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org.biomage.Common
Class Extendable  view Extendable download Extendable.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
All Implemented Interfaces:
org.biomage.Interface.HasPropertySets, java.io.Serializable
Direct Known Subclasses:
Describable

public abstract class Extendable
extends java.lang.Object
implements java.io.Serializable, org.biomage.Interface.HasPropertySets

Abstract class that specifies for subclasses an association to NameValueTypes. These can be used, for instance, to specify proprietary properties and in-house processing hints.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasPropertySets.PropertySets_list propertySets
          Allows specification of name/value pairs.
 
Constructor Summary
Extendable()
          Default constructor.
Extendable(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToPropertySets(int position, NameValueType nameValueType)
          Method to add NameValueType at position to PropertySets_list
 void addToPropertySets(NameValueType nameValueType)
          Method to add NameValueType to PropertySets_list
 NameValueType getFromPropertySets(int position)
          Method to get NameValueType from PropertySets_list
 org.biomage.Interface.HasPropertySets.PropertySets_list getPropertySets()
          Get method for propertySets
 void removeElementAtFromPropertySets(int position)
          Method to remove by position from PropertySets_list
 void removeFromPropertySets(NameValueType nameValueType)
          Method to remove first NameValueType from PropertySets_list
 void setPropertySets(org.biomage.Interface.HasPropertySets.PropertySets_list propertySets)
          Set method for propertySets
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

propertySets

private org.biomage.Interface.HasPropertySets.PropertySets_list propertySets
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

Constructor Detail

Extendable

public Extendable()
Default constructor.


Extendable

public Extendable(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML

This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.


writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes

This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.


writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations

This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.


setPropertySets

public void setPropertySets(org.biomage.Interface.HasPropertySets.PropertySets_list propertySets)
Set method for propertySets

Specified by:
setPropertySets in interface org.biomage.Interface.HasPropertySets

getPropertySets

public org.biomage.Interface.HasPropertySets.PropertySets_list getPropertySets()
Get method for propertySets

Specified by:
getPropertySets in interface org.biomage.Interface.HasPropertySets

addToPropertySets

public void addToPropertySets(NameValueType nameValueType)
Method to add NameValueType to PropertySets_list

Specified by:
addToPropertySets in interface org.biomage.Interface.HasPropertySets

addToPropertySets

public void addToPropertySets(int position,
                              NameValueType nameValueType)
Method to add NameValueType at position to PropertySets_list

Specified by:
addToPropertySets in interface org.biomage.Interface.HasPropertySets

getFromPropertySets

public NameValueType getFromPropertySets(int position)
Method to get NameValueType from PropertySets_list

Specified by:
getFromPropertySets in interface org.biomage.Interface.HasPropertySets

removeElementAtFromPropertySets

public void removeElementAtFromPropertySets(int position)
Method to remove by position from PropertySets_list

Specified by:
removeElementAtFromPropertySets in interface org.biomage.Interface.HasPropertySets

removeFromPropertySets

public void removeFromPropertySets(NameValueType nameValueType)
Method to remove first NameValueType from PropertySets_list

Specified by:
removeFromPropertySets in interface org.biomage.Interface.HasPropertySets