uk.ac.man.bioinf.apps.cinema.consensus
Class CinemaConsensus

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.consensus.CinemaConsensus

All Implemented Interfaces:

AlignmentEventProvider

public class CinemaConsensus

extends CinemaModule

Constructor Summary

CinemaConsensus()

Method Summary

Collection	getAllMetaData()
CinemaConsensusCalculatorMetaData	getDefaultMetaData()
CinemaConsensusCalculatorMetaData	getMetaData(ConsensusCalculator calc)
CinemaConsensusCalculatorMetaData	getMetaData(ConsensusSequence sequence)
CinemaConsensusCalculatorMetaData	getMetaData(String name)
ModuleIdentifierList	getRequiredIdentifiers() Returns the module identifiers for the required modules.
String	getVersion() Returns the version of this module.
void	start() The method called externally to initiate the modules function.

Methods inherited from class uk.ac.man.bioinf.apps.cinema.CinemaModule

addAlignmentListener, addCinemaPropertyChangeListener, addCinemaPropertyChangeListener, addVetoableAlignmentListener, clearSequenceTitleColor, destroy, 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, hasListeners, isDestroyed, isStarted, load, removePropertyChangeListener, removePropertyChangeListener, runStart, setContext

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CinemaConsensus

public CinemaConsensus()

Method Detail

start

public void start()

Description copied from class: Module

The method called externally to initiate the modules function.

Overrides:

start in class Module

getAllMetaData

public Collection getAllMetaData()

getDefaultMetaData

public CinemaConsensusCalculatorMetaData getDefaultMetaData()

getMetaData

public CinemaConsensusCalculatorMetaData getMetaData(ConsensusSequence sequence)

getMetaData

public CinemaConsensusCalculatorMetaData getMetaData(ConsensusCalculator calc)

getMetaData

public CinemaConsensusCalculatorMetaData getMetaData(String name)

getVersion

public String getVersion()

Description copied from class: Module

Returns the version of this module.

Specified by:

getVersion in class Module

Returns:

the version

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 CinemaModule

Returns:

the required module identifiers