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   Color resBoxColour;
  70
  71   AlignmentPanel ap;
  72
  73   /**
  74    * Creates a new FeatureRenderer object
  75    *
  76    * @param alignPanel
  77    */
  78   public FeatureRenderer(AlignmentPanel alignPanel)
  79   {
  80     super(alignPanel.av);
  81     this.ap = alignPanel;
  82     if (alignPanel.getSeqPanel() != null
  83             && alignPanel.getSeqPanel().seqCanvas != null
  84             && alignPanel.getSeqPanel().seqCanvas.fr != null)
  85     {
  86       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
  87     }
  88   }
  89
  90   // // /////////////
  91   // // Feature Editing Dialog
  92   // // Will be refactored in next release.
  93
  94   static String lastFeatureAdded;
  95
  96   static String lastFeatureGroupAdded;
  97
  98   static String lastDescriptionAdded;
  99
 100   FeatureColourI oldcol, fcol;
 101
 102   int featureIndex = 0;
 103
 104   /**
 105    * Presents a dialog allowing the user to add new features, or amend or delete
 106    * existing features. Currently this can be on
 107    * <ul>
 108    * <li>double-click on a sequence - Amend/Delete features at position</li>
 109    * <li>Create sequence feature from pop-up menu on selected region</li>
 110    * <li>Create features for pattern matches from Find</li>
 111    * </ul>
 112    *
 113    * @param sequences
 114    *          the sequences features are to be created on (if creating
 115    *          features), or a single sequence (if amending features)
 116    * @param features
 117    *          the current features at the position (if amending), or template
 118    *          new features with start/end position set (if creating)
 119    * @param create
 120    *          true to create features, false to amend or delete
 121    * @param featureType
 122    *          the feature type to set on new features; if null, defaults to the
 123    *          type of the last new feature created if any, failing that to
 124    *          "feature_1"
 125    * @param alignPanel
 126    * @return
 127    */
 128   protected boolean amendFeatures(final List<SequenceI> sequences,
 129           final List<SequenceFeature> features, boolean create,
 130           final AlignmentPanel alignPanel, String featureType)
 131   {
 132
 133     featureIndex = 0;
 134
 135     final JPanel mainPanel = new JPanel(new BorderLayout());
 136
 137     final JTextField name = new JTextField(25);
 138     name.getDocument().addDocumentListener(new DocumentListener()
 139     {
 140       @Override
 141       public void insertUpdate(DocumentEvent e)
 142       {
 143         warnIfTypeHidden(mainPanel, name.getText());
 144       }
 145
 146       @Override
 147       public void removeUpdate(DocumentEvent e)
 148       {
 149         warnIfTypeHidden(mainPanel, name.getText());
 150       }
 151
 152       @Override
 153       public void changedUpdate(DocumentEvent e)
 154       {
 155         warnIfTypeHidden(mainPanel, name.getText());
 156       }
 157     });
 158
 159     final JTextField group = new JTextField(25);
 160     group.getDocument().addDocumentListener(new DocumentListener()
 161     {
 162       @Override
 163       public void insertUpdate(DocumentEvent e)
 164       {
 165         warnIfGroupHidden(mainPanel, group.getText());
 166       }
 167
 168       @Override
 169       public void removeUpdate(DocumentEvent e)
 170       {
 171         warnIfGroupHidden(mainPanel, group.getText());
 172       }
 173
 174       @Override
 175       public void changedUpdate(DocumentEvent e)
 176       {
 177         warnIfGroupHidden(mainPanel, group.getText());
 178       }
 179     });
 180
 181     final JTextArea description = new JTextArea(3, 25);
 182     final JSpinner start = new JSpinner();
 183     final JSpinner end = new JSpinner();
 184     start.setPreferredSize(new Dimension(80, 20));
 185     end.setPreferredSize(new Dimension(80, 20));
 186     final FeatureRenderer me = this;
 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       FeatureColourChooser fcc = null;
 194
 195       @Override
 196       public void mousePressed(MouseEvent evt)
 197       {
 198         if (fcol.isSimpleColour())
 199         {
 200           Color col = JColorChooser.showDialog(Desktop.desktop,
 201                   MessageManager.getString("label.select_feature_colour"),
 202                   fcol.getColour());
 203           if (col != null)
 204           {
 205             fcol = new FeatureColour(col);
 206             updateColourButton(mainPanel, colour, new FeatureColour(col));
 207           }
 208         }
 209         else
 210         {
 211           if (fcc == null)
 212           {
 213             final String ft = features.get(featureIndex).getType();
 214             final String type = ft == null ? lastFeatureAdded : ft;
 215             fcc = new FeatureColourChooser(me, type);
