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