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.HashMap;
  48 import java.util.List;
  49 import java.util.Map;
  50 import java.util.Map.Entry;
  51
  52 import javax.swing.JColorChooser;
  53 import javax.swing.JComboBox;
  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    * the colour scheme selected by the user for the current feature type
  87    * when amending features
  88    */
  89   FeatureColourI fcol;
  90
  91   int featureIndex = 0;
  92
  93   /**
  94    * Creates a new FeatureRenderer object
  95    *
  96    * @param alignPanel
  97    */
  98   public FeatureRenderer(AlignmentPanel alignPanel)
  99   {
 100     super(alignPanel.av);
 101     this.ap = alignPanel;
 102     if (alignPanel.getSeqPanel() != null
 103             && alignPanel.getSeqPanel().seqCanvas != null
 104             && alignPanel.getSeqPanel().seqCanvas.fr != null)
 105     {
 106       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
 107     }
 108   }
 109
 110   /**
 111    * Presents a dialog allowing the user to add new features, or amend or delete
 112    * existing features. Currently this can be on
 113    * <ul>
 114    * <li>double-click on a sequence - Amend/Delete features at position</li>
 115    * <li>Create sequence feature from pop-up menu on selected region</li>
 116    * <li>Create features for pattern matches from Find</li>
 117    * </ul>
 118    * If the supplied feature type is null, show (and update on confirm) the type
 119    * and group of the last new feature created (with initial defaults of
 120    * "feature_1" and "Jalview").
 121    *
 122    * @param sequences
 123    *          the sequences features are to be created on (if creating
 124    *          features), or a single sequence (if amending features)
 125    * @param features
 126    *          the current features at the position (if amending), or template
 127    *          new feature(s) with start/end position set (if creating)
 128    * @param create
 129    *          true to create features, false to amend or delete
 130    * @param alignPanel
 131    * @return
 132    */
 133   protected boolean amendFeatures(final List<SequenceI> sequences,
 134           final List<SequenceFeature> features, boolean create,
 135           final AlignmentPanel alignPanel)
 136   {
 137     /*
 138      * save original colours, for reset on Cancel
 139      */
 140     Map<String, FeatureColourI> oldColours = new HashMap<>();
 141     for (SequenceFeature sf : features)
 142     {
 143       String type = sf.getType();
 144       if (type != null)
 145       {
 146         oldColours.put(type, getFeatureStyle(type));
 147       }
 148     }
 149
 150     featureIndex = 0;
 151
 152     final JPanel mainPanel = new JPanel(new BorderLayout());
 153
 154     final JTextField name = new JTextField(25);
 155     name.getDocument().addDocumentListener(new DocumentListener()
 156     {
 157       @Override
 158       public void insertUpdate(DocumentEvent e)
 159       {
 160         warnIfTypeHidden(mainPanel, name.getText());
 161       }
 162
 163       @Override
 164       public void removeUpdate(DocumentEvent e)
 165       {
 166         warnIfTypeHidden(mainPanel, name.getText());
 167       }
 168
 169       @Override
 170       public void changedUpdate(DocumentEvent e)
 171       {
 172         warnIfTypeHidden(mainPanel, name.getText());
 173       }
 174     });
 175
 176     final JTextField group = new JTextField(25);
 177     group.getDocument().addDocumentListener(new DocumentListener()
 178     {
 179       @Override
 180       public void insertUpdate(DocumentEvent e)
 181       {
 182         warnIfGroupHidden(mainPanel, group.getText());
 183       }
 184
 185       @Override
 186       public void removeUpdate(DocumentEvent e)
 187       {
 188         warnIfGroupHidden(mainPanel, group.getText());
 189       }
 190
 191       @Override
 192       public void changedUpdate(DocumentEvent e)
 193       {
 194         warnIfGroupHidden(mainPanel, group.getText());
 195       }
 196     });
 197
 198     final JTextArea description = new JTextArea(3, 25);
 199     final JSpinner start = new JSpinner();
 200     final JSpinner end = new JSpinner();
 201     start.setPreferredSize(new Dimension(80, 20));
 202     end.setPreferredSize(new Dimension(80, 20));
 203     final FeatureRenderer me = this;
 204     final JLabel colour = new JLabel();
 205     colour.setOpaque(true);
 206     // colour.setBorder(BorderFactory.createEtchedBorder());
 207     colour.setMaximumSize(new Dimension(30, 16));
 208     colour.addMouseListener(new MouseAdapter()
 209     {
 210       FeatureColourChooser fcc = null;
 211
 212       @Override
 213       public void mousePressed(MouseEvent evt)
 214       {
 215         final String ft = features.get(featureIndex).getType();
