FeatureEdit.java

/* FeatureEdit.java
 *
 * created: Tue Dec  1 1998
 *
 * This file is part of Artemis
 *
 * Copyright (C) 1998,1999,2000,2001,2002  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/FeatureEdit.java,v 1.70 2009-09-24 15:01:27 tjc Exp $
 **/

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.MarkerRange;

import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.GFFDocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.OutOfDateException;
import uk.ac.sanger.artemis.io.LocationParseException;
import uk.ac.sanger.artemis.io.PartialSequence;
import uk.ac.sanger.artemis.io.QualifierLazyLoading;
import uk.ac.sanger.artemis.io.QualifierParseException;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.KeyVector;
import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.StreamQualifier;
import uk.ac.sanger.artemis.io.QualifierInfo;
import uk.ac.sanger.artemis.io.ValidateFeature;

import uk.ac.sanger.artemis.components.ProgressThread;
import uk.ac.sanger.artemis.components.genebuilder.BasicGeneBuilderFrame;
import uk.ac.sanger.artemis.components.genebuilder.GeneBuilderFrame;
import uk.ac.sanger.artemis.components.genebuilder.GeneEditorPanel;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.components.genebuilder.ProteinMapPanel;
import uk.ac.sanger.artemis.components.genebuilder.ReferencesPanel;
import uk.ac.sanger.artemis.components.genebuilder.cv.CVPanel;
import uk.ac.sanger.artemis.components.genebuilder.gff.PropertiesPanel;
import uk.ac.sanger.artemis.components.genebuilder.ortholog.MatchPanel;

import java.awt.*;
import java.awt.event.*;
import java.io.*;
import java.util.Date;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Set;
import java.util.Vector;
import java.util.Collections;
import java.util.Comparator;

import javax.swing.*;


/**
 *  FeatureEdit class
 *
 *  @author Kim Rutherford
 *  @version $Id: FeatureEdit.java,v 1.70 2009-09-24 15:01:27 tjc Exp $
 **/
public class FeatureEdit extends JPanel
                         implements EntryChangeListener, FeatureChangeListener 
{

  /**
   * 
   */
  private static final long serialVersionUID = 1L;


  /** The choice of feature keys - created in createComponents(). */
  private KeyChoice key_choice;

  /** The choice of qualifiers - created in createComponents(). */
  private QualifierChoice qualifier_choice = null;

  private final static int LOCATION_TEXT_WIDTH = 80;

  /** The location text - set by updateLocation(). */
  private JTextField location_text = new JTextField(LOCATION_TEXT_WIDTH);

  /** When pressed - apply changes and dispose of the component. */
  private JButton ok_button = new JButton("OK");

  /** When pressed - discard changes and dispose of the component. */
  private JButton cancel_button = new JButton("Cancel");

  /** When pressed - apply changes and keep the component open. */
  private JButton apply_button = new JButton("Apply");

  /** Edit area for qualifiers - created by createComponents(). */
  private QualifierTextArea qualifier_text_area;

  /** The Feature this object is displaying. */
  private Feature edit_feature;

  /**
   *  The GotoEventSource that was passed to the constructor - used for the
   *  "Goto Feature" button.
   **/
  private GotoEventSource goto_event_source;

  /** Entry containing the Feature this object is displaying. */
  private Entry edit_entry;

  /** EntryGroup that contains this Feature (passed to the constructor). */
  private EntryGroup entry_group;

  /**
   *  The datestamp of the RWCorbaFeature when updateFromFeature() was last
   *  called or null if this is not a RWCorbaFeature.
   **/
  private Date datestamp = null;

  /** The Selection that was passed to the constructor. */
  private Selection selection;

  /**
   *  The contents of the QualifierTextArea before the user edits anything.
   *  This is used to work out if anything has changed since the creation of
   *  the FeatureEdit.
   **/
  final String orig_qualifier_text;

  private JFrame frame;
  
  /** controlled vocabulary tab */
  private CVPanel cvForm;
  
  /** GFF tab */
  private PropertiesPanel propertiesPanel;
  
