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

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
                                |
                                +--uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput
All Implemented Interfaces:
AlignmentEventProvider, CinemaActionProvider

public class FileSequenceInput
extends AbstractSequenceInput

FileSequenceInput is a that module covers sequence input into Cinema via files. It extends the abstract sequence input module which provides the basics of any sequence input method into Cinema. It is currently Cinema only the abstract sequence input module extends the Cinema GUI module. Created: Thu Jun 15 15:07:12 2000

Version:
$Id: FileSequenceInput.java,v 1.15 2002/04/20 14:58:56 lord Exp $
Author:
Julian Selley

Field Summary
 
Fields inherited from class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
eh
 
Constructor Summary
FileSequenceInput()
           
 
Method Summary
 String getVersion()
          Returns the version of this module.
 SequenceAlignment openAlignment()
          Obtains the sequence alignment by the relevent method.
 SequenceAlignment openFile(File file, AlignmentInputParser parser, Identifier ident)
          Opens a file using a parser.
 void start()
          The method called externally to initiate the modules function.
 
Methods inherited from class uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
getActions, getAvailableParsers, getExceptionHandler, getParser, getParserDescription, getRequiredIdentifiers, load, setExceptionHandler
 
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, hasListeners, isDestroyed, isStarted, removePropertyChangeListener, removePropertyChangeListener, runStart, setContext
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

FileSequenceInput

public FileSequenceInput()
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

openFile

public SequenceAlignment openFile(File file,
                                  AlignmentInputParser parser,
                                  Identifier ident)
                           throws IOException
Opens a file using a parser. This method was generated to allow file parsing without the need for the open dialog - i.e., it will make the passing of arguments to Cinema of the file name a lot easier, or even possible.

Parameters:
file - the file
parser - the input parser
ident - the identifier for the alignment
Returns:
the sequence alignment
IOException

openAlignment

public SequenceAlignment openAlignment()
Description copied from class: AbstractSequenceInput
Obtains the sequence alignment by the relevent method.

Specified by:
openAlignment in class AbstractSequenceInput
Returns:
the sequence alignment

getVersion

public String getVersion()
Description copied from class: Module
Returns the version of this module.

Specified by:
getVersion in class Module
Returns:
the version