com.rubecula.darwin.domain.genetics
Class Allele_

java.lang.Object
  net.sf.tostring0.AToString
      com.rubecula.darwin.domain.helper.Attribute_
          com.rubecula.darwin.domain.genetics.Allele_

All Implemented Interfaces:

Allele, Attribute, Basic, CacheSignature, Censusible, net.sf.tostring0.Identifiable, net.sf.tostring0.IToString

Direct Known Subclasses:

Allele_Binary, Allele_Number

public abstract class Allele_
extends Attribute_
implements Allele

This abstract provides base operations for implementations of Allele, which are specific, competing genes which may appear at a Locus.

In general, an allele can have a key and a value, both being objects. If the key is null, then the value, reduced to a String, serves as its key. Normally, known alleles are defined via configuration. But new alleles (mutants) can arise during an evolution. For these, there is an AlleleFactory.

In all cases, however, an Allele is immutable regarding its value. Once constructed, the value cannot be changed. The value of the (parent) locus is set once and once only.

Version:

$Revision: 1.29 $

Author:

Robin Hillyard

Field Summary

protected static org.apache.commons.logging.Log

LOG The logger for this class.

Fields inherited from interface net.sf.tostring0.IToString

ANGBR_OPEN, ANGBRA_CLSE, BRA_CLSE, BRA_OPEN, BRCE_OPEN, BRCS_CLSE, COLON, LIST_SEPARATOR, MAX_ELEMENTS_DEFAULT, S_MT, S_PERCENT, SEPARATOR, SPACE

Constructor Summary

protected	Allele_(java.lang.Object value) Constructor of an Allele_ based on a specific value.
protected	Allele_(java.lang.Object key, java.lang.Object value) Primary Private constructor of an Allele_ based on a specific value.

Method Summary

boolean	censusMe(Census census, java.lang.Object context) Method to census this object.
java.util.Collection<? extends Censusible>	getCensusibleChildren() Method to return a list of censusible children of this object.
Locus	getLocus() Return the value of locus.
java.lang.String	getSignature()
protected int	getStringChars()
void	setLocus(Locus locus) Set the value of the locus for this Allele.
void	setStringChars(int stringChars) Set the number of characters that we should see when we create a string of this Allele.
void	setValue(java.lang.Object value) set the field Attribute_.value.
java.lang.String	toString(boolean showDetail, boolean showClass, boolean showIdentifier, boolean includeParent, boolean includeChildren, java.lang.String prefix, boolean recurse, int maxElements, int maxChars)

Methods inherited from class com.rubecula.darwin.domain.helper.Attribute_

equals, getAttribute, getIdentifier, getValue, hashCode

Methods inherited from class net.sf.tostring0.AToString

toString, toStringBrief, toStringId

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.rubecula.darwin.domain.helper.Attribute

getAttribute, getValue

Methods inherited from interface net.sf.tostring0.IToString

toStringBrief, toStringId

Methods inherited from interface com.rubecula.darwin.domain.helper.Basic

getBases

Methods inherited from interface net.sf.tostring0.Identifiable

getIdentifier

Field Detail

LOG

protected static final org.apache.commons.logging.Log LOG

The logger for this class.

Constructor Detail

Allele_

protected Allele_(java.lang.Object value)

Constructor of an Allele_ based on a specific value. The key will be the value, in the form of a String. XXX this constructor is used only by unit tests.

Parameters:

value - the value for the new Allele_, as an Object.

Allele_

protected Allele_(java.lang.Object key,
                  java.lang.Object value)

Primary Private constructor of an Allele_ based on a specific value.

Parameters:

key - the key for the new Allele_, as an Object.

value - the value for the new Allele_, as an Object.

Method Detail

censusMe

public boolean censusMe(Census census,
                        java.lang.Object context)

Description copied from interface: Censusible

Method to census this object.

Specified by:

censusMe in interface Censusible

Parameters:

census - the census object which will present the results of taking this census

context - an arbitrary object which can be used by the census object to provide appropriate context for this object.

Returns:

true if we should continue censusing this object at deeper levels. If the result is false, then we do not call Censusible.getCensusibleChildren().

See Also:

Censusible.censusMe(com.rubecula.darwin.domain.helper.Census, java.lang.Object)

getCensusibleChildren

public java.util.Collection<? extends Censusible> getCensusibleChildren()

Description copied from interface: Censusible

Method to return a list of censusible children of this object.

Specified by:

getCensusibleChildren in interface Censusible

Returns:

either null or an ArrayList of censusible objects.

See Also:

Censusible.getCensusibleChildren()

getLocus

public Locus getLocus()

Return the value of locus.

Specified by:

getLocus in interface Allele

Returns:

the locus to which this allele can belong.

See Also:

Allele.getLocus()

getSignature

public java.lang.String getSignature()

Specified by:

getSignature in interface CacheSignature

Returns:

a "signature" for this object which can be used to form part of a cache key. The signature is similar in a sense to the hash code but typically, it is based more on mutable components of an object than is the hash code.

See Also:

CacheSignature.getSignature()

setLocus

public void setLocus(Locus locus)

Set the value of the locus for this Allele. This is not set in the constructor. TODO why is it not set in the constructor?

Specified by:

setLocus in interface Allele

See Also:

Allele.setLocus(com.rubecula.darwin.domain.helper.Locus)

setStringChars

public void setStringChars(int stringChars)

Set the number of characters that we should see when we create a string of this Allele. By default, the number is 1. We only increase it to N+1 if there are allele identifiers that share the first N characters.

Parameters:

stringChars - the stringChars to set

setValue

public void setValue(java.lang.Object value)

Description copied from class: Attribute_

set the field Attribute_.value.

Specified by:

setValue in interface Attribute

Overrides:

setValue in class Attribute_

Parameters:

value - the new value for the attribute.

See Also:

Attribute_.setValue(java.lang.Object)

toString

public java.lang.String toString(boolean showDetail,
                                 boolean showClass,
                                 boolean showIdentifier,
                                 boolean includeParent,
                                 boolean includeChildren,
                                 java.lang.String prefix,
                                 boolean recurse,
                                 int maxElements,
                                 int maxChars)

Specified by:

toString in interface net.sf.tostring0.IToString

Overrides:

toString in class Attribute_

See Also:

Attribute_.toString(boolean, boolean, boolean, boolean, boolean, java.lang.String, boolean, int, int)

getStringChars

protected int getStringChars()

Returns:

the stringChars