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.AlignedCodonFrame;
  25 import jalview.datamodel.Mapping;
  26 import jalview.datamodel.SearchResultMatchI;
  27 import jalview.datamodel.SearchResults;
  28 import jalview.datamodel.SearchResultsI;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.io.FeaturesFile;
  32 import jalview.schemes.FeatureColour;
  33 import jalview.util.ColorUtils;
  34 import jalview.util.MessageManager;
  35
  36 import java.awt.BorderLayout;
  37 import java.awt.Color;
  38 import java.awt.Dimension;
  39 import java.awt.Font;
  40 import java.awt.GridLayout;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.ItemEvent;
  44 import java.awt.event.ItemListener;
  45 import java.awt.event.MouseAdapter;
  46 import java.awt.event.MouseEvent;
  47 import java.util.ArrayList;
  48 import java.util.Arrays;
  49 import java.util.Comparator;
  50 import java.util.List;
  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    * 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    * @return
 128    */
 129   protected boolean amendFeatures(final List<SequenceI> sequences,
 130           final List<SequenceFeature> features, boolean create,
 131           final AlignmentPanel alignPanel)
 132   {
 133     featureIndex = 0;
 134
 135     final JPanel mainPanel = new JPanel(new BorderLayout());
 136
 137     final JTextField name = new JTextField(25);
 138     name.getDocument().addDocumentListener(new DocumentListener()
 139     {
 140       @Override
 141       public void insertUpdate(DocumentEvent e)
 142       {
 143         warnIfTypeHidden(mainPanel, name.getText());
 144       }
 145
 146       @Override
 147       public void removeUpdate(DocumentEvent e)
 148       {
 149         warnIfTypeHidden(mainPanel, name.getText());
 150       }
 151
 152       @Override
 153       public void changedUpdate(DocumentEvent e)
 154       {
 155         warnIfTypeHidden(mainPanel, name.getText());
 156       }
 157     });
 158
 159     final JTextField group = new JTextField(25);
 160     group.getDocument().addDocumentListener(new DocumentListener()
 161     {
 162       @Override
 163       public void insertUpdate(DocumentEvent e)
 164       {
 165         warnIfGroupHidden(mainPanel, group.getText());
 166       }
 167
 168       @Override
 169       public void removeUpdate(DocumentEvent e)
 170       {
 171         warnIfGroupHidden(mainPanel, group.getText());
 172       }
 173
 174       @Override
 175       public void changedUpdate(DocumentEvent e)
 176       {
 177         warnIfGroupHidden(mainPanel, group.getText());
 178       }
 179     });
 180
 181     final JTextArea description = new JTextArea(3, 25);
 182     final JSpinner start = new JSpinner();
 183     final JSpinner end = new JSpinner();
 184     start.setPreferredSize(new Dimension(80, 20));
 185     end.setPreferredSize(new Dimension(80, 20));
 186     final JLabel colour = new JLabel();
 187     colour.setOpaque(true);
 188     // colour.setBorder(BorderFactory.createEtchedBorder());
 189     colour.setMaximumSize(new Dimension(30, 16));
 190     colour.addMouseListener(new MouseAdapter()
 191     {
 192       /*
 193        * open colour chooser on click in colour panel
 194        */
 195       @Override
 196       public void mousePressed(MouseEvent evt)
 197       {
 198         if (fcol.isSimpleColour())
 199         {
 200           Color col = JColorChooser.showDialog(Desktop.desktop,
 201                   MessageManager.getString("label.select_feature_colour"),
 202                   fcol.getColour());
 203           if (col != null)
 204           {
 205             fcol = new FeatureColour(col);
 206             updateColourButton(mainPanel, colour, fcol);
 207           }
 208         }
 209         else
 210         {
 211           /*
 212            * variable colour dialog - on OK, refetch the updated
 213            * feature colour and update this display
 214            */
 215           final String ft = features.get(featureIndex).getType();
 216           final String type = ft == null ? lastFeatureAdded : ft;
 217           FeatureTypeSettings fcc = new FeatureTypeSettings(
 218                   FeatureRenderer.this, type);
 219           fcc.setRequestFocusEnabled(true);
 220           fcc.requestFocus();
 221           fcc.addActionListener(new ActionListener()
 222           {
 223             @Override
 224             public void actionPerformed(ActionEvent e)
 225             {
 226               fcol = FeatureRenderer.this.getFeatureStyle(ft);
 227               setColour(type, fcol);
 228               updateColourButton(mainPanel, colour, fcol);
 229             }
 230           });
 231         }
 232       }
