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 ft = features.get(featureIndex).getType();
 169             final String type = ft == null ? lastFeatureAdded : ft;
 170             fcc = new FeatureColourChooser(me, type);
 171             fcc.setRequestFocusEnabled(true);
 172             fcc.requestFocus();
 173
 174             fcc.addActionListener(new ActionListener()
 175             {
 176
 177               @Override
 178               public void actionPerformed(ActionEvent e)
 179               {
 180                 fcol = fcc.getLastColour();
 181                 fcc = null;
 182                 setColour(type, fcol);
 183                 updateColourButton(mainPanel, colour, fcol);
 184               }
 185             });
 186
 187           }
 188         }
 189       }
 190     });
 191     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 192
 193     if (!create && features.size() > 1)
 194     {
 195       /*
 196        * more than one feature at selected position - add a drop-down
 197        * to choose the feature to amend
 198        */
 199       gridPanel = new JPanel(new GridLayout(4, 1));
 200       JPanel choosePanel = new JPanel();
 201       choosePanel.add(new JLabel(MessageManager
 202               .getString("label.select_feature")
 203               + ":"));
 204       final JComboBox<String> overlaps = new JComboBox<String>();
 205       for (SequenceFeature sf : features)
 206       {
 207         String text = sf.getType() + "/" + sf.getBegin() + "-"
 208                 + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
 209         overlaps.addItem(text);
 210       }
 211       choosePanel.add(overlaps);
 212
 213       overlaps.addItemListener(new ItemListener()
 214       {
 215         @Override
 216         public void itemStateChanged(ItemEvent e)
 217         {
 218           int index = overlaps.getSelectedIndex();
 219           if (index != -1)
 220           {
 221             featureIndex = index;
 222             SequenceFeature sf = features.get(index);
 223             name.setText(sf.getType());
 224             description.setText(sf.getDescription());
 225             source.setText(sf.getFeatureGroup());
 226             start.setValue(new Integer(sf.getBegin()));
 227             end.setValue(new Integer(sf.getEnd()));
 228
 229             SearchResultsI highlight = new SearchResults();
 230             highlight.addResult(sequences.get(0), sf.getBegin(),
 231                     sf.getEnd());
 232
 233             alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 234
 235           }
 236           FeatureColourI col = getFeatureStyle(name.getText());
 237           if (col == null)
 238           {
 239             col = new FeatureColour(ColorUtils
 240                     .createColourFromName(name.getText()));
 241           }
 242           oldcol = fcol = col;
 243           updateColourButton(mainPanel, colour, col);
 244         }
 245       });
 246
 247       gridPanel.add(choosePanel);
 248     }
 249     // ////////
 250     // ////////////////////////////////////
 251
 252     JPanel namePanel = new JPanel();
 253     gridPanel.add(namePanel);
 254     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 255             JLabel.RIGHT));
 256     namePanel.add(name);
 257
 258     JPanel groupPanel = new JPanel();
 259     gridPanel.add(groupPanel);
 260     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 261             JLabel.RIGHT));
 262     groupPanel.add(source);
 263
 264     JPanel colourPanel = new JPanel();
 265     gridPanel.add(colourPanel);
 266     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 267             JLabel.RIGHT));
 268     colourPanel.add(colour);
 269     colour.setPreferredSize(new Dimension(150, 15));
 270     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 271     colour.setForeground(Color.black);
 272     colour.setHorizontalAlignment(SwingConstants.CENTER);
 273     colour.setVerticalAlignment(SwingConstants.CENTER);
 274     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 275     colour.setVerticalTextPosition(SwingConstants.CENTER);
 276     mainPanel.add(gridPanel, BorderLayout.NORTH);
 277
 278     JPanel descriptionPanel = new JPanel();
 279     descriptionPanel.add(new JLabel(MessageManager
 280             .getString("label.description:"),
 281             JLabel.RIGHT));
 282     description.setFont(JvSwingUtils.getTextAreaFont());
 283     description.setLineWrap(true);
 284     descriptionPanel.add(new JScrollPane(description));
 285
 286     if (!create)
 287     {
 288       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 289
 290       JPanel startEndPanel = new JPanel();
 291       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 292               JLabel.RIGHT));
 293       startEndPanel.add(start);
 294       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 295               JLabel.RIGHT));
 296       startEndPanel.add(end);
 297       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 298     }
 299     else
 300     {
 301       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 302     }
 303
 304     SequenceFeature firstFeature = features.get(0);
 305     if (featureType != null)
 306     {
 307       lastFeatureAdded = featureType;
 308     }
 309     else
 310     {
 311       if (lastFeatureAdded == null)
 312       {
 313         if (firstFeature.type != null)
 314         {
 315           lastFeatureAdded = firstFeature.type;
 316         }
 317         else
 318         {
 319           lastFeatureAdded = "feature_1";
 320         }
 321       }
 322     }
 323
 324     if (lastFeatureGroupAdded == null)
 325     {
 326       if (firstFeature.featureGroup != null)
