src/jalview/gui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.api.FeatureColourI;
  24 import jalview.datamodel.SearchResults;
  25 import jalview.datamodel.SearchResultsI;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.JalviewColourChooser.ColourChooserListener;
  29 import jalview.io.FeaturesFile;
  30 import jalview.schemes.FeatureColour;
  31 import jalview.util.ColorUtils;
  32 import jalview.util.MessageManager;
  33 import jalview.util.dialogrunner.RunResponse;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.Dimension;
  38 import java.awt.Font;
  39 import java.awt.GridLayout;
  40 import java.awt.event.ActionEvent;
  41 import java.awt.event.ActionListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.util.ArrayList;
  47 import java.util.Arrays;
  48 import java.util.Comparator;
  49 import java.util.List;
  50
  51 import javax.swing.JColorChooser;
  52 import javax.swing.JComboBox;
  53 import javax.swing.JDialog;
  54 import javax.swing.JLabel;
  55 import javax.swing.JPanel;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSpinner;
  58 import javax.swing.JTextArea;
  59 import javax.swing.JTextField;
  60 import javax.swing.SwingConstants;
  61 import javax.swing.event.DocumentEvent;
  62 import javax.swing.event.DocumentListener;
  63
  64 /**
  65  * DOCUMENT ME!
  66  *
  67  * @author $author$
  68  * @version $Revision$
  69  */
  70 public class FeatureRenderer
  71         extends jalview.renderer.seqfeatures.FeatureRenderer
  72 {
  73   /*
  74    * defaults for creating a new feature are the last created
  75    * feature type and group
  76    */
  77   static String lastFeatureAdded = "feature_1";
  78
  79   static String lastFeatureGroupAdded = "Jalview";
  80
  81   Color resBoxColour;
  82
  83   AlignmentPanel ap;
  84
  85   /**
  86    * Creates a new FeatureRenderer object
  87    *
  88    * @param alignPanel
  89    */
  90   public FeatureRenderer(AlignmentPanel alignPanel)
  91   {
  92     super(alignPanel.av);
  93     this.ap = alignPanel;
  94     if (alignPanel.getSeqPanel() != null
  95             && alignPanel.getSeqPanel().seqCanvas != null
  96             && alignPanel.getSeqPanel().seqCanvas.fr != null)
  97     {
  98       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
  99     }
 100   }
 101
 102   FeatureColourI oldcol, fcol;
 103
 104   int featureIndex = 0;
 105
 106   /**
 107    * Presents a dialog allowing the user to add new features, or amend or delete
 108    * existing features. Currently this can be on
 109    * <ul>
 110    * <li>double-click on a sequence - Amend/Delete features at position</li>
 111    * <li>Create sequence feature from pop-up menu on selected region</li>
 112    * <li>Create features for pattern matches from Find</li>
 113    * </ul>
 114    * If the supplied feature type is null, show (and update on confirm) the type
 115    * and group of the last new feature created (with initial defaults of
 116    * "feature_1" and "Jalview").
 117    *
 118    * @param sequences
 119    *          the sequences features are to be created on (if creating
 120    *          features), or a single sequence (if amending features)
 121    * @param features
 122    *          the current features at the position (if amending), or template
 123    *          new feature(s) with start/end position set (if creating)
 124    * @param create
 125    *          true to create features, false to amend or delete
 126    * @param alignPanel
 127    * @param responseHandler
 128    *          boolean true RunResponse is run if features are created
 129    */
 130   protected boolean amendFeatures(final List<SequenceI> sequences,
 131           final List<SequenceFeature> features, boolean create,
 132           final AlignmentPanel alignPanel, final Runnable responseHandler)
 133   {
 134     featureIndex = 0;
 135
 136     final JPanel mainPanel = new JPanel(new BorderLayout());
 137
 138     final JTextField name = new JTextField(25);
 139     name.getDocument().addDocumentListener(new DocumentListener()
 140     {
 141       @Override
 142       public void insertUpdate(DocumentEvent e)
 143       {
 144         warnIfTypeHidden(mainPanel, name.getText());
 145       }
 146
 147       @Override
 148       public void removeUpdate(DocumentEvent e)
 149       {
 150         warnIfTypeHidden(mainPanel, name.getText());
 151       }
 152
 153       @Override
 154       public void changedUpdate(DocumentEvent e)
 155       {
 156         warnIfTypeHidden(mainPanel, name.getText());
 157       }
 158     });
 159
 160     final JTextField group = new JTextField(25);
 161     group.getDocument().addDocumentListener(new DocumentListener()
 162     {
 163       @Override
 164       public void insertUpdate(DocumentEvent e)
 165       {
 166         warnIfGroupHidden(mainPanel, group.getText());
 167       }
 168
 169       @Override
 170       public void removeUpdate(DocumentEvent e)
 171       {
 172         warnIfGroupHidden(mainPanel, group.getText());
 173       }
 174
 175       @Override
 176       public void changedUpdate(DocumentEvent e)
 177       {
 178         warnIfGroupHidden(mainPanel, group.getText());
 179       }
 180     });
 181
 182     final JTextArea description = new JTextArea(3, 25);
 183     final JSpinner start = new JSpinner();
 184     final JSpinner end = new JSpinner();
 185     start.setPreferredSize(new Dimension(80, 20));
