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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--org.xml.sax.HandlerBase | +--org.concord.biologica.engine.EngineObject | +--org.concord.biologica.engine.OrganismAllelePair
This class represents a pair of organism alleles or, in the case of sex chromosomes, it can represent a single allele on a single chromosome. This type of object should only exist for organisms of a diploid species.
In general this object is created when the organism is created and never changes from that time on. It's essentially a convenience object, especially for the tree view as this object represents a node in the tree view.
An instance of this class is contained by one organism chromosome pair.
An object of this class will generate the following property change events:
EngineProp.DELETED
,
EngineProp.ID
,
EngineProp.LOCKED_STATE
,
PropertyChangeListener
, Serialized FormFields 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 | |
OrganismAllelePair(OrganismChromosomePair anOrganismChromosomePair,
OrganismAllele aFirstOrganismAllele,
OrganismAllele aSecondOrganismAllele)
Create a new organism allele pair from the two given organism alleles. |
|
OrganismAllelePair(OrganismChromosomePair anOrganismChromosomePair,
java.lang.String anElementName,
int anElementID,
com.sun.xml.parser.Parser anXMLParser,
ImportContext importContext)
Create a new organism allele pair 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. |
OrganismAllele |
getFirstOrganismAllele()
Get the first organism allele of this pair. |
Organism |
getOrganism()
Returns the allele pair's organism. |
OrganismChromosomePair |
getOrganismChromosomePair()
Returns the organism allele pair's chromosome organism pair. |
OrganismAllele |
getSecondOrganismAllele()
Get the second organism allele of this pair. |
Species |
getSpecies()
Returns the organism chromosome pair's species. |
World |
getWorld()
Get the world containing this object. |
void |
ignorableWhitespace(char[] ch,
int start,
int length)
Receive notification of ignorable white space character data. |
void |
propertyChange(java.beans.PropertyChangeEvent event)
Handle property change events |
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, setAutomaticLocked, setID, setLockedState, setLockedStateAsString, setManualLocked |
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 |
Constructor Detail |
public OrganismAllelePair(OrganismChromosomePair anOrganismChromosomePair, OrganismAllele aFirstOrganismAllele, OrganismAllele aSecondOrganismAllele)
anOrganismChromosomePair
- OrganismChromosomePair - containing organism chromosome pair, may not be nullaFirstOrganismAllele
- OrganismAllele - a first organism allele, may not be nullaSecondOrganismAllele
- OrganismAllele - a second organism allele, may be nulljava.lang.IllegalArgumentException
- - input argument(s) illegalpublic OrganismAllelePair(OrganismChromosomePair anOrganismChromosomePair, java.lang.String anElementName, int anElementID, com.sun.xml.parser.Parser anXMLParser, ImportContext importContext)
anOrganismChromosomePair
- OrganismChromosomePair - the enclosing organism chromosome pair for this new organism allele pairanElementName
- String - the element nameanElementID
- int - the element idanXMLParser
- com.sun.xml.parser.Parser - the element parserimportContext
- ImportContext - import context for mapping ids from file to this worldjava.lang.IllegalArgumentException
- - input arguments illegalMethod Detail |
public void startElement(java.lang.String anElementName, org.xml.sax.AttributeList amap) throws org.xml.sax.SAXException
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.
startElement
in class org.xml.sax.HandlerBase
anElementName
- String - name of elementamap
- AttributeList - an attribute listpublic void characters(char[] ch, int start, int length) throws org.xml.sax.SAXException
characters
in class org.xml.sax.HandlerBase
ch
- char[] - charactersstart
- int - start of stringlength
- int - length of stringpublic void ignorableWhitespace(char[] ch, int start, int length) throws org.xml.sax.SAXException
ignorableWhitespace
in class org.xml.sax.HandlerBase
ch
- char[] - charactersstart
- int - start of stringlength
- int - length of stringpublic void endElement(java.lang.String anElementName) throws org.xml.sax.SAXException
endElement
in class org.xml.sax.HandlerBase
anElementName
- String - the element namepublic void delete()
When this method is called, a property change event is generated for the property named EngineProp.DELETED.
delete
in class EngineObject
public void delete(boolean notifyChange)
public java.lang.String toString()
toString
in class EngineObject
public OrganismChromosomePair getOrganismChromosomePair()
public Organism getOrganism()
public Species getSpecies()
public World getWorld()
getWorld
in class EngineObject
public OrganismAllele getFirstOrganismAllele()
public OrganismAllele getSecondOrganismAllele()
public void propertyChange(java.beans.PropertyChangeEvent event)
propertyChange
in interface java.beans.PropertyChangeListener
event
- PropertyChangeEvent - the property change eventpublic void writeToStream(java.io.PrintWriter stream) throws java.io.IOException
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.
writeToStream
in class EngineObject
stream
- PrintWriter - print streamjava.lang.IllegalArgumentException
- - input arguments illegaljava.io.IOException
- - an IO error occurred in java libraries
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