  /** similarity/ortholog/paralog tab */
  private MatchPanel matchForm;
  
  private ReferencesPanel refPanel;
  
  private EntryInformation entry_information;
  
  private static boolean isTabbedView = false;
  
  private GeneEditorPanel editorPanel;
  
  private static UserDefinedQualifier userDefinedQualifierFrame;
  
  /**
   *  Create a new FeatureEdit object from the given Feature.
   *  @param entry_group The EntryGroup that contains this Feature.
   *  @param selection The Selection operate on.  The operations are "Remove
   *    Range" and "Grab Range"
   *  @param goto_event_source The object the we will call gotoBase() on.
   **/
  public FeatureEdit(final Feature edit_feature,
                     final EntryGroup entry_group,
                     final Selection selection,
                     final GotoEventSource goto_event_source,
                     final JFrame frame) 
  {
    this(edit_feature, entry_group, selection, 
         goto_event_source, frame, 
         edit_feature.getEntry().getEntryInformation());
  }
  
  public FeatureEdit(final Feature edit_feature,
      final EntryGroup entry_group,
      final Selection selection,
      final GotoEventSource goto_event_source,
      final JFrame frame, final EntryInformation entry_information) 
  {
    this.entry_information = entry_information;
    this.frame = frame;
    this.edit_feature = edit_feature;
    this.edit_entry   = edit_feature.getEntry();
    this.entry_group  = entry_group;
    this.selection    = selection;
    this.goto_event_source = goto_event_source;

    setLayout(new BorderLayout());
    createComponents();
    updateFromFeature();

    orig_qualifier_text = qualifier_text_area.getText();
  
    if(edit_feature.getEntry() != null)
    {
      edit_feature.getEntry().addEntryChangeListener(this);
      edit_feature.addFeatureChangeListener(this);

      frame.addWindowListener(new WindowAdapter()
      {
        public void windowClosing(WindowEvent event)
        {
          stopListening();
          frame.dispose();
          if(userDefinedQualifierFrame != null)
            userDefinedQualifierFrame.setVisible(false);
        }
      });
    }
    
    qualifier_text_area.requestFocus();
  }
  
  private boolean isPartialSequence()
  {
    return entry_group.getSequenceEntry().getBases().getSequence() instanceof PartialSequence;
  }
  
  /**
   * Set the feature to edit
   * @param edit_feature
   * @param isSet
   */
  public void setActiveFeature(final Feature edit_feature,
                               final boolean isSet)
  {
    if(!isPartialSequence() && isSet)
      setFeature();
    this.edit_feature = edit_feature;
    this.edit_entry   = edit_feature.getEntry();
    
    if(edit_feature.getEntry() != null)
    {
      edit_feature.getEntry().addEntryChangeListener(this);
      edit_feature.addFeatureChangeListener(this);
    }
    updateFromFeature();
  }

  /**
   *  Remove this object as a feature and entry change listener.
   **/
  public void stopListening() 
  {
    getEntry().removeEntryChangeListener(this);
    getFeature().removeFeatureChangeListener(this);
    if(cvForm != null)
      getFeature().removeFeatureChangeListener(cvForm);
    if(propertiesPanel != null)
      getFeature().removeFeatureChangeListener(propertiesPanel);
    if(matchForm != null)
      getFeature().removeFeatureChangeListener(matchForm);
  }

  /**
   *  Implementation of the EntryChangeListener interface.  We listen to
   *  EntryChange events so we can notify the user if of this component if the
   *  feature gets deleted.
   **/
  public void entryChanged(EntryChangeEvent event) 
  {
    switch(event.getType())
    {
      case EntryChangeEvent.FEATURE_DELETED:
        if(event.getFeature() == edit_feature) 
        {
          stopListening();
          frame.dispose();
        }
        break;
      default:
        // do nothing;
        break;
    }
  }

  /**
   *  Add an ActionListener to the Cancel JButton of this FeatureEdit.
   **/
  public void addCancelActionListener(final ActionListener l) 
  {
    cancel_button.addActionListener(l);
  }

  /**
   *  Remove an ActionListener from the Cancel JButton of this FeatureEdit.
   **/
  public void removeCancelActionListener(final ActionListener l) 
  {
    cancel_button.removeActionListener(l);
  }

