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 import jalview.util.dialogrunner.RunResponse;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.Dimension;
  38 import java.awt.Font;
  39 import java.awt.GridLayout;
  40 import java.awt.event.ActionEvent;
  41 import java.awt.event.ActionListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.util.ArrayList;
  47 import java.util.Arrays;
  48 import java.util.Comparator;
  49 import java.util.List;
  50
  51 import javax.swing.JColorChooser;
  52 import javax.swing.JComboBox;
  53 import javax.swing.JDialog;
  54 import javax.swing.JLabel;
  55 import javax.swing.JPanel;
  56 import javax.swing.JScrollPane;
  57 import javax.swing.JSpinner;
  58 import javax.swing.JTextArea;
  59 import javax.swing.JTextField;
  60 import javax.swing.SwingConstants;
  61 import javax.swing.event.DocumentEvent;
  62 import javax.swing.event.DocumentListener;
  63
  64 /**
  65  * DOCUMENT ME!
  66  *
  67  * @author $author$
  68  * @version $Revision$
  69  */
  70 public class FeatureRenderer
  71         extends jalview.renderer.seqfeatures.FeatureRenderer
  72 {
  73   /*
  74    * defaults for creating a new feature are the last created
  75    * feature type and group
  76    */
  77   static String lastFeatureAdded = "feature_1";
  78
  79   static String lastFeatureGroupAdded = "Jalview";
  80
  81   Color resBoxColour;
  82
  83   AlignmentPanel ap;
  84
  85   /**
  86    * Creates a new FeatureRenderer object
  87    *
  88    * @param alignPanel
  89    */
  90   public FeatureRenderer(AlignmentPanel alignPanel)
  91   {
  92     super(alignPanel.av);
  93     this.ap = alignPanel;
  94     if (alignPanel.getSeqPanel() != null
  95             && alignPanel.getSeqPanel().seqCanvas != null
  96             && alignPanel.getSeqPanel().seqCanvas.fr != null)
  97     {
  98       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
  99     }
 100   }
 101
 102   FeatureColourI oldcol, fcol;
 103
 104   int featureIndex = 0;
 105
 106   /**
 107    * Presents a dialog allowing the user to add new features, or amend or delete
 108    * existing features. Currently this can be on
 109    * <ul>
 110    * <li>double-click on a sequence - Amend/Delete features at position</li>
 111    * <li>Create sequence feature from pop-up menu on selected region</li>
 112    * <li>Create features for pattern matches from Find</li>
 113    * </ul>
 114    * If the supplied feature type is null, show (and update on confirm) the type
 115    * and group of the last new feature created (with initial defaults of
 116    * "feature_1" and "Jalview").
 117    *
 118    * @param sequences
 119    *          the sequences features are to be created on (if creating
 120    *          features), or a single sequence (if amending features)
 121    * @param features
 122    *          the current features at the position (if amending), or template
 123    *          new feature(s) with start/end position set (if creating)
 124    * @param create
 125    *          true to create features, false to amend or delete
 126    * @param alignPanel
 127    * @param responseHandler
 128    *          boolean true RunResponse is run if features are created
 129    */
 130   protected boolean amendFeatures(final List<SequenceI> sequences,
 131           final List<SequenceFeature> features, boolean create,
 132           final AlignmentPanel alignPanel, final Runnable responseHandler)
 133   {
 134     featureIndex = 0;
 135
 136     final JPanel mainPanel = new JPanel(new BorderLayout());
 137
 138     final JTextField name = new JTextField(25);
 139     name.getDocument().addDocumentListener(new DocumentListener()
 140     {
 141       @Override
 142       public void insertUpdate(DocumentEvent e)
 143       {
 144         warnIfTypeHidden(mainPanel, name.getText());
 145       }
 146
 147       @Override
 148       public void removeUpdate(DocumentEvent e)
 149       {
 150         warnIfTypeHidden(mainPanel, name.getText());
 151       }
 152
 153       @Override
 154       public void changedUpdate(DocumentEvent e)
 155       {
 156         warnIfTypeHidden(mainPanel, name.getText());
 157       }
 158     });
 159
 160     final JTextField group = new JTextField(25);
 161     group.getDocument().addDocumentListener(new DocumentListener()
 162     {
 163       @Override
 164       public void insertUpdate(DocumentEvent e)
 165       {
 166         warnIfGroupHidden(mainPanel, group.getText());
 167       }
 168
 169       @Override
 170       public void removeUpdate(DocumentEvent e)
 171       {
 172         warnIfGroupHidden(mainPanel, group.getText());
 173       }
 174
 175       @Override
 176       public void changedUpdate(DocumentEvent e)
 177       {
 178         warnIfGroupHidden(mainPanel, group.getText());
 179       }
 180     });
 181
 182     final JTextArea description = new JTextArea(3, 25);
 183     final JSpinner start = new JSpinner();
 184     final JSpinner end = new JSpinner();
 185     start.setPreferredSize(new Dimension(80, 20));
 186     end.setPreferredSize(new Dimension(80, 20));
 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       /*
 194        * open colour chooser on click in colour panel
 195        */
 196       @Override
