ca.cas.nucleus
Class GenomeReader

java.lang.Object
  ca.cas.nucleus.GenomeReader

public class GenomeReader
extends java.lang.Object

The GenomeReader class is used for its static readGenome method which reads a Genome object from a file

Constructor Summary

GenomeReader()

Method Summary

static Genome<Chromosome>

readGenome(java.lang.String f) Creates a Genome object from a file which must follow a particular format There is a separate line in the file for each Chromosome in the Genome each line must be written in the following way: [name]:[homologue # (0 or 1)]:[# base pairs]:[index # of centromere]:[circularity (true or false)]

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeReader

public GenomeReader()

Method Detail

readGenome

public static Genome<Chromosome> readGenome(java.lang.String f)
                                     throws java.io.IOException

Creates a Genome object from a file which must follow a particular format There is a separate line in the file for each Chromosome in the Genome each line must be written in the following way: [name]:[homologue # (0 or 1)]:[# base pairs]:[index # of centromere]:[circularity (true or false)]

Parameters:

f - a file to be read from

Returns:

a Genome object representing the data read from the file

Throws:

java.io.IOException