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   public void amendFeatures(final List<SequenceI> sequences,
  79           final List<SequenceFeature> features,
  80           final Runnable responseHandler)
  81   {
  82     amendFeatures(sequences, features, false, responseHandler);
  83   }
  84
  85   public void createFeatures(final List<SequenceI> sequences,
  86           final List<SequenceFeature> features,
  87           final Runnable responseHandler)
  88   {
  89     amendFeatures(sequences, features, true, responseHandler);
  90   }
  91
  92   /**
  93    * Presents a dialog allowing the user to add new features, or amend or delete
  94    * existing features. Currently this can be on
  95    * <ul>
  96    * <li>double-click on a sequence - Amend/Delete features at position</li>
  97    * <li>Create sequence feature from pop-up menu on selected region</li>
  98    * <li>Create features for pattern matches from Find</li>
  99    * </ul>
 100    * If the supplied feature type is null, show (and update on confirm) the type
 101    * and group of the last new feature created (with initial defaults of
 102    * "feature_1" and "Jalview").
 103    *
 104    * @param sequences
 105    *          the sequences features are to be created on (if creating
 106    *          features), or a single sequence (if amending features)
 107    * @param features
 108    *          the current features at the position (if amending), or template
 109    *          new feature(s) with start/end position set (if creating)
 110    * @param create
 111    *          true to create features, false to amend or delete
 112    * @param alignPanel
 113    * @param responseHandler
 114    *          boolean true RunResponse is run if features are created
 115    */
 116   private void amendFeatures(final List<SequenceI> sequences,
 117           final List<SequenceFeature> features, boolean create,
 118           final Runnable responseHandler)
 119   {
 120     featureIndex = 0;
 121
 122     final JPanel mainPanel = new JPanel(new BorderLayout());
 123
 124     final JTextField name = new JTextField(25);
 125     name.getDocument().addDocumentListener(new DocumentListener()
 126     {
 127       @Override
 128       public void insertUpdate(DocumentEvent e)
 129       {
 130         warnIfTypeHidden(mainPanel, name.getText());
 131       }
 132
 133       @Override
 134       public void removeUpdate(DocumentEvent e)
 135       {
 136         warnIfTypeHidden(mainPanel, name.getText());
 137       }
 138
 139       @Override
 140       public void changedUpdate(DocumentEvent e)
 141       {
 142         warnIfTypeHidden(mainPanel, name.getText());
 143       }
 144     });
 145
 146     final JTextField group = new JTextField(25);
 147     group.getDocument().addDocumentListener(new DocumentListener()
 148     {
 149       @Override
 150       public void insertUpdate(DocumentEvent e)
 151       {
 152         warnIfGroupHidden(mainPanel, group.getText());
 153       }
 154
 155       @Override
 156       public void removeUpdate(DocumentEvent e)
 157       {
 158         warnIfGroupHidden(mainPanel, group.getText());
 159       }
 160
 161       @Override
 162       public void changedUpdate(DocumentEvent e)
 163       {
 164         warnIfGroupHidden(mainPanel, group.getText());
 165       }
 166     });
 167
 168     final JTextArea description = new JTextArea(3, 25);
 169     final JSpinner start = new JSpinner();
 170     final JSpinner end = new JSpinner();
 171     start.setPreferredSize(new Dimension(80, 20));
 172     end.setPreferredSize(new Dimension(80, 20));
 173     final JLabel colour = new JLabel();
 174     colour.setOpaque(true);
 175     // colour.setBorder(BorderFactory.createEtchedBorder());
 176     colour.setMaximumSize(new Dimension(30, 16));
 177     colour.addMouseListener(new MouseAdapter()
 178     {
 179       /*
 180        * open colour chooser on click in colour panel
 181        */
 182       @Override
 183       public void mousePressed(MouseEvent evt)
 184       {
 185         if (featureColour.isSimpleColour())
 186         {
 187           String title = MessageManager
 188                   .getString("label.select_feature_colour");
 189           ColourChooserListener listener = new ColourChooserListener()
 190           {
 191             @Override
 192             public void colourSelected(Color c)
 193             {
 194               featureColour = new FeatureColour(c);
 195               updateColourButton(mainPanel, colour, featureColour);
 196             };
 197           };
 198           JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
 199                   title, featureColour.getColour(), listener);
 200         }
 201         else
 202         {
 203           /*
 204            * variable colour dialog - on OK, refetch the updated
 205            * feature colour and update this display
 206            */
 207           final String ft = features.get(featureIndex).getType();
 208           final String type = ft == null ? lastFeatureAdded : ft;
 209           FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
 210           fcc.setRequestFocusEnabled(true);
 211           fcc.requestFocus();
 212           fcc.addActionListener(new ActionListener()
 213           {
 214             @Override
 215             public void actionPerformed(ActionEvent e)
 216             {
 217               featureColour = fr.getFeatureStyle(ft);
 218               fr.setColour(type, featureColour);