 186     end.setPreferredSize(new Dimension(80, 20));
 187     final JLabel colour = new JLabel();
 188     colour.setOpaque(true);
 189     // colour.setBorder(BorderFactory.createEtchedBorder());
 190     colour.setMaximumSize(new Dimension(30, 16));
 191     colour.addMouseListener(new MouseAdapter()
 192     {
 193       /*
 194        * open colour chooser on click in colour panel
 195        */
 196       @Override
 197       public void mousePressed(MouseEvent evt)
 198       {
 199         if (fcol.isSimpleColour())
 200         {
 201           String title = MessageManager
 202                   .getString("label.select_feature_colour");
 203           ColourChooserListener listener = new ColourChooserListener()
 204           {
 205             @Override
 206             public void colourSelected(Color c)
 207             {
 208               updateColourButton(mainPanel, colour, new FeatureColour(c));
 209             };
 210           };
 211           JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
 212                   title, fcol.getColour(), listener);
 213         }
 214         else
 215         {
 216           /*
 217            * variable colour dialog - on OK, refetch the updated
 218            * feature colour and update this display
 219            */
 220           final String ft = features.get(featureIndex).getType();
 221           final String type = ft == null ? lastFeatureAdded : ft;
 222           FeatureTypeSettings fcc = new FeatureTypeSettings(
 223                   FeatureRenderer.this, type);
 224           fcc.setRequestFocusEnabled(true);
 225           fcc.requestFocus();
 226           fcc.addActionListener(new ActionListener()
 227           {
 228             @Override
 229             public void actionPerformed(ActionEvent e)
 230             {
 231               fcol = FeatureRenderer.this.getFeatureStyle(ft);
 232               setColour(type, fcol);
 233               updateColourButton(mainPanel, colour, fcol);
 234             }
 235           });
 236         }
 237       }
 238     });
 239     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 240
 241     if (!create && features.size() > 1)
 242     {
 243       /*
 244        * more than one feature at selected position -
 245        * add a drop-down to choose the feature to amend
 246        * space pad text if necessary to make entries distinct
 247        */
 248       gridPanel = new JPanel(new GridLayout(4, 1));
 249       JPanel choosePanel = new JPanel();
 250       choosePanel.add(new JLabel(
 251               MessageManager.getString("label.select_feature") + ":"));
 252       final JComboBox<String> overlaps = new JComboBox<>();
 253       List<String> added = new ArrayList<>();
 254       for (SequenceFeature sf : features)
 255       {
 256         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 257                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 258         while (added.contains(text))
 259         {
 260           text += " ";
 261         }
 262         overlaps.addItem(text);
 263         added.add(text);
 264       }
 265       choosePanel.add(overlaps);
 266
 267       overlaps.addItemListener(new ItemListener()
 268       {
 269         @Override
 270         public void itemStateChanged(ItemEvent e)
 271         {
 272           int index = overlaps.getSelectedIndex();
 273           if (index != -1)
 274           {
 275             featureIndex = index;
 276             SequenceFeature sf = features.get(index);
 277             name.setText(sf.getType());
 278             description.setText(sf.getDescription());
 279             group.setText(sf.getFeatureGroup());
 280             start.setValue(new Integer(sf.getBegin()));
 281             end.setValue(new Integer(sf.getEnd()));
 282
 283             SearchResultsI highlight = new SearchResults();
 284             highlight.addResult(sequences.get(0), sf.getBegin(),
 285                     sf.getEnd());
 286
 287             alignPanel.getSeqPanel().seqCanvas
 288                     .highlightSearchResults(highlight, false);
 289           }
 290           FeatureColourI col = getFeatureStyle(name.getText());
 291           if (col == null)
 292           {
 293             col = new FeatureColour(
 294                     ColorUtils.createColourFromName(name.getText()));
 295           }
 296           oldcol = fcol = col;
 297           updateColourButton(mainPanel, colour, col);
 298         }
 299       });
 300
 301       gridPanel.add(choosePanel);
 302     }
 303
 304     JPanel namePanel = new JPanel();
 305     gridPanel.add(namePanel);
 306     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 307             JLabel.RIGHT));
 308     namePanel.add(name);
 309
 310     JPanel groupPanel = new JPanel();
 311     gridPanel.add(groupPanel);
 312     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 313             JLabel.RIGHT));
 314     groupPanel.add(group);
 315
 316     JPanel colourPanel = new JPanel();
 317     gridPanel.add(colourPanel);
 318     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 319             JLabel.RIGHT));
 320     colourPanel.add(colour);
 321     colour.setPreferredSize(new Dimension(150, 15));
 322     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 323     colour.setForeground(Color.black);
 324     colour.setHorizontalAlignment(SwingConstants.CENTER);
