org.concord.biologica.engine
Class Gene

java.lang.Object
  |
  +--org.xml.sax.HandlerBase
        |
        +--org.concord.biologica.engine.EngineObject
              |
              +--org.concord.biologica.engine.Gene

All Implemented Interfaces:

org.xml.sax.DocumentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler, java.io.Serializable

public final class Gene

extends EngineObject

implements java.io.Serializable

This class represents a gene.

This class does not implement INucleicAcid because a gene is considered to be an abstract relationship between different alleles where the alleles are the actual nucleic acids.

A gene MAY change after it has been created, especially new alleles may be created and added to the gene. This is possible due to mutations.

An object of this class will generate the following property change events:

• EngineProp.DELETED - object has been deleted
• EngineProp.DESCRIPTION - the object description has changed
• EngineProp.ID - object's id has changed
• EngineProp.LENGTH_IN_BASES - length of this gene in bases has changed
• EngineProp.LOCKED_STATE - object has been locked or unlocked
• EngineProp.NAME - name of this gene has changed
• EngineProp.SPECIES_ALLELE_ADDED - a species allele was added
• EngineProp.SPECIES_ALLELE_REMOVED - a species allele was removed
• EngineProp.START_INDEX_IN_HOLDER - index of this gene in its chromosome has changed
• EngineProp.STRAND - top or bottom strand?
• EngineProp.VISIBLE - gene visibility has changed

Version:

$Revision: 1.1.1.1 $ $Date: 2001/04/28 00:39:12 $

Author:

$Author: ed $

See Also:

EngineProp.DELETED, EngineProp.DESCRIPTION, EngineProp.ID, EngineProp.LENGTH_IN_BASES, EngineProp.LOCKED_STATE, EngineProp.NAME, EngineProp.SPECIES_ALLELE_ADDED, EngineProp.SPECIES_ALLELE_REMOVED, EngineProp.START_INDEX_IN_HOLDER, EngineProp.STRAND, EngineProp.VISIBLE, PropertyChangeListener, Serialized Form

Field Summary

static int	BOTTOM_STRAND Top strand
static int	TOP_STRAND Bottom strand

Fields inherited from class org.concord.biologica.engine.EngineObject

AUTOMATIC_LOCKED, AUTOMATIC_LOCKED_STRING, changes, deleted, FALSE, id, lockedState, MANUAL_AND_AUTOMATIC_LOCKED, MANUAL_AND_AUTOMATIC_LOCKED_STRING, MANUAL_LOCKED, MANUAL_LOCKED_STRING, NULL_ID, TRUE, UNLOCKED, UNLOCKED_STRING, xmlElementContext

Constructor Summary

Gene(SpeciesChromosome aSpeciesChromosome, java.lang.String aName, int aStartIndexInHolder, int aLengthInBases)
Create a new gene given a species chromosome.

Gene(SpeciesChromosome aSpeciesChromosome, java.lang.String anElementName, int anElementID, com.sun.xml.parser.Parser anXMLParser, ImportContext importContext)
Create a new gene and start handling XML parsing events to set the properties of this object.

Method Summary

void	characters(char[] ch, int start, int length) Receive notification of character data.
void	delete() Delete this object, notifying parent objects and deleting any child objects.
void	delete(boolean notifyChange)
void	endElement(java.lang.String anElementName) Handle notification that the parsing of the given element has ended.
java.lang.String	getDescription() Return the description of this gene.
int	getLengthInBases() Returns the length of this gene in bases.
SpeciesAllele	getMutationSpeciesAllele() Returns the mutation species allele for this gene, if there is one.
java.lang.String	getName() Return the name of this gene.
int	getNumberOfSpeciesAlleles() Return the number of species alleles of this gene.
Species	getSpecies() Get the species containing this object.
java.util.Enumeration	getSpeciesAlleles() Returns an enumeration over the gene's species alleles.
SpeciesChromosome	getSpeciesChromosome() Get the species chromosome containing this gene.
int	getStartIndexInHolder() Returns the start index of this gene acid in its chromosome.
int	getStrand() Get the strand of this gene.
World	getWorld() Get the world containing this object.
void	ignorableWhitespace(char[] ch, int start, int length) Receive notification of ignorable white space character data.
boolean	isVisible() Get whether this gene is visible.
void	setAutomaticLocked(boolean automaticLocked) Set or unset the automatic locked state of this object, leaving other components of the locked state untouched.
void	setDescription(java.lang.String aDescription) Set the description of this gene.
void	setLengthInBases(int aLengthInBases) Set the length in bases of this gene.
void	setLockedState(int aLockedState) Set the locked state of the object, recursively setting the locked state of children objects.
void	setManualLocked(boolean manualLocked) Set or unset the manual locked state of this object, leaving other components of the locked state untouched.
void	setName(java.lang.String aName) Set the name of this gene.
void	setStartIndexInHolder(int anIndex) Set the start index of this gene in its chromosome.
void	setStrand(int aStrand) Set the strand of this gene.
void	setVisible(boolean TorF) Set whether this gene is visible.
void	startElement(java.lang.String anElementName, org.xml.sax.AttributeList amap) Handle notification that the parser has hit the start of a new element with the given name and attributes.
java.lang.String	toString() Return a string representation of this object, usually the object's name.
void	writeToStream(java.io.PrintWriter stream) Writes this object to the given stream in XML format.

