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           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           /*
 209            * variable colour dialog - on OK, refetch the updated
 210            * feature colour and update this display
 211            */
 212           final String ft = features.get(featureIndex).getType();
 213           final String type = ft == null ? lastFeatureAdded : ft;
 214           FeatureTypeSettings fcc = new FeatureTypeSettings(
 215                   FeatureRenderer.this, type);
 216           fcc.setRequestFocusEnabled(true);
 217           fcc.requestFocus();
 218           fcc.addActionListener(new ActionListener()
 219           {
 220             @Override
 221             public void actionPerformed(ActionEvent e)
 222             {
 223               fcol = FeatureRenderer.this.getFeatureStyle(ft);
 224               setColour(type, fcol);
 225               updateColourButton(mainPanel, colour, fcol);
 226             }
 227           });
 228         }
 229       }
 230     });
 231     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 232
 233     if (!create && features.size() > 1)
 234     {
 235       /*
 236        * more than one feature at selected position -
 237        * add a drop-down to choose the feature to amend
 238        * space pad text if necessary to make entries distinct
 239        */
 240       gridPanel = new JPanel(new GridLayout(4, 1));
 241       JPanel choosePanel = new JPanel();
 242       choosePanel.add(new JLabel(
 243               MessageManager.getString("label.select_feature") + ":"));
 244       final JComboBox<String> overlaps = new JComboBox<>();
 245       List<String> added = new ArrayList<>();
 246       for (SequenceFeature sf : features)
 247       {
 248         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 249                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 250         while (added.contains(text))
 251         {
 252           text += " ";
 253         }
 254         overlaps.addItem(text);
 255         added.add(text);
 256       }
 257       choosePanel.add(overlaps);
 258
 259       overlaps.addItemListener(new ItemListener()
 260       {
 261         @Override
 262         public void itemStateChanged(ItemEvent e)
 263         {
 264           int index = overlaps.getSelectedIndex();
 265           if (index != -1)
 266           {
 267             featureIndex = index;
 268             SequenceFeature sf = features.get(index);
 269             name.setText(sf.getType());
 270             description.setText(sf.getDescription());
 271             group.setText(sf.getFeatureGroup());
 272             start.setValue(new Integer(sf.getBegin()));
 273             end.setValue(new Integer(sf.getEnd()));
 274
 275             SearchResultsI highlight = new SearchResults();
 276             highlight.addResult(sequences.get(0), sf.getBegin(),
 277                     sf.getEnd());
 278
 279             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
 280                     highlight, false);
 281           }
 282           FeatureColourI col = getFeatureStyle(name.getText());
 283           if (col == null)
 284           {
 285             col = new FeatureColour(
 286                     ColorUtils.createColourFromName(name.getText()));
 287           }
 288           oldcol = fcol = col;
 289           updateColourButton(mainPanel, colour, col);
 290         }
 291       });
 292
 293       gridPanel.add(choosePanel);
 294     }
 295
 296     JPanel namePanel = new JPanel();
 297     gridPanel.add(namePanel);
 298     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 299             JLabel.RIGHT));
 300     namePanel.add(name);
 301
 302     JPanel groupPanel = new JPanel();
 303     gridPanel.add(groupPanel);
 304     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 305             JLabel.RIGHT));
 306     groupPanel.add(group);
 307
 308     JPanel colourPanel = new JPanel();
 309     gridPanel.add(colourPanel);
 310     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 311             JLabel.RIGHT));
 312     colourPanel.add(colour);
 313     colour.setPreferredSize(new Dimension(150, 15));
 314     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 315     colour.setForeground(Color.black);
 316     colour.setHorizontalAlignment(SwingConstants.CENTER);
 317     colour.setVerticalAlignment(SwingConstants.CENTER);
 318     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 319     colour.setVerticalTextPosition(SwingConstants.CENTER);
 320     mainPanel.add(gridPanel, BorderLayout.NORTH);
 321
 322     JPanel descriptionPanel = new JPanel();
 323     descriptionPanel.add(new JLabel(
 324             MessageManager.getString("label.description:"), 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     /*
 348      * default feature type and group to that of the first feature supplied,
 349      * or to the last feature created if not supplied (null value)
 350      */
 351     SequenceFeature firstFeature = features.get(0);
 352     boolean useLastDefaults = firstFeature.getType() == null;
 353     final String featureType = useLastDefaults ? lastFeatureAdded
 354             : firstFeature.getType();
 355     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 356             : firstFeature.getFeatureGroup();
 357     name.setText(featureType);
 358     group.setText(featureGroup);
 359
 360     start.setValue(new Integer(firstFeature.getBegin()));
 361     end.setValue(new Integer(firstFeature.getEnd()));
 362     description.setText(firstFeature.getDescription());
 363     updateColourButton(mainPanel, colour,
 364             (oldcol = fcol = getFeatureStyle(featureType)));
 365     Object[] options;
 366     if (!create)
 367     {
 368       options = new Object[] { MessageManager.getString("label.amend"),
 369           MessageManager.getString("action.delete"),
 370           MessageManager.getString("action.cancel") };
 371     }
 372     else
 373     {
 374       options = new Object[] { MessageManager.getString("action.ok"),
 375           MessageManager.getString("action.cancel") };
 376     }
 377
 378     String title = create
 379             ? MessageManager.getString("label.create_new_sequence_features")
 380             : MessageManager.formatMessage("label.amend_delete_features",
 381                     new String[]
 382                     { sequences.get(0).getName() });
