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

Class TreesBlock

java.lang.Object

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

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, Tiago Antao

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
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

Fields

Modifier and Type	Field	Description
static String	TREES_BLOCK	A constant representing the name of Trees blocks.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
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.
void	addTree(String label, org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph)	Deprecated.
void	addTree(String label, org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph, String topLabel)	Add a tree, converting weighted graph (JGraphT) to NewickString.
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.
String	getNodePrefix()	Returns the node prefix.
String	getTopNode()	Returns the top node of the previously requested graph.
Map	getTranslations()	Get the translations added so far.
Object	getTree(String label)	Returns a tree for given label
org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge>	getTreeAsWeightedJGraphT(String label)	Get given (NewickString) tree by label, converts it to weighted graph (JGraphT).
Map	getTrees()	Returns all trees.
String	getTreeText(org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> treegraph, String node, String parent)
String	getTreeText(org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph, String node, String parent)
void	removeComment(NexusComment comment)	Removes a comment.
void	removeTranslation(String label)	Removes the given translation.
void	removeTree(String label)	Removes a tree.
void	setNodePrefix(String prefix)	Sets the node prefix of intermediate nodes for returned graphs.
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.

getTree

public Object getTree(String label)

Returns a tree for given label

Parameters:

label - the label to select.

Returns:

selected tree.

getTreeText

public String getTreeText(org.jgrapht.UndirectedGraph<String,org.jgrapht.graph.DefaultEdge> treegraph,
                          String node,
                          String parent)

addTree

public void addTree(String label,
                    org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph)

Deprecated.

Add a tree, converting weighted graph (JGraphT) to NewickString This will assume a (arbitrary) root node using the old convention of labeling intermediate nodes as p*.

Parameters:

label - the label to add

treegraph - the treegraph to convert.

getTreeText

public String getTreeText(org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph,
                          String node,
                          String parent)

addTree

public void addTree(String label,
                    org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> treegraph,
                    String topLabel)

Add a tree, converting weighted graph (JGraphT) to NewickString.

Parameters:

label - the label to add

treegraph - the treegraph to convert.

topLabel - the label of the top (root if rooted tree) node.

getTreeAsWeightedJGraphT

public org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge> getTreeAsWeightedJGraphT(String label)
                                                                                                       throws ParseException

Get given (NewickString) tree by label, converts it to weighted graph (JGraphT). Alters this.weighted!

Parameters:

label - label for tree selection

Returns:

converted tree as undirectedGraph

Throws:

ParseException

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.

getTopNode

public String getTopNode()

Returns the top node of the previously requested graph. The topNode will be the root node if the tree is rooted, if not then it will just be the top most node of the newick string with no biological meaning. The top node from the #getTreeAsJGraphT(java.lang.String) and getTreeAsWeightedJGraphT(java.lang.String) might vary, and this function will return the top node of the previously called method only. If no method was called, null is returned. Note: the top node between graphs, probably does not vary, but, just in case, the note is here and the user should get a different top for each type of graph.

Returns:

the top node.

setNodePrefix

public void setNodePrefix(String prefix)

Sets the node prefix of intermediate nodes for returned graphs. The intermediate nodes of graphs have to be named, the conventions being: 1. Generate a new node name using a prefix plus an integer 2. If the node name clashes with any taxon name, use another integer

Parameters:

prefix - The prefix

getNodePrefix

public String getNodePrefix()

Returns the node prefix.

Returns:

the node prefix