Methods inherited from class org.concord.biologica.engine.EngineObject

addPropertyChangeListener, getID, getLockedState, getLockedStateAsString, isAutomaticLocked, isDeleted, isLocked, isManualLocked, notifySelected, release, removePropertyChangeListener, setID, setLockedStateAsString

Methods inherited from class org.xml.sax.HandlerBase

endDocument, error, fatalError, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, startDocument, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Field Detail

BOTTOM_STRAND

public static final int BOTTOM_STRAND

Top strand

TOP_STRAND

public static final int TOP_STRAND

Bottom strand

Constructor Detail

Gene

public Gene(SpeciesChromosome aSpeciesChromosome,
            java.lang.String aName,
            int aStartIndexInHolder,
            int aLengthInBases)

Create a new gene given a species chromosome.

Parameters:

aSpeciesChromosome - SpeciesChromosome - the species chromosome of this gene, may not be null

aName - String - the name for this gene, may not be null

aStartIndexInHolder - int - the start index of the gene in bases on its chromosome, must be greater than zero

aLengthInBases - int - the "normal" length of the gene, must be zero or greater

Throws:

java.lang.IllegalArgumentException - - input argument(s) illegal

Gene

public Gene(SpeciesChromosome aSpeciesChromosome,
            java.lang.String anElementName,
            int anElementID,
            com.sun.xml.parser.Parser anXMLParser,
            ImportContext importContext)

Create a new gene and start handling XML parsing events to set the properties of this object.

Parameters:

aSpeciesChromosome - SpeciesChromosome - the enclosing species chromosome for this new gene

anElementName - String - the element name

anElementID - int - the element id

anXMLParser - com.sun.xml.parser.Parser - the element parser

importContext - ImportContext - import context for mapping ids from file to this world

Throws:

java.lang.IllegalArgumentException - - input arguments illegal

Method Detail

startElement

public void startElement(java.lang.String anElementName,
                         org.xml.sax.AttributeList amap)
                  throws org.xml.sax.SAXException

Handle notification that the parser has hit the start of a new element with the given name and attributes.

For internal elements (elements that are non-EngineObject instance variables of this object), call xmlElementContext.startElement() and xmlElementContext will receive the remaining element notifications. For external elements (elements that are EngineObject instance variables of this object), create an object of the appropriate class and that object will receive the remaining element notifications.

Overrides:

startElement in class org.xml.sax.HandlerBase

Parameters:

anElementName - String - name of element

amap - AttributeList - an attribute list

characters

public void characters(char[] ch,
                       int start,
                       int length)
                throws org.xml.sax.SAXException

Receive notification of character data.

Overrides:

characters in class org.xml.sax.HandlerBase

Parameters:

ch - char[] - characters

start - int - start of string

length - int - length of string

ignorableWhitespace

public void ignorableWhitespace(char[] ch,
                                int start,
                                int length)
                         throws org.xml.sax.SAXException

Receive notification of ignorable white space character data.

Overrides:

ignorableWhitespace in class org.xml.sax.HandlerBase

Parameters:

ch - char[] - characters

start - int - start of string

length - int - length of string

endElement

public void endElement(java.lang.String anElementName)
                throws org.xml.sax.SAXException

Handle notification that the parsing of the given element has ended.

Overrides:

endElement in class org.xml.sax.HandlerBase

Parameters:

anElementName - String - the element name

delete

public void delete()

Delete this object, notifying parent objects and deleting any child objects.

When this method is called, a property change event is generated for the property named EngineProp.DELETED.

Overrides:

delete in class EngineObject

delete

public void delete(boolean notifyChange)

getSpeciesChromosome

public SpeciesChromosome getSpeciesChromosome()

Get the species chromosome containing this gene.

Returns:

SpeciesChromosome - the chromosome containing this gene

getSpecies

public Species getSpecies()

Get the species containing this object.

Returns:

Species - the species containing this object, never null.

getWorld

public World getWorld()

Get the world containing this object.

Overrides:

getWorld in class EngineObject

Returns:

World - the world containing this object, never null.

setAutomaticLocked

public void setAutomaticLocked(boolean automaticLocked)

Set or unset the automatic locked state of this object, leaving other components of the locked state untouched. Recursively sets the automatic locked state of children of this object.

When this property is changed, a property change event is fired for the property named EngineProp.LOCKED_STATE.

Overrides:

setAutomaticLocked in class EngineObject

Parameters:

automaticLocked - boolean - object should be automatic locked (true) or not (false)

setManualLocked

public void setManualLocked(boolean manualLocked)

Set or unset the manual locked state of this object, leaving other components of the locked state untouched. Recursively sets the manual locked state of children of this object.

When this property is changed, a property change event is fired for the property named EngineProp.LOCKED_STATE.

Overrides:

setManualLocked in class EngineObject

Parameters:

manualLocked - boolean - object should be manually locked (true) or not (false)

setLockedState

public void setLockedState(int aLockedState)

Set the locked state of the object, recursively setting the locked state of children objects.