 216         final String type = ft == null ? lastFeatureAdded : ft;
 217         if (fcol.isSimpleColour())
 218         {
 219           Color col = JColorChooser.showDialog(Desktop.desktop,
 220                   MessageManager.getString("label.select_feature_colour"),
 221                   fcol.getColour());
 222           if (col != null)
 223           {
 224             fcol = new FeatureColour(col);
 225             setColour(type, fcol);
 226             alignPanel.paintAlignment(true, true);
 227             updateColourButton(mainPanel, colour, fcol);
 228           }
 229         }
 230         else
 231         {
 232           if (fcc == null)
 233           {
 234             fcc = new FeatureColourChooser(me, type);
 235             fcc.setRequestFocusEnabled(true);
 236             fcc.requestFocus();
 237
 238             fcc.addActionListener(new ActionListener()
 239             {
 240
 241               @Override
 242               public void actionPerformed(ActionEvent e)
 243               {
 244                 fcol = fcc.getLastColour();
 245                 fcc = null;
 246                 setColour(type, fcol);
 247                 updateColourButton(mainPanel, colour, fcol);
 248               }
 249             });
 250
 251           }
 252         }
 253       }
 254     });
 255     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 256
 257     if (!create && features.size() > 1)
 258     {
 259       /*
 260        * more than one feature at selected position -
 261        * add a drop-down to choose the feature to amend
 262        * space pad text if necessary to make entries distinct
 263        */
 264       gridPanel = new JPanel(new GridLayout(4, 1));
 265       JPanel choosePanel = new JPanel();
 266       choosePanel.add(new JLabel(
 267               MessageManager.getString("label.select_feature") + ":"));
 268       final JComboBox<String> overlaps = new JComboBox<>();
 269       List<String> added = new ArrayList<>();
 270       for (SequenceFeature sf : features)
 271       {
 272         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 273                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 274         while (added.contains(text))
 275         {
 276           text += " ";
 277         }
 278         overlaps.addItem(text);
 279         added.add(text);
 280       }
 281       choosePanel.add(overlaps);
 282
 283       overlaps.addItemListener(new ItemListener()
 284       {
 285         @Override
 286         public void itemStateChanged(ItemEvent e)
 287         {
 288           int index = overlaps.getSelectedIndex();
 289           if (index != -1)
 290           {
 291             featureIndex = index;
 292             SequenceFeature sf = features.get(index);
 293             name.setText(sf.getType());
 294             description.setText(sf.getDescription());
 295             group.setText(sf.getFeatureGroup());
 296             start.setValue(new Integer(sf.getBegin()));
 297             end.setValue(new Integer(sf.getEnd()));
 298
 299             SearchResultsI highlight = new SearchResults();
 300             highlight.addResult(sequences.get(0), sf.getBegin(),
 301                     sf.getEnd());
 302
 303             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
 304                     highlight, false);
 305           }
 306           FeatureColourI col = getFeatureStyle(name.getText());
 307           if (col == null)
 308           {
 309             col = new FeatureColour(
 310                     ColorUtils.createColourFromName(name.getText()));
 311           }
 312           fcol = col;
 313           updateColourButton(mainPanel, colour, col);
 314         }
 315       });
 316
 317       gridPanel.add(choosePanel);
 318     }
 319
 320     JPanel namePanel = new JPanel();
 321     gridPanel.add(namePanel);
 322     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 323             JLabel.RIGHT));
 324     namePanel.add(name);
 325
 326     JPanel groupPanel = new JPanel();
 327     gridPanel.add(groupPanel);
 328     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 329             JLabel.RIGHT));
 330     groupPanel.add(group);
 331
 332     JPanel colourPanel = new JPanel();
 333     gridPanel.add(colourPanel);
 334     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 335             JLabel.RIGHT));
 336     colourPanel.add(colour);
 337     colour.setPreferredSize(new Dimension(150, 15));
 338     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 339     colour.setForeground(Color.black);
 340     colour.setHorizontalAlignment(SwingConstants.CENTER);
 341     colour.setVerticalAlignment(SwingConstants.CENTER);
 342     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 343     colour.setVerticalTextPosition(SwingConstants.CENTER);
