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.Arrays;
  45 import java.util.Comparator;
  46 import java.util.HashMap;
  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
  59 /**
  60  * DOCUMENT ME!
  61  *
  62  * @author $author$
  63  * @version $Revision$
  64  */
  65 public class FeatureRenderer extends
  66         jalview.renderer.seqfeatures.FeatureRenderer
  67 {
  68   Color resBoxColour;
  69
  70   AlignmentPanel ap;
  71
  72   /**
  73    * Creates a new FeatureRenderer object
  74    *
  75    * @param alignPanel
  76    */
  77   public FeatureRenderer(AlignmentPanel alignPanel)
  78   {
  79     super(alignPanel.av);
  80     this.ap = alignPanel;
  81     if (alignPanel.getSeqPanel() != null
  82             && alignPanel.getSeqPanel().seqCanvas != null
  83             && alignPanel.getSeqPanel().seqCanvas.fr != null)
  84     {
  85       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
  86     }
  87   }
  88
  89   // // /////////////
  90   // // Feature Editing Dialog
  91   // // Will be refactored in next release.
  92
  93   static String lastFeatureAdded;
  94
  95   static String lastFeatureGroupAdded;
  96
  97   static String lastDescriptionAdded;
  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    *
 112    * @param sequences
 113    *          the sequences features are to be created on (if creating
 114    *          features), or a single sequence (if amending features)
 115    * @param features
 116    *          the current features at the position (if amending), or template
 117    *          new features with start/end position set (if creating)
 118    * @param create
 119    *          true to create features, false to amend or delete
 120    * @param featureType
 121    *          the feature type to set on new features; if null, defaults to the
 122    *          type of the last new feature created if any, failing that to
 123    *          "feature_1"
 124    * @param alignPanel
 125    * @return
 126    */
 127   protected boolean amendFeatures(final List<SequenceI> sequences,
 128           final List<SequenceFeature> features, boolean create,
 129           final AlignmentPanel alignPanel, String featureType)
 130   {
 131
 132     featureIndex = 0;
 133
 134     final JPanel mainPanel = new JPanel(new BorderLayout());
 135     final JTextField name = new JTextField(25);
 136     final JTextField source = new JTextField(25);
 137     final JTextArea description = new JTextArea(3, 25);
 138     final JSpinner start = new JSpinner();
 139     final JSpinner end = new JSpinner();
 140     start.setPreferredSize(new Dimension(80, 20));
 141     end.setPreferredSize(new Dimension(80, 20));
 142     final FeatureRenderer me = this;
 143     final JLabel colour = new JLabel();
 144     colour.setOpaque(true);
 145     // colour.setBorder(BorderFactory.createEtchedBorder());
 146     colour.setMaximumSize(new Dimension(30, 16));
 147     colour.addMouseListener(new MouseAdapter()
 148     {
 149       FeatureColourChooser fcc = null;
 150
 151       @Override
 152       public void mousePressed(MouseEvent evt)
 153       {
 154         if (fcol.isSimpleColour())
 155         {
 156           Color col = JColorChooser.showDialog(Desktop.desktop,
 157                   MessageManager.getString("label.select_feature_colour"),
 158                   fcol.getColour());
 159           if (col != null)
 160           {
 161             fcol = new FeatureColour(col);
 162             updateColourButton(mainPanel, colour, new FeatureColour(col));
 163           }
 164         }
 165         else
 166         {
 167           if (fcc == null)
 168           {
 169             final String ft = features.get(featureIndex).getType();
 170             final String type = ft == null ? lastFeatureAdded : ft;
 171             fcc = new FeatureColourChooser(me, type);
 172             fcc.setRequestFocusEnabled(true);
 173             fcc.requestFocus();
 174
 175             fcc.addActionListener(new ActionListener()
 176             {
 177
 178               @Override
 179               public void actionPerformed(ActionEvent e)
 180               {
 181                 fcol = fcc.getLastColour();
 182                 fcc = null;
 183                 setColour(type, fcol);
 184                 updateColourButton(mainPanel, colour, fcol);
 185               }
 186             });
 187
 188           }
 189         }
 190       }
 191     });
 192     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 193
 194     if (!create && features.size() > 1)
 195     {
 196       /*
 197        * more than one feature at selected position - add a drop-down
 198        * to choose the feature to amend
 199        */
 200       gridPanel = new JPanel(new GridLayout(4, 1));
 201       JPanel choosePanel = new JPanel();
 202       choosePanel.add(new JLabel(MessageManager
 203               .getString("label.select_feature")
 204               + ":"));
 205       final JComboBox<String> overlaps = new JComboBox<String>();
 206       for (SequenceFeature sf : features)
 207       {
 208         String text = sf.getType() + "/" + sf.getBegin() + "-"
 209                 + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
 210         overlaps.addItem(text);
 211       }
 212       choosePanel.add(overlaps);
 213
 214       overlaps.addItemListener(new ItemListener()
 215       {
