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  1. Project Clover database Wed Nov 13 2024 16:21:17 GMT
  2. Package jalview.gui

File FeatureEditor.java

 

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../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

50
224
25
1
732
493
52
0.23
8.96
25
2.08

Classes

Class Line # Actions
FeatureEditor 66 224 52
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Dimension;
26    import java.awt.Font;
27    import java.awt.GridLayout;
28    import java.awt.event.ActionEvent;
29    import java.awt.event.ActionListener;
30    import java.awt.event.ItemEvent;
31    import java.awt.event.ItemListener;
32    import java.awt.event.MouseAdapter;
33    import java.awt.event.MouseEvent;
34    import java.util.ArrayList;
35    import java.util.List;
36   
37    import javax.swing.JComboBox;
38    import javax.swing.JLabel;
39    import javax.swing.JPanel;
40    import javax.swing.JScrollPane;
41    import javax.swing.JSpinner;
42    import javax.swing.JTextArea;
43    import javax.swing.JTextField;
44    import javax.swing.SpinnerNumberModel;
45    import javax.swing.SwingConstants;
46    import javax.swing.event.ChangeEvent;
47    import javax.swing.event.ChangeListener;
48    import javax.swing.event.DocumentEvent;
49    import javax.swing.event.DocumentListener;
50   
51    import jalview.api.FeatureColourI;
52    import jalview.datamodel.SearchResults;
53    import jalview.datamodel.SearchResultsI;
54    import jalview.datamodel.SequenceFeature;
55    import jalview.datamodel.SequenceI;
56    import jalview.gui.JalviewColourChooser.ColourChooserListener;
57    import jalview.io.FeaturesFile;
58    import jalview.schemes.FeatureColour;
59    import jalview.util.ColorUtils;
60    import jalview.util.MessageManager;
61   
62    /**
63    * Provides a dialog allowing the user to add new features, or amend or delete
64    * existing features
65    */
 
66    public class FeatureEditor
67    {
68    /*
69    * defaults for creating a new feature are the last created
70    * feature type and group
71    */
72    static String lastFeatureAdded = "feature_1";
73   
74    static String lastFeatureGroupAdded = "Jalview";
75   
76    /*
77    * the sequence(s) with features to be created / amended
78    */
79    final List<SequenceI> sequences;
80   
81    /*
82    * the features (or template features) to be created / amended
83    */
84    final List<SequenceFeature> features;
85   
86    /*
87    * true if the dialog is to create a new feature, false if
88    * for amend or delete of existing feature(s)
89    */
90    final boolean forCreate;
91   
92    /*
93    * index into the list of features
94    */
95    int featureIndex;
96   
97    FeatureColourI oldColour;
98   
99    FeatureColourI featureColour;
100   
101    FeatureRenderer fr;
102   
103    AlignmentPanel ap;
104   
105    JTextField name;
106   
107    JTextField group;
108   
109    JTextArea description;
110   
111    JSpinner start;
112   
113    JSpinner end;
114   
115    JPanel mainPanel;
116   
117    /**
118    * Constructor
119    *
120    * @param alignPanel
121    * @param seqs
122    * @param feats
123    * @param create
124    * if true create a new feature, else amend or delete an existing
125    * feature
126    */
 
127  0 toggle public FeatureEditor(AlignmentPanel alignPanel, List<SequenceI> seqs,
128    List<SequenceFeature> feats, boolean create)
129    {
130  0 ap = alignPanel;
131  0 fr = alignPanel.getSeqPanel().seqCanvas.fr;
132  0 sequences = seqs;
133  0 features = feats;
134  0 this.forCreate = create;
135   
136  0 init();
137    }
138   
139    /**
140    * Initialise the layout and controls
141    */
 
142  0 toggle protected void init()
143    {
144  0 featureIndex = 0;
145   
146  0 mainPanel = new JPanel(new BorderLayout());
147   
148  0 name = new JTextField(25);
149  0 name.getDocument().addDocumentListener(new DocumentListener()
150    {
 
