edu.rit.compbio.phyl

Class DrawTree

java.lang.Object

edu.rit.compbio.phyl.DrawTree

public class DrawTree
extends java.lang.Object

Class DrawTree is a program that draws a phylogenetic tree. The tree is specified on the command line in a subset of Newick Standard format. The drawing is stored in a file specified on the command line as a serialized Drawing object. The View program can be used to view the drawing file and save it in an image file in several formats.

Usage: java edu.rit.compbio.phyl.DrawTree "tree" file [ format ]
tree = Tree in Newick Standard format
file = Drawing file name
format = DecimalFormat string for branch lengths (default: "0.00")

Newick Standard format. The subset of Newick Standard format class DrawTree supports is described by this BNF syntax. Nonterminal symbols are in italic font, terminal symbols are in typewriter font, | designates alternatives.

tree ::= node ;
node ::= ( childList ) nameLength
childList ::= child | child , childList
child ::= tip | node
tip ::= nameLength
nameLength ::= empty | name | : length | name : length
name ::= Any sequence of non-whitespace characters except ( ) , : ;
length ::= Floating point number, as in the Double.valueOf() method

This subset only supports non-quoted names with no whitespace; however, any underscore character _ in a name is replaced with a space character. The full Newick Standard format supports quoted names including whitespace. For further information about Newick Standard format, see:

• http://evolution.gs.washington.edu/phylip/newicktree.html

Here is an example command to draw a tree and store it in the file "tree.dwg":

java edu.rit.compbio.phyl.DrawTree \
"(Gibbon:10,(Orangutan:8,(Gorilla:6,(Chimp:4,Human:4)))apes)primates;" tree.dwg

Here is the command to view the tree drawing:

java View tree.dwg

Here is the resulting drawing:

Method Summary

Modifier and Type	Method and Description
static void	main(java.lang.String[] args) Main program.

Methods inherited from class java.lang.Object

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

Method Detail

main

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

Main program.

Throws:

java.lang.Exception