Trees

Class TreeFigure

java.lang.Object

Trees.TreeFigure

public class TreeFigure
extends java.lang.Object

Class for visualising trees. Produces a SVG file.
Note this class is still being developed. It works but may not have all appropriate error checking nor have all needed methods been written. I make no guarantees that future versions will have the same methods.

Version:

2.0

Constructor Summary

Constructors

Constructor and Description
TreeFigure(Tree t) Constructor

Method Summary

Methods

Modifier and Type	Method and Description
void	printSVG(java.io.File f, boolean showLengths) Prints the tree to the given file
void	setBranchColors(java.util.Map<Branch,java.lang.String> colors) Sets the colour of branches.
void	setLeafColor(java.util.Map<java.lang.String,java.lang.String> colors) Sets the colour of the leaf text.
void	setLeavesText(java.util.Map<java.lang.String,java.lang.String> names) Overwrites the default leaf text (the taxa names).
void	setRootBranchColor(java.lang.String color) Sets the colour of the root branch.
void	setVerticalSpacing(int spacing) Sets the spacing (in co-ordinate terms) between the horizontal lines

Methods inherited from class java.lang.Object

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

Constructor Detail

TreeFigure

public TreeFigure(Tree t)
           throws TreeException

Constructor

Parameters:

t - The tree to visualise

Throws:

TreeException - If the tree does not have branch lengths

Method Detail

setBranchColors

public void setBranchColors(java.util.Map<Branch,java.lang.String> colors)

Sets the colour of branches. Default is black, either if this method is not called at all or it is not passed a colour for a branch. Colours should be defined as in a SVG file.

Parameters:

colors - Map from branch to colour

setLeafColor

public void setLeafColor(java.util.Map<java.lang.String,java.lang.String> colors)

Sets the colour of the leaf text. Default is black, either if this method is not called at all or it is not passed a colour for a leaf.

Parameters:

colors - Map from leaf name to colour. Colours should be defined as in a SVG file.

setRootBranchColor

public void setRootBranchColor(java.lang.String color)

Sets the colour of the root branch. Defaults to black if this method is not called

Parameters:

color - The colour of the branch. Colour should be defined as in a SVG file.

setLeavesText

public void setLeavesText(java.util.Map<java.lang.String,java.lang.String> names)

Overwrites the default leaf text (the taxa names).

Parameters:

names - Map from taxa name to string where the string is the new text for each leaf. Should include new text for every leaf.

setVerticalSpacing

public void setVerticalSpacing(int spacing)

Sets the spacing (in co-ordinate terms) between the horizontal lines

Parameters:

spacing - The spacing to use

printSVG

public void printSVG(java.io.File f,
            boolean showLengths)
              throws java.io.IOException,
                     TreeException

Prints the tree to the given file

Parameters:

f - The file to print to

showLengths - Display branch lengths on output

Throws:

java.io.IOException - Thrown if there is a problem writing the file

TreeException - Thrown if there is a problem with the tree