  /**
   *  Add an ActionListener to the Apply JButton of this FeatureEdit.
   **/
  public void addApplyActionListener(final ActionListener l) 
  {
    apply_button.addActionListener(l);
  }

  /**
   *  Remove an ActionListener from the Apply JButton of this FeatureEdit.
   **/
  public void removeApplyActionListener(final ActionListener l) 
  {
    apply_button.removeActionListener(l);
  }

  /**
   *  Implementation of the FeatureChangeListener interface.  We need to
   *  listen to feature change events from the Features in this object so that
   *  we can update the display.
   *  @param event The change event.
   **/
  public void featureChanged(FeatureChangeEvent event) 
  {
    getFeature().resetColour();
    // re-read the information from the feature
    switch(event.getType()) 
    {
      case FeatureChangeEvent.LOCATION_CHANGED:
        updateLocation();
        break;
      case FeatureChangeEvent.SEGMENT_CHANGED:
        updateLocation();
        break;
      case FeatureChangeEvent.KEY_CHANGED:
        updateKey();
        break;
      case FeatureChangeEvent.QUALIFIER_CHANGED:
        if(qualifier_text_area.getText().equals(orig_qualifier_text)) 
          updateFromFeature();
        else
        {
          if(!event.getFeature().getIDString().equals(getFeature().getIDString()))
            break;
          
          final String message =
            "warning: the qualifiers have changed outside the editor - " +
            "view now?";

          final YesNoDialog yes_no_dialog =
            new YesNoDialog(frame, message);

          if(yes_no_dialog.getResult()) 
            new FeatureViewer(getFeature());
        }
        break;
      default:
        updateFromFeature();
        break;
    }
  }


  /**
   *  Create all the components for this FeatureEdit component.
   **/
  private void createComponents()
  {
    qualifier_text_area = new QualifierTextArea();
    //qualifier_text_area.setWrapStyleWord(true);

    FlowLayout flowLayoutZeroHVgap = new FlowLayout(FlowLayout.LEADING, 0, 0);

    key_choice =
      new KeyChoice(getEntryInformation(),getFeature().getKey());
    key_choice.setLayout(flowLayoutZeroHVgap);
    final JPanel key_and_qualifier_panel = new JPanel();
    location_text.setBackground(Color.white);

    final JPanel key_panel = new JPanel(flowLayoutZeroHVgap);
    final JLabel locLabel = new JLabel("Location: ");
    final JLabel keyLabel = new JLabel("Key: ");
    keyLabel.setHorizontalAlignment(SwingConstants.RIGHT);
    keyLabel.setPreferredSize(locLabel.getPreferredSize());
    
    key_panel.add(keyLabel);
    key_panel.add(key_choice);

    key_and_qualifier_panel.setLayout(new BorderLayout());
    key_and_qualifier_panel.add(key_panel, "West");

    boolean isGFF = false;
    if(edit_feature.getEmblFeature().getEntry() instanceof GFFDocumentEntry)
      isGFF = true;
    
    qualifier_choice = new QualifierChoice(getEntryInformation(),
                                  key_choice.getSelectedItem(),null,
                                  isGFF);
    
    final JPanel qualifier_panel = new JPanel(new FlowLayout(FlowLayout.TRAILING,0,0));
    final JButton qualifier_add_button = new JButton("Add Qualifier:");

    qualifier_panel.add(qualifier_add_button);
    qualifier_panel.add(qualifier_choice);

    key_and_qualifier_panel.add(qualifier_panel, "East");

    key_choice.addItemListener(new ItemListener() 
    {
      public void itemStateChanged(ItemEvent _) 
      {
        qualifier_choice.setKey(key_choice.getSelectedItem());
      }
    });

    qualifier_add_button.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent e)
      {
        final String qualifier_name =
          (String)qualifier_choice.getSelectedItem();

