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