edu.rit.compbio.phyl.test

Class Test04

java.lang.Object

edu.rit.compbio.phyl.test.Test04

public class Test04
extends java.lang.Object

Class Test04 is a unit test program for classes DnaSequenceList, DnaSequenceTree, FitchParsimony, and Upgma. The program:

1. Reads a DnaSequenceList from the input file in interleaved PHYLIP format.
2. Constructs a phylogenetic tree using the UPGMA algorithm.
3. Computes and prints the tree's Fitch parsimony score.
4. Reorders the list of DNA sequences into descending order of branch length and stores the list in an output file.
5. Stores a picture of the tree in an output file 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.test.Test04 infile outfile drawfile [ format ]
infile = Input DNA sequence list file name
outfile = Output DNA sequence list file name
drawfile = Output drawing file name
format = DecimalFormat string for branch lengths (default: "0.00")

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