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