src/jalview/gui/FeatureEditor.java

   1 package jalview.gui;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.datamodel.SearchResults;
   5 import jalview.datamodel.SearchResultsI;
   6 import jalview.datamodel.SequenceFeature;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.JalviewColourChooser.ColourChooserListener;
   9 import jalview.io.FeaturesFile;
  10 import jalview.schemes.FeatureColour;
  11 import jalview.util.ColorUtils;
  12 import jalview.util.MessageManager;
  13 import jalview.util.dialogrunner.RunResponse;
  14
  15 import java.awt.BorderLayout;
  16 import java.awt.Color;
  17 import java.awt.Dimension;
  18 import java.awt.Font;
  19 import java.awt.GridLayout;
  20 import java.awt.event.ActionEvent;
  21 import java.awt.event.ActionListener;
  22 import java.awt.event.ItemEvent;
  23 import java.awt.event.ItemListener;
  24 import java.awt.event.MouseAdapter;
  25 import java.awt.event.MouseEvent;
  26 import java.util.ArrayList;
  27 import java.util.List;
  28
  29 import javax.swing.JComboBox;
  30 import javax.swing.JLabel;
  31 import javax.swing.JPanel;
  32 import javax.swing.JScrollPane;
  33 import javax.swing.JSpinner;
  34 import javax.swing.JTextArea;
  35 import javax.swing.JTextField;
  36 import javax.swing.SwingConstants;
  37 import javax.swing.event.DocumentEvent;
  38 import javax.swing.event.DocumentListener;
  39
  40 /**
  41  * Provides a dialog allowing the user to add new features, or amend or delete
  42  * existing features
  43  */
  44 public class FeatureEditor
  45 {
  46   /*
  47    * defaults for creating a new feature are the last created
  48    * feature type and group
  49    */
  50   static String lastFeatureAdded = "feature_1";
  51
  52   static String lastFeatureGroupAdded = "Jalview";
  53
  54   /*
  55    * index into a list of features if more than one selected for editing
  56    */
  57   int featureIndex;
  58
  59   FeatureColourI oldColour;
  60
  61   FeatureColourI featureColour;
  62
  63   FeatureRenderer fr;
  64
  65   AlignmentPanel ap;
  66
  67   /**
  68    * Constructor
  69    *
  70    * @param alignPanel
  71    */
  72   public FeatureEditor(AlignmentPanel alignPanel)
  73   {
  74     ap = alignPanel;
  75     fr = alignPanel.getSeqPanel().seqCanvas.fr;
  76   }
  77
  78   /**
  79    * Presents a dialog allowing the user to add new features, or amend or delete
  80    * existing features. Currently this can be on
  81    * <ul>
  82    * <li>double-click on a sequence - Amend/Delete features at position</li>
  83    * <li>Create sequence feature from pop-up menu on selected region</li>
  84    * <li>Create features for pattern matches from Find</li>
  85    * </ul>
  86    * If the supplied feature type is null, show (and update on confirm) the type
  87    * and group of the last new feature created (with initial defaults of
  88    * "feature_1" and "Jalview").
  89    *
  90    * @param sequences
  91    *          the sequences features are to be created on (if creating
  92    *          features), or a single sequence (if amending features)
  93    * @param features
  94    *          the current features at the position (if amending), or template
  95    *          new feature(s) with start/end position set (if creating)
  96    * @param create
  97    *          true to create features, false to amend or delete
  98    * @param alignPanel
  99    * @param responseHandler
 100    *          boolean true RunResponse is run if features are created
 101    */
 102   public boolean amendFeatures(final List<SequenceI> sequences,
 103           final List<SequenceFeature> features, boolean create,
 104           final Runnable responseHandler)
 105   {
 106     featureIndex = 0;
 107
 108     final JPanel mainPanel = new JPanel(new BorderLayout());
 109
 110     final JTextField name = new JTextField(25);
 111     name.getDocument().addDocumentListener(new DocumentListener()
 112     {
 113       @Override
 114       public void insertUpdate(DocumentEvent e)
 115       {
 116         warnIfTypeHidden(mainPanel, name.getText());
 117       }
 118
 119       @Override
 120       public void removeUpdate(DocumentEvent e)
 121       {
 122         warnIfTypeHidden(mainPanel, name.getText());
 123       }
 124
 125       @Override
 126       public void changedUpdate(DocumentEvent e)
 127       {
 128         warnIfTypeHidden(mainPanel, name.getText());
 129       }
 130     });
 131
 132     final JTextField group = new JTextField(25);
 133     group.getDocument().addDocumentListener(new DocumentListener()
 134     {
 135       @Override
 136       public void insertUpdate(DocumentEvent e)
 137       {
 138         warnIfGroupHidden(mainPanel, group.getText());
 139       }
 140
 141       @Override
 142       public void removeUpdate(DocumentEvent e)
 143       {
 144         warnIfGroupHidden(mainPanel, group.getText());
 145       }
 146
 147       @Override
 148       public void changedUpdate(DocumentEvent e)
 149       {
 150         warnIfGroupHidden(mainPanel, group.getText());
 151       }
 152     });
 153
 154     final JTextArea description = new JTextArea(3, 25);
 155     final JSpinner start = new JSpinner();
 156     final JSpinner end = new JSpinner();
 157     start.setPreferredSize(new Dimension(80, 20));
 158     end.setPreferredSize(new Dimension(80, 20));