151  0 toggle @Override
152    public void insertUpdate(DocumentEvent e)
153    {
154  0 warnIfTypeHidden(mainPanel, name.getText());
155    }
156   
 
157  0 toggle @Override
158    public void removeUpdate(DocumentEvent e)
159    {
160  0 warnIfTypeHidden(mainPanel, name.getText());
161    }
162   
 
163  0 toggle @Override
164    public void changedUpdate(DocumentEvent e)
165    {
166  0 warnIfTypeHidden(mainPanel, name.getText());
167    }
168    });
169   
170  0 group = new JTextField(25);
171  0 group.getDocument().addDocumentListener(new DocumentListener()
172    {
 
173  0 toggle @Override
174    public void insertUpdate(DocumentEvent e)
175    {
176  0 warnIfGroupHidden(mainPanel, group.getText());
177    }
178   
 
179  0 toggle @Override
180    public void removeUpdate(DocumentEvent e)
181    {
182  0 warnIfGroupHidden(mainPanel, group.getText());
183    }
184   
 
185  0 toggle @Override
186    public void changedUpdate(DocumentEvent e)
187    {
188  0 warnIfGroupHidden(mainPanel, group.getText());
189    }
190    });
191   
192  0 description = new JTextArea(3, 25);
193   
194  0 start = new JSpinner();
195  0 end = new JSpinner();
196  0 start.setPreferredSize(new Dimension(80, 20));
197  0 end.setPreferredSize(new Dimension(80, 20));
198   
199    /*
200    * ensure that start can never be more than end
201    */
202  0 start.addChangeListener(new ChangeListener()
203    {
 
204  0 toggle @Override
205    public void stateChanged(ChangeEvent e)
206    {
207  0 Integer startVal = (Integer) start.getValue();
208  0 ((SpinnerNumberModel) end.getModel()).setMinimum(startVal);
209    }
210    });
211  0 end.addChangeListener(new ChangeListener()
212    {
 
213  0 toggle @Override
214    public void stateChanged(ChangeEvent e)
215    {
216  0 Integer endVal = (Integer) end.getValue();
217  0 ((SpinnerNumberModel) start.getModel()).setMaximum(endVal);
218    }
219    });
220   
221  0 final JLabel colour = new JLabel();
222  0 colour.setOpaque(true);
223  0 colour.setMaximumSize(new Dimension(30, 16));
224  0 colour.addMouseListener(new MouseAdapter()
225    {
 
226  0 toggle @Override
227    public void mousePressed(MouseEvent evt)
228    {
229  0 if (featureColour.isSimpleColour())
230    {
231    /*
232    * open colour chooser on click in colour panel
233    */
234  0 String title = MessageManager
235    .getString("label.select_feature_colour");
236  0 ColourChooserListener listener = new ColourChooserListener()
237    {
 
238  0 toggle @Override
239    public void colourSelected(Color c)
240    {
241  0 featureColour = new FeatureColour(c);
242  0 updateColourButton(mainPanel, colour, featureColour);
243    };
244    };
245  0 JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
246    title, featureColour.getColour(), listener);
247    }
248    else
249    {
250    /*
251    * variable colour dialog - on OK, refetch the updated
252    * feature colour and update this display
253    */
254  0 final String ft = features.get(featureIndex).getType();
255  0 final String type = ft == null ? lastFeatureAdded : ft;
256  0 FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type, true);
257  0 fcc.setRequestFocusEnabled(true);
258  0 fcc.requestFocus();
259  0 fcc.addActionListener(new ActionListener()
260    {
 