 233     });
 234     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 235
 236     if (!create && features.size() > 1)
 237     {
 238       /*
 239        * more than one feature at selected position -
 240        * add a drop-down to choose the feature to amend
 241        * space pad text if necessary to make entries distinct
 242        */
 243       gridPanel = new JPanel(new GridLayout(4, 1));
 244       JPanel choosePanel = new JPanel();
 245       choosePanel.add(new JLabel(
 246               MessageManager.getString("label.select_feature") + ":"));
 247       final JComboBox<String> overlaps = new JComboBox<>();
 248       List<String> added = new ArrayList<>();
 249       for (SequenceFeature sf : features)
 250       {
 251         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 252                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 253         while (added.contains(text))
 254         {
 255           text += " ";
 256         }
 257         overlaps.addItem(text);
 258         added.add(text);
 259       }
 260       choosePanel.add(overlaps);
 261
 262       overlaps.addItemListener(new ItemListener()
 263       {
 264         @Override
 265         public void itemStateChanged(ItemEvent e)
 266         {
 267           int index = overlaps.getSelectedIndex();
 268           if (index != -1)
 269           {
 270             featureIndex = index;
 271             SequenceFeature sf = features.get(index);
 272             name.setText(sf.getType());
 273             description.setText(sf.getDescription());
 274             group.setText(sf.getFeatureGroup());
 275             start.setValue(new Integer(sf.getBegin()));
 276             end.setValue(new Integer(sf.getEnd()));
 277
 278             SearchResultsI highlight = new SearchResults();
 279             highlight.addResult(sequences.get(0), sf.getBegin(),
 280                     sf.getEnd());
 281
 282             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
 283                     highlight, false);
 284           }
 285           FeatureColourI col = getFeatureStyle(name.getText());
 286           if (col == null)
 287           {
 288             col = new FeatureColour(
 289                     ColorUtils.createColourFromName(name.getText()));
 290           }
 291           oldcol = fcol = col;
 292           updateColourButton(mainPanel, colour, col);
 293         }
 294       });
 295
 296       gridPanel.add(choosePanel);
 297     }
 298
 299     JPanel namePanel = new JPanel();
 300     gridPanel.add(namePanel);
 301     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 302             JLabel.RIGHT));
 303     namePanel.add(name);
 304
 305     JPanel groupPanel = new JPanel();
 306     gridPanel.add(groupPanel);
 307     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 308             JLabel.RIGHT));
 309     groupPanel.add(group);
 310
 311     JPanel colourPanel = new JPanel();
 312     gridPanel.add(colourPanel);
 313     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 314             JLabel.RIGHT));
 315     colourPanel.add(colour);
 316     colour.setPreferredSize(new Dimension(150, 15));
 317     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 318     colour.setForeground(Color.black);
 319     colour.setHorizontalAlignment(SwingConstants.CENTER);
 320     colour.setVerticalAlignment(SwingConstants.CENTER);
 321     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 322     colour.setVerticalTextPosition(SwingConstants.CENTER);
 323     mainPanel.add(gridPanel, BorderLayout.NORTH);
 324
 325     JPanel descriptionPanel = new JPanel();
 326     descriptionPanel.add(new JLabel(
 327             MessageManager.getString("label.description:"), JLabel.RIGHT));
 328     description.setFont(JvSwingUtils.getTextAreaFont());
 329     description.setLineWrap(true);
 330     descriptionPanel.add(new JScrollPane(description));
 331
 332     if (!create)
 333     {
 334       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 335
 336       JPanel startEndPanel = new JPanel();
 337       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 338               JLabel.RIGHT));
 339       startEndPanel.add(start);
 340       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 341               JLabel.RIGHT));
 342       startEndPanel.add(end);
 343       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 344     }
 345     else
 346     {
 347       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 348     }
 349
 350     /*
 351      * default feature type and group to that of the first feature supplied,
 352      * or to the last feature created if not supplied (null value)
 353      */
