exe
Class GAIGSphylogenetic_tree

java.lang.Object
  exe.Tree
      exe.GAIGStree
          exe.GAIGSphylogenetic_tree

All Implemented Interfaces:

GAIGSdatastr

public class GAIGSphylogenetic_tree
extends GAIGStree
implements GAIGSdatastr

GAIGSphylogenetic_tree extends the GAIGStree class, providing a uniform interface for that class in generating GAIGS XML code. Use the various constructors to specify the general parameters for the tree visualization, and use the toXML method to actually generate the tree XML for snapshots.

Many of the more standard tree methods themselves are contained within the GAIGStree and Tree classes. Consult the documentation of those classes

. The unique aspect of phylogenetic trees is there layout in which only leaf nodes contain data and edgeweights are proportional to distances between gene sequences.

Version:

10/20/2007

Author:

Tom Naps

Field Summary

Fields inherited from class exe.Tree

binary, font_size, lines_per_node, out, root, x_spacing, x1, x2, y_spacing, y1, y2

Fields inherited from interface exe.GAIGSdatastr

DEFAULT_COLOR, DEFAULT_FONT_SIZE, DEFAULT_NAME, DEFAULT_X1, DEFAULT_X2, DEFAULT_Y1, DEFAULT_Y2

Constructor Summary

GAIGSphylogenetic_tree(boolean b)
Set the type of phylogenetic tree (binary or general), otherwise use default values.

GAIGSphylogenetic_tree(boolean b, java.lang.String name, java.lang.String color, double x1, double y1, double x2, double y2, double fontSize)
Set all instance variables.

Method Summary

protected int	size_helper(TreeNode the_root) Recursive helper function
int	size()
java.lang.String	toXML() Creates and returns GAIGS XML code for the current state of the tree

Methods inherited from class exe.GAIGStree

getName, setName

Methods inherited from class exe.Tree

getRoot, isBinary, setBinary, setBounds, setFontSize, setLinesPerNode, setOut, setRoot, setSpacing, writeGAIGSTree, writeGAIGSXMLTree, writeGAIGSXMLTree

Methods inherited from class java.lang.Object

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

Methods inherited from interface exe.GAIGSdatastr

getName, setName

Constructor Detail

GAIGSphylogenetic_tree

public GAIGSphylogenetic_tree(boolean b)

Set the type of phylogenetic tree (binary or general), otherwise use default values. Most phylogenetic trees should be binary and the layout algorithm is designed for such.

Parameters:

b - Whether this tree is binary (true) or general (false).

GAIGSphylogenetic_tree

public GAIGSphylogenetic_tree(boolean b,
                              java.lang.String name,
                              java.lang.String color,
                              double x1,
                              double y1,
                              double x2,
                              double y2,
                              double fontSize)

Set all instance variables.

Parameters:

b - Whether this tree is binary (true) or general (false).

name - Display name of this structure.

color - Color for items unless locally overridden.

x1 - Left display bound.

y1 - Bottom display bound.

x2 - Top display bound.

y2 - Right display bound.

fontSize - Font size for display.

Method Detail

size

public int size()

Returns:

the number of nodes in the tree

size_helper

protected int size_helper(TreeNode the_root)

Recursive helper function

Returns:

the number of nodes in the tree

toXML

public java.lang.String toXML()

Creates and returns GAIGS XML code for the current state of the tree

Specified by:

toXML in interface GAIGSdatastr

Overrides:

toXML in class GAIGStree

Returns:

A String containing GAIGS XML code for the tree