        QualifierInfo qualifier_info =
          getEntryInformation().getQualifierInfo(qualifier_name);

        if(qualifier_info == null) 
          qualifier_info = new QualifierInfo(qualifier_name,
                              QualifierInfo.OPTIONAL_QUOTED_TEXT,
                              null, null, false);

        qualifier_text_area.append("/" + qualifier_name);

        switch(qualifier_info.getType()) 
        {
          case QualifierInfo.QUOTED_TEXT:
            if(qualifier_name.equals("GO")) 
            {
              // special case for /GO
              final java.util.Calendar calendar =
                      java.util.Calendar.getInstance();
                
              final Date current_time = calendar.getTime();
            
              final java.text.SimpleDateFormat date_format =
                  new java.text.SimpleDateFormat("yyyyMMdd");
            
              final StringBuffer result_buffer = new StringBuffer();
            
              date_format.format(current_time, result_buffer,
                                 new java.text.FieldPosition(java.text.DateFormat.DATE_FIELD));
            
              final String go_string = "aspect=; term=; GOid=GO:; "+
                                       "evidence=ISS; db_xref=GO_REF:0000001; " +
                                       "with=UniProtKB:; date=" + result_buffer;
              qualifier_text_area.append("=\"" + go_string + "\"");
            } 
            else if(qualifier_name.equals("controlled_curation"))
            {
              final java.util.Calendar calendar =
                      java.util.Calendar.getInstance();

              final Date current_time = calendar.getTime();

              final java.text.SimpleDateFormat date_format =
                  new java.text.SimpleDateFormat("yyyyMMdd");

              final StringBuffer result_buffer = new StringBuffer();

              date_format.format(current_time, result_buffer,
                                 new java.text.FieldPosition(java.text.DateFormat.DATE_FIELD));

              final String cc_string = "term=; db_xref=; date="+ result_buffer;
              qualifier_text_area.append("=\"" + cc_string + "\"");
            }
            else 
              qualifier_text_area.append ("=\"\"");
            break;

          case QualifierInfo.NO_VALUE:
          case QualifierInfo.OPTIONAL_QUOTED_TEXT:
            break;

          default:
            qualifier_text_area.append("=");
        }

        qualifier_text_area.append("\n");
      }
    });

    final JPanel middle_panel = new JPanel();
    middle_panel.setLayout(new BorderLayout(0,0));

    final JPanel lower_panel = new JPanel();
    lower_panel.setLayout(new BorderLayout(0,0));

    //final JPanel outer_location_button_panel = new JPanel(flowLayoutZeroHgap);
    //outer_location_button_panel.setLayout(new BorderLayout(0,0));

    final JToolBar location_button_panel = new JToolBar();
    location_button_panel.setRollover(true);
    //outer_location_button_panel.add(location_button_panel, "West");
    lower_panel.add(location_button_panel, "North");
    
    final JPanel location_panel = new JPanel(new BorderLayout(0,0));
    location_panel.add(locLabel, "West");
    location_panel.add(location_text, "Center");

    final JButton complement_button = new JButton("Complement");
    complement_button.setToolTipText("Complement position");
    location_button_panel.add(complement_button);
    complement_button.addActionListener(new ActionListener () 
    {
      public void actionPerformed(ActionEvent e) 
      {
        complementLocation();
      }
    });
    
    if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
    {
      final JButton refresh_button = new JButton("Refresh");
      location_button_panel.add(refresh_button);
      refresh_button.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          refresh();
        }
      });
    }

    final JButton grab_button = new JButton("Grab Range");
    grab_button.setToolTipText("Add selected base range from feature coordinates");
    location_button_panel.add(grab_button);
    grab_button.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        grabSelectedRange();
      }
    });

    final JButton remove_button = new JButton("Remove Range");
    remove_button.setToolTipText("Remove selected base range from feature coordinates");
    location_button_panel.add(remove_button);
    remove_button.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent e)
      {
        removeSelectedRange();
      }
    });

    final JButton goto_button = new JButton("Goto Feature");
    goto_button.setToolTipText("Goto and select this feature");
    location_button_panel.add(goto_button);
    goto_button.addActionListener(new ActionListener() 
    {
      public void actionPerformed(ActionEvent e)
      {
        goto_event_source.gotoBase(getFeature().getFirstBaseMarker());
        getSelection().set(getFeature());
      }
    });