 159     final JLabel colour = new JLabel();
 160     colour.setOpaque(true);
 161     // colour.setBorder(BorderFactory.createEtchedBorder());
 162     colour.setMaximumSize(new Dimension(30, 16));
 163     colour.addMouseListener(new MouseAdapter()
 164     {
 165       /*
 166        * open colour chooser on click in colour panel
 167        */
 168       @Override
 169       public void mousePressed(MouseEvent evt)
 170       {
 171         if (featureColour.isSimpleColour())
 172         {
 173           String title = MessageManager
 174                   .getString("label.select_feature_colour");
 175           ColourChooserListener listener = new ColourChooserListener()
 176           {
 177             @Override
 178             public void colourSelected(Color c)
 179             {
 180               featureColour = new FeatureColour(c);
 181               updateColourButton(mainPanel, colour, featureColour);
 182             };
 183           };
 184           JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
 185                   title, featureColour.getColour(), listener);
 186         }
 187         else
 188         {
 189           /*
 190            * variable colour dialog - on OK, refetch the updated
 191            * feature colour and update this display
 192            */
 193           final String ft = features.get(featureIndex).getType();
 194           final String type = ft == null ? lastFeatureAdded : ft;
 195           FeatureTypeSettings fcc = new FeatureTypeSettings(
 196                   fr, type);
 197           fcc.setRequestFocusEnabled(true);
 198           fcc.requestFocus();
 199           fcc.addActionListener(new ActionListener()
 200           {
 201             @Override
 202             public void actionPerformed(ActionEvent e)
 203             {
 204               featureColour = fr.getFeatureStyle(ft);
 205               fr.setColour(type, featureColour);
 206               updateColourButton(mainPanel, colour, featureColour);
 207             }
 208           });
 209         }
 210       }
 211     });
 212     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 213
 214     if (!create && features.size() > 1)
 215     {
 216       /*
 217        * more than one feature at selected position -
 218        * add a drop-down to choose the feature to amend
 219        * space pad text if necessary to make entries distinct
 220        */
 221       gridPanel = new JPanel(new GridLayout(4, 1));
 222       JPanel choosePanel = new JPanel();
 223       choosePanel.add(new JLabel(
 224               MessageManager.getString("label.select_feature") + ":"));
 225       final JComboBox<String> overlaps = new JComboBox<>();
 226       List<String> added = new ArrayList<>();
 227       for (SequenceFeature sf : features)
 228       {
 229         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 230                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 231         while (added.contains(text))
 232         {
 233           text += " ";
 234         }
 235         overlaps.addItem(text);
 236         added.add(text);
 237       }
 238       choosePanel.add(overlaps);
 239
 240       overlaps.addItemListener(new ItemListener()
 241       {
 242         @Override
 243         public void itemStateChanged(ItemEvent e)
 244         {
 245           int index = overlaps.getSelectedIndex();
 246           if (index != -1)
 247           {
 248             featureIndex = index;
 249             SequenceFeature sf = features.get(index);
 250             name.setText(sf.getType());
 251             description.setText(sf.getDescription());
 252             group.setText(sf.getFeatureGroup());
 253             start.setValue(new Integer(sf.getBegin()));
 254             end.setValue(new Integer(sf.getEnd()));
 255
 256             SearchResultsI highlight = new SearchResults();
 257             highlight.addResult(sequences.get(0), sf.getBegin(),
 258                     sf.getEnd());
 259
 260             ap.getSeqPanel().seqCanvas
 261                     .highlightSearchResults(highlight, false);
 262           }
 263           FeatureColourI col = fr.getFeatureStyle(name.getText());
 264           if (col == null)
 265           {
 266             col = new FeatureColour(
 267                     ColorUtils.createColourFromName(name.getText()));
 268           }
 269           oldColour = featureColour = col;
 270           updateColourButton(mainPanel, colour, col);
 271         }
 272       });
 273
 274       gridPanel.add(choosePanel);
 275     }
 276
 277     JPanel namePanel = new JPanel();
 278     gridPanel.add(namePanel);
 279     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 280             JLabel.RIGHT));
 281     namePanel.add(name);
 282
 283     JPanel groupPanel = new JPanel();
 284     gridPanel.add(groupPanel);
 285     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 286             JLabel.RIGHT));
 287     groupPanel.add(group);
 288
 289     JPanel colourPanel = new JPanel();
 290     gridPanel.add(colourPanel);
 291     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 292             JLabel.RIGHT));
 293     colourPanel.add(colour);
 294     colour.setPreferredSize(new Dimension(150, 15));
 295     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 296     colour.setForeground(Color.black);