 325     colour.setVerticalAlignment(SwingConstants.CENTER);
 326     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 327     colour.setVerticalTextPosition(SwingConstants.CENTER);
 328     mainPanel.add(gridPanel, BorderLayout.NORTH);
 329
 330     JPanel descriptionPanel = new JPanel();
 331     descriptionPanel.add(new JLabel(
 332             MessageManager.getString("label.description:"), JLabel.RIGHT));
 333     description.setFont(JvSwingUtils.getTextAreaFont());
 334     description.setLineWrap(true);
 335     descriptionPanel.add(new JScrollPane(description));
 336
 337     if (!create)
 338     {
 339       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 340
 341       JPanel startEndPanel = new JPanel();
 342       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 343               JLabel.RIGHT));
 344       startEndPanel.add(start);
 345       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 346               JLabel.RIGHT));
 347       startEndPanel.add(end);
 348       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 349     }
 350     else
 351     {
 352       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 353     }
 354
 355     /*
 356      * default feature type and group to that of the first feature supplied,
 357      * or to the last feature created if not supplied (null value)
 358      */
 359     SequenceFeature firstFeature = features.get(0);
 360     boolean useLastDefaults = firstFeature.getType() == null;
 361     final String featureType = useLastDefaults ? lastFeatureAdded
 362             : firstFeature.getType();
 363     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 364             : firstFeature.getFeatureGroup();
 365     name.setText(featureType);
 366     group.setText(featureGroup);
 367
 368     start.setValue(new Integer(firstFeature.getBegin()));
 369     end.setValue(new Integer(firstFeature.getEnd()));
 370     description.setText(firstFeature.getDescription());
 371     updateColourButton(mainPanel, colour,
 372             (oldcol = fcol = getFeatureStyle(featureType)));
 373     Object[] options;
 374     if (!create)
 375     {
 376       options = new Object[] { MessageManager.getString("label.amend"),
 377           MessageManager.getString("action.delete"),
 378           MessageManager.getString("action.cancel") };
 379     }
 380     else
 381     {
 382       options = new Object[] { MessageManager.getString("action.ok"),
 383           MessageManager.getString("action.cancel") };
 384     }
 385
 386     String title = create
 387             ? MessageManager.getString("label.create_new_sequence_features")
 388             : MessageManager.formatMessage("label.amend_delete_features",
 389                     new String[]
 390                     { sequences.get(0).getName() });
 391
 392     /*
 393      * register responses and show the dialog
 394      */
 395     JvOptionPane.newOptionDialog(Desktop.desktop).response(
 396
 397             new RunResponse(JvOptionPane.OK_OPTION)
 398             {
 399               public void run()
 400               {
 401                 final String enteredType = name.getText().trim();
 402                 final String enteredGroup = group.getText().trim();
 403                 final String enteredDescription = description.getText()
 404                         .replaceAll("\n", " ");
 405                 if (enteredType.length() > 0)
 406
 407                 {
 408                   /*
 409                    * update default values only if creating using default values
 410                    */
 411                   if (useLastDefaults)
 412                   {
 413                     lastFeatureAdded = enteredType;
 414                     lastFeatureGroupAdded = enteredGroup;
 415                     // TODO: determine if the null feature group is valid
 416                     if (lastFeatureGroupAdded.length() < 1)
 417                     {
 418                       lastFeatureGroupAdded = null;
 419                     }
 420                   }
 421                 }
 422
 423                 if (create)
 424                 {
 425                   // NEW FEATURES ADDED
 426                   if (enteredType.length() > 0)
 427                   {
 428                     for (int i = 0; i < sequences.size(); i++)
 429                     {
 430                       SequenceFeature sf = features.get(i);
 431                       SequenceFeature sf2 = new SequenceFeature(enteredType,
 432                               enteredDescription, sf.getBegin(),
 433                               sf.getEnd(), enteredGroup);
 434                       new FeaturesFile().parseDescriptionHTML(sf2, false);
 435                       sequences.get(i).addSequenceFeature(sf2);
 436                     }
 437
 438                     setColour(enteredType, fcol);
 439
 440                     featuresAdded();
 441
 442                     responseHandler.run();
 443                   }
 444                 } else {
 445                   SequenceFeature sf = features.get(featureIndex);
 446                   /*
 447                    * Feature amended - YES_OPTION corresponds to the Amend button
 448                    * need to refresh Feature Settings if type, group or colour changed;
 449                    * note we don't force the feature to be visible - the user has been