/*    final JButton select_button = new JButton("Select Feature");
    location_button_panel.add(select_button);
    select_button.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e) 
      {
        getSelection().set(getFeature());
      }
    });*/

    if(Options.getOptions().getPropertyTruthValue("sanger_options"))
    {
      // a PSU only hack 
      final JButton tidy_button = new JButton("Tidy");
      location_button_panel.add(tidy_button);
      tidy_button.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e) 
        {
          try 
          {
            tidy();
            tidyGO();
          } 
          catch(QualifierParseException exception) 
          {
            new MessageDialog(frame,
                 "Cannot tidy - qualifier error: " +
                  exception.getMessage());
          }
        }
      });
    }
    
    final JButton transferAnnotationBbutton = new JButton("TAT");
    location_button_panel.add(transferAnnotationBbutton);
    transferAnnotationBbutton.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e) 
      {
      	new TransferAnnotationTool(getFeature(), entry_group, matchForm);
      }
    });


    if(Options.isUnixHost())
    {
      JButton oo_edit_button = new JButton("ObjectEdit");
      location_button_panel.add(oo_edit_button);
      final uk.ac.sanger.artemis.editor.BigPane bp =
                   new uk.ac.sanger.artemis.editor.BigPane(getEntryInformation());

      oo_edit_button.addActionListener(new ActionListener ()
      {
        public void actionPerformed(ActionEvent e)
        {
          String qualifier_txt = qualifier_text_area.getText();
        
          File base_dir = getBaseDirectoryFromEntry(edit_entry);
          String baseDirStr = "";

          if(base_dir != null)
            baseDirStr = base_dir.getAbsolutePath() + 
                              System.getProperty("file.separator");

          StringReader strRead = new StringReader(qualifier_txt);
          BufferedReader buff = new BufferedReader(strRead);
          String line;
          final Hashtable<String, Vector<String>> dataFile = new Hashtable<String, Vector<String>>();
          try
          {
            int ind;
            while((line = buff.readLine()) != null)
            {
              if(line.startsWith("/fasta_file="))
              {
                if((ind = line.indexOf(':'))>-1)
                  line = baseDirStr+line.substring(ind+1);
                else
                  line = baseDirStr+line.substring(13);
                
                ind = line.lastIndexOf("\"");
                if(ind > -1)
                  line = line.substring(0, ind);
                
                Vector<String> v;
                if(dataFile.containsKey("fasta"))
                  v = dataFile.get("fasta");
                else
                  v = new Vector<String>();
                v.add(line);
                dataFile.put("fasta",v);
              }
              else if(line.startsWith("/blastp_file="))
              {
                if((ind = line.indexOf(':'))>-1)
                  line = baseDirStr+line.substring(ind+1);
                else
                  line = baseDirStr+line.substring(14);
                
                ind = line.lastIndexOf("\"");
                if(ind > -1)
                  line = line.substring(0, ind);
                
                Vector<String> v;
                if(dataFile.containsKey("blastp"))
                  v = dataFile.get("blastp");
                else
                  v = new Vector<String>();
                v.add(line);
                dataFile.put("blastp",v);
              }
              else if(line.startsWith("/blastp+go_file="))
              {
                if((ind = line.indexOf(':'))>-1)
                  line = line.substring(ind+1);
                else
                  line = baseDirStr+line.substring(17);
                ind = line.lastIndexOf("\"");
                if(ind > -1)
                  line = line.substring(0, ind);
                
                Vector<String> v;
                if(dataFile.containsKey("blastp+go"))
                  v = dataFile.get("blastp+go");
                else
                  v = new Vector<String>();
                v.add(line);
                dataFile.put("blastp+go",v);
              }   
            }
          }
          catch(IOException ioe){}
 
          FeatureEdit.this.setCursor(new Cursor(Cursor.WAIT_CURSOR)); 
          final ProgressThread progress = new ProgressThread(null,
                                        "Loading Data....");
          progress.start();
          SwingWorker ooEd = new SwingWorker()
          {
            public Object construct()
            {
              // find overlaping features
              final Location this_loc = edit_feature.getLocation();
              final int this_start = this_loc.getFirstBase();
              final int this_end   = this_loc.getLastBase();