261  0 toggle @Override
262    public void actionPerformed(ActionEvent e)
263    {
264  0 featureColour = fr.getFeatureStyle(ft);
265  0 fr.setColour(type, featureColour);
266  0 updateColourButton(mainPanel, colour, featureColour);
267    }
268    });
269    }
270    }
271    });
272  0 JPanel gridPanel = new JPanel(new GridLayout(3, 1));
273   
274  0 if (!forCreate && features.size() > 1)
275    {
276    /*
277    * more than one feature at selected position -
278    * add a drop-down to choose the feature to amend
279    * space pad text if necessary to make entries distinct
280    */
281  0 gridPanel = new JPanel(new GridLayout(4, 1));
282  0 JPanel choosePanel = new JPanel();
283  0 choosePanel.add(new JLabel(
284    MessageManager.getString("label.select_feature") + ":"));
285  0 final JComboBox<String> overlaps = new JComboBox<>();
286  0 List<String> added = new ArrayList<>();
287  0 for (SequenceFeature sf : features)
288    {
289  0 String text = String.format("%s/%d-%d (%s)", sf.getType(),
290    sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
291  0 while (added.contains(text))
292    {
293  0 text += " ";
294    }
295  0 overlaps.addItem(text);
296  0 added.add(text);
297    }
298  0 choosePanel.add(overlaps);
299   
300  0 overlaps.addItemListener(new ItemListener()
301    {
 
302  0 toggle @Override
303    public void itemStateChanged(ItemEvent e)
304    {
305  0 int index = overlaps.getSelectedIndex();
306  0 if (index != -1)
307    {
308  0 featureIndex = index;
309  0 SequenceFeature sf = features.get(index);
310  0 name.setText(sf.getType());
311  0 description.setText(sf.getDescription());
312  0 group.setText(sf.getFeatureGroup());
313  0 start.setValue(new Integer(sf.getBegin()));
314  0 end.setValue(new Integer(sf.getEnd()));
315  0 ((SpinnerNumberModel) start.getModel()).setMaximum(sf.getEnd());
316  0 ((SpinnerNumberModel) end.getModel()).setMinimum(sf.getBegin());
317   
318  0 SearchResultsI highlight = new SearchResults();
319  0 highlight.addResult(sequences.get(0), sf.getBegin(),
320    sf.getEnd());
321   
322  0 ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
323    }
324  0 FeatureColourI col = fr.getFeatureStyle(name.getText());
325  0 if (col == null)
326    {
327  0 col = new FeatureColour(
328    ColorUtils.createColourFromName(name.getText()));
329    }
330  0 oldColour = featureColour = col;
331  0 updateColourButton(mainPanel, colour, col);
332    }
333    });
334   
335  0 gridPanel.add(choosePanel);
336    }
337   
338  0 JPanel namePanel = new JPanel();
339  0 gridPanel.add(namePanel);
340  0 namePanel.add(new JLabel(MessageManager.getString("label.name:"),
341    JLabel.RIGHT));
342  0 namePanel.add(name);
343   
344  0 JPanel groupPanel = new JPanel();
345  0 gridPanel.add(groupPanel);
346  0 groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
347    JLabel.RIGHT));
348  0 groupPanel.add(group);
349   
350  0 JPanel colourPanel = new JPanel();
351  0 gridPanel.add(colourPanel);
352  0 colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
353    JLabel.RIGHT));
354  0 colourPanel.add(colour);
355  0 colour.setPreferredSize(new Dimension(150, 15));
356  0 colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
357  0 colour.setForeground(Color.black);
358  0 colour.setHorizontalAlignment(SwingConstants.CENTER);
359  0 colour.setVerticalAlignment(SwingConstants.CENTER);
360  0 colour.setHorizontalTextPosition(SwingConstants.CENTER);
361  0 colour.setVerticalTextPosition(SwingConstants.CENTER);
362  0 mainPanel.add(gridPanel, BorderLayout.NORTH);
363   
364  0 JPanel descriptionPanel = new JPanel();
365  0 descriptionPanel.add(new JLabel(
366    MessageManager.getString("label.description:"), JLabel.RIGHT));
367  0 description.setFont(JvSwingUtils.getTextAreaFont());
368  0 description.setLineWrap(true);
369  0 descriptionPanel.add(new JScrollPane(description));
370   
371  0 if (!forCreate)
372    {
373  0 mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
374   
375  0 JPanel startEndPanel = new JPanel();
376  0 startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
377    JLabel.RIGHT));
378  0 startEndPanel.add(start);
379  0 startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
380    JLabel.RIGHT));
381  0 startEndPanel.add(end);
382  0 mainPanel.add(startEndPanel, BorderLayout.CENTER);
383    }
384    else
385    {
386  0 mainPanel.add(descriptionPanel, BorderLayout.CENTER);
387    }
388   
389    /*
390    * default feature type and group to that of the first feature supplied,
391    * or to the last feature created if not supplied (null value)
392    */
393  0 SequenceFeature firstFeature = features.get(0);
394  0 boolean useLastDefaults = firstFeature.getType() == null;
395  0 final String featureType = useLastDefaults ? lastFeatureAdded
396    : firstFeature.getType();
397  0 final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
398    : firstFeature.getFeatureGroup();
399  0 name.setText(featureType);
400  0 group.setText(featureGroup);
401   
402  0 start.setValue(new Integer(firstFeature.getBegin()));
403  0 end.setValue(new Integer(firstFeature.getEnd()));
404  0 ((SpinnerNumberModel) start.getModel())
405    .setMaximum(firstFeature.getEnd());
406  0 ((SpinnerNumberModel) end.getModel())
407    .setMinimum(firstFeature.getBegin());
408   
409  0 description.setText(firstFeature.getDescription());
410  0 featureColour = fr.getFeatureStyle(featureType);
411  0 oldColour = featureColour;
412  0 updateColourButton(mainPanel, colour, oldColour);
413    }
414   
415    /**
416    * Presents a dialog allowing the user to add new features, or amend or delete
417    * an existing feature. Currently this can be on
418    * <ul>
419    * <li>double-click on a sequence - Amend/Delete a selected feature at the
420    * position</li>
421    * <li>Create sequence feature(s) from pop-up menu on selected region</li>
422    * <li>Create features for pattern matches from Find</li>
423    * </ul>
424    * If the supplied feature type is null, show (and update on confirm) the type
425    * and group of the last new feature created (with initial defaults of
426    * "feature_1" and "Jalview").
427    */
 
