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 FeatureRenderer me = this;
 184     final JLabel colour = new JLabel();
 185     colour.setOpaque(true);
 186     // colour.setBorder(BorderFactory.createEtchedBorder());
 187     colour.setMaximumSize(new Dimension(30, 16));
 188     colour.addMouseListener(new MouseAdapter()
 189     {
 190       FeatureColourChooser fcc = null;
 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           if (fcc == null)
 209           {
 210             final String ft = features.get(featureIndex).getType();
 211             final String type = ft == null ? lastFeatureAdded : ft;
 212             fcc = new FeatureColourChooser(me, type);
 213             fcc.setRequestFocusEnabled(true);
 214             fcc.requestFocus();
 215
 216             fcc.addActionListener(new ActionListener()
 217             {
 218
 219               @Override
 220               public void actionPerformed(ActionEvent e)
 221               {
 222                 fcol = fcc.getLastColour();
 223                 fcc = null;
 224                 setColour(type, fcol);
 225                 updateColourButton(mainPanel, colour, fcol);
 226               }
 227             });
 228
 229           }
 230         }
 231       }
 232     });
 233     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 234
 235     if (!create && features.size() > 1)
 236     {
 237       /*
 238        * more than one feature at selected position -
 239        * add a drop-down to choose the feature to amend
 240        * space pad text if necessary to make entries distinct
 241        */
 242       gridPanel = new JPanel(new GridLayout(4, 1));
 243       JPanel choosePanel = new JPanel();
 244       choosePanel.add(new JLabel(
 245               MessageManager.getString("label.select_feature") + ":"));
 246       final JComboBox<String> overlaps = new JComboBox<>();
 247       List<String> added = new ArrayList<>();
 248       for (SequenceFeature sf : features)
 249       {
 250         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 251                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 252         while (added.contains(text))
 253         {
 254           text += " ";
 255         }
 256         overlaps.addItem(text);
 257         added.add(text);
 258       }
 259       choosePanel.add(overlaps);
 260
 261       overlaps.addItemListener(new ItemListener()
 262       {
 263         @Override
 264         public void itemStateChanged(ItemEvent e)
 265         {
 266           int index = overlaps.getSelectedIndex();
 267           if (index != -1)
 268           {
 269             featureIndex = index;
 270             SequenceFeature sf = features.get(index);
 271             name.setText(sf.getType());
 272             description.setText(sf.getDescription());
 273             group.setText(sf.getFeatureGroup());
 274             start.setValue(new Integer(sf.getBegin()));
 275             end.setValue(new Integer(sf.getEnd()));
 276
 277             SearchResultsI highlight = new SearchResults();
 278             highlight.addResult(sequences.get(0), sf.getBegin(),
 279                     sf.getEnd());
 280
 281             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
 282                     highlight, false);
 283           }
 284           FeatureColourI col = getFeatureStyle(name.getText());
 285           if (col == null)
 286           {
 287             col = new FeatureColour(
 288                     ColorUtils.createColourFromName(name.getText()));
 289           }
 290           oldcol = fcol = col;
 291           updateColourButton(mainPanel, colour, col);
 292         }
 293       });
 294
 295       gridPanel.add(choosePanel);
 296     }
 297
 298     JPanel namePanel = new JPanel();
 299     gridPanel.add(namePanel);
 300     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 301             JLabel.RIGHT));
 302     namePanel.add(name);
 303
 304     JPanel groupPanel = new JPanel();
 305     gridPanel.add(groupPanel);
 306     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 307             JLabel.RIGHT));
 308     groupPanel.add(group);
 309
 310     JPanel colourPanel = new JPanel();
 311     gridPanel.add(colourPanel);
 312     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 313             JLabel.RIGHT));
 314     colourPanel.add(colour);
 315     colour.setPreferredSize(new Dimension(150, 15));
 316     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 317     colour.setForeground(Color.black);
 318     colour.setHorizontalAlignment(SwingConstants.CENTER);
