edu.uconn.mcb.lineageevolver.config
Class Configuration

java.lang.Object
  edu.uconn.mcb.lineageevolver.config.Configuration

All Implemented Interfaces:

java.io.Serializable

public class Configuration

extends java.lang.Object

implements java.io.Serializable

Common superclass for all configuration objects. Contains everything necessary for a Lineage.

Author:

Hasan Khalil

See Also:

Serialized Form

Field Summary

protected int[]	_hgtCounts Our breakpoints for HGT.
protected Genome	_rootGenome The root genome.
protected int	_totalTime The total time to process evolution.
protected GraphTopology	_tree The topology.

Constructor Summary

Configuration()
Default constructor for Configuration objects.

Method Summary

int[]	getHGTCounts()
Genome	getRootGenome() Returns the root Genome.
int	getTotalTime()
GraphTopology	getTree()
void	setHGTCounts(int[] counts)
void	setRootGenome(Genome genome) Sets the root genome.
void	setTotalTime(int time)

Methods inherited from class java.lang.Object

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

Field Detail

_tree

protected GraphTopology _tree

The topology.

_hgtCounts

protected int[] _hgtCounts

Our breakpoints for HGT.

_totalTime

protected int _totalTime

The total time to process evolution.

_rootGenome

protected Genome _rootGenome

The root genome.

Constructor Detail

Configuration

public Configuration()

Default constructor for Configuration objects. Creates a configuration with an empty topology and no HGT.

Method Detail

getHGTCounts

public int[] getHGTCounts()

Returns:

Returns the _hgtCounts.

setHGTCounts

public void setHGTCounts(int[] counts)

Parameters:

counts - The _hgtCounts to set.

getTotalTime

public int getTotalTime()

Returns:

Returns the _totalTime.

setTotalTime

public void setTotalTime(int time)

Parameters:

time - The _totalTime to set.

getTree

public GraphTopology getTree()

Returns:

Returns the _tree.

getRootGenome

public Genome getRootGenome()

Returns the root Genome.

Returns:

Returns the root Genome.

setRootGenome

public void setRootGenome(Genome genome)

Sets the root genome.

Parameters:

genome - The root Genome to set.