 383
 384     /*
 385      * show the dialog
 386      */
 387     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 388             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 389             JvOptionPane.QUESTION_MESSAGE, null, options,
 390             MessageManager.getString("action.ok"));
 391
 392     FeaturesFile ffile = new FeaturesFile();
 393
 394     final String enteredType = name.getText().trim();
 395     final String enteredGroup = group.getText().trim();
 396     final String enteredDescription = description.getText().replaceAll("\n", " ");
 397
 398     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 399     {
 400       /*
 401        * update default values only if creating using default values
 402        */
 403       if (useLastDefaults)
 404       {
 405         lastFeatureAdded = enteredType;
 406         lastFeatureGroupAdded = enteredGroup;
 407         // TODO: determine if the null feature group is valid
 408         if (lastFeatureGroupAdded.length() < 1)
 409         {
 410           lastFeatureGroupAdded = null;
 411         }
 412       }
 413     }
 414
 415     if (!create)
 416     {
 417       SequenceFeature sf = features.get(featureIndex);
 418
 419       if (reply == JvOptionPane.NO_OPTION)
 420       {
 421         /*
 422          * NO_OPTION corresponds to the Delete button
 423          */
 424         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 425         // update Feature Settings for removal of feature / group
 426         featuresAdded();
 427       }
 428       else if (reply == JvOptionPane.YES_OPTION)
 429       {
 430         /*
 431          * YES_OPTION corresponds to the Amend button
 432          * need to refresh Feature Settings if type, group or colour changed;
 433          * note we don't force the feature to be visible - the user has been
 434          * warned if a hidden feature type or group was entered
 435          */
 436         boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
 437                 .equals(enteredGroup));
 438         refreshSettings |= (fcol != oldcol);
 439         setColour(enteredType, fcol);
 440         int newBegin = sf.begin;
 441         int newEnd = sf.end;
 442         try
 443         {
 444           newBegin = ((Integer) start.getValue()).intValue();
 445           newEnd = ((Integer) end.getValue()).intValue();
 446         } catch (NumberFormatException ex)
 447         {
 448           // JSpinner doesn't accept invalid format data :-)
 449         }
 450
 451         /*
 452          * replace the feature by deleting it and adding a new one
 453          * (to ensure integrity of SequenceFeatures data store)
 454          */
 455         sequences.get(0).deleteFeature(sf);
 456         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 457                 newBegin, newEnd, enteredGroup, sf.getScore());
 458         newSf.setDescription(enteredDescription);
 459         ffile.parseDescriptionHTML(newSf, false);
 460         // amend features dialog only updates one sequence at a time
 461         sequences.get(0).addSequenceFeature(newSf);
 462
 463         if (refreshSettings)
 464         {
 465           featuresAdded();
 466         }
 467       }
 468     }
 469     else
 470     // NEW FEATURES ADDED
 471     {
 472       if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 473       {
 474         for (int i = 0; i < sequences.size(); i++)
 475         {
 476           SequenceFeature sf = features.get(i);
 477           SequenceFeature sf2 = new SequenceFeature(enteredType,
 478                   enteredDescription, sf.getBegin(), sf.getEnd(),
 479                   enteredGroup);
 480           ffile.parseDescriptionHTML(sf2, false);
 481           sequences.get(i).addSequenceFeature(sf2);
 482         }
 483
 484         setColour(enteredType, fcol);
 485
 486         featuresAdded();
 487
 488         alignPanel.paintAlignment(true, true);
 489
 490         return true;
 491       }
 492       else
 493       {
 494         return false;
 495       }
 496     }
 497
 498     alignPanel.paintAlignment(true, true);
 499
 500     return true;
 501   }
 502
 503   /**
 504    * Show a warning message if the entered type is one that is currently hidden
 505    *
 506    * @param panel
 507    * @param type
 508    */
 509   protected void warnIfTypeHidden(JPanel panel, String type)
 510   {
 511     if (getRenderOrder().contains(type))
 512     {
 513       if (!showFeatureOfType(type))
 514       {
 515         String msg = MessageManager.formatMessage("label.warning_hidden",
 516                 MessageManager.getString("label.feature_type"), type);
 517         JvOptionPane.showMessageDialog(panel, msg, "",
 518                 JvOptionPane.OK_OPTION);
 519       }
 520     }
 521   }
 522
 523   /**
 524    * Show a warning message if the entered group is one that is currently hidden
 525    *
 526    * @param panel
 527    * @param group
 528    */
 529   protected void warnIfGroupHidden(JPanel panel, String group)
 530   {
 531     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 532     {
 533       String msg = MessageManager.formatMessage("label.warning_hidden",
 534               MessageManager.getString("label.group"), group);
 535       JvOptionPane.showMessageDialog(panel, msg, "",
 536               JvOptionPane.OK_OPTION);
 537     }
 538   }
 539
 540   /**
 541    * update the amend feature button dependent on the given style
 542    *
 543    * @param bigPanel
 544    * @param col
 545    * @param col
 546    */
 547   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 548           FeatureColourI col)
 549   {
 550     colour.removeAll();
 551     colour.setIcon(null);
 552     colour.setToolTipText(null);
 553     colour.setText("");
 554
 555     if (col.isSimpleColour())
 556     {
 557       colour.setBackground(col.getColour());
 558     }
 559     else
 560     {
 561       colour.setBackground(bigPanel.getBackground());
 562       colour.setForeground(Color.black);
 563       FeatureSettings.renderGraduatedColor(colour, col);
 564     }
 565   }
 566
 567   /**
 568    * Orders features in render precedence (last in order is last to render, so
 569    * displayed on top of other features)
 570    *
 571    * @param order
 572    */
 573   public void orderFeatures(Comparator<String> order)
 574   {
 575     Arrays.sort(renderOrder, order);
 576   }
 577 }