              FeaturePredicate predicate = new FeaturePredicate()
              {
                public boolean testPredicate (final Feature feature) 
                {
                  final Location loc = feature.getLocation();

                  final int start = loc.getFirstBase();
                  final int end   = loc.getLastBase();

                  if((start > this_start &&
                      start < this_end) ||
                     (end > this_start &&
                      end < this_end))
                  {
                    final String note = feature.getNote();
                    if(note != null &&
                       note.indexOf("Pfam")>-1)
                      return true;
                  }
                  
                  return false;
                }
              };

              final FeatureVector overlapFeatures = new FeatureVector();
              final FeatureEnumeration featureEnum = entry_group.features();
              while(featureEnum.hasMoreFeatures()) 
              {
                Feature this_feature = featureEnum.nextFeature();
                if(predicate.testPredicate(this_feature))
                  overlapFeatures.add(this_feature);
              }

              // show object editor
              try
              {
                if(dataFile.size() > 0)
                  bp.set(dataFile, qualifier_text_area, overlapFeatures,
                         edit_feature, matchForm, cvForm);
                else
                  JOptionPane.showMessageDialog(null,"No results files.",
                      "Warning",
                      JOptionPane.WARNING_MESSAGE); 
              }
              catch(ArrayIndexOutOfBoundsException e)
              {
                JOptionPane.showMessageDialog(null,"No results files.",
                        "Warning",
                        JOptionPane.WARNING_MESSAGE);
              }

              progress.finished();
              FeatureEdit.this.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
              return null;
            }
          };
          ooEd.start();   
        }
      });
    }

    final JButton userQualifiers = new JButton("User Qualifiers");
    userQualifiers.setToolTipText("User defined qualifier selection");
    location_button_panel.add(userQualifiers);
    userQualifiers.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e) 
      {
        if(userDefinedQualifierFrame == null) 
        {
          userDefinedQualifierFrame = new UserDefinedQualifier();
          userDefinedQualifierFrame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
        }

        userDefinedQualifierFrame.pack();
        final JFrame topFrame = 
              (JFrame) SwingUtilities.getWindowAncestor(FeatureEdit.this);
        Point p = topFrame.getLocationOnScreen();
        p.x -= userDefinedQualifierFrame.getWidth();
        if(p.x < 10)
          p.x = 10;
        userDefinedQualifierFrame.setLocation(p);

        userDefinedQualifierFrame.setQualifierTextArea(qualifier_text_area);
        userDefinedQualifierFrame.setVisible(true);
      }
    });
    
    middle_panel.add(location_panel, "North");
    add(key_and_qualifier_panel, "North");

    cancel_button.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e) 
      {
        if(edit_feature.getEntry() != null)
          stopListening();
        frame.dispose();
        if(userDefinedQualifierFrame != null)
          userDefinedQualifierFrame.setVisible(false);
      }
    });

    if(!getFeature().isReadOnly())
    {
      ok_button.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          if(setFeature()) 
          {
            stopListening();
            
            if(propertiesPanel != null)
              propertiesPanel.updateSettings();
            
            frame.dispose();
            if(userDefinedQualifierFrame != null)
              userDefinedQualifierFrame.setVisible(false);
          }
        }
      });

      apply_button.addActionListener(new ActionListener() 
      {
        public void actionPerformed(ActionEvent e) 
        {
          setFeature();
        }
      });
    }

    final FlowLayout flow_layout =
                 new FlowLayout(FlowLayout.CENTER, 18, 1);

    final JPanel ok_cancel_update_panel = new JPanel(flow_layout);
    Box fillerBox = Box.createHorizontalBox();
    if(GeneUtils.isDatabaseEntry(getFeature().getEmblFeature()))
    {
      cvForm = new CVPanel(getFeature());
      cvForm.setBackground(Color.WHITE);

      matchForm = new MatchPanel(getFeature(), 
          (DocumentEntry)getFeature().getEmblFeature().getEntry());
      matchForm.setBackground(Color.WHITE);
      
      propertiesPanel = new PropertiesPanel(getFeature());
      propertiesPanel.setBackground(Color.WHITE);

      refPanel = new ReferencesPanel(getFeature());
      refPanel.setBackground(Color.WHITE);
      
      addGffAnnotationView(lower_panel);
      
      final JCheckBox tabbedView = new JCheckBox("Tab View", isTabbedView);
      tabbedView.addItemListener(new ItemListener()
      {
        public void itemStateChanged(ItemEvent e)
        {
          isTabbedView = tabbedView.isSelected();
          addGffAnnotationView(lower_panel);
          lower_panel.revalidate();
          lower_panel.repaint();
        }
      });


