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.ArrayList;
  45 import java.util.Arrays;
  46 import java.util.Comparator;
  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
  68         extends 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 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       /*
 190        * open colour chooser on click in colour panel
 191        */
 192       @Override
 193       public void mousePressed(MouseEvent evt)
 194       {
 195         if (fcol.isSimpleColour())
 196         {
 197           // BH 2018 JavaScript-compatible color dialog
 198           Desktop.desktop.dialogData = new Object[] {
 199               "label.select_feature_colour", this, mainPanel, colour };
 200           Desktop.desktop
 201                   .onDialogReturn(JColorChooser.showDialog(Desktop.desktop,
 202                   MessageManager.getString("label.select_feature_colour"),
 203                           fcol.getColour()));
 204         }
 205         else
 206         {
 207           /*
 208            * variable colour dialog - on OK, refetch the updated
 209            * feature colour and update this display
 210            */
 211           final String ft = features.get(featureIndex).getType();
 212           final String type = ft == null ? lastFeatureAdded : ft;
 213           FeatureTypeSettings fcc = new FeatureTypeSettings(
 214                   FeatureRenderer.this, type);
 215           fcc.setRequestFocusEnabled(true);
 216           fcc.requestFocus();
 217           fcc.addActionListener(new ActionListener()
 218           {
 219             @Override
 220             public void actionPerformed(ActionEvent e)
 221             {
 222               fcol = FeatureRenderer.this.getFeatureStyle(ft);
 223               setColour(type, fcol);
 224               updateColourButton(mainPanel, colour, fcol);
 225             }
 226           });
 227         }
 228       }
 229     });
 230     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 231
 232     if (!create && features.size() > 1)
 233     {
 234       /*
 235        * more than one feature at selected position -
 236        * add a drop-down to choose the feature to amend
 237        * space pad text if necessary to make entries distinct
 238        */
 239       gridPanel = new JPanel(new GridLayout(4, 1));
 240       JPanel choosePanel = new JPanel();
 241       choosePanel.add(new JLabel(
 242               MessageManager.getString("label.select_feature") + ":"));
 243       final JComboBox<String> overlaps = new JComboBox<>();
 244       List<String> added = new ArrayList<>();
 245       for (SequenceFeature sf : features)
 246       {
 247         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 248                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 249         while (added.contains(text))
 250         {
 251           text += " ";
 252         }
 253         overlaps.addItem(text);
 254         added.add(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(
 279                     highlight, false);
 280           }
 281           FeatureColourI col = getFeatureStyle(name.getText());
 282           if (col == null)
 283           {
 284             col = new FeatureColour(
 285                     ColorUtils.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(
 323             MessageManager.getString("label.description:"), JLabel.RIGHT));
 324     description.setFont(JvSwingUtils.getTextAreaFont());
 325     description.setLineWrap(true);
 326     descriptionPanel.add(new JScrollPane(description));
 327
 328     if (!create)
 329     {
 330       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 331
 332       JPanel startEndPanel = new JPanel();
 333       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 334               JLabel.RIGHT));
 335       startEndPanel.add(start);
 336       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 337               JLabel.RIGHT));
 338       startEndPanel.add(end);
 339       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 340     }
 341     else
 342     {
 343       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 344     }
 345
 346     /*
 347      * default feature type and group to that of the first feature supplied,
 348      * or to the last feature created if not supplied (null value)
 349      */
 350     SequenceFeature firstFeature = features.get(0);
 351     boolean useLastDefaults = firstFeature.getType() == null;
 352     final String featureType = useLastDefaults ? lastFeatureAdded
 353             : firstFeature.getType();
 354     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 355             : firstFeature.getFeatureGroup();
 356     name.setText(featureType);
 357     group.setText(featureGroup);
 358
 359     start.setValue(new Integer(firstFeature.getBegin()));
 360     end.setValue(new Integer(firstFeature.getEnd()));
 361     description.setText(firstFeature.getDescription());
 362     updateColourButton(mainPanel, colour,
 363             (oldcol = fcol = getFeatureStyle(featureType)));
 364     Object[] options;
 365     if (!create)
 366     {
 367       options = new Object[] { MessageManager.getString("label.amend"),
 368           MessageManager.getString("action.delete"),
 369           MessageManager.getString("action.cancel") };
 370     }
 371     else
 372     {
 373       options = new Object[] { MessageManager.getString("action.ok"),
 374           MessageManager.getString("action.cancel") };
 375     }
 376
 377     String title = create
 378             ? MessageManager.getString("label.create_new_sequence_features")
 379             : MessageManager.formatMessage("label.amend_delete_features",
 380                     new String[]
 381                     { sequences.get(0).getName() });
 382
 383     /*
 384      * show the dialog
 385      */
 386     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 387             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 388             JvOptionPane.QUESTION_MESSAGE, null, options,
 389             MessageManager.getString("action.ok"));
 390
 391     FeaturesFile ffile = new FeaturesFile();
 392
 393     final String enteredType = name.getText().trim();
 394     final String enteredGroup = group.getText().trim();
