uk.ac.man.bioinf.apps.cinema.io
Class AbstractSequenceOutput

java.lang.Object
  |
  +--uk.ac.man.bioinf.module.Module
        |
        +--uk.ac.man.bioinf.apps.xml.XMLModule
              |
              +--uk.ac.man.bioinf.apps.cinema.CinemaModule
                    |
                    +--uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
                          |
                          +--uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput
All Implemented Interfaces:
AlignmentEventProvider, CinemaActionProvider
Direct Known Subclasses:
FileSequenceOutput

public abstract class AbstractSequenceOutput
extends CinemaGuiModule
implements CinemaActionProvider

This class is abstract and will be extended by any sequence output modules. It merely provides the action stuff for the menu system, and describes an abstract method run by the actionPerformed(...) and implemented by the children of this class. Created: Mon Jul 31 22:22:33 2000

Version:
$Id: AbstractSequenceOutput.java,v 1.5 2001/07/06 11:48:08 lord Exp $
Author:
Julian Selley

Field Summary
protected  AbstractSequenceParserExceptionHandler eh
           
 
Constructor Summary
AbstractSequenceOutput()
           
 
Method Summary
 Action[] getActions()
           
 String[] getAvailableParsers()
           
 ParserExceptionHandler getExceptionHandler()
           
 AlignmentOutputParser getParser(String keyOfParser)
           
 String getParserDescription(String keyOfParser)
           
 ModuleIdentifierList getRequiredIdentifiers()
          Returns the module identifiers for the required modules.
 void load()
          The method called for the load of this module.
abstract  void saveAlignment(SequenceAlignment sa)
           
abstract  void saveAlignmentAs(SequenceAlignment sa)
           
 void setExceptionHandler(AbstractSequenceParserExceptionHandler exceptionHandler)
           
 
Methods inherited from class uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
destroy, getAlignmentFrame, getFrame, getJMenuBar, getRowHeaders, getRuler, getRulerPanel, getScrollPane, getStatusBar, getViewer, setFrameTitle
 
Methods inherited from class uk.ac.man.bioinf.apps.cinema.CinemaModule
addAlignmentListener, addCinemaPropertyChangeListener, addCinemaPropertyChangeListener, addVetoableAlignmentListener, clearSequenceTitleColor, fireCinemaPropertyChange, getAlignmentSelectionModel, getColorMap, getSequenceAlignment, removeAlignmentListener, removeCinemaPropertyChangeListener, removeCinemaPropertyChangeListener, removeVetoableAlignmentListener, sendStatusMessage, setAlignmentSelectionModel, setColorMap, setSequenceAlignment, setSequenceTitleColor
 
Methods inherited from class uk.ac.man.bioinf.apps.xml.XMLModule
getConfigProperties, getConfigTree
 
Methods inherited from class uk.ac.man.bioinf.module.Module
addPropertyChangeListener, addPropertyChangeListener, finalize, firePropertyChange, firePropertyChange, firePropertyChange, getContext, getIdentifier, getRequiredModule, getRequiredModules, getVersion, hasListeners, isDestroyed, isStarted, removePropertyChangeListener, removePropertyChangeListener, runStart, setContext, start
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

eh

protected AbstractSequenceParserExceptionHandler eh
Constructor Detail

AbstractSequenceOutput

public AbstractSequenceOutput()
Method Detail

getAvailableParsers

public final String[] getAvailableParsers()

getParser

public final AlignmentOutputParser getParser(String keyOfParser)

load

public void load()
          throws ModuleException
Description copied from class: Module
The method called for the load of this module.

Overrides:
load in class Module
ModuleException

getParserDescription

public final String getParserDescription(String keyOfParser)

getActions

public Action[] getActions()
Specified by:
getActions in interface CinemaActionProvider

saveAlignment

public abstract void saveAlignment(SequenceAlignment sa)

saveAlignmentAs

public abstract void saveAlignmentAs(SequenceAlignment sa)

setExceptionHandler

public void setExceptionHandler(AbstractSequenceParserExceptionHandler exceptionHandler)

getExceptionHandler

public ParserExceptionHandler getExceptionHandler()

getRequiredIdentifiers

public ModuleIdentifierList getRequiredIdentifiers()
Description copied from class: Module
Returns the module identifiers for the required modules. This places a call on getRequiredModules, which is delegated to the module context. It may require over-riding inorder to improve the efficiency of the method.

Overrides:
getRequiredIdentifiers in class CinemaGuiModule
Returns:
the required module identifiers