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.List;
  47
  48 import javax.swing.JColorChooser;
  49 import javax.swing.JComboBox;
  50 import javax.swing.JLabel;
  51 import javax.swing.JPanel;
  52 import javax.swing.JScrollPane;
  53 import javax.swing.JSpinner;
  54 import javax.swing.JTextArea;
  55 import javax.swing.JTextField;
  56 import javax.swing.SwingConstants;
  57
  58 /**
  59  * DOCUMENT ME!
  60  *
  61  * @author $author$
  62  * @version $Revision$
  63  */
  64 public class FeatureRenderer extends
  65         jalview.renderer.seqfeatures.FeatureRenderer
  66 {
  67   Color resBoxColour;
  68
  69   AlignmentPanel ap;
  70
  71   /**
  72    * Creates a new FeatureRenderer object
  73    *
  74    * @param alignPanel
  75    */
  76   public FeatureRenderer(AlignmentPanel alignPanel)
  77   {
  78     super(alignPanel.av);
  79     this.ap = alignPanel;
  80     if (alignPanel.getSeqPanel() != null
  81             && alignPanel.getSeqPanel().seqCanvas != null
  82             && alignPanel.getSeqPanel().seqCanvas.fr != null)
  83     {
  84       transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
  85     }
  86   }
  87
  88   // // /////////////
  89   // // Feature Editing Dialog
  90   // // Will be refactored in next release.
  91
  92   static String lastFeatureAdded;
  93
  94   static String lastFeatureGroupAdded;
  95
  96   static String lastDescriptionAdded;
  97
  98   FeatureColourI oldcol, fcol;
  99
 100   int featureIndex = 0;
 101
 102   /**
 103    * Presents a dialog allowing the user to add new features, or amend or delete
 104    * existing features. Currently this can be on
 105    * <ul>
 106    * <li>double-click on a sequence - Amend/Delete features at position</li>
 107    * <li>Create sequence feature from pop-up menu on selected region</li>
 108    * <li>Create features for pattern matches from Find</li>
 109    * </ul>
 110    *
 111    * @param sequences
 112    *          the sequences features are to be created on (if creating
 113    *          features), or a single sequence (if amending features)
 114    * @param features
 115    *          the current features at the position (if amending), or template
 116    *          new features with start/end position set (if creating)
 117    * @param create
 118    *          true to create features, false to amend or delete
 119    * @param featureType
 120    *          the feature type to set on new features; if null, defaults to the
 121    *          type of the last new feature created if any, failing that to
 122    *          "feature_1"
 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, String featureType)
 129   {
 130
 131     featureIndex = 0;
 132
 133     final JPanel mainPanel = new JPanel(new BorderLayout());
 134     final JTextField name = new JTextField(25);
 135     final JTextField source = new JTextField(25);
 136     final JTextArea description = new JTextArea(3, 25);
 137     final JSpinner start = new JSpinner();
 138     final JSpinner end = new JSpinner();
 139     start.setPreferredSize(new Dimension(80, 20));
 140     end.setPreferredSize(new Dimension(80, 20));
 141     final FeatureRenderer me = this;
 142     final JLabel colour = new JLabel();
 143     colour.setOpaque(true);
 144     // colour.setBorder(BorderFactory.createEtchedBorder());
 145     colour.setMaximumSize(new Dimension(30, 16));
 146     colour.addMouseListener(new MouseAdapter()
 147     {
 148       FeatureColourChooser fcc = null;
 149
 150       @Override
 151       public void mousePressed(MouseEvent evt)
 152       {
 153         if (fcol.isSimpleColour())
 154         {
 155           Color col = JColorChooser.showDialog(Desktop.desktop,
 156                   MessageManager.getString("label.select_feature_colour"),
 157                   fcol.getColour());
 158           if (col != null)
 159           {
 160             fcol = new FeatureColour(col);
 161             updateColourButton(mainPanel, colour, new FeatureColour(col));
 162           }
 163         }
 164         else
 165         {
 166           if (fcc == null)
 167           {
 168             final String type = features.get(featureIndex).getType();
 169             fcc = new FeatureColourChooser(me, type);
 170             fcc.setRequestFocusEnabled(true);
 171             fcc.requestFocus();
 172
 173             fcc.addActionListener(new ActionListener()
 174             {
 175
 176               @Override
 177               public void actionPerformed(ActionEvent e)
 178               {
 179                 fcol = fcc.getLastColour();
 180                 fcc = null;
 181                 setColour(type, fcol);
 182                 updateColourButton(mainPanel, colour, fcol);
 183               }
 184             });
 185
 186           }
 187         }
 188       }
 189     });
 190     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 191
 192     if (!create && features.size() > 1)
 193     {
 194       /*
 195        * more than one feature at selected position - add a drop-down