 216             fcc.setRequestFocusEnabled(true);
 217             fcc.requestFocus();
 218
 219             fcc.addActionListener(new ActionListener()
 220             {
 221
 222               @Override
 223               public void actionPerformed(ActionEvent e)
 224               {
 225                 fcol = fcc.getLastColour();
 226                 fcc = null;
 227                 setColour(type, fcol);
 228                 updateColourButton(mainPanel, colour, fcol);
 229               }
 230             });
 231
 232           }
 233         }
 234       }
 235     });
 236     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 237
 238     if (!create && features.size() > 1)
 239     {
 240       /*
 241        * more than one feature at selected position - add a drop-down
 242        * to choose the feature to amend
 243        */
 244       gridPanel = new JPanel(new GridLayout(4, 1));
 245       JPanel choosePanel = new JPanel();
 246       choosePanel.add(new JLabel(MessageManager
 247               .getString("label.select_feature")
 248               + ":"));
 249       final JComboBox<String> overlaps = new JComboBox<String>();
 250       for (SequenceFeature sf : features)
 251       {
 252         String text = sf.getType() + "/" + sf.getBegin() + "-"
 253                 + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
 254         overlaps.addItem(text);
 255       }
 256       choosePanel.add(overlaps);
 257
 258       overlaps.addItemListener(new ItemListener()
 259       {
 260         @Override
 261         public void itemStateChanged(ItemEvent e)
 262         {
 263           int index = overlaps.getSelectedIndex();
 264           if (index != -1)
 265           {
 266             featureIndex = index;
 267             SequenceFeature sf = features.get(index);
 268             name.setText(sf.getType());
 269             description.setText(sf.getDescription());
 270             group.setText(sf.getFeatureGroup());
 271             start.setValue(new Integer(sf.getBegin()));
 272             end.setValue(new Integer(sf.getEnd()));
 273
 274             SearchResultsI highlight = new SearchResults();
 275             highlight.addResult(sequences.get(0), sf.getBegin(),
 276                     sf.getEnd());
 277
 278             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 279
 280           }
 281           FeatureColourI col = getFeatureStyle(name.getText());
 282           if (col == null)
 283           {
 284             col = new FeatureColour(ColorUtils
 285                     .createColourFromName(name.getText()));
 286           }
 287           oldcol = fcol = col;
 288           updateColourButton(mainPanel, colour, col);
 289         }
 290       });
 291
 292       gridPanel.add(choosePanel);
 293     }
 294
 295     JPanel namePanel = new JPanel();
 296     gridPanel.add(namePanel);
 297     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 298             JLabel.RIGHT));
 299     namePanel.add(name);
 300
 301     JPanel groupPanel = new JPanel();
 302     gridPanel.add(groupPanel);
 303     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 304             JLabel.RIGHT));
 305     groupPanel.add(group);
 306
 307     JPanel colourPanel = new JPanel();
 308     gridPanel.add(colourPanel);
 309     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 310             JLabel.RIGHT));
 311     colourPanel.add(colour);
 312     colour.setPreferredSize(new Dimension(150, 15));
 313     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 314     colour.setForeground(Color.black);
 315     colour.setHorizontalAlignment(SwingConstants.CENTER);
 316     colour.setVerticalAlignment(SwingConstants.CENTER);
 317     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 318     colour.setVerticalTextPosition(SwingConstants.CENTER);
 319     mainPanel.add(gridPanel, BorderLayout.NORTH);
 320
 321     JPanel descriptionPanel = new JPanel();
 322     descriptionPanel.add(new JLabel(MessageManager
 323             .getString("label.description:"),
 324             JLabel.RIGHT));
 325     description.setFont(JvSwingUtils.getTextAreaFont());
 326     description.setLineWrap(true);
 327     descriptionPanel.add(new JScrollPane(description));
 328
 329     if (!create)
 330     {
 331       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 332
 333       JPanel startEndPanel = new JPanel();
 334       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 335               JLabel.RIGHT));
 336       startEndPanel.add(start);
 337       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 338               JLabel.RIGHT));
 339       startEndPanel.add(end);
 340       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 341     }
 342     else
 343     {
 344       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 345     }
 346
 347     SequenceFeature firstFeature = features.get(0);