428  0 toggle public void showDialog()
429    {
430  0 Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
431  0 Runnable cancelAction = getCancelAction();
432   
433    /*
434    * set dialog action handlers for OK (create/Amend) and Cancel options
435    * also for Delete if applicable (when amending features)
436    */
437  0 JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame)
438    .setResponseHandler(0, okAction)
439    .setResponseHandler(2, cancelAction);
440  0 if (!forCreate)
441    {
442  0 dialog.setResponseHandler(1, getDeleteAction());
443    }
444   
445  0 String title = null;
446  0 Object[] options = null;
447  0 if (forCreate)
448    {
449  0 title = MessageManager
450    .getString("label.create_new_sequence_features");
451  0 options = new Object[] { MessageManager.getString("action.ok"),
452    MessageManager.getString("action.cancel") };
453    }
454    else
455    {
456  0 title = MessageManager.formatMessage("label.amend_delete_features",
457    new String[]
458    { sequences.get(0).getName() });
459  0 options = new Object[] { MessageManager.getString("label.amend"),
460    MessageManager.getString("action.delete"),
461    MessageManager.getString("action.cancel") };
462    }
463   
464  0 dialog.showInternalDialog(mainPanel, title,
465    JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
466    null, options, MessageManager.getString("action.ok"));
467    }
468   
469    /**
470    * Answers an action to run on Cancel in the dialog. This is just to remove
471    * any feature highlighting from the display. Changes in the dialog are not
472    * applied until it is dismissed with OK, Amend or Delete, so there are no
473    * updates to reset on Cancel.
474    *
475    * @return
476    */
 
477  0 toggle protected Runnable getCancelAction()
478    {
479  0 Runnable okAction = () -> {
480  0 ap.highlightSearchResults(null);
481  0 ap.paintAlignment(false, false);
482    };
483  0 return okAction;
484    }
485   
486    /**
487    * Returns the action to be run on OK in the dialog when creating one or more
488    * sequence features. Note these may have a pre-supplied feature type (such as
489    * a Find pattern), or none, in which case the feature type and group default
490    * to those last added through this dialog. The action includes refreshing the
491    * Feature Settings panel (if it is open), to show any new feature type, or
492    * amended colour for an existing type.
493    *
494    * @return
495    */
 