 354     SequenceFeature firstFeature = features.get(0);
 355     boolean useLastDefaults = firstFeature.getType() == null;
 356     final String featureType = useLastDefaults ? lastFeatureAdded
 357             : firstFeature.getType();
 358     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 359             : firstFeature.getFeatureGroup();
 360     name.setText(featureType);
 361     group.setText(featureGroup);
 362
 363     start.setValue(new Integer(firstFeature.getBegin()));
 364     end.setValue(new Integer(firstFeature.getEnd()));
 365     description.setText(firstFeature.getDescription());
 366     updateColourButton(mainPanel, colour,
 367             (oldcol = fcol = getFeatureStyle(featureType)));
 368     Object[] options;
 369     if (!create)
 370     {
 371       options = new Object[] { MessageManager.getString("label.amend"),
 372           MessageManager.getString("action.delete"),
 373           MessageManager.getString("action.cancel") };
 374     }
 375     else
 376     {
 377       options = new Object[] { MessageManager.getString("action.ok"),
 378           MessageManager.getString("action.cancel") };
 379     }
 380
 381     String title = create
 382             ? MessageManager.getString("label.create_new_sequence_features")
 383             : MessageManager.formatMessage("label.amend_delete_features",
 384                     new String[]
 385                     { sequences.get(0).getName() });
 386
 387     /*
 388      * show the dialog
 389      */
 390     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 391             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 392             JvOptionPane.QUESTION_MESSAGE, null, options,
 393             MessageManager.getString("action.ok"));
 394
 395     FeaturesFile ffile = new FeaturesFile();
 396
 397     final String enteredType = name.getText().trim();
 398     final String enteredGroup = group.getText().trim();
 399     final String enteredDescription = description.getText().replaceAll("\n", " ");
 400
 401     if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 402     {
 403       /*
 404        * update default values only if creating using default values
 405        */
 406       if (useLastDefaults)
 407       {
 408         lastFeatureAdded = enteredType;
 409         lastFeatureGroupAdded = enteredGroup;
 410         // TODO: determine if the null feature group is valid
 411         if (lastFeatureGroupAdded.length() < 1)
 412         {
 413           lastFeatureGroupAdded = null;
 414         }
 415       }
 416     }
 417
 418     if (!create)
 419     {
 420       SequenceFeature sf = features.get(featureIndex);
 421
 422       if (reply == JvOptionPane.NO_OPTION)
 423       {
 424         /*
 425          * NO_OPTION corresponds to the Delete button
 426          */
 427         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 428         // update Feature Settings for removal of feature / group
 429         featuresAdded();
 430       }
 431       else if (reply == JvOptionPane.YES_OPTION)
 432       {
 433         /*
 434          * YES_OPTION corresponds to the Amend button
 435          * need to refresh Feature Settings if type, group or colour changed;
 436          * note we don't force the feature to be visible - the user has been
 437          * warned if a hidden feature type or group was entered
 438          */
 439         boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
 440                 .equals(enteredGroup));
 441         refreshSettings |= (fcol != oldcol);
 442         setColour(enteredType, fcol);
 443         int newBegin = sf.begin;
 444         int newEnd = sf.end;
 445         try
 446         {
 447           newBegin = ((Integer) start.getValue()).intValue();
 448           newEnd = ((Integer) end.getValue()).intValue();
 449         } catch (NumberFormatException ex)
 450         {
 451           // JSpinner doesn't accept invalid format data :-)
 452         }
 453
 454         /*
 455          * replace the feature by deleting it and adding a new one
 456          * (to ensure integrity of SequenceFeatures data store)
 457          */
 458         sequences.get(0).deleteFeature(sf);
 459         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 460                 newBegin, newEnd, enteredGroup, sf.getScore());
 461         newSf.setDescription(enteredDescription);
 462         ffile.parseDescriptionHTML(newSf, false);
 463         // amend features dialog only updates one sequence at a time
 464         sequences.get(0).addSequenceFeature(newSf);
 465
 466         if (refreshSettings)
 467         {
 468           featuresAdded();
 469         }
 470       }
 471     }
 472     else
 473     // NEW FEATURES ADDED