 395     final String enteredDescription = description.getText().replaceAll("\n", " ");
 396
 397     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 398     {
 399       /*
 400        * update default values only if creating using default values
 401        */
 402       if (useLastDefaults)
 403       {
 404         lastFeatureAdded = enteredType;
 405         lastFeatureGroupAdded = enteredGroup;
 406         // TODO: determine if the null feature group is valid
 407         if (lastFeatureGroupAdded.length() < 1)
 408         {
 409           lastFeatureGroupAdded = null;
 410         }
 411       }
 412     }
 413
 414     if (!create)
 415     {
 416       SequenceFeature sf = features.get(featureIndex);
 417
 418       if (reply == JvOptionPane.NO_OPTION)
 419       {
 420         /*
 421          * NO_OPTION corresponds to the Delete button
 422          */
 423         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 424         // update Feature Settings for removal of feature / group
 425         featuresAdded();
 426       }
 427       else if (reply == JvOptionPane.YES_OPTION)
 428       {
 429         /*
 430          * YES_OPTION corresponds to the Amend button
 431          * need to refresh Feature Settings if type, group or colour changed;
 432          * note we don't force the feature to be visible - the user has been
 433          * warned if a hidden feature type or group was entered
 434          */
 435         boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
 436                 .equals(enteredGroup));
 437         refreshSettings |= (fcol != oldcol);
 438         setColour(enteredType, fcol);
 439         int newBegin = sf.begin;
 440         int newEnd = sf.end;
 441         try
 442         {
 443           newBegin = ((Integer) start.getValue()).intValue();
 444           newEnd = ((Integer) end.getValue()).intValue();
 445         } catch (NumberFormatException ex)
 446         {
 447           // JSpinner doesn't accept invalid format data :-)
 448         }
 449
 450         /*
 451          * replace the feature by deleting it and adding a new one
 452          * (to ensure integrity of SequenceFeatures data store)
 453          */
 454         sequences.get(0).deleteFeature(sf);
 455         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 456                 newBegin, newEnd, enteredGroup, sf.getScore());
 457         newSf.setDescription(enteredDescription);
 458         ffile.parseDescriptionHTML(newSf, false);
 459         // amend features dialog only updates one sequence at a time
 460         sequences.get(0).addSequenceFeature(newSf);
 461
 462         if (refreshSettings)
 463         {
 464           featuresAdded();
 465         }
 466       }
 467     }
 468     else
 469     // NEW FEATURES ADDED
 470     {
 471       if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 472       {
 473         for (int i = 0; i < sequences.size(); i++)
 474         {
 475           SequenceFeature sf = features.get(i);
 476           SequenceFeature sf2 = new SequenceFeature(enteredType,
 477                   enteredDescription, sf.getBegin(), sf.getEnd(),
 478                   enteredGroup);
 479           ffile.parseDescriptionHTML(sf2, false);
 480           sequences.get(i).addSequenceFeature(sf2);
 481         }
 482
 483         setColour(enteredType, fcol);
 484
 485         featuresAdded();
 486
 487         alignPanel.paintAlignment(true, true);
 488
 489         return true;
 490       }
 491       else
 492       {
 493         return false;
 494       }
 495     }
 496
 497     alignPanel.paintAlignment(true, true);
 498
 499     return true;
 500   }
 501
 502   void processColorDialog(Color col)
 503   {
 504     JPanel mainPanel = (JPanel) Desktop.desktop.dialogData[2];
 505     JLabel colour = (JLabel) Desktop.desktop.dialogData[3];
 506     if (col != null)
 507     {
 508       fcol = new FeatureColour(col);
 509       updateColourButton(mainPanel, colour, fcol);
 510     }
 511   }
 512
 513   /**
 514    * Show a warning message if the entered type is one that is currently hidden
 515    *
 516    * @param panel
 517    * @param type
 518    */
 519   protected void warnIfTypeHidden(JPanel panel, String type)
 520   {
 521     if (getRenderOrder().contains(type))
 522     {
 523       if (!showFeatureOfType(type))
 524       {
 525         String msg = MessageManager.formatMessage("label.warning_hidden",
 526                 MessageManager.getString("label.feature_type"), type);
 527         JvOptionPane.showMessageDialog(panel, msg, "",
 528                 JvOptionPane.OK_OPTION);
 529       }
 530     }
 531   }
 532
 533   /**
 534    * Show a warning message if the entered group is one that is currently hidden
 535    *
 536    * @param panel
 537    * @param group
 538    */
 539   protected void warnIfGroupHidden(JPanel panel, String group)
 540   {
 541     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 542     {
 543       String msg = MessageManager.formatMessage("label.warning_hidden",
 544               MessageManager.getString("label.group"), group);
 545       JvOptionPane.showMessageDialog(panel, msg, "",
 546               JvOptionPane.OK_OPTION);
 547     }
 548   }
 549
 550   /**
 551    * update the amend feature button dependent on the given style
 552    *
 553    * @param bigPanel
 554    * @param col
 555    * @param col
 556    */
 557   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 558           FeatureColourI col)
 559   {
 560     colour.removeAll();
 561     colour.setIcon(null);
 562     colour.setToolTipText(null);
 563     colour.setText("");
 564
 565     if (col.isSimpleColour())
 566     {
 567       colour.setBackground(col.getColour());
 568     }
 569     else
 570     {
 571       colour.setBackground(bigPanel.getBackground());
 572       colour.setForeground(Color.black);
 573       FeatureSettings.renderGraduatedColor(colour, col);
 574     }
 575   }
 576
 577   /**
 578    * Orders features in render precedence (last in order is last to render, so
 579    * displayed on top of other features)
 580    *
 581    * @param order
 582    */
 583   public void orderFeatures(Comparator<String> order)
 584   {
 585     Arrays.sort(renderOrder, order);
 586   }
 587 }