 450                    * warned if a hidden feature type or group was entered
 451                    */
 452                   boolean refreshSettings = (!featureType.equals(enteredType)
 453                           || !featureGroup.equals(enteredGroup));
 454                   refreshSettings |= (fcol != oldcol);
 455                   setColour(enteredType, fcol);
 456                   int newBegin = sf.begin;
 457                   int newEnd = sf.end;
 458                   try
 459                   {
 460                     newBegin = ((Integer) start.getValue()).intValue();
 461                     newEnd = ((Integer) end.getValue()).intValue();
 462                   } catch (NumberFormatException ex)
 463                   {
 464                     // JSpinner doesn't accept invalid format data :-)
 465                   }
 466
 467                   /*
 468                    * replace the feature by deleting it and adding a new one
 469                    * (to ensure integrity of SequenceFeatures data store)
 470                    */
 471                   sequences.get(0).deleteFeature(sf);
 472                   SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 473                           newBegin, newEnd, enteredGroup, sf.getScore());
 474                   newSf.setDescription(enteredDescription);
 475                   new FeaturesFile().parseDescriptionHTML(newSf, false);
 476                   // amend features dialog only updates one sequence at a time
 477                   sequences.get(0).addSequenceFeature(newSf);
 478
 479                   if (refreshSettings)
 480                   {
 481                     featuresAdded();
 482                   }
 483                 }
 484                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 485                 alignPanel.paintAlignment(true, true);
 486               }
 487             }).response(new RunResponse(JvOptionPane.NO_OPTION)
 488             {
 489               public void run()
 490               {
 491                 SequenceFeature sf = features.get(featureIndex);
 492                 /*
 493                  * NO_OPTION corresponds to the Delete button
 494                  */
 495                 sequences.get(0).getDatasetSequence().deleteFeature(sf);
 496                 // update Feature Settings for removal of feature / group
 497                 featuresAdded();
 498                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 499                 alignPanel.paintAlignment(true, true);
 500               }
 501             }).defaultResponse(new Runnable()
 502             {
 503               public void run()
 504               {
 505                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 506                 alignPanel.paintAlignment(true, true);
 507               }
 508             }).showInternalDialog(mainPanel, title,
 509                     JvOptionPane.YES_NO_CANCEL_OPTION,
 510                     JvOptionPane.QUESTION_MESSAGE, null, options,
 511                     MessageManager.getString("action.ok"));
 512     return true;
 513   }
 514
 515   /**
 516    * Show a warning message if the entered type is one that is currently hidden
 517    *
 518    * @param panel
 519    * @param type
 520    */
 521   protected void warnIfTypeHidden(JPanel panel, String type)
 522   {
 523     if (getRenderOrder().contains(type))
 524     {
 525       if (!showFeatureOfType(type))
 526       {
 527         String msg = MessageManager.formatMessage("label.warning_hidden",
 528                 MessageManager.getString("label.feature_type"), type);
 529         JvOptionPane.showMessageDialog(panel, msg, "",
 530                 JvOptionPane.OK_OPTION);
 531       }
 532     }
 533   }
 534
 535   /**
 536    * Show a warning message if the entered group is one that is currently hidden
 537    *
 538    * @param panel
 539    * @param group
 540    */
 541   protected void warnIfGroupHidden(JPanel panel, String group)
 542   {
 543     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 544     {
 545       String msg = MessageManager.formatMessage("label.warning_hidden",
 546               MessageManager.getString("label.group"), group);
 547       JvOptionPane.showMessageDialog(panel, msg, "",
 548               JvOptionPane.OK_OPTION);
 549     }
 550   }
 551
 552   /**
 553    * update the amend feature button dependent on the given style
 554    *
 555    * @param bigPanel
 556    * @param col
 557    * @param col
 558    */
 559   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 560           FeatureColourI col)
 561   {
 562     colour.removeAll();
 563     colour.setIcon(null);
 564     colour.setToolTipText(null);
 565     colour.setText("");
 566
 567     if (col.isSimpleColour())
 568     {
 569       colour.setBackground(col.getColour());
 570     }
 571     else
 572     {
 573       colour.setBackground(bigPanel.getBackground());
 574       colour.setForeground(Color.black);
 575       FeatureSettings.renderGraduatedColor(colour, col);
 576     }
 577   }
 578
 579   /**
 580    * Orders features in render precedence (last in order is last to render, so
 581    * displayed on top of other features)
 582    *
 583    * @param order
 584    */
 585   public void orderFeatures(Comparator<String> order)
 586   {
 587     Arrays.sort(renderOrder, order);
 588   }
 589 }