 297     colour.setHorizontalAlignment(SwingConstants.CENTER);
 298     colour.setVerticalAlignment(SwingConstants.CENTER);
 299     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 300     colour.setVerticalTextPosition(SwingConstants.CENTER);
 301     mainPanel.add(gridPanel, BorderLayout.NORTH);
 302
 303     JPanel descriptionPanel = new JPanel();
 304     descriptionPanel.add(new JLabel(
 305             MessageManager.getString("label.description:"), JLabel.RIGHT));
 306     description.setFont(JvSwingUtils.getTextAreaFont());
 307     description.setLineWrap(true);
 308     descriptionPanel.add(new JScrollPane(description));
 309
 310     if (!create)
 311     {
 312       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 313
 314       JPanel startEndPanel = new JPanel();
 315       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 316               JLabel.RIGHT));
 317       startEndPanel.add(start);
 318       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 319               JLabel.RIGHT));
 320       startEndPanel.add(end);
 321       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 322     }
 323     else
 324     {
 325       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 326     }
 327
 328     /*
 329      * default feature type and group to that of the first feature supplied,
 330      * or to the last feature created if not supplied (null value)
 331      */
 332     SequenceFeature firstFeature = features.get(0);
 333     boolean useLastDefaults = firstFeature.getType() == null;
 334     final String featureType = useLastDefaults ? lastFeatureAdded
 335             : firstFeature.getType();
 336     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 337             : firstFeature.getFeatureGroup();
 338     name.setText(featureType);
 339     group.setText(featureGroup);
 340
 341     start.setValue(new Integer(firstFeature.getBegin()));
 342     end.setValue(new Integer(firstFeature.getEnd()));
 343     description.setText(firstFeature.getDescription());
 344     featureColour = fr.getFeatureStyle(featureType);
 345     oldColour = featureColour;
 346     updateColourButton(mainPanel, colour, oldColour);
 347     Object[] options;
 348     if (!create)
 349     {
 350       options = new Object[] { MessageManager.getString("label.amend"),
 351           MessageManager.getString("action.delete"),
 352           MessageManager.getString("action.cancel") };
 353     }
 354     else
 355     {
 356       options = new Object[] { MessageManager.getString("action.ok"),
 357           MessageManager.getString("action.cancel") };
 358     }
 359
 360     String title = create
 361             ? MessageManager.getString("label.create_new_sequence_features")
 362             : MessageManager.formatMessage("label.amend_delete_features",
 363                     new String[]
 364                     { sequences.get(0).getName() });
 365
 366     /*
 367      * register responses and show the dialog
 368      */
 369     JvOptionPane.newOptionDialog(Desktop.desktop).response(
 370
 371             new RunResponse(JvOptionPane.OK_OPTION)
 372             {
 373               public void run()
 374               {
 375                 final String enteredType = name.getText().trim();
 376                 final String enteredGroup = group.getText().trim();
 377                 final String enteredDescription = description.getText()
 378                         .replaceAll("\n", " ");
 379                 if (enteredType.length() > 0)
 380
 381                 {
 382                   /*
 383                    * update default values only if creating using default values
 384                    */
 385                   if (useLastDefaults)
 386                   {
 387                     lastFeatureAdded = enteredType;
 388                     lastFeatureGroupAdded = enteredGroup;
 389                     // TODO: determine if the null feature group is valid
 390                     if (lastFeatureGroupAdded.length() < 1)
 391                     {
 392                       lastFeatureGroupAdded = null;
 393                     }
 394                   }
 395                 }
 396
 397                 if (create)
 398                 {
 399                   // NEW FEATURES ADDED
 400                   if (enteredType.length() > 0)
 401                   {
 402                     for (int i = 0; i < sequences.size(); i++)
 403                     {
 404                       SequenceFeature sf = features.get(i);
 405                       SequenceFeature sf2 = new SequenceFeature(enteredType,
 406                               enteredDescription, sf.getBegin(),
 407                               sf.getEnd(), enteredGroup);
 408                       new FeaturesFile().parseDescriptionHTML(sf2, false);
 409                       sequences.get(i).addSequenceFeature(sf2);
 410                     }
 411
 412                     fr.setColour(enteredType, featureColour);
 413
 414                     fr.featuresAdded();
 415
 416                     responseHandler.run();
 417                   }
 418                 } else {
 419                   SequenceFeature sf = features.get(featureIndex);
 420                   /*
 421                    * Feature amended - YES_OPTION corresponds to the Amend button