      final JCheckBox oneView = new JCheckBox("Overview", false);
      oneView.addItemListener(new ItemListener()
      {
        public void itemStateChanged(ItemEvent e)
        {
          if(setFeature()) 
          {
            stopListening();
            
            if(propertiesPanel != null)
              propertiesPanel.updateSettings();
            
            frame.dispose();
            System.setProperty("basic", "true");
            new BasicGeneBuilderFrame(getFeature(), entry_group,
                selection, null);
          }
        }
      });

      if(((GFFStreamFeature)getFeature().getEmblFeature()).getChadoGene() != null)
        ok_cancel_update_panel.add(oneView);
      ok_cancel_update_panel.add(tabbedView);
      fillerBox.add(Box.createHorizontalStrut( 
          tabbedView.getPreferredSize().width ));
    }
    else
      lower_panel.add(new JScrollPane(qualifier_text_area), "Center");
    
    if(!getFeature().isReadOnly()) 
      ok_cancel_update_panel.add(ok_button);

    ok_cancel_update_panel.add(cancel_button);

    if(!getFeature().isReadOnly()) 
      ok_cancel_update_panel.add(apply_button);
    ok_cancel_update_panel.add(fillerBox);
    
    add(ok_cancel_update_panel, "South");
    
    middle_panel.add(lower_panel, "Center");

    add(middle_panel, "Center");
  }

  /**
   * Refresh the annotation for the active feature
   */
  private void refresh()
  {
    // refresh from the database
    final DatabaseDocument originalDocument =
      (DatabaseDocument)((DocumentEntry)edit_feature.getEmblFeature().getEntry()).getDocument();

    final Set<String> uniquenames = ((GFFStreamFeature)edit_feature.getEmblFeature()).getSegmentRangeStore().keySet();
    final Iterator<String> it = uniquenames.iterator();
    final String uniquename = it.next();
    final DatabaseDocument newDocument = new DatabaseDocument(originalDocument,
        uniquename, null, true, null);
    newDocument.setLazyFeatureLoad(false);
    newDocument.setReadChildren(false);
    
    try
    {
      DatabaseDocumentEntry dbentry = new DatabaseDocumentEntry(newDocument, null);
      uk.ac.sanger.artemis.io.Feature databaseFeature = dbentry.getAllFeatures().featureAt(0);
      
      // compare timelastmodified
      Qualifier qualifier = edit_feature.getQualifierByName("timelastmodified");
      String active_timelastmodified = (String)qualifier.getValues().get(0);
      qualifier = databaseFeature.getQualifierByName("timelastmodified");
      String database_timelastmodified = (String)qualifier.getValues().get(0);
      
      if(active_timelastmodified.equals(database_timelastmodified))
      {
        JOptionPane.showMessageDialog(this, 
            "No new changes found for the feature\n"+
            uniquename+"\n"+
            "in the database since:\n"+database_timelastmodified, 
            "No Updates", JOptionPane.INFORMATION_MESSAGE);
        return;
      }
      else
      {
        JOptionPane.showMessageDialog(this, 
            "Changes found for the feature\n"+
            uniquename+"\n"+
            "in the database at:\n"+database_timelastmodified, 
            "Changes Found", JOptionPane.INFORMATION_MESSAGE);
      }
      
      final QualifierVector db_qv = databaseFeature.getQualifiers();
      final QualifierVector qv = edit_feature.getQualifiers();
      final QualifierVector new_qv = new QualifierVector();
      
      for(int i=0; i<qv.size(); i++)
      {
        Qualifier q = (Qualifier)qv.get(i);
        if(q.getName().equals("Parent") ||
           q.getName().equals("Derives_from") ||
           q.getName().equals("ID")  )
          new_qv.addQualifierValues(q);
      }
      
      
      for(int i=0; i<db_qv.size(); i++)
      {
        Qualifier q = (Qualifier)db_qv.get(i);
        if(q.getName().equals("Parent") ||
           q.getName().equals("Derives_from") ||
           q.getName().equals("ID")  )
          continue;
        new_qv.add(q);