 196        * to choose the feature to amend
 197        */
 198       gridPanel = new JPanel(new GridLayout(4, 1));
 199       JPanel choosePanel = new JPanel();
 200       choosePanel.add(new JLabel(MessageManager
 201               .getString("label.select_feature")
 202               + ":"));
 203       final JComboBox<String> overlaps = new JComboBox<String>();
 204       for (SequenceFeature sf : features)
 205       {
 206         String text = sf.getType() + "/" + sf.getBegin() + "-"
 207                 + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
 208         overlaps.addItem(text);
 209       }
 210       choosePanel.add(overlaps);
 211
 212       overlaps.addItemListener(new ItemListener()
 213       {
 214         @Override
 215         public void itemStateChanged(ItemEvent e)
 216         {
 217           int index = overlaps.getSelectedIndex();
 218           if (index != -1)
 219           {
 220             featureIndex = index;
 221             SequenceFeature sf = features.get(index);
 222             name.setText(sf.getType());
 223             description.setText(sf.getDescription());
 224             source.setText(sf.getFeatureGroup());
 225             start.setValue(new Integer(sf.getBegin()));
 226             end.setValue(new Integer(sf.getEnd()));
 227
 228             SearchResultsI highlight = new SearchResults();
 229             highlight.addResult(sequences.get(0), sf.getBegin(),
 230                     sf.getEnd());
 231
 232             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 233
 234           }
 235           FeatureColourI col = getFeatureStyle(name.getText());
 236           if (col == null)
 237           {
 238             col = new FeatureColour(ColorUtils
 239                     .createColourFromName(name.getText()));
 240           }
 241           oldcol = fcol = col;
 242           updateColourButton(mainPanel, colour, col);
 243         }
 244       });
 245
 246       gridPanel.add(choosePanel);
 247     }
 248     // ////////
 249     // ////////////////////////////////////
 250
 251     JPanel namePanel = new JPanel();
 252     gridPanel.add(namePanel);
 253     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 254             JLabel.RIGHT));
 255     namePanel.add(name);
 256
 257     JPanel groupPanel = new JPanel();
 258     gridPanel.add(groupPanel);
 259     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 260             JLabel.RIGHT));
 261     groupPanel.add(source);
 262
 263     JPanel colourPanel = new JPanel();
 264     gridPanel.add(colourPanel);
 265     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 266             JLabel.RIGHT));
 267     colourPanel.add(colour);
 268     colour.setPreferredSize(new Dimension(150, 15));
 269     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 270     colour.setForeground(Color.black);
 271     colour.setHorizontalAlignment(SwingConstants.CENTER);
 272     colour.setVerticalAlignment(SwingConstants.CENTER);
 273     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 274     colour.setVerticalTextPosition(SwingConstants.CENTER);
 275     mainPanel.add(gridPanel, BorderLayout.NORTH);
 276
 277     JPanel descriptionPanel = new JPanel();
 278     descriptionPanel.add(new JLabel(MessageManager
 279             .getString("label.description:"),
 280             JLabel.RIGHT));
 281     description.setFont(JvSwingUtils.getTextAreaFont());
 282     description.setLineWrap(true);
 283     descriptionPanel.add(new JScrollPane(description));
 284
 285     if (!create)
 286     {
 287       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 288
 289       JPanel startEndPanel = new JPanel();
 290       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 291               JLabel.RIGHT));
 292       startEndPanel.add(start);
 293       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 294               JLabel.RIGHT));
 295       startEndPanel.add(end);
 296       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 297     }
 298     else
 299     {
 300       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 301     }
 302
 303     SequenceFeature firstFeature = features.get(0);
 304     if (featureType != null)
 305     {
 306       lastFeatureAdded = featureType;
 307     }
 308     else
 309     {
 310       if (lastFeatureAdded == null)
 311       {
 312         if (firstFeature.type != null)
 313         {
 314           lastFeatureAdded = firstFeature.type;
 315         }
 316         else
 317         {
 318           lastFeatureAdded = "feature_1";
 319         }
 320       }
 321     }
 322
 323     if (lastFeatureGroupAdded == null)
 324     {
 325       if (firstFeature.featureGroup != null)
 326       {
 327         lastFeatureGroupAdded = firstFeature.featureGroup;
 328       }
 329       else
 330       {
 331         lastFeatureGroupAdded = "Jalview";
 332       }
 333     }
 334
 335     if (create)
 336     {
 337       name.setText(lastFeatureAdded);