 319     colour.setVerticalAlignment(SwingConstants.CENTER);
 320     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 321     colour.setVerticalTextPosition(SwingConstants.CENTER);
 322     mainPanel.add(gridPanel, BorderLayout.NORTH);
 323
 324     JPanel descriptionPanel = new JPanel();
 325     descriptionPanel.add(new JLabel(
 326             MessageManager.getString("label.description:"), JLabel.RIGHT));
 327     description.setFont(JvSwingUtils.getTextAreaFont());
 328     description.setLineWrap(true);
 329     descriptionPanel.add(new JScrollPane(description));
 330
 331     if (!create)
 332     {
 333       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 334
 335       JPanel startEndPanel = new JPanel();
 336       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 337               JLabel.RIGHT));
 338       startEndPanel.add(start);
 339       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 340               JLabel.RIGHT));
 341       startEndPanel.add(end);
 342       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 343     }
 344     else
 345     {
 346       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 347     }
 348
 349     /*
 350      * default feature type and group to that of the first feature supplied,
 351      * or to the last feature created if not supplied (null value)
 352      */
 353     SequenceFeature firstFeature = features.get(0);
 354     boolean useLastDefaults = firstFeature.getType() == null;
 355     final String featureType = useLastDefaults ? lastFeatureAdded
 356             : firstFeature.getType();
 357     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 358             : firstFeature.getFeatureGroup();
 359     name.setText(featureType);
 360     group.setText(featureGroup);
 361
 362     start.setValue(new Integer(firstFeature.getBegin()));
 363     end.setValue(new Integer(firstFeature.getEnd()));
 364     description.setText(firstFeature.getDescription());
 365     updateColourButton(mainPanel, colour,
 366             (oldcol = fcol = getFeatureStyle(featureType)));
 367     Object[] options;
 368     if (!create)
 369     {
 370       options = new Object[] { MessageManager.getString("label.amend"),
 371           MessageManager.getString("action.delete"),
 372           MessageManager.getString("action.cancel") };
 373     }
 374     else
 375     {
 376       options = new Object[] { MessageManager.getString("action.ok"),
 377           MessageManager.getString("action.cancel") };
 378     }
 379
 380     String title = create
 381             ? MessageManager.getString("label.create_new_sequence_features")
 382             : MessageManager.formatMessage("label.amend_delete_features",
 383                     new String[]
 384                     { sequences.get(0).getName() });
 385
 386     /*
 387      * show the dialog
 388      */
 389     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 390             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 391             JvOptionPane.QUESTION_MESSAGE, null, options,
 392             MessageManager.getString("action.ok"));
 393
 394     FeaturesFile ffile = new FeaturesFile();
 395
 396     final String enteredType = name.getText().trim();
 397     final String enteredGroup = group.getText().trim();
 398     final String enteredDescription = description.getText().replaceAll("\n", " ");
 399
 400     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 401     {
 402       /*
 403        * update default values only if creating using default values
 404        */
 405       if (useLastDefaults)
 406       {
 407         lastFeatureAdded = enteredType;
 408         lastFeatureGroupAdded = enteredGroup;
 409         // TODO: determine if the null feature group is valid
 410         if (lastFeatureGroupAdded.length() < 1)
 411         {
 412           lastFeatureGroupAdded = null;
 413         }
 414       }
 415     }
 416
 417     if (!create)
 418     {
 419       SequenceFeature sf = features.get(featureIndex);
 420
 421       if (reply == JvOptionPane.NO_OPTION)
 422       {
 423         /*
 424          * NO_OPTION corresponds to the Delete button
 425          */
 426         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 427         // update Feature Settings for removal of feature / group
 428         featuresAdded();
 429       }
 430       else if (reply == JvOptionPane.YES_OPTION)
 431       {
 432         /*
 433          * YES_OPTION corresponds to the Amend button
 434          * need to refresh Feature Settings if type, group or colour changed;
 435          * note we don't force the feature to be visible - the user has been