 219               updateColourButton(mainPanel, colour, featureColour);
 220             }
 221           });
 222         }
 223       }
 224     });
 225     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 226
 227     if (!create && features.size() > 1)
 228     {
 229       /*
 230        * more than one feature at selected position -
 231        * add a drop-down to choose the feature to amend
 232        * space pad text if necessary to make entries distinct
 233        */
 234       gridPanel = new JPanel(new GridLayout(4, 1));
 235       JPanel choosePanel = new JPanel();
 236       choosePanel.add(new JLabel(
 237               MessageManager.getString("label.select_feature") + ":"));
 238       final JComboBox<String> overlaps = new JComboBox<>();
 239       List<String> added = new ArrayList<>();
 240       for (SequenceFeature sf : features)
 241       {
 242         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 243                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 244         while (added.contains(text))
 245         {
 246           text += " ";
 247         }
 248         overlaps.addItem(text);
 249         added.add(text);
 250       }
 251       choosePanel.add(overlaps);
 252
 253       overlaps.addItemListener(new ItemListener()
 254       {
 255         @Override
 256         public void itemStateChanged(ItemEvent e)
 257         {
 258           int index = overlaps.getSelectedIndex();
 259           if (index != -1)
 260           {
 261             featureIndex = index;
 262             SequenceFeature sf = features.get(index);
 263             name.setText(sf.getType());
 264             description.setText(sf.getDescription());
 265             group.setText(sf.getFeatureGroup());
 266             start.setValue(new Integer(sf.getBegin()));
 267             end.setValue(new Integer(sf.getEnd()));
 268
 269             SearchResultsI highlight = new SearchResults();
 270             highlight.addResult(sequences.get(0), sf.getBegin(),
 271                     sf.getEnd());
 272
 273             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight,
 274                     true);
 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 (!create)
 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     Object[] options;
 361     if (!create)
 362     {
 363       options = new Object[] { MessageManager.getString("label.amend"),
 364           MessageManager.getString("action.delete"),
 365           MessageManager.getString("action.cancel") };
 366     }
 367     else
 368     {
 369       options = new Object[] { MessageManager.getString("action.ok"),
 370           MessageManager.getString("action.cancel") };
 371     }
 372
 373     String title = create
 374             ? MessageManager.getString("label.create_new_sequence_features")
 375             : MessageManager.formatMessage("label.amend_delete_features",
 376                     new String[]
 377                     { sequences.get(0).getName() });
 378
 379     /*
 380      * register responses and show the dialog
 381      */
 382     JvOptionPane.newOptionDialog(Desktop.desktop).response(
 383
 384             new RunResponse(JvOptionPane.OK_OPTION)
 385             {
 386               public void run()
 387               {
 388                 final String enteredType = name.getText().trim();
 389                 final String enteredGroup = group.getText().trim();
 390                 final String enteredDescription = description.getText()
 391                         .replaceAll("\n", " ");
 392                 if (enteredType.length() > 0)
 393
 394                 {
 395                   /*
 396                    * update default values only if creating using default values
 397                    */
 398                   if (useLastDefaults)
 399                   {
 400                     lastFeatureAdded = enteredType;
 401                     lastFeatureGroupAdded = enteredGroup;
 402                     // TODO: determine if the null feature group is valid
 403                     if (lastFeatureGroupAdded.length() < 1)
 404                     {
 405                       lastFeatureGroupAdded = null;
 406                     }
 407                   }
 408                 }
 409
 410                 if (create)
 411                 {
 412                   // NEW FEATURES ADDED
 413                   if (enteredType.length() > 0)
 414                   {
 415                     for (int i = 0; i < sequences.size(); i++)
 416                     {
 417                       SequenceFeature sf = features.get(i);
 418                       SequenceFeature sf2 = new SequenceFeature(enteredType,
 419                               enteredDescription, sf.getBegin(),
 420                               sf.getEnd(), enteredGroup);
 421                       new FeaturesFile().parseDescriptionHTML(sf2, false);
 422                       sequences.get(i).addSequenceFeature(sf2);
 423                     }
 424
 425                     fr.setColour(enteredType, featureColour);
 426
 427                     fr.featuresAdded();
 428
 429                     responseHandler.run();
 430                   }
 431                 }
 432                 else
 433                 {
 434                   SequenceFeature sf = features.get(featureIndex);
 435                   /*
 436                    * Feature amended - YES_OPTION corresponds to the Amend button
 437                    * need to refresh Feature Settings if type, group or colour changed;