 197       public void mousePressed(MouseEvent evt)
 198       {
 199         if (fcol.isSimpleColour())
 200         {
 201           String title = MessageManager
 202                   .getString("label.select_feature_colour");
 203           ColourChooserListener listener = new ColourChooserListener()
 204           {
 205             @Override
 206             public void colourSelected(Color c)
 207             {
 208               fcol = new FeatureColour(c);
 209               updateColourButton(mainPanel, colour, fcol);
 210             };
 211           };
 212           JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
 213                   title, fcol.getColour(), listener);
 214         }
 215         else
 216         {
 217           /*
 218            * variable colour dialog - on OK, refetch the updated
 219            * feature colour and update this display
 220            */
 221           final String ft = features.get(featureIndex).getType();
 222           final String type = ft == null ? lastFeatureAdded : ft;
 223           FeatureTypeSettings fcc = new FeatureTypeSettings(
 224                   FeatureRenderer.this, type);
 225           fcc.setRequestFocusEnabled(true);
 226           fcc.requestFocus();
 227           fcc.addActionListener(new ActionListener()
 228           {
 229             @Override
 230             public void actionPerformed(ActionEvent e)
 231             {
 232               fcol = FeatureRenderer.this.getFeatureStyle(ft);
 233               setColour(type, fcol);
 234               updateColourButton(mainPanel, colour, fcol);
 235             }
 236           });
 237         }
 238       }
 239     });
 240     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 241
 242     if (!create && features.size() > 1)
 243     {
 244       /*
 245        * more than one feature at selected position -
 246        * add a drop-down to choose the feature to amend
 247        * space pad text if necessary to make entries distinct
 248        */
 249       gridPanel = new JPanel(new GridLayout(4, 1));
 250       JPanel choosePanel = new JPanel();
 251       choosePanel.add(new JLabel(
 252               MessageManager.getString("label.select_feature") + ":"));
 253       final JComboBox<String> overlaps = new JComboBox<>();
 254       List<String> added = new ArrayList<>();
 255       for (SequenceFeature sf : features)
 256       {
 257         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 258                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 259         while (added.contains(text))
 260         {
 261           text += " ";
 262         }
 263         overlaps.addItem(text);
 264         added.add(text);
 265       }
 266       choosePanel.add(overlaps);
 267
 268       overlaps.addItemListener(new ItemListener()
 269       {
 270         @Override
 271         public void itemStateChanged(ItemEvent e)
 272         {
 273           int index = overlaps.getSelectedIndex();
 274           if (index != -1)
 275           {
 276             featureIndex = index;
 277             SequenceFeature sf = features.get(index);
 278             name.setText(sf.getType());
 279             description.setText(sf.getDescription());
 280             group.setText(sf.getFeatureGroup());
 281             start.setValue(new Integer(sf.getBegin()));
 282             end.setValue(new Integer(sf.getEnd()));
 283
 284             SearchResultsI highlight = new SearchResults();
 285             highlight.addResult(sequences.get(0), sf.getBegin(),
 286                     sf.getEnd());
 287
 288             alignPanel.getSeqPanel().seqCanvas
 289                     .highlightSearchResults(highlight, false);
 290           }
 291           FeatureColourI col = getFeatureStyle(name.getText());
 292           if (col == null)
 293           {
 294             col = new FeatureColour(
 295                     ColorUtils.createColourFromName(name.getText()));
 296           }
 297           oldcol = fcol = col;
 298           updateColourButton(mainPanel, colour, col);
 299         }
 300       });
 301
 302       gridPanel.add(choosePanel);
 303     }
 304
 305     JPanel namePanel = new JPanel();
 306     gridPanel.add(namePanel);
 307     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 308             JLabel.RIGHT));
 309     namePanel.add(name);
 310
 311     JPanel groupPanel = new JPanel();
 312     gridPanel.add(groupPanel);
 313     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 314             JLabel.RIGHT));
 315     groupPanel.add(group);
 316
 317     JPanel colourPanel = new JPanel();
 318     gridPanel.add(colourPanel);
 319     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 320             JLabel.RIGHT));
 321     colourPanel.add(colour);
 322     colour.setPreferredSize(new Dimension(150, 15));
 323     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 324     colour.setForeground(Color.black);
 325     colour.setHorizontalAlignment(SwingConstants.CENTER);
 326     colour.setVerticalAlignment(SwingConstants.CENTER);
 327     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 328     colour.setVerticalTextPosition(SwingConstants.CENTER);
 329     mainPanel.add(gridPanel, BorderLayout.NORTH);
 330
