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