496  0 toggle protected Runnable getCreateAction()
497    {
498  0 Runnable okAction = new Runnable()
499    {
500    boolean useLastDefaults = features.get(0).getType() == null;
501   
 
502  0 toggle @Override
503    public void run()
504    {
505  0 final String enteredType = name.getText().trim();
506  0 final String enteredGroup = group.getText().trim();
507  0 final String enteredDescription = description.getText()
508    .replaceAll("\n", " ");
509  0 if (enteredType.length() > 0)
510    {
511    /*
512    * update default values only if creating using default values
513    */
514  0 if (useLastDefaults)
515    {
516  0 lastFeatureAdded = enteredType;
517  0 lastFeatureGroupAdded = enteredGroup;
518    // TODO: determine if the null feature group is valid
519  0 if (lastFeatureGroupAdded.length() < 1)
520    {
521  0 lastFeatureGroupAdded = null;
522    }
523    }
524    }
525   
526  0 if (enteredType.length() > 0)
527    {
528  0 for (int i = 0; i < sequences.size(); i++)
529    {
530  0 SequenceFeature sf = features.get(i);
531  0 SequenceFeature sf2 = new SequenceFeature(enteredType,
532    enteredDescription, sf.getBegin(), sf.getEnd(),
533    enteredGroup);
534  0 new FeaturesFile().parseDescriptionHTML(sf2, false);
535  0 sequences.get(i).addSequenceFeature(sf2);
536    }
537   
538  0 fr.setColour(enteredType, featureColour);
539  0 fr.featuresAdded();
540   
541  0 repaintPanel();
542    }
543    }
544    };
545  0 return okAction;
546    }
547   
548    /**
549    * Answers the action to run on Delete in the dialog. Note this includes
550    * refreshing the Feature Settings (if open) in case the only instance of a
551    * feature type or group has been deleted.
552    *
553    * @return
554    */
 
555  0 toggle protected Runnable getDeleteAction()
556    {
557  0 Runnable deleteAction = () -> {
558  0 SequenceFeature sf = features.get(featureIndex);
559  0 sequences.get(0).getDatasetSequence().deleteFeature(sf);
560  0 fr.featuresAdded();
561  0 ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
562  0 ap.paintAlignment(true, true);
563    };
564  0 return deleteAction;
565    }
566   
567    /**
568    * update the amend feature button dependent on the given style
569    *
570    * @param bigPanel
571    * @param col
572    * @param col
573    */
 
574  0 toggle protected void updateColourButton(JPanel bigPanel, JLabel colour,
575    FeatureColourI col)
576    {
577  0 colour.removeAll();
578  0 colour.setIcon(null);
579  0 colour.setText("");
580   
581  0 if (col.isSimpleColour())
582    {
583  0 colour.setToolTipText(null);
584  0 colour.setBackground(col.getColour());
585    }
586    else
587    {
588  0 colour.setBackground(bigPanel.getBackground());
589  0 colour.setForeground(Color.black);
590  0 colour.setToolTipText(FeatureSettings.getColorTooltip(col, false));
591  0 FeatureSettings.renderGraduatedColor(colour, col);
592    }
593    }
594   
595    /**
596    * Show a warning message if the entered group is one that is currently hidden
597    *
598    * @param panel
599    * @param group
600    */
 
601  0 toggle protected void warnIfGroupHidden(JPanel panel, String group)
602    {
603  0 if (!fr.isGroupVisible(group))
604    {
605  0 String msg = MessageManager.formatMessage("label.warning_hidden",
606    MessageManager.getString("label.group"), group);
607  0 JvOptionPane.showMessageDialog(panel, msg, "",
608    JvOptionPane.OK_OPTION);
609    }
610    }
611   
612    /**
613    * Show a warning message if the entered type is one that is currently hidden
614    *
615    * @param panel
616    * @param type
617    */
 
