uk.ac.man.bioinf.apps.cinema.io
Class FileSequenceInput
java.lang.Object
|
+--uk.ac.man.bioinf.module.Module
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+--uk.ac.man.bioinf.apps.xml.XMLModule
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+--uk.ac.man.bioinf.apps.cinema.CinemaModule
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+--uk.ac.man.bioinf.apps.cinema.CinemaGuiModule
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+--uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput
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+--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
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.module.Module |
addPropertyChangeListener, addPropertyChangeListener, finalize, firePropertyChange, firePropertyChange, firePropertyChange, getContext, getIdentifier, getRequiredModule, getRequiredModules, hasListeners, isDestroyed, isStarted, removePropertyChangeListener, removePropertyChangeListener, runStart, setContext |
FileSequenceInput
public FileSequenceInput()
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 fileparser
- the input parserident
- 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