 436          * warned if a hidden feature type or group was entered
 437          */
 438         boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
 439                 .equals(enteredGroup));
 440         refreshSettings |= (fcol != oldcol);
 441         setColour(enteredType, fcol);
 442         int newBegin = sf.begin;
 443         int newEnd = sf.end;
 444         try
 445         {
 446           newBegin = ((Integer) start.getValue()).intValue();
 447           newEnd = ((Integer) end.getValue()).intValue();
 448         } catch (NumberFormatException ex)
 449         {
 450           // JSpinner doesn't accept invalid format data :-)
 451         }
 452
 453         /*
 454          * replace the feature by deleting it and adding a new one
 455          * (to ensure integrity of SequenceFeatures data store)
 456          */
 457         sequences.get(0).deleteFeature(sf);
 458         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 459                 newBegin, newEnd, enteredGroup, sf.getScore());
 460         newSf.setDescription(enteredDescription);
 461         ffile.parseDescriptionHTML(newSf, false);
 462         // amend features dialog only updates one sequence at a time
 463         sequences.get(0).addSequenceFeature(newSf);
 464
 465         if (refreshSettings)
 466         {
 467           featuresAdded();
 468         }
 469       }
 470     }
 471     else
 472     // NEW FEATURES ADDED
 473     {
 474       if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 475       {
 476         for (int i = 0; i < sequences.size(); i++)
 477         {
 478           SequenceFeature sf = features.get(i);
 479           SequenceFeature sf2 = new SequenceFeature(enteredType,
 480                   enteredDescription, sf.getBegin(), sf.getEnd(),
 481                   enteredGroup);
 482           ffile.parseDescriptionHTML(sf2, false);
 483           sequences.get(i).addSequenceFeature(sf2);
 484         }
 485
 486         setColour(enteredType, fcol);
 487
 488         featuresAdded();
 489
 490         alignPanel.paintAlignment(true, true);
 491
 492         return true;
 493       }
 494       else
 495       {
 496         return false;
 497       }
 498     }
 499
 500     alignPanel.paintAlignment(true, true);
 501
 502     return true;
 503   }
 504
 505   /**
 506    * Show a warning message if the entered type is one that is currently hidden
 507    *
 508    * @param panel
 509    * @param type
 510    */
 511   protected void warnIfTypeHidden(JPanel panel, String type)
 512   {
 513     if (getRenderOrder().contains(type))
 514     {
 515       if (!showFeatureOfType(type))
 516       {
 517         String msg = MessageManager.formatMessage("label.warning_hidden",
 518                 MessageManager.getString("label.feature_type"), type);
 519         JvOptionPane.showMessageDialog(panel, msg, "",
 520                 JvOptionPane.OK_OPTION);
 521       }
 522     }
 523   }
 524
 525   /**
 526    * Show a warning message if the entered group is one that is currently hidden
 527    *
 528    * @param panel
 529    * @param group
 530    */
 531   protected void warnIfGroupHidden(JPanel panel, String group)
 532   {
 533     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 534     {
 535       String msg = MessageManager.formatMessage("label.warning_hidden",
 536               MessageManager.getString("label.group"), group);
 537       JvOptionPane.showMessageDialog(panel, msg, "",
 538               JvOptionPane.OK_OPTION);
 539     }
 540   }
 541
 542   /**
 543    * update the amend feature button dependent on the given style
 544    *
 545    * @param bigPanel
 546    * @param col
 547    * @param col
 548    */
 549   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 550           FeatureColourI col)
 551   {
 552     colour.removeAll();
 553     colour.setIcon(null);
 554     colour.setToolTipText(null);
 555     colour.setText("");
 556
 557     if (col.isSimpleColour())
 558     {
 559       colour.setBackground(col.getColour());
 560     }
 561     else
 562     {
 563       colour.setBackground(bigPanel.getBackground());
 564       colour.setForeground(Color.black);
 565       FeatureSettings.renderGraduatedColor(colour, col);
 566     }
 567   }
 568
 569   /**
 570    * Orders features in render precedence (last in order is last to render, so
 571    * displayed on top of other features)
 572    *
 573    * @param order
 574    */
 575   public void orderFeatures(Comparator<String> order)
 576   {
 577     Arrays.sort(renderOrder, order);
 578   }
 579 }