 344     mainPanel.add(gridPanel, BorderLayout.NORTH);
 345
 346     JPanel descriptionPanel = new JPanel();
 347     descriptionPanel.add(new JLabel(
 348             MessageManager.getString("label.description:"), JLabel.RIGHT));
 349     description.setFont(JvSwingUtils.getTextAreaFont());
 350     description.setLineWrap(true);
 351     descriptionPanel.add(new JScrollPane(description));
 352
 353     if (!create)
 354     {
 355       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 356
 357       JPanel startEndPanel = new JPanel();
 358       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 359               JLabel.RIGHT));
 360       startEndPanel.add(start);
 361       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 362               JLabel.RIGHT));
 363       startEndPanel.add(end);
 364       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 365     }
 366     else
 367     {
 368       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 369     }
 370
 371     /*
 372      * default feature type and group to that of the first feature supplied,
 373      * or to the last feature created if not supplied (null value)
 374      */
 375     SequenceFeature firstFeature = features.get(0);
 376     boolean useLastDefaults = firstFeature.getType() == null;
 377     final String featureType = useLastDefaults ? lastFeatureAdded
 378             : firstFeature.getType();
 379     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 380             : firstFeature.getFeatureGroup();
 381     name.setText(featureType);
 382     group.setText(featureGroup);
 383
 384     start.setValue(new Integer(firstFeature.getBegin()));
 385     end.setValue(new Integer(firstFeature.getEnd()));
 386     description.setText(firstFeature.getDescription());
 387     fcol = getFeatureStyle(featureType);
 388     oldColours.put(featureType, fcol);
 389     updateColourButton(mainPanel, colour, fcol);
 390     Object[] options;
 391     if (!create)
 392     {
 393       options = new Object[] { MessageManager.getString("label.amend"),
 394           MessageManager.getString("action.delete"),
 395           MessageManager.getString("action.cancel") };
 396     }
 397     else
 398     {
 399       options = new Object[] { MessageManager.getString("action.ok"),
 400           MessageManager.getString("action.cancel") };
 401     }
 402
 403     String title = create
 404             ? MessageManager.getString("label.create_new_sequence_features")
 405             : MessageManager.formatMessage("label.amend_delete_features",
 406                     new String[]
 407                     { sequences.get(0).getName() });
 408
 409     /*
 410      * show the dialog
 411      */
 412     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 413             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 414             JvOptionPane.QUESTION_MESSAGE, null, options,
 415             MessageManager.getString("action.ok"));
 416
 417     FeaturesFile ffile = new FeaturesFile();
 418
 419     final String enteredType = name.getText().trim();
 420     final String enteredGroup = group.getText().trim();
 421     final String enteredDescription = description.getText().replaceAll("\n", " ");
 422
 423     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 424     {
 425       /*
 426        * update default values only if creating using default values
 427        */
 428       if (useLastDefaults)
 429       {
 430         lastFeatureAdded = enteredType;
 431         lastFeatureGroupAdded = enteredGroup;
 432         // TODO: determine if the null feature group is valid
 433         if (lastFeatureGroupAdded.length() < 1)
 434         {
 435           lastFeatureGroupAdded = null;
 436         }
 437       }
 438     }
 439
 440     if (!create)
 441     {
 442       SequenceFeature sf = features.get(featureIndex);
 443
 444       if (reply == JvOptionPane.NO_OPTION)
 445       {
 446         /*
 447          * NO_OPTION corresponds to the Delete button
 448          */
 449         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 450         // update Feature Settings for removal of feature / group
 451         featuresAdded();
 452       }
 453       else if (reply == JvOptionPane.YES_OPTION)
 454       {
 455         /*
 456          * YES_OPTION corresponds to the Amend button
 457          * need to refresh Feature Settings if type, group or colour changed;
 458          * note we don't force the feature to be visible - the user has been
 459          * warned if a hidden feature type or group was entered
 460          */
 461         boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
 462                 .equals(enteredGroup));
 463         refreshSettings |= (fcol != oldColours.get(featureType));
 464         setColour(enteredType, fcol);
 465         int newBegin = sf.begin;
