uk.ac.vamsas.objects.utils.trees
Class NewickFile

java.lang.Object
  uk.ac.vamsas.objects.utils.trees.NewickFile

public class NewickFile

extends java.lang.Object

DOCUMENT ME!

Version:

$Revision: 1.12 $

Author:

$author$

Constructor Summary

NewickFile(java.io.File inFile)

NewickFile(SequenceNode newtree)
Creates a new NewickFile object.

NewickFile(SequenceNode newtree, boolean bootstrap)
Creates a new NewickFile object.

NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
Creates a new NewickFile object.

NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances, boolean rootdistance)
Creates a new NewickFile object.

NewickFile(java.lang.String inStr)
Creates a new NewickFile object

Method Summary

void	_print(java.lang.StringBuffer tf, SequenceNode c)
java.util.Vector	attachTreeMap(Treenode[] tn) re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode.
java.util.Vector	findLeaves(SequenceNode node, java.util.Vector leaves) Search for leaf nodes.
SequenceNode	getTree() DOCUMENT ME!
boolean	HasBootstrap()
boolean	HasDistances()
boolean	HasRootDistance()
static void	main(java.lang.String[] args)
Treenode[]	makeTreeNodes() make tree node vector from a newick tree structure with associated vamsas objects
Treenode[]	makeTreeNodes(boolean ignoreplaceholders) make treenode vector for a parsed tree with/out leaf node associations
Treenode[]	matchTreeNodeNames(java.lang.String[] names, Vobject[] boundObjects)
java.lang.String	nextLine()
void	parse() call this to convert the newick string into a binary node linked tree Note: this is automatically called by the constructors, so you normally wouldn't need to use this.
java.lang.String	print() Generate a newick format tree according to internal flags for bootstraps, distances and root distances.
java.lang.String	print(boolean withbootstraps) Generate a newick format tree according to internal flags for distances and root distances and user specificied writing of bootstraps.
java.lang.String	print(boolean withbootstraps, boolean withdists) Generate newick format tree according to internal flags for writing root node distances.
java.lang.String	print(boolean withbootstraps, boolean withdists, boolean printRootInfo) Generate newick format tree according to user specified flags
void	print(java.lang.StringBuffer tf, SequenceNode root)

Methods inherited from class java.lang.Object

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

Constructor Detail

NewickFile

public NewickFile(java.lang.String inStr)
           throws java.io.IOException

Creates a new NewickFile object

Parameters:

inStr - Newick style tree string

Throws:

java.io.IOException - if string is not a valid newick file

NewickFile

public NewickFile(java.io.File inFile)
           throws java.io.IOException

NewickFile

public NewickFile(SequenceNode newtree)

Creates a new NewickFile object.

Parameters:

newtree - DOCUMENT ME!

NewickFile

public NewickFile(SequenceNode newtree,
                  boolean bootstrap)

Creates a new NewickFile object.

Parameters:

newtree - DOCUMENT ME!

bootstrap - DOCUMENT ME!

NewickFile

public NewickFile(SequenceNode newtree,
                  boolean bootstrap,
                  boolean distances)

Creates a new NewickFile object.

Parameters:

newtree - DOCUMENT ME!

bootstrap - DOCUMENT ME!

distances - DOCUMENT ME!

NewickFile

public NewickFile(SequenceNode newtree,
                  boolean bootstrap,
                  boolean distances,
                  boolean rootdistance)

Creates a new NewickFile object.

Parameters:

newtree - DOCUMENT ME!

bootstrap - DOCUMENT ME!

distances - DOCUMENT ME!

rootdistance - DOCUMENT ME!

Method Detail

HasBootstrap

public boolean HasBootstrap()

Returns:

true if tree has bootstrap values

HasDistances

public boolean HasDistances()

Returns:

true if tree has distances on branches

HasRootDistance

public boolean HasRootDistance()

Returns:

true if root has a stem distance

nextLine

public java.lang.String nextLine()
                          throws java.io.IOException

Throws:

java.io.IOException

parse

public void parse()
           throws java.io.IOException

call this to convert the newick string into a binary node linked tree Note: this is automatically called by the constructors, so you normally wouldn't need to use this.

Throws:

java.io.IOException - if the newick string cannot be parsed.

getTree

public SequenceNode getTree()

DOCUMENT ME!

Returns:

DOCUMENT ME!

matchTreeNodeNames

public Treenode[] matchTreeNodeNames(java.lang.String[] names,
                                     Vobject[] boundObjects)

print

public java.lang.String print()

Generate a newick format tree according to internal flags for bootstraps, distances and root distances.

Returns:

new hampshire tree in a single line

print

public java.lang.String print(boolean withbootstraps)

Generate a newick format tree according to internal flags for distances and root distances and user specificied writing of bootstraps.

Parameters:

withbootstraps - controls if bootstrap values are explicitly written.

Returns:

new hampshire tree in a single line

print

public java.lang.String print(boolean withbootstraps,
                              boolean withdists)

Generate newick format tree according to internal flags for writing root node distances.

Parameters:

withbootstraps - explicitly write bootstrap values

withdists - explicitly write distances

Returns:

new hampshire tree in a single line

print

public java.lang.String print(boolean withbootstraps,
                              boolean withdists,
                              boolean printRootInfo)

Generate newick format tree according to user specified flags

Parameters:

withbootstraps - explicitly write bootstrap values

withdists - explicitly write distances

printRootInfo - explicitly write root distance

Returns:

new hampshire tree in a single line

print

public void print(java.lang.StringBuffer tf,
                  SequenceNode root)

_print

public void _print(java.lang.StringBuffer tf,
                   SequenceNode c)

main

public static void main(java.lang.String[] args)

findLeaves

public java.util.Vector findLeaves(SequenceNode node,
                                   java.util.Vector leaves)

Search for leaf nodes.

Parameters:

node - root node to search from

leaves - Vector of leaves to add leaf node objects too.

Returns:

Vector of leaf nodes on binary tree

makeTreeNodes

public Treenode[] makeTreeNodes()

make tree node vector from a newick tree structure with associated vamsas objects

Returns:

Treenode definitions for nodes with associated objects

makeTreeNodes

public Treenode[] makeTreeNodes(boolean ignoreplaceholders)

make treenode vector for a parsed tree with/out leaf node associations

Parameters:

ignoreplaceholders - if true means only associated nodes are returned

Returns:

treenode vector for associated or all leaves

attachTreeMap

public java.util.Vector attachTreeMap(Treenode[] tn)

re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode. Note: this only takes the first object in the first set of references.

Parameters:

tn -

Returns:

vector of mappings { treenode, SequenceNode, Vobject for VorbaId on sequence node }