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

java.lang.Object
  extended by org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
      extended by org.biojavax.bio.phylo.io.nexus.TreesBlock
All Implemented Interfaces:
NexusBlock, NexusObject

public class TreesBlock
extends NexusBlock.Abstract

Represents Nexus trees blocks.

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

Nested Class Summary
static class TreesBlock.NewickTreeString
          A simple representation of a Newick tree as a single string.
 
Nested classes/interfaces inherited from interface org.biojavax.bio.phylo.io.nexus.NexusBlock
NexusBlock.Abstract
 
Field Summary
static String TREES_BLOCK
          A constant representing the name of Trees blocks.
 
Constructor Summary
TreesBlock()
          Delegates to NexusBlock.Abstract constructor using TreesBlock.TREES_BLOCK as the name.
 
Method Summary
 void addComment(NexusComment comment)
          Adds a comment.
 void addTranslation(String label, String taxa)
          Add a translation.
 void addTree(String label, TreesBlock.NewickTreeString tree)
          Adds a tree.
 boolean containsTranslation(String label)
          Checks to see if we contain the given translation.
 boolean containsTree(String label)
          Checks to see if we contain the given tree.
 List getComments()
          Returns all comments.
 Map getTranslations()
          Get the translations added so far.
 Map getTrees()
          Returns all trees.
 void removeComment(NexusComment comment)
          Removes a comment.
 void removeTranslation(String label)
          Removes the given translation.
 void removeTree(String label)
          Removes a tree.
protected  void writeBlockContents(Writer writer)
          Implement this to write out block contents, not including the BEGIN and END tags.
 
Methods inherited from class org.biojavax.bio.phylo.io.nexus.NexusBlock.Abstract
getBlockName, writeObject, writeToken
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

TREES_BLOCK

public static final String TREES_BLOCK
A constant representing the name of Trees blocks.

See Also:
Constant Field Values
Constructor Detail

TreesBlock

public TreesBlock()
Delegates to NexusBlock.Abstract constructor using TreesBlock.TREES_BLOCK as the name.

Method Detail

addTranslation

public void addTranslation(String label,
                           String taxa)
Add a translation.

Parameters:
label - the label to add.
taxa - the taxa name this label will represent.

removeTranslation

public void removeTranslation(String label)
Removes the given translation.

Parameters:
label - the label to remove.

containsTranslation

public boolean containsTranslation(String label)
Checks to see if we contain the given translation.

Parameters:
label - the label to check for.
Returns:
true if we already contain it.

getTranslations

public Map getTranslations()
Get the translations added so far.

Returns:
the translations added so far.

addTree

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

Parameters:
label - the label to give the tree.
tree - the tree to add.

removeTree

public void removeTree(String label)
Removes a tree.

Parameters:
label - the label to remove.

containsTree

public boolean containsTree(String label)
Checks to see if we contain the given tree.

Parameters:
label - the label to check for.
Returns:
true if we already contain it.

getTrees

public Map getTrees()
Returns all trees.

Returns:
all the selected trees.

addComment

public void addComment(NexusComment comment)
Adds a comment.

Parameters:
comment - the comment to add.

removeComment

public void removeComment(NexusComment comment)
Removes a comment.

Parameters:
comment - the comment to remove.

getComments

public List getComments()
Returns all comments.

Returns:
all the selected comments.

writeBlockContents

protected void writeBlockContents(Writer writer)
                           throws IOException
Description copied from class: NexusBlock.Abstract
Implement this to write out block contents, not including the BEGIN and END tags.

Specified by:
writeBlockContents in class NexusBlock.Abstract
Parameters:
writer - the writer to write to.
Throws:
IOException - if writing failed.