 327       {
 328         lastFeatureGroupAdded = firstFeature.featureGroup;
 329       }
 330       else
 331       {
 332         lastFeatureGroupAdded = "Jalview";
 333       }
 334     }
 335
 336     if (create)
 337     {
 338       name.setText(lastFeatureAdded);
 339       source.setText(lastFeatureGroupAdded);
 340     }
 341     else
 342     {
 343       name.setText(firstFeature.getType());
 344       source.setText(firstFeature.getFeatureGroup());
 345     }
 346
 347     start.setValue(new Integer(firstFeature.getBegin()));
 348     end.setValue(new Integer(firstFeature.getEnd()));
 349     description.setText(firstFeature.getDescription());
 350     updateColourButton(mainPanel, colour,
 351             (oldcol = fcol = getFeatureStyle(name.getText())));
 352     Object[] options;
 353     if (!create)
 354     {
 355       options = new Object[] { MessageManager.getString("label.amend"),
 356           MessageManager.getString("action.delete"),
 357           MessageManager.getString("action.cancel") };
 358     }
 359     else
 360     {
 361       options = new Object[] { MessageManager.getString("action.ok"),
 362           MessageManager.getString("action.cancel") };
 363     }
 364
 365     String title = create ? MessageManager
 366             .getString("label.create_new_sequence_features")
 367             : MessageManager.formatMessage("label.amend_delete_features",
 368                     new String[] { sequences.get(0).getName() });
 369
 370     /*
 371      * show the dialog
 372      */
 373     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 374             mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 375             JvOptionPane.QUESTION_MESSAGE, null, options,
 376             MessageManager.getString("action.ok"));
 377
 378     FeaturesFile ffile = new FeaturesFile();
 379
 380     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 381     {
 382       lastFeatureAdded = name.getText().trim();
 383       lastFeatureGroupAdded = source.getText().trim();
 384       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 385       // TODO: determine if the null feature group is valid
 386       if (lastFeatureGroupAdded.length() < 1)
 387       {
 388         lastFeatureGroupAdded = null;
 389       }
 390     }
 391
 392     if (!create)
 393     {
 394       SequenceFeature sf = features.get(featureIndex);
 395
 396       if (reply == JvOptionPane.NO_OPTION)
 397       {
 398         /*
 399          * NO_OPTION corresponds to the Delete button
 400          */
 401         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 402       }
 403       else if (reply == JvOptionPane.YES_OPTION)
 404       {
 405         /*
 406          * YES_OPTION corresponds to the Amend button
 407          */
 408         boolean typeChanged = !lastFeatureAdded.equals(sf.type);
 409         sf.type = lastFeatureAdded;
 410         sf.featureGroup = lastFeatureGroupAdded;
 411         sf.description = lastDescriptionAdded;
 412
 413         setColour(sf.type, fcol);
 414         getFeaturesDisplayed().setVisible(sf.type);
 415
 416         try
 417         {
 418           sf.begin = ((Integer) start.getValue()).intValue();
 419           sf.end = ((Integer) end.getValue()).intValue();
 420         } catch (NumberFormatException ex)
 421         {
 422         }
 423
 424         ffile.parseDescriptionHTML(sf, false);
 425         if (typeChanged)
 426         {
 427           findAllFeatures();
 428         }
 429       }
 430     }
 431     else
 432     // NEW FEATURES ADDED
 433     {
 434       if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 435       {
 436         for (int i = 0; i < sequences.size(); i++)
 437         {
 438           SequenceFeature sf = features.get(i);
 439           sf.type = lastFeatureAdded;
 440           // fix for JAL-1538 - always set feature group here
 441           sf.featureGroup = lastFeatureGroupAdded;
 442           sf.description = lastDescriptionAdded;
 443           sequences.get(i).addSequenceFeature(sf);
 444           ffile.parseDescriptionHTML(sf, false);
 445         }
 446
 447         if (lastFeatureGroupAdded != null)
 448         {
 449           setGroupVisibility(lastFeatureGroupAdded, true);
 450         }
 451         setColour(lastFeatureAdded, fcol);
 452         setVisible(lastFeatureAdded);
 453
 454         findAllFeatures(false);
 455
 456         alignPanel.paintAlignment(true);
 457
 458         return true;
 459       }
 460       else
 461       {
 462         return false;
 463       }
 464     }
 465
 466     alignPanel.paintAlignment(true);
 467
 468     return true;
 469   }
 470
 471   /**
 472    * update the amend feature button dependent on the given style
 473    *
 474    * @param bigPanel
 475    * @param col
 476    * @param col
 477    */
 478   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 479           FeatureColourI col)
 480   {
 481     colour.removeAll();
 482     colour.setIcon(null);
 483     colour.setToolTipText(null);
 484     colour.setText("");
 485
 486     if (col.isSimpleColour())
 487     {
 488       colour.setBackground(col.getColour());
 489     }
 490     else
 491     {
 492       colour.setBackground(bigPanel.getBackground());
 493       colour.setForeground(Color.black);
 494       FeatureSettings.renderGraduatedColor(colour, col);
 495     }
 496   }
 497
 498   /**
 499    * Orders features in render precedence (last in order is last to render, so
 500    * displayed on top of other features)
 501    *
 502    * @param order
 503    */
 504   public void orderFeatures(Comparator<String> order)
 505   {
 506     Arrays.sort(renderOrder, order);
 507   }
 508 }