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