 331     JPanel descriptionPanel = new JPanel();
 332     descriptionPanel.add(new JLabel(
 333             MessageManager.getString("label.description:"), JLabel.RIGHT));
 334     description.setFont(JvSwingUtils.getTextAreaFont());
 335     description.setLineWrap(true);
 336     descriptionPanel.add(new JScrollPane(description));
 337
 338     if (!create)
 339     {
 340       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 341
 342       JPanel startEndPanel = new JPanel();
 343       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 344               JLabel.RIGHT));
 345       startEndPanel.add(start);
 346       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 347               JLabel.RIGHT));
 348       startEndPanel.add(end);
 349       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 350     }
 351     else
 352     {
 353       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 354     }
 355
 356     /*
 357      * default feature type and group to that of the first feature supplied,
 358      * or to the last feature created if not supplied (null value)
 359      */
 360     SequenceFeature firstFeature = features.get(0);
 361     boolean useLastDefaults = firstFeature.getType() == null;
 362     final String featureType = useLastDefaults ? lastFeatureAdded
 363             : firstFeature.getType();
 364     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 365             : firstFeature.getFeatureGroup();
 366     name.setText(featureType);
 367     group.setText(featureGroup);
 368
 369     start.setValue(new Integer(firstFeature.getBegin()));
 370     end.setValue(new Integer(firstFeature.getEnd()));
 371     description.setText(firstFeature.getDescription());
 372     updateColourButton(mainPanel, colour,
 373             (oldcol = fcol = getFeatureStyle(featureType)));
 374     Object[] options;
 375     if (!create)
 376     {
 377       options = new Object[] { MessageManager.getString("label.amend"),
 378           MessageManager.getString("action.delete"),
 379           MessageManager.getString("action.cancel") };
 380     }
 381     else
 382     {
 383       options = new Object[] { MessageManager.getString("action.ok"),
 384           MessageManager.getString("action.cancel") };
 385     }
 386
 387     String title = create
 388             ? MessageManager.getString("label.create_new_sequence_features")
 389             : MessageManager.formatMessage("label.amend_delete_features",
 390                     new String[]
 391                     { sequences.get(0).getName() });
 392
 393     /*
 394      * register responses and show the dialog
 395      */
 396     JvOptionPane.newOptionDialog(Desktop.desktop).response(
 397
 398             new RunResponse(JvOptionPane.OK_OPTION)
 399             {
 400               public void run()
 401               {
 402                 final String enteredType = name.getText().trim();
 403                 final String enteredGroup = group.getText().trim();
 404                 final String enteredDescription = description.getText()
 405                         .replaceAll("\n", " ");
 406                 if (enteredType.length() > 0)
 407
 408                 {
 409                   /*
 410                    * update default values only if creating using default values
 411                    */
 412                   if (useLastDefaults)
 413                   {
 414                     lastFeatureAdded = enteredType;
 415                     lastFeatureGroupAdded = enteredGroup;
 416                     // TODO: determine if the null feature group is valid
 417                     if (lastFeatureGroupAdded.length() < 1)
 418                     {
 419                       lastFeatureGroupAdded = null;
 420                     }
 421                   }
 422                 }
 423
 424                 if (create)
 425                 {
 426                   // NEW FEATURES ADDED
 427                   if (enteredType.length() > 0)
 428                   {
 429                     for (int i = 0; i < sequences.size(); i++)
 430                     {
 431                       SequenceFeature sf = features.get(i);
 432                       SequenceFeature sf2 = new SequenceFeature(enteredType,
 433                               enteredDescription, sf.getBegin(),
 434                               sf.getEnd(), enteredGroup);
 435                       new FeaturesFile().parseDescriptionHTML(sf2, false);
 436                       sequences.get(i).addSequenceFeature(sf2);
 437                     }
 438
 439                     setColour(enteredType, fcol);
 440
 441                     featuresAdded();
 442
 443                     responseHandler.run();
 444                   }
 445                 } else {
 446                   SequenceFeature sf = features.get(featureIndex);
 447                   /*
 448                    * Feature amended - YES_OPTION corresponds to the Amend button
 449                    * need to refresh Feature Settings if type, group or colour changed;
 450                    * note we don't force the feature to be visible - the user has been
 451                    * warned if a hidden feature type or group was entered
 452                    */
