilder.Abstract

endBlock

public void endBlock()

Description copied from interface: NexusBlockListener

Notifies the parser that a block is ending.

Specified by:

endBlock in interface NexusBlockListener

endTokenGroup

public void endTokenGroup()

Description copied from interface: NexusBlockListener

Closing a line (semi-colon encountered). This indicates that anything received after it is on the next logical line of the block.

Specified by:

endTokenGroup in interface NexusBlockListener

addTranslation

public void addTranslation(String label,
                           String taxa)

Description copied from interface: TreesBlockListener

Add a translation.

Specified by:

addTranslation in interface TreesBlockListener

Parameters:

label - the label to add.

taxa - the taxa name this label will represent.

addTree

public void addTree(String label,
                    TreesBlock.NewickTreeString tree)

Description copied from interface: TreesBlockListener

Adds a tree.

Specified by:

addTree in interface TreesBlockListener

Parameters:

label - the label to give the tree.

tree - the tree to add.