618  0 toggle protected void warnIfTypeHidden(JPanel panel, String type)
619    {
620  0 if (fr.getRenderOrder().contains(type))
621    {
622  0 if (!fr.showFeatureOfType(type))
623    {
624  0 String msg = MessageManager.formatMessage("label.warning_hidden",
625    MessageManager.getString("label.feature_type"), type);
626  0 JvOptionPane.showMessageDialog(panel, msg, "",
627    JvOptionPane.OK_OPTION);
628    }
629    }
630    }
631   
632    /**
633    * On closing the dialog - ensure feature display is turned on, to show any
634    * new features - remove highlighting of the last selected feature - repaint
635    * the panel to show any changes
636    */
 
637  0 toggle protected void repaintPanel()
638    {
639  0 ap.alignFrame.showSeqFeatures.setSelected(true);
640  0 ap.av.setShowSequenceFeatures(true);
641  0 ap.av.setSearchResults(null);
642  0 ap.paintAlignment(true, true);
643    }
644   
645    /**
646    * Returns the action to be run on OK in the dialog when amending a feature.
647    * Note this may include refreshing the Feature Settings panel (if it is
648    * open), if feature type, group or colour has changed (but not for
649    * description or extent).
650    *
651    * @return
652    */
 
653  0 toggle protected Runnable getAmendAction()
654    {
655  0 Runnable okAction = new Runnable()
656    {
657    boolean useLastDefaults = features.get(0).getType() == null;
658   
659    String featureType = name.getText();
660   
661    String featureGroup = group.getText();
662   
 
663  0 toggle @Override
664    public void run()
665    {
666  0 final String enteredType = name.getText().trim();
667  0 final String enteredGroup = group.getText().trim();
668  0 final String enteredDescription = description.getText()
669    .replaceAll("\n", " ");
670  0 if (enteredType.length() > 0)
671   
672    {
673    /*
674    * update default values only if creating using default values
675    */
676  0 if (useLastDefaults)
677    {
678  0 lastFeatureAdded = enteredType;
679  0 lastFeatureGroupAdded = enteredGroup;
680    // TODO: determine if the null feature group is valid
681  0 if (lastFeatureGroupAdded.length() < 1)
682    {
683  0 lastFeatureGroupAdded = null;
684    }
685    }
686    }
687   
688  0 SequenceFeature sf = features.get(featureIndex);
689   
690    /*
691    * Need to refresh Feature Settings if type, group or colour changed;
692    * note we don't force the feature to be visible - the user has been
693    * warned if a hidden feature type or group was entered
694    */
695  0 boolean refreshSettings = (!featureType.equals(enteredType)
696    || !featureGroup.equals(enteredGroup));
697  0 refreshSettings |= (featureColour != oldColour);
698  0 fr.setColour(enteredType, featureColour);
699  0 int newBegin = sf.begin;
700  0 int newEnd = sf.end;
701  0 try
702    {
703  0 newBegin = ((Integer) start.getValue()).intValue();
704  0 newEnd = ((Integer) end.getValue()).intValue();
705    } catch (NumberFormatException ex)
706    {
707    // JSpinner doesn't accept invalid format data :-)
708    }
709   
710    /*
711    * 'amend' the feature by deleting it and adding a new one
712    * (to ensure integrity of SequenceFeatures data store)
713    * note this dialog only updates one sequence at a time
714    */
715  0 sequences.get(0).deleteFeature(sf);
716  0 SequenceFeature newSf = new SequenceFeature(sf, enteredType,
717    newBegin, newEnd, enteredGroup, sf.getScore());
718  0 newSf.setDescription(enteredDescription);
719  0 new FeaturesFile().parseDescriptionHTML(newSf, false);
720  0 sequences.get(0).addSequenceFeature(newSf);
721   
722  0 if (refreshSettings)
723    {
724  0 fr.featuresAdded();
725    }
726  0 repaintPanel();
727    }
728    };
729  0 return okAction;
730    }
731   
732    }