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

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.AbstractSequenceInput

All Implemented Interfaces:

AlignmentEventProvider, CinemaActionProvider

Direct Known Subclasses:

FileSequenceInput

public abstract class AbstractSequenceInput

extends CinemaGuiModule

implements CinemaActionProvider

This class is abstract and will be extended by any sequence input 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: Wed Jun 14 15:26:56 2000

Version:

$Id: AbstractSequenceInput.java,v 1.13 2002/04/20 14:59:05 lord Exp $

Author:

Julian Selley

Field Summary

protected AbstractSequenceParserExceptionHandler

eh

Constructor Summary

AbstractSequenceInput()

Method Summary

Action[]	getActions() Supplies the action for the menu system/whatever else wishes to invoke this modules action.
String[]	getAvailableParsers()
ParserExceptionHandler	getExceptionHandler() Returns the parser exception handler.
AlignmentInputParser	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 SequenceAlignment	openAlignment() Obtains the sequence alignment by the relevent method.
void	setExceptionHandler(AbstractSequenceParserExceptionHandler exceptionHandler) Sets the parser exception handler.

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

AbstractSequenceInput

public AbstractSequenceInput()

Method Detail

getAvailableParsers

public final String[] getAvailableParsers()

getParser

public final AlignmentInputParser getParser(String keyOfParser)

getParserDescription

public final String getParserDescription(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

getActions

public Action[] getActions()

Supplies the action for the menu system/whatever else wishes to invoke this modules action.

Specified by:

getActions in interface CinemaActionProvider

Returns:

the possible actions

openAlignment

public abstract SequenceAlignment openAlignment()

Obtains the sequence alignment by the relevent method.

Returns:

the sequence alignment

setExceptionHandler

public void setExceptionHandler(AbstractSequenceParserExceptionHandler exceptionHandler)

Sets the parser exception handler.

getExceptionHandler

public ParserExceptionHandler getExceptionHandler()

Returns the parser exception handler.

Returns:

the exception handler

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