 438                    * note we don't force the feature to be visible - the user has been
 439                    * warned if a hidden feature type or group was entered
 440                    */
 441                   boolean refreshSettings = (!featureType
 442                           .equals(enteredType)
 443                           || !featureGroup.equals(enteredGroup));
 444                   refreshSettings |= (featureColour != oldColour);
 445                   fr.setColour(enteredType, featureColour);
 446                   int newBegin = sf.begin;
 447                   int newEnd = sf.end;
 448                   try
 449                   {
 450                     newBegin = ((Integer) start.getValue()).intValue();
 451                     newEnd = ((Integer) end.getValue()).intValue();
 452                   } catch (NumberFormatException ex)
 453                   {
 454                     // JSpinner doesn't accept invalid format data :-)
 455                   }
 456
 457                   /*
 458                    * replace the feature by deleting it and adding a new one
 459                    * (to ensure integrity of SequenceFeatures data store)
 460                    */
 461                   sequences.get(0).deleteFeature(sf);
 462                   SequenceFeature newSf = new SequenceFeature(sf,
 463                           enteredType, newBegin, newEnd, enteredGroup,
 464                           sf.getScore());
 465                   newSf.setDescription(enteredDescription);
 466                   new FeaturesFile().parseDescriptionHTML(newSf, false);
 467                   // amend features dialog only updates one sequence at a time
 468                   sequences.get(0).addSequenceFeature(newSf);
 469
 470                   if (refreshSettings)
 471                   {
 472                     fr.featuresAdded();
 473                   }
 474                 }
 475
 476                 /*
 477                  * suppress fastPaint here - if feature colour changed,
 478                  * we need to repaint the whole alignment
 479                  */
 480                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 481                         true);
 482                 ap.paintAlignment(true, true);
 483               }
 484             }).response(new RunResponse(JvOptionPane.NO_OPTION)
 485             {
 486               public void run()
 487               {
 488                 SequenceFeature sf = features.get(featureIndex);
 489                 /*
 490                  * NO_OPTION corresponds to the Delete button
 491                  */
 492                 sequences.get(0).getDatasetSequence().deleteFeature(sf);
 493                 // update Feature Settings for removal of feature / group
 494                 fr.featuresAdded();
 495                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 496                         true);
 497                 ap.paintAlignment(true, true);
 498               }
 499             }).defaultResponse(new Runnable()
 500             {
 501               public void run()
 502               {
 503                 ap.getSeqPanel().seqCanvas.highlightSearchResults(null,
 504                         true);
 505                 ap.paintAlignment(true, true);
 506               }
 507             }).showInternalDialog(mainPanel, title,
 508                     JvOptionPane.YES_NO_CANCEL_OPTION,
 509                     JvOptionPane.QUESTION_MESSAGE, null, options,
 510                     MessageManager.getString("action.ok"));
 511   }
 512
 513   /**
 514    * update the amend feature button dependent on the given style
 515    *
 516    * @param bigPanel
 517    * @param col
 518    * @param col
 519    */
 520   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 521           FeatureColourI col)
 522   {
 523     colour.removeAll();
 524     colour.setIcon(null);
 525     colour.setToolTipText(null);
 526     colour.setText("");
 527
 528     if (col.isSimpleColour())
 529     {
 530       colour.setBackground(col.getColour());
 531     }
 532     else
 533     {
 534       colour.setBackground(bigPanel.getBackground());
 535       colour.setForeground(Color.black);
 536       FeatureSettings.renderGraduatedColor(colour, col);
 537     }
 538   }
 539
 540   /**
 541    * Show a warning message if the entered group is one that is currently hidden
 542    *
 543    * @param panel
 544    * @param group
 545    */
 546   protected void warnIfGroupHidden(JPanel panel, String group)
 547   {
 548     if (!fr.isGroupVisible(group))
 549     {
 550       String msg = MessageManager.formatMessage("label.warning_hidden",
 551               MessageManager.getString("label.group"), group);
 552       JvOptionPane.showMessageDialog(panel, msg, "",
 553               JvOptionPane.OK_OPTION);
 554     }
 555   }
 556
 557   /**
 558    * Show a warning message if the entered type is one that is currently hidden
 559    *
 560    * @param panel
 561    * @param type
 562    */
 563   protected void warnIfTypeHidden(JPanel panel, String type)
 564   {
 565     if (fr.getRenderOrder().contains(type))
 566     {
 567       if (!fr.showFeatureOfType(type))
 568       {
 569         String msg = MessageManager.formatMessage("label.warning_hidden",
 570                 MessageManager.getString("label.feature_type"), type);
 571         JvOptionPane.showMessageDialog(panel, msg, "",
 572                 JvOptionPane.OK_OPTION);
 573       }
 574     }
 575   }
 576
 577 }