 453                   boolean refreshSettings = (!featureType.equals(enteredType)
 454                           || !featureGroup.equals(enteredGroup));
 455                   refreshSettings |= (fcol != oldcol);
 456                   setColour(enteredType, fcol);
 457                   int newBegin = sf.begin;
 458                   int newEnd = sf.end;
 459                   try
 460                   {
 461                     newBegin = ((Integer) start.getValue()).intValue();
 462                     newEnd = ((Integer) end.getValue()).intValue();
 463                   } catch (NumberFormatException ex)
 464                   {
 465                     // JSpinner doesn't accept invalid format data :-)
 466                   }
 467
 468                   /*
 469                    * replace the feature by deleting it and adding a new one
 470                    * (to ensure integrity of SequenceFeatures data store)
 471                    */
 472                   sequences.get(0).deleteFeature(sf);
 473                   SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 474                           newBegin, newEnd, enteredGroup, sf.getScore());
 475                   newSf.setDescription(enteredDescription);
 476                   new FeaturesFile().parseDescriptionHTML(newSf, false);
 477                   // amend features dialog only updates one sequence at a time
 478                   sequences.get(0).addSequenceFeature(newSf);
 479
 480                   if (refreshSettings)
 481                   {
 482                     featuresAdded();
 483                   }
 484                 }
 485                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 486                 alignPanel.paintAlignment(true, true);
 487               }
 488             }).response(new RunResponse(JvOptionPane.NO_OPTION)
 489             {
 490               public void run()
 491               {
 492                 SequenceFeature sf = features.get(featureIndex);
 493                 /*
 494                  * NO_OPTION corresponds to the Delete button
 495                  */
 496                 sequences.get(0).getDatasetSequence().deleteFeature(sf);
 497                 // update Feature Settings for removal of feature / group
 498                 featuresAdded();
 499                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 500                 alignPanel.paintAlignment(true, true);
 501               }
 502             }).defaultResponse(new Runnable()
 503             {
 504               public void run()
 505               {
 506                 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(null, false);
 507                 alignPanel.paintAlignment(true, true);
 508               }
 509             }).showInternalDialog(mainPanel, title,
 510                     JvOptionPane.YES_NO_CANCEL_OPTION,
 511                     JvOptionPane.QUESTION_MESSAGE, null, options,
 512                     MessageManager.getString("action.ok"));
 513     return true;
 514   }
 515
 516   /**
 517    * Show a warning message if the entered type is one that is currently hidden
 518    *
 519    * @param panel
 520    * @param type
 521    */
 522   protected void warnIfTypeHidden(JPanel panel, String type)
 523   {
 524     if (getRenderOrder().contains(type))
 525     {
 526       if (!showFeatureOfType(type))
 527       {
 528         String msg = MessageManager.formatMessage("label.warning_hidden",
 529                 MessageManager.getString("label.feature_type"), type);
 530         JvOptionPane.showMessageDialog(panel, msg, "",
 531                 JvOptionPane.OK_OPTION);
 532       }
 533     }
 534   }
 535
 536   /**
 537    * Show a warning message if the entered group is one that is currently hidden
 538    *
 539    * @param panel
 540    * @param group
 541    */
 542   protected void warnIfGroupHidden(JPanel panel, String group)
 543   {
 544     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 545     {
 546       String msg = MessageManager.formatMessage("label.warning_hidden",
 547               MessageManager.getString("label.group"), group);
 548       JvOptionPane.showMessageDialog(panel, msg, "",
 549               JvOptionPane.OK_OPTION);
 550     }
 551   }
 552
 553   /**
 554    * update the amend feature button dependent on the given style
 555    *
 556    * @param bigPanel
 557    * @param col
 558    * @param col
 559    */
 560   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 561           FeatureColourI col)
 562   {
 563     colour.removeAll();
 564     colour.setIcon(null);
 565     colour.setToolTipText(null);
 566     colour.setText("");
 567
 568     if (col.isSimpleColour())
 569     {
 570       colour.setBackground(col.getColour());
 571     }
 572     else
 573     {
 574       colour.setBackground(bigPanel.getBackground());
 575       colour.setForeground(Color.black);
 576       FeatureSettings.renderGraduatedColor(colour, col);
 577     }
 578   }
 579
 580   /**
 581    * Orders features in render precedence (last in order is last to render, so
 582    * displayed on top of other features)
 583    *
 584    * @param order
 585    */
 586   public void orderFeatures(Comparator<String> order)
 587   {
 588     Arrays.sort(renderOrder, order);
 589   }
 590 }