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## org.biojavax.ga.impl
Class AbstractOrganism

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojavax.ga.impl.AbstractOrganism

All Implemented Interfaces:
  Changeable, Organism

Direct Known Subclasses:
  SimpleOrganism

    public abstract class AbstractOrganism

extends AbstractChangeable
implements Organism

Abstract implementation of Organism. Most implementations would want to inherit from here.

Since:
  1.5
Version:
  1.0
Author:
  Mark Schreiber

Field Summary
`protected SymbolList[]` | `chromosomes`

Fields inherited from interface org.biojavax.ga.Organism
`CHROMOSOMES, NAME`

Constructor Summary
`protected` | `AbstractOrganism()`
`protected` | `AbstractOrganism(Organism org, String name)`

Method Summary
`SymbolList[]` | `getChromosomes()` Gets the organisms 'chromosome' sequences
`double[]` | `getFitness()` Returns the current fitness of this organism.
`String` | `getName()` Gets the organisms name
`abstract boolean` | `isHaploid()` Is the organism Haploid?
`protected abstract void` | `setChromImpl(SymbolList[] chromosomes)`
`void` | `setChromosomes(SymbolList[] chromosomes)` Sets the organisms 'chromosome' sequences.
`void` | `setFitness(double[] fitness)` This method allows to set the fitness of this organism to the specified value.
`void` | `setName(String name)` Sets the organisms name

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface org.biojavax.ga.Organism
`replicate`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Field Detail

### chromosomes

    protected SymbolList[] chromosomes

Constructor Detail

### AbstractOrganism

    protected AbstractOrganism()

### AbstractOrganism

    protected AbstractOrganism(Organism org,
                               String name)

Method Detail

### getChromosomes

    public final SymbolList[] getChromosomes()

  Description copied from interface: `Organism`
  Gets the organisms 'chromosome' sequences

  Specified by:
    `getChromosomes` in interface `Organism`
  Returns:
    a `SymbolList[]`

### getFitness

    public final double[] getFitness()

  Description copied from interface: `Organism`
  Returns the current fitness of this organism. This is an array. Note that in the most cases this array may only contain one single value, but for multi-objective optimization it is necessary to store multiple fitness values.

  Specified by:
    `getFitness` in interface `Organism`
  Returns:
    the fitness of the organism

### getName

    public String getName()

  Description copied from interface: `Organism`
  Gets the organisms name

  Specified by:
    `getName` in interface `Organism`
  Returns:
    the name String

### isHaploid

    public abstract boolean isHaploid()

  Description copied from interface: `Organism`
  Is the organism Haploid?

  Specified by:
    `isHaploid` in interface `Organism`
  Returns:
    true if it is.

### setChromImpl

    protected abstract void setChromImpl(SymbolList[] chromosomes)

### setChromosomes

    public final void setChromosomes(SymbolList[] chromosomes)
                              throws ChangeVetoException

  Description copied from interface: `Organism`
  Sets the organisms 'chromosome' sequences.

  Specified by:
    `setChromosomes` in interface `Organism`
  Parameters:
    `chromosomes` - a `SymbolList[]`
  Throws:
    `ChangeVetoException` - if the Chromosome collection of the Organism is unchangable

### setFitness

    public final void setFitness(double[] fitness)

  Description copied from interface: `Organism`
  This method allows to set the fitness of this organism to the specified value. Generally this will be an array, which in the most cases contains just a single entry. In cases where we want to have multi-objective optimization we may want to make use of a more general fitness array with mutliple entries.

  Specified by:
    `setFitness` in interface `Organism`

### setName

    public final void setName(String name)
                       throws ChangeVetoException

  Description copied from interface: `Organism`
  Sets the organisms name

  Specified by:
    `setName` in interface `Organism`
  Parameters:
    `name` - the name of the organism.
  Throws:
    `ChangeVetoException` - if the name may not be changed.

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