 216         @Override
 217         public void itemStateChanged(ItemEvent e)
 218         {
 219           int index = overlaps.getSelectedIndex();
 220           if (index != -1)
 221           {
 222             featureIndex = index;
 223             SequenceFeature sf = features.get(index);
 224             name.setText(sf.getType());
 225             description.setText(sf.getDescription());
 226             source.setText(sf.getFeatureGroup());
 227             start.setValue(new Integer(sf.getBegin()));
 228             end.setValue(new Integer(sf.getEnd()));
 229
 230             SearchResultsI highlight = new SearchResults();
 231             highlight.addResult(sequences.get(0), sf.getBegin(),
 232                     sf.getEnd());
 233
 234             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 235
 236           }
 237           FeatureColourI col = getFeatureStyle(name.getText());
 238           if (col == null)
 239           {
 240             col = new FeatureColour(ColorUtils
 241                     .createColourFromName(name.getText()));
 242           }
 243           oldcol = fcol = col;
 244           updateColourButton(mainPanel, colour, col);
 245         }
 246       });
 247
 248       gridPanel.add(choosePanel);
 249     }
 250     // ////////
 251     // ////////////////////////////////////
 252
 253     JPanel namePanel = new JPanel();
 254     gridPanel.add(namePanel);
 255     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 256             JLabel.RIGHT));
 257     namePanel.add(name);
 258
 259     JPanel groupPanel = new JPanel();
 260     gridPanel.add(groupPanel);
 261     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 262             JLabel.RIGHT));
 263     groupPanel.add(source);
 264
 265     JPanel colourPanel = new JPanel();
 266     gridPanel.add(colourPanel);
 267     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 268             JLabel.RIGHT));
 269     colourPanel.add(colour);
 270     colour.setPreferredSize(new Dimension(150, 15));
 271     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 272     colour.setForeground(Color.black);
 273     colour.setHorizontalAlignment(SwingConstants.CENTER);
 274     colour.setVerticalAlignment(SwingConstants.CENTER);
 275     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 276     colour.setVerticalTextPosition(SwingConstants.CENTER);
 277     mainPanel.add(gridPanel, BorderLayout.NORTH);
 278
 279     JPanel descriptionPanel = new JPanel();
 280     descriptionPanel.add(new JLabel(MessageManager
 281             .getString("label.description:"),
 282             JLabel.RIGHT));
 283     description.setFont(JvSwingUtils.getTextAreaFont());
 284     description.setLineWrap(true);
 285     descriptionPanel.add(new JScrollPane(description));
 286
 287     if (!create)
 288     {
 289       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 290
 291       JPanel startEndPanel = new JPanel();
 292       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 293               JLabel.RIGHT));
 294       startEndPanel.add(start);
 295       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 296               JLabel.RIGHT));
 297       startEndPanel.add(end);
 298       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 299     }
 300     else
 301     {
 302       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 303     }
 304
 305     SequenceFeature firstFeature = features.get(0);
 306     if (featureType != null)
 307     {
 308       lastFeatureAdded = featureType;
 309     }
 310     else
 311     {
 312       if (lastFeatureAdded == null)
 313       {
 314         if (firstFeature.type != null)
 315         {
 316           lastFeatureAdded = firstFeature.type;
 317         }
 318         else
 319         {
 320           lastFeatureAdded = "feature_1";
 321         }
 322       }
 323     }
 324
 325     if (lastFeatureGroupAdded == null)
 326     {
 327       if (firstFeature.featureGroup != null)
 328       {
 329         lastFeatureGroupAdded = firstFeature.featureGroup;
 330       }
 331       else
 332       {
 333         lastFeatureGroupAdded = "Jalview";
 334       }
 335     }
 336
 337     if (create)
 338     {
 339       name.setText(lastFeatureAdded);
 340       source.setText(lastFeatureGroupAdded);
 341     }
 342     else
 343     {
 344       name.setText(firstFeature.getType());
 345       source.setText(firstFeature.getFeatureGroup());
 346     }
 347
 348     start.setValue(new Integer(firstFeature.getBegin()));
 349     end.setValue(new Integer(firstFeature.getEnd()));
 350     description.setText(firstFeature.getDescription());
 351     updateColourButton(mainPanel, colour,
 352             (oldcol = fcol = getFeatureStyle(name.getText())));
 353     Object[] options;
 354     if (!create)
 355     {
 356       options = new Object[] { MessageManager.getString("label.amend"),
 357           MessageManager.getString("action.delete"),
 358           MessageManager.getString("action.cancel") };
 359     }
 360     else
 361     {
 362       options = new Object[] { MessageManager.getString("action.ok"),
 363           MessageManager.getString("action.cancel") };
 364     }
 365
 366     String title = create ? MessageManager
 367             .getString("label.create_new_sequence_features")
 368             : MessageManager.formatMessage("label.amend_delete_features",