 348     if (featureType != null)
 349     {
 350       lastFeatureAdded = featureType;
 351     }
 352     else
 353     {
 354       if (lastFeatureAdded == null)
 355       {
 356         if (firstFeature.type != null)
 357         {
 358           lastFeatureAdded = firstFeature.type;
 359         }
 360         else
 361         {
 362           lastFeatureAdded = "feature_1";
 363         }
 364       }
 365     }
 366
 367     if (lastFeatureGroupAdded == null)
 368     {
 369       if (firstFeature.featureGroup != null)
 370       {
 371         lastFeatureGroupAdded = firstFeature.featureGroup;
 372       }
 373       else
 374       {
 375         lastFeatureGroupAdded = "Jalview";
 376       }
 377     }
 378
 379     if (create)
 380     {
 381       name.setText(lastFeatureAdded);
 382       group.setText(lastFeatureGroupAdded);
 383     }
 384     else
 385     {
 386       name.setText(firstFeature.getType());
 387       group.setText(firstFeature.getFeatureGroup());
 388     }
 389
 390     start.setValue(new Integer(firstFeature.getBegin()));
 391     end.setValue(new Integer(firstFeature.getEnd()));
 392     description.setText(firstFeature.getDescription());
 393     updateColourButton(mainPanel, colour,
 394             (oldcol = fcol = getFeatureStyle(name.getText())));
 395     Object[] options;
 396     if (!create)
 397     {
 398       options = new Object[] { MessageManager.getString("label.amend"),
 399           MessageManager.getString("action.delete"),
 400           MessageManager.getString("action.cancel") };
 401     }
 402     else
 403     {
 404       options = new Object[] { MessageManager.getString("action.ok"),
 405           MessageManager.getString("action.cancel") };
 406     }
 407
 408     String title = create ? MessageManager
 409             .getString("label.create_new_sequence_features")
 410             : MessageManager.formatMessage("label.amend_delete_features",
 411                     new String[] { sequences.get(0).getName() });
 412
 413     /*
 414      * show the dialog
 415      */
 416     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 417             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 418             JvOptionPane.QUESTION_MESSAGE, null, options,
 419             MessageManager.getString("action.ok"));
 420
 421     FeaturesFile ffile = new FeaturesFile();
 422
 423     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 424     {
 425       lastFeatureAdded = name.getText().trim();
 426       lastFeatureGroupAdded = group.getText().trim();
 427       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 428       // TODO: determine if the null feature group is valid
 429       if (lastFeatureGroupAdded.length() < 1)
 430       {
 431         lastFeatureGroupAdded = null;
 432       }
 433     }
 434
 435     if (!create)
 436     {
 437       SequenceFeature sf = features.get(featureIndex);
 438
 439       if (reply == JvOptionPane.NO_OPTION)
 440       {
 441         /*
 442          * NO_OPTION corresponds to the Delete button
 443          */
 444         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 445         // update Feature Settings for removal of feature / group
 446         featuresAdded();
 447       }
 448       else if (reply == JvOptionPane.YES_OPTION)
 449       {
 450         /*
 451          * YES_OPTION corresponds to the Amend button
 452          */
 453         boolean refreshSettings = (!lastFeatureAdded.equals(sf.type) || !lastFeatureGroupAdded
 454                 .equals(sf.featureGroup));
 455         refreshSettings |= (fcol != oldcol);
 456         sf.type = lastFeatureAdded;
 457         sf.featureGroup = lastFeatureGroupAdded;
 458         sf.description = lastDescriptionAdded;
 459
 460         setColour(sf.type, fcol);
 461
 462         try
 463         {
 464           sf.begin = ((Integer) start.getValue()).intValue();
 465           sf.end = ((Integer) end.getValue()).intValue();
 466         } catch (NumberFormatException ex)
 467         {
 468         }
 469
 470         ffile.parseDescriptionHTML(sf, false);
 471         if (refreshSettings)
 472         {
 473           featuresAdded();
 474         }
 475       }
 476     }
 477     else
 478     // NEW FEATURES ADDED
 479     {
 480       if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 481       {
 482         for (int i = 0; i < sequences.size(); i++)
 483         {
 484           SequenceFeature sf = features.get(i);
 485           sf.type = lastFeatureAdded;
 486           // fix for JAL-1538 - always set feature group here
 487           sf.featureGroup = lastFeatureGroupAdded;
 488           sf.description = lastDescriptionAdded;
 489           sequences.get(i).addSequenceFeature(sf);
 490           ffile.parseDescriptionHTML(sf, false);
 491         }
 492
 493         setColour(lastFeatureAdded, 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 }