When this property is changed, a property change event is fired for the property named EngineProp.LOCKED_STATE.

Overrides:

setLockedState in class EngineObject

Parameters:

aLockedState - int - new locked state of this object

Throws:

java.lang.IllegalArgumentException - - new locked state invalid

toString

public java.lang.String toString()

Return a string representation of this object, usually the object's name.

Overrides:

toString in class EngineObject

Returns:

String - string representation of object

getName

public java.lang.String getName()

Return the name of this gene. May be null.

Returns:

String - name of this gene, may not be null.

setName

public void setName(java.lang.String aName)

Set the name of this gene.

When this method is successful, a property change event is fired for the property named EngineProp.NAME.

Parameters:

aName - String - the new name of this gene, may not be null

Throws:

java.lang.IllegalArgumentException - - input argument illegal

ObjectDeletedException - - object is deleted and cannot be modified

ObjectLockedException - - object is locked and cannot be deleted

getDescription

public java.lang.String getDescription()

Return the description of this gene. May be null.

Returns:

String - description of this gene, may not be null.

setDescription

public void setDescription(java.lang.String aDescription)

Set the description of this gene.

When this method is successful, a property change event is fired for the property named EngineProp.DESCRIPTION.

Parameters:

aDescription - String - the new description of this gene, may not be null

Throws:

java.lang.IllegalArgumentException - - input argument illegal

ObjectDeletedException - - object is deleted and cannot be modified

ObjectLockedException - - object is locked and cannot be modified

getStartIndexInHolder

public int getStartIndexInHolder()

Returns the start index of this gene acid in its chromosome.

Returns:

int - index in holder, in bases

setStartIndexInHolder

public void setStartIndexInHolder(int anIndex)

Set the start index of this gene in its chromosome.

When this property is changed, a property change event is generated for the property named EngineProp.START_INDEX_IN_HOLDER.

Parameters:

int - - new index in holder, must be between 0 and the length in bases

Throws:

java.lang.IllegalArgumentException - - input argument(s) illegal

ObjectDeletedException - - object is deleted and cannot be modified

ObjectLockedException - - object is locked and cannot be deleted

getLengthInBases

public int getLengthInBases()

Returns the length of this gene in bases.

Returns:

int - length of this gene in bases

setLengthInBases

public void setLengthInBases(int aLengthInBases)

Set the length in bases of this gene.

When this property is changed, a property change event is generated for the property named EngineProp.LENGTH_IN_BASES.

Parameters:

aLengthInBases - int - new length in bases for gene

Throws:

java.lang.IllegalArgumentException - - input argument(s) illegal

ObjectDeletedException - - object is deleted and cannot be modified

ObjectLockedException - - object is locked and cannot be deleted

getMutationSpeciesAllele

public SpeciesAllele getMutationSpeciesAllele()

Returns the mutation species allele for this gene, if there is one.

The mutation species allele is the allele that will be assumed when the user manually mutates an existing allele of this gene into something that isn't recognizable as a known allele. In this case, the mutation allele will be used for purposes of genotype to phenotype calculations, etc.

Returns:

SpeciesAllele - the mutation species allele, may be null

getSpeciesAlleles

public java.util.Enumeration getSpeciesAlleles()

Returns an enumeration over the gene's species alleles.

If there are no alleles of this gene, an enumeration with no elements is returned.

If there are alleles of this gene, the vector of alleles is cloned and an enumeration over that clone is returned. This enables you to safely modify the gene and its alleles while using the enumeration.

Returns:

Enumeration - an enumeration over the vector of alleles of this gene, never null

getNumberOfSpeciesAlleles

public int getNumberOfSpeciesAlleles()

Return the number of species alleles of this gene.

Returns:

int - the number of species alleles of this gene

isVisible

public boolean isVisible()

Get whether this gene is visible.

Returns:

boolean - whether this gene is visible (true) or not visible (false)

setVisible

public void setVisible(boolean TorF)

Set whether this gene is visible.

Parameters:

TorF - boolean - visible (true) or not visible (false)

getStrand

public int getStrand()

Get the strand of this gene.

Returns:

int - the strand of this gene, TOP_STRAND or BOTTOM_STRAND

See Also:

BOTTOM_STRAND, TOP_STRAND

setStrand

public void setStrand(int aStrand)

Set the strand of this gene.

Parameters:

aStrand - int - strand of gene

writeToStream

public void writeToStream(java.io.PrintWriter stream)
                   throws java.io.IOException

Writes this object to the given stream in XML format. Usually this method is used to write the object to a file for saving it, but that is potentially not the only use.

We could supply a default implementation that knows how to write the id value. But that convenience is not chosen because it's never correct to use just this implementation of these methods, so I'd rather have a compilation fail if a derived class fails to implement this method.

The inverse of this method is a constructor that takes a org.xml.sax.Parser argument and other arguments.

Overrides:

writeToStream in class EngineObject

Parameters:

stream - PrintWriter - print stream

Throws:

java.lang.IllegalArgumentException - - input arguments illegal

java.io.IOException - - an IO error occurred in java libraries