 338       source.setText(lastFeatureGroupAdded);
 339     }
 340     else
 341     {
 342       name.setText(firstFeature.getType());
 343       source.setText(firstFeature.getFeatureGroup());
 344     }
 345
 346     start.setValue(new Integer(firstFeature.getBegin()));
 347     end.setValue(new Integer(firstFeature.getEnd()));
 348     description.setText(firstFeature.getDescription());
 349     updateColourButton(mainPanel, colour,
 350             (oldcol = fcol = getFeatureStyle(name.getText())));
 351     Object[] options;
 352     if (!create)
 353     {
 354       options = new Object[] { MessageManager.getString("label.amend"),
 355           MessageManager.getString("action.delete"),
 356           MessageManager.getString("action.cancel") };
 357     }
 358     else
 359     {
 360       options = new Object[] { MessageManager.getString("action.ok"),
 361           MessageManager.getString("action.cancel") };
 362     }
 363
 364     String title = create ? MessageManager
 365             .getString("label.create_new_sequence_features")
 366             : MessageManager.formatMessage("label.amend_delete_features",
 367                     new String[] { sequences.get(0).getName() });
 368
 369     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 370             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 371             JvOptionPane.QUESTION_MESSAGE, null, options,
 372             MessageManager.getString("action.ok"));
 373
 374     FeaturesFile ffile = new FeaturesFile();
 375
 376     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 377     {
 378       lastFeatureAdded = name.getText().trim();
 379       lastFeatureGroupAdded = source.getText().trim();
 380       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 381       // TODO: determine if the null feature group is valid
 382       if (lastFeatureGroupAdded.length() < 1)
 383       {
 384         lastFeatureGroupAdded = null;
 385       }
 386     }
 387
 388     if (!create)
 389     {
 390       SequenceFeature sf = features.get(featureIndex);
 391
 392       if (reply == JvOptionPane.NO_OPTION)
 393       {
 394         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 395       }
 396       else if (reply == JvOptionPane.YES_OPTION)
 397       {
 398         sf.type = lastFeatureAdded;
 399         sf.featureGroup = lastFeatureGroupAdded;
 400         sf.description = lastDescriptionAdded;
 401
 402         setColour(sf.type, fcol);
 403         getFeaturesDisplayed().setVisible(sf.type);
 404
 405         try
 406         {
 407           sf.begin = ((Integer) start.getValue()).intValue();
 408           sf.end = ((Integer) end.getValue()).intValue();
 409         } catch (NumberFormatException ex)
 410         {
 411         }
 412
 413         ffile.parseDescriptionHTML(sf, false);
 414       }
 415     }
 416     else
 417     // NEW FEATURES ADDED
 418     {
 419       if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 420       {
 421         for (int i = 0; i < sequences.size(); i++)
 422         {
 423           SequenceFeature sf = features.get(i);
 424           sf.type = lastFeatureAdded;
 425           // fix for JAL-1538 - always set feature group here
 426           sf.featureGroup = lastFeatureGroupAdded;
 427           sf.description = lastDescriptionAdded;
 428           sequences.get(i).addSequenceFeature(sf);
 429           ffile.parseDescriptionHTML(sf, false);
 430         }
 431
 432         if (lastFeatureGroupAdded != null)
 433         {
 434           setGroupVisibility(lastFeatureGroupAdded, true);
 435         }
 436         setColour(lastFeatureAdded, fcol);
 437         setVisible(lastFeatureAdded);
 438
 439         findAllFeatures(false);
 440
 441         alignPanel.paintAlignment(true);
 442
 443         return true;
 444       }
 445       else
 446       {
 447         return false;
 448       }
 449     }
 450
 451     alignPanel.paintAlignment(true);
 452
 453     return true;
 454   }
 455
 456   /**
 457    * update the amend feature button dependent on the given style
 458    *
 459    * @param bigPanel
 460    * @param col
 461    * @param col
 462    */
 463   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 464           FeatureColourI col)
 465   {
 466     colour.removeAll();
 467     colour.setIcon(null);
 468     colour.setToolTipText(null);
 469     colour.setText("");
 470
 471     if (col.isSimpleColour())
 472     {
 473       colour.setBackground(col.getColour());
 474     }
 475     else
 476     {
 477       colour.setBackground(bigPanel.getBackground());
 478       colour.setForeground(Color.black);
 479       FeatureSettings.renderGraduatedColor(colour, col);
 480     }
 481   }
 482
 483   /**
 484    * Orders features in render precedence (last in order is last to render, so
 485    * displayed on top of other features)
 486    *
 487    * @param order
 488    */
 489   public void orderFeatures(Comparator<String> order)
 490   {
 491     Arrays.sort(renderOrder, order);
 492   }
 493 }