 422                    * need to refresh Feature Settings if type, group or colour changed;
 423                    * note we don't force the feature to be visible - the user has been
 424                    * warned if a hidden feature type or group was entered
 425                    */
 426                   boolean refreshSettings = (!featureType.equals(enteredType)
 427                           || !featureGroup.equals(enteredGroup));
 428                   refreshSettings |= (featureColour != oldColour);
 429                   fr.setColour(enteredType, featureColour);
 430                   int newBegin = sf.begin;
 431                   int newEnd = sf.end;
 432                   try
 433                   {
 434                     newBegin = ((Integer) start.getValue()).intValue();
 435                     newEnd = ((Integer) end.getValue()).intValue();
 436                   } catch (NumberFormatException ex)
 437                   {
 438                     // JSpinner doesn't accept invalid format data :-)
 439                   }
 440
 441                   /*
 442                    * replace the feature by deleting it and adding a new one
 443                    * (to ensure integrity of SequenceFeatures data store)
 444                    */
 445                   sequences.get(0).deleteFeature(sf);
 446                   SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 447                           newBegin, newEnd, enteredGroup, sf.getScore());
 448                   newSf.setDescription(enteredDescription);
 449                   new FeaturesFile().parseDescriptionHTML(newSf, false);
 450                   // amend features dialog only updates one sequence at a time
 451                   sequences.get(0).addSequenceFeature(newSf);
 452
 453                   if (refreshSettings)
 454                   {
 455                     fr.featuresAdded();
 456                   }
 457                 }
 458                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 459                         false);
 460                 ap.paintAlignment(true, true);
 461               }
 462             }).response(new RunResponse(JvOptionPane.NO_OPTION)
 463             {
 464               public void run()
 465               {
 466                 SequenceFeature sf = features.get(featureIndex);
 467                 /*
 468                  * NO_OPTION corresponds to the Delete button
 469                  */
 470                 sequences.get(0).getDatasetSequence().deleteFeature(sf);
 471                 // update Feature Settings for removal of feature / group
 472                 fr.featuresAdded();
 473                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 474                         false);
 475                 ap.paintAlignment(true, true);
 476               }
 477             }).defaultResponse(new Runnable()
 478             {
 479               public void run()
 480               {
 481                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 482                         false);
 483                 ap.paintAlignment(true, true);
 484               }
 485             }).showInternalDialog(mainPanel, title,
 486                     JvOptionPane.YES_NO_CANCEL_OPTION,
 487                     JvOptionPane.QUESTION_MESSAGE, null, options,
 488                     MessageManager.getString("action.ok"));
 489     return true;
 490   }
 491
 492   /**
 493    * update the amend feature button dependent on the given style
 494    *
 495    * @param bigPanel
 496    * @param col
 497    * @param col
 498    */
 499   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 500           FeatureColourI col)
 501   {
 502     colour.removeAll();
 503     colour.setIcon(null);
 504     colour.setToolTipText(null);
 505     colour.setText("");
 506
 507     if (col.isSimpleColour())
 508     {
 509       colour.setBackground(col.getColour());
 510     }
 511     else
 512     {
 513       colour.setBackground(bigPanel.getBackground());
 514       colour.setForeground(Color.black);
 515       FeatureSettings.renderGraduatedColor(colour, col);
 516     }
 517   }
 518
 519   /**
 520    * Show a warning message if the entered group is one that is currently hidden
 521    *
 522    * @param panel
 523    * @param group
 524    */
 525   protected void warnIfGroupHidden(JPanel panel, String group)
 526   {
 527     if (!fr.isGroupVisible(group))
 528     {
 529       String msg = MessageManager.formatMessage("label.warning_hidden",
 530               MessageManager.getString("label.group"), group);
 531       JvOptionPane.showMessageDialog(panel, msg, "",
 532               JvOptionPane.OK_OPTION);
 533     }
 534   }
 535
 536   /**
 537    * Show a warning message if the entered type is one that is currently hidden
 538    *
 539    * @param panel
 540    * @param type
 541    */
 542   protected void warnIfTypeHidden(JPanel panel, String type)
 543   {
 544     if (fr.getRenderOrder().contains(type))
 545     {
 546       if (!fr.showFeatureOfType(type))
 547       {
 548         String msg = MessageManager.formatMessage("label.warning_hidden",
 549                 MessageManager.getString("label.feature_type"), type);
 550         JvOptionPane.showMessageDialog(panel, msg, "",
 551                 JvOptionPane.OK_OPTION);
 552       }
 553     }
 554   }
 555
 556 }