FeatureAminoAcidViewer.java

/* FeatureAminoAcidViewer.java
 *
 * created: Sat Dec 19 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureAminoAcidViewer.java,v 1.2 2008-11-12 16:49:58 tjc Exp $
 */

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.*;
import java.awt.event.*;

/**
 *  A component for viewing the amino acids of a protein feature.  Once
 *  created this component listens for FeatureChange events to keep the the
 *  sequence up to date.
 *
 *  @author Kim Rutherford
 *  @version $Id: FeatureAminoAcidViewer.java,v 1.2 2008-11-12 16:49:58 tjc Exp $
 **/

public class FeatureAminoAcidViewer
    implements EntryChangeListener, FeatureChangeListener {
  /**
   *  Create a new FeatureAminoAcidViewer component to display the amino acids
   *  of the given Feature.
   *  @param feature The feature to view.
   *  @param include_numbers If true then the amino acids will be numbered
   *    (every second line of the display will be numbers rather than
   *    sequence).
   **/
  public FeatureAminoAcidViewer (final Feature feature,
                                 final boolean include_numbers) {
    this.feature = feature;
    this.entry = feature.getEntry ();

    sequence_viewer =
      new SequenceViewer ("Feature base viewer for feature:" +
                          getFeature ().getIDString (), include_numbers);

    redisplay ();

    getFeature ().getEntry ().addEntryChangeListener (this);
    getFeature ().addFeatureChangeListener (this);

    sequence_viewer.addWindowListener (new WindowAdapter () {
      public void windowClosed (WindowEvent event) {
        stopListening ();
      }
    });
  }

  /**
   *  Remove this object as a entry and feature change listener.
   **/
  private void stopListening () {
    getEntry ().removeEntryChangeListener (this);
    getFeature ().removeFeatureChangeListener (this);
  }

  /**
   *  Implementation of the EntryChangeListener interface.  We listen to
   *  EntryChange events so we can delete this component if the feature gets
   *  deleted.
   **/
  public void entryChanged (EntryChangeEvent event) {
    switch (event.getType ()) {
    case EntryChangeEvent.FEATURE_DELETED:
      if (event.getFeature () == getFeature ()) {
        stopListening ();
        sequence_viewer.dispose ();
      }
      break;
    default:
      // do nothing;
      break;
    }
  }
  /**
   *  Implementation of the FeatureChangeListener interface.  We need to
   *  listen to feature change events from the Features in this object so that
   *  we can keep the display up to date.
   *  @param event The change event.
   **/
  public void featureChanged (FeatureChangeEvent event) {
//       System.out.println ("FeatureViewer: feature change event type: " +
//                           event.getType ());

    // re-read the information from the feature
    redisplay ();
  }

  /**
   *  Redisplay the amino acids.
   **/
  private void redisplay () {
    String small_note = getFeature ().getNote ();

    if (small_note == null) {
      small_note = getFeature ().getIDString ();
    } else {
      if (small_note.length () > 50) {
        small_note = small_note.substring (0, 50);
      }
    }

    final String comment = ">" + small_note + "   - " +
      getFeature ().getFirstBase () + ": " +
      getFeature ().getLastBase () + "  MW: " +
      getFeature ().getMolecularWeight ();

    final String sequence =
      getFeature ().getTranslation ().toString ().toUpperCase ();

    sequence_viewer.setSequence (comment, sequence);
  }


  /**
   *  Return the feature this component is showing information about.
   **/
  private Feature getFeature () {
    return feature;
  }

  /**
   *  Return the Entry that contains the Feature this object is displaying.
   **/
  private Entry getEntry () {
    return entry;
  }

  /**
   *  The Feature that this component is showing information about.
   **/
  private Feature feature = null;

  /**
   *  The SequenceViewer object that is displaying the feature bases.
   **/
  private SequenceViewer sequence_viewer;

  /**
   *  The Entry that contains the Feature this object is displaying.
   **/
  private Entry entry;

}