 466         int newEnd = sf.end;
 467         try
 468         {
 469           newBegin = ((Integer) start.getValue()).intValue();
 470           newEnd = ((Integer) end.getValue()).intValue();
 471         } catch (NumberFormatException ex)
 472         {
 473           // JSpinner doesn't accept invalid format data :-)
 474         }
 475
 476         /*
 477          * replace the feature by deleting it and adding a new one
 478          * (to ensure integrity of SequenceFeatures data store)
 479          */
 480         sequences.get(0).deleteFeature(sf);
 481         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 482                 newBegin, newEnd, enteredGroup, sf.getScore());
 483         newSf.setDescription(enteredDescription);
 484         ffile.parseDescriptionHTML(newSf, false);
 485         // amend features dialog only updates one sequence at a time
 486         sequences.get(0).addSequenceFeature(newSf);
 487
 488         if (refreshSettings)
 489         {
 490           featuresAdded();
 491         }
 492       }
 493       else
 494       {
 495         // Cancel: reset any colour changes applied
 496         resetColours(oldColours);
 497       }
 498     }
 499     else
 500     // NEW FEATURES ADDED
 501     {
 502       if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 503       {
 504         for (int i = 0; i < sequences.size(); i++)
 505         {
 506           SequenceFeature sf = features.get(i);
 507           SequenceFeature sf2 = new SequenceFeature(enteredType,
 508                   enteredDescription, sf.getBegin(), sf.getEnd(),
 509                   enteredGroup);
 510           ffile.parseDescriptionHTML(sf2, false);
 511           sequences.get(i).addSequenceFeature(sf2);
 512         }
 513
 514         setColour(enteredType, fcol);
 515
 516         featuresAdded();
 517
 518         alignPanel.paintAlignment(true, true);
 519
 520         return true;
 521       }
 522       else
 523       {
 524         // Cancel: reset any colour changes applied
 525         resetColours(oldColours);
 526         return false;
 527       }
 528     }
 529
 530     alignPanel.paintAlignment(true, true);
 531
 532     return true;
 533   }
 534
 535   /**
 536    * Reset features to their original colours (on Cancel)
 537    *
 538    * @param colours
 539    */
 540   private void resetColours(Map<String, FeatureColourI> colours)
 541   {
 542     for (Entry<String, FeatureColourI> entry : colours.entrySet())
 543     {
 544       setColour(entry.getKey(), entry.getValue());
 545     }
 546   }
 547
 548   /**
 549    * Show a warning message if the entered type is one that is currently hidden
 550    *
 551    * @param panel
 552    * @param type
 553    */
 554   protected void warnIfTypeHidden(JPanel panel, String type)
 555   {
 556     if (getRenderOrder().contains(type))
 557     {
 558       if (!showFeatureOfType(type))
 559       {
 560         String msg = MessageManager.formatMessage("label.warning_hidden",
 561                 MessageManager.getString("label.feature_type"), type);
 562         JvOptionPane.showMessageDialog(panel, msg, "",
 563                 JvOptionPane.OK_OPTION);
 564       }
 565     }
 566   }
 567
 568   /**
 569    * Show a warning message if the entered group is one that is currently hidden
 570    *
 571    * @param panel
 572    * @param group
 573    */
 574   protected void warnIfGroupHidden(JPanel panel, String group)
 575   {
 576     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 577     {
 578       String msg = MessageManager.formatMessage("label.warning_hidden",
 579               MessageManager.getString("label.group"), group);
 580       JvOptionPane.showMessageDialog(panel, msg, "",
 581               JvOptionPane.OK_OPTION);
 582     }
 583   }
 584
 585   /**
 586    * update the amend feature button dependent on the given style
 587    *
 588    * @param bigPanel
 589    * @param col
 590    * @param col
 591    */
 592   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 593           FeatureColourI col)
 594   {
 595     colour.removeAll();
 596     colour.setIcon(null);
 597     colour.setToolTipText(null);
 598     colour.setText("");
 599
 600     if (col.isSimpleColour())
 601     {
 602       colour.setBackground(col.getColour());
 603     }
 604     else
 605     {
 606       colour.setBackground(bigPanel.getBackground());
 607       colour.setForeground(Color.black);
 608       FeatureSettings.renderGraduatedColor(colour, col);
 609     }
 610   }
 611
 612   /**
 613    * Orders features in render precedence (last in order is last to render, so
 614    * displayed on top of other features)
 615    *
 616    * @param order
 617    */
 618   public void orderFeatures(Comparator<String> order)
 619   {
 620     Arrays.sort(renderOrder, order);
 621   }
 622 }