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