 474     {
 475       if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
 476       {
 477         for (int i = 0; i < sequences.size(); i++)
 478         {
 479           SequenceFeature sf = features.get(i);
 480           SequenceFeature sf2 = new SequenceFeature(enteredType,
 481                   enteredDescription, sf.getBegin(), sf.getEnd(),
 482                   enteredGroup);
 483           ffile.parseDescriptionHTML(sf2, false);
 484           sequences.get(i).addSequenceFeature(sf2);
 485         }
 486
 487         setColour(enteredType, fcol);
 488
 489         featuresAdded();
 490
 491         alignPanel.paintAlignment(true, true);
 492
 493         return true;
 494       }
 495       else
 496       {
 497         return false;
 498       }
 499     }
 500
 501     alignPanel.paintAlignment(true, true);
 502
 503     return true;
 504   }
 505
 506   /**
 507    * Show a warning message if the entered type is one that is currently hidden
 508    *
 509    * @param panel
 510    * @param type
 511    */
 512   protected void warnIfTypeHidden(JPanel panel, String type)
 513   {
 514     if (getRenderOrder().contains(type))
 515     {
 516       if (!showFeatureOfType(type))
 517       {
 518         String msg = MessageManager.formatMessage("label.warning_hidden",
 519                 MessageManager.getString("label.feature_type"), type);
 520         JvOptionPane.showMessageDialog(panel, msg, "",
 521                 JvOptionPane.OK_OPTION);
 522       }
 523     }
 524   }
 525
 526   /**
 527    * Show a warning message if the entered group is one that is currently hidden
 528    *
 529    * @param panel
 530    * @param group
 531    */
 532   protected void warnIfGroupHidden(JPanel panel, String group)
 533   {
 534     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 535     {
 536       String msg = MessageManager.formatMessage("label.warning_hidden",
 537               MessageManager.getString("label.group"), group);
 538       JvOptionPane.showMessageDialog(panel, msg, "",
 539               JvOptionPane.OK_OPTION);
 540     }
 541   }
 542
 543   /**
 544    * update the amend feature button dependent on the given style
 545    *
 546    * @param bigPanel
 547    * @param col
 548    * @param col
 549    */
 550   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 551           FeatureColourI col)
 552   {
 553     colour.removeAll();
 554     colour.setIcon(null);
 555     colour.setToolTipText(null);
 556     colour.setText("");
 557
 558     if (col.isSimpleColour())
 559     {
 560       colour.setBackground(col.getColour());
 561     }
 562     else
 563     {
 564       colour.setBackground(bigPanel.getBackground());
 565       colour.setForeground(Color.black);
 566       FeatureSettings.renderGraduatedColor(colour, col);
 567     }
 568   }
 569
 570   /**
 571    * Orders features in render precedence (last in order is last to render, so
 572    * displayed on top of other features)
 573    *
 574    * @param order
 575    */
 576   public void orderFeatures(Comparator<String> order)
 577   {
 578     Arrays.sort(renderOrder, order);
 579   }
 580
 581   /**
 582    * Answers a (possibly empty) list of features in this alignment at a position
 583    * (or range) which is mappable from the given sequence residue position in a
 584    * mapped alignment.
 585    *
 586    * @param sequence
 587    * @param pos
 588    * @return
 589    */
 590   public List<SequenceFeature> findComplementFeaturesAtResidue(
 591           SequenceI sequence, int pos)
 592   {
 593     SequenceI ds = sequence.getDatasetSequence();
 594     List<SequenceFeature> result = new ArrayList<>();
 595     List<AlignedCodonFrame> mappings = this.av.getAlignment()
 596             .getCodonFrame(sequence);
 597     for (AlignedCodonFrame acf : mappings)
 598     {
 599       Mapping mapping = acf.getMappingForSequence(sequence);
 600       if (mapping.getMap().getFromRatio() == mapping.getMap().getToRatio())
 601       {
 602         continue; // we are only looking for 3:1 or 1:3 mappings
 603       }
 604       SearchResultsI sr = new SearchResults();
 605       acf.markMappedRegion(ds, pos, sr);
 606       for (SearchResultMatchI match : sr.getResults())
 607       {
 608         for (int i = match.getStart(); i <= match.getEnd(); i++)
 609         {
 610           List<SequenceFeature> fs = findFeaturesAtResidue(
 611                   match.getSequence(), i);
 612           for (SequenceFeature sf : fs)
 613           {
 614             if (!result.contains(sf))
 615             {
 616               result.addAll(fs);
 617             }
 618           }
 619         }
 620       }
 621     }
 622
 623     return result;
 624   }
 625 }