 369                     new String[] { sequences.get(0).getName() });
 370
 371     /*
 372      * show the dialog
 373      */
 374     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 375             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 376             JvOptionPane.QUESTION_MESSAGE, null, options,
 377             MessageManager.getString("action.ok"));
 378
 379     FeaturesFile ffile = new FeaturesFile();
 380
 381     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 382     {
 383       lastFeatureAdded = name.getText().trim();
 384       lastFeatureGroupAdded = source.getText().trim();
 385       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 386       // TODO: determine if the null feature group is valid
 387       if (lastFeatureGroupAdded.length() < 1)
 388       {
 389         lastFeatureGroupAdded = null;
 390       }
 391     }
 392
 393     if (!create)
 394     {
 395       SequenceFeature sf = features.get(featureIndex);
 396
 397       if (reply == JvOptionPane.NO_OPTION)
 398       {
 399         /*
 400          * NO_OPTION corresponds to the Delete button
 401          */
 402         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 403       }
 404       else if (reply == JvOptionPane.YES_OPTION)
 405       {
 406         /*
 407          * YES_OPTION corresponds to the Amend button
 408          */
 409         boolean typeChanged = !lastFeatureAdded.equals(sf.type);
 410         String newType = lastFeatureAdded;
 411         String newFeatureGroup = lastFeatureGroupAdded;
 412         String newDescription = lastDescriptionAdded;
 413
 414         setColour(newType, fcol);
 415         getFeaturesDisplayed().setVisible(newType);
 416         int newBegin = sf.begin;
 417         int newEnd = sf.end;
 418         try
 419         {
 420           newBegin = ((Integer) start.getValue()).intValue();
 421           newEnd = ((Integer) end.getValue()).intValue();
 422         } catch (NumberFormatException ex)
 423         {
 424           // JSpinner doesn't accept invalid format data :-)
 425         }
 426
 427         /*
 428          * replace the feature by deleting it and adding a new one
 429          * (to ensure integrity of SequenceFeatures data store)
 430          */
 431         sequences.get(0).deleteFeature(sf);
 432         SequenceFeature newSf = new SequenceFeature(newType,
 433                 newDescription, newBegin, newEnd, sf.getScore(),
 434                 newFeatureGroup);
 435         // ensure any additional properties are copied
 436         if (sf.otherDetails != null)
 437         {
 438           newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
 439         }
 440         ffile.parseDescriptionHTML(newSf, false);
 441         // add any additional links not parsed from description
 442         if (sf.links != null)
 443         {
 444           for (String link : sf.links)
 445           {
 446             newSf.addLink(link);
 447           }
 448         }
 449         // amend features only gets one sequence to act on
 450         sequences.get(0).addSequenceFeature(newSf);
 451
 452         if (typeChanged)
 453         {
 454           findAllFeatures();
 455         }
 456       }
 457     }
 458     else
 459     // NEW FEATURES ADDED
 460     {
 461       if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 462       {
 463         for (int i = 0; i < sequences.size(); i++)
 464         {
 465           SequenceFeature sf = features.get(i);
 466           sf.type = lastFeatureAdded;
 467           // fix for JAL-1538 - always set feature group here
 468           sf.featureGroup = lastFeatureGroupAdded;
 469           sf.description = lastDescriptionAdded;
 470           sequences.get(i).addSequenceFeature(sf);
 471           ffile.parseDescriptionHTML(sf, false);
 472         }
 473
 474         if (lastFeatureGroupAdded != null)
 475         {
 476           setGroupVisibility(lastFeatureGroupAdded, true);
 477         }
 478         setColour(lastFeatureAdded, fcol);
 479         setVisible(lastFeatureAdded);
 480
 481         findAllFeatures(false);
 482
 483         alignPanel.paintAlignment(true);
 484
 485         return true;
 486       }
 487       else
 488       {
 489         return false;
 490       }
 491     }
 492
 493     alignPanel.paintAlignment(true);
 494
 495     return true;
 496   }
 497
 498   /**
 499    * update the amend feature button dependent on the given style
 500    *
 501    * @param bigPanel
 502    * @param col
 503    * @param col
 504    */
 505   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 506           FeatureColourI col)
 507   {
 508     colour.removeAll();
 509     colour.setIcon(null);
 510     colour.setToolTipText(null);
 511     colour.setText("");
 512
 513     if (col.isSimpleColour())
 514     {
 515       colour.setBackground(col.getColour());
 516     }
 517     else
 518     {
 519       colour.setBackground(bigPanel.getBackground());
 520       colour.setForeground(Color.black);
 521       FeatureSettings.renderGraduatedColor(colour, col);
 522     }
 523   }
 524
 525   /**
 526    * Orders features in render precedence (last in order is last to render, so
 527    * displayed on top of other features)
 528    *
 529    * @param order
 530    */
 531   public void orderFeatures(Comparator<String> order)
 532   {
 533     Arrays.sort(renderOrder, order);
 534   }
 535 }