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.SequenceFeature;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.schemes.Colour;
  28 import jalview.schemes.FeatureColour;
  29 import jalview.schemes.UserColourScheme;
  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
  47 import javax.swing.JColorChooser;
  48 import javax.swing.JComboBox;
  49 import javax.swing.JLabel;
  50 import javax.swing.JOptionPane;
  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 implements
  66         jalview.api.FeatureRenderer
  67 {
  68   Color resBoxColour;
  69
  70   AlignmentPanel ap;
  71
  72   /**
  73    * Creates a new FeatureRenderer object.
  74    *
  75    * @param av
  76    *          DOCUMENT ME!
  77    */
  78   public FeatureRenderer(AlignmentPanel ap)
  79   {
  80     super(ap.av);
  81     this.ap = ap;
  82     if (ap != null && ap.getSeqPanel() != null
  83             && ap.getSeqPanel().seqCanvas != null
  84             && ap.getSeqPanel().seqCanvas.fr != null)
  85     {
  86       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  87     }
  88   }
  89
  90   // // /////////////
  91   // // Feature Editing Dialog
  92   // // Will be refactored in next release.
  93
  94   static String lastFeatureAdded;
  95
  96   static String lastFeatureGroupAdded;
  97
  98   static String lastDescriptionAdded;
  99
 100   FeatureColourI oldcol, fcol;
 101
 102   int featureIndex = 0;
 103
 104   boolean amendFeatures(final SequenceI[] sequences,
 105           final SequenceFeature[] features, boolean newFeatures,
 106           final AlignmentPanel ap)
 107   {
 108
 109     featureIndex = 0;
 110
 111     final JPanel bigPanel = new JPanel(new BorderLayout());
 112     final JComboBox overlaps;
 113     final JTextField name = new JTextField(25);
 114     final JTextField source = new JTextField(25);
 115     final JTextArea description = new JTextArea(3, 25);
 116     final JSpinner start = new JSpinner();
 117     final JSpinner end = new JSpinner();
 118     start.setPreferredSize(new Dimension(80, 20));
 119     end.setPreferredSize(new Dimension(80, 20));
 120     final FeatureRenderer me = this;
 121     final JLabel colour = new JLabel();
 122     colour.setOpaque(true);
 123     // colour.setBorder(BorderFactory.createEtchedBorder());
 124     colour.setMaximumSize(new Dimension(30, 16));
 125     colour.addMouseListener(new MouseAdapter()
 126     {
 127       FeatureColourChooser fcc = null;
 128
 129       @Override
 130       public void mousePressed(MouseEvent evt)
 131       {
 132         if (fcol.isSimpleColour())
 133         {
 134           Color col = JColorChooser.showDialog(Desktop.desktop,
 135                   MessageManager.getString("label.select_feature_colour"),
 136                   ColorUtils.getColor(fcol.getColour()));
 137           if (col != null)
 138           {
 139             fcol = new FeatureColour(new Colour(col));
 140             updateColourButton(bigPanel, colour, fcol);
 141           }
 142         }
 143         else
 144         {
 145           if (fcc == null)
 146           {
 147             final String type = features[featureIndex].getType();
 148             fcc = new FeatureColourChooser(me, type);
 149             fcc.setRequestFocusEnabled(true);
 150             fcc.requestFocus();
 151
 152             fcc.addActionListener(new ActionListener()
 153             {
 154
 155               @Override
 156               public void actionPerformed(ActionEvent e)
 157               {
 158                 fcol = fcc.getLastColour();
 159                 fcc = null;
 160                 setColour(type, fcol);
 161                 updateColourButton(bigPanel, colour, fcol);
 162               }
 163             });
 164
 165           }
 166         }
 167       }
 168     });
 169     JPanel tmp = new JPanel();
 170     JPanel panel = new JPanel(new GridLayout(3, 1));
 171
 172     // /////////////////////////////////////
 173     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 174     if (!newFeatures && features.length > 1)
 175     {
 176       panel = new JPanel(new GridLayout(4, 1));
 177       tmp = new JPanel();
 178       tmp.add(new JLabel(MessageManager.getString("label.select_feature")
 179               + ":"));
 180       overlaps = new JComboBox();
 181       for (int i = 0; i < features.length; i++)
 182       {
 183         overlaps.addItem(features[i].getType() + "/"
 184                 + features[i].getBegin() + "-" + features[i].getEnd()
 185                 + " (" + features[i].getFeatureGroup() + ")");
 186       }
 187
 188       tmp.add(overlaps);
 189
 190       overlaps.addItemListener(new ItemListener()
 191       {
 192         @Override
 193         public void itemStateChanged(ItemEvent e)
 194         {
 195           int index = overlaps.getSelectedIndex();
 196           if (index != -1)
 197           {
 198             featureIndex = index;
 199             name.setText(features[index].getType());
 200             description.setText(features[index].getDescription());
 201             source.setText(features[index].getFeatureGroup());
 202             start.setValue(new Integer(features[index].getBegin()));
 203             end.setValue(new Integer(features[index].getEnd()));
 204
 205             SearchResults highlight = new SearchResults();
 206             highlight.addResult(sequences[0], features[index].getBegin(),
 207                     features[index].getEnd());
 208
 209             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 210
 211           }
 212           FeatureColourI col = getFeatureStyle(name.getText());
 213           if (col == null)
 214           {
 215             col = new FeatureColour(new Colour(UserColourScheme
 216                     .createColourFromName(name.getText())));
 217           }
 218           oldcol = fcol = col;
 219           updateColourButton(bigPanel, colour, col);
 220         }
 221       });
 222
 223       panel.add(tmp);
 224     }
 225     // ////////
 226     // ////////////////////////////////////
 227
 228     tmp = new JPanel();
 229     panel.add(tmp);
 230     tmp.add(new JLabel(MessageManager.getString("label.name:"),
 231             JLabel.RIGHT));
 232     tmp.add(name);
 233
 234     tmp = new JPanel();
 235     panel.add(tmp);
 236     tmp.add(new JLabel(MessageManager.getString("label.group:"),
 237             JLabel.RIGHT));
 238     tmp.add(source);
 239
 240     tmp = new JPanel();
 241     panel.add(tmp);
 242     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 243             JLabel.RIGHT));
 244     tmp.add(colour);
 245     colour.setPreferredSize(new Dimension(150, 15));
 246     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 247     colour.setForeground(Color.black);
 248     colour.setHorizontalAlignment(SwingConstants.CENTER);
 249     colour.setVerticalAlignment(SwingConstants.CENTER);
 250     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 251     colour.setVerticalTextPosition(SwingConstants.CENTER);
 252     bigPanel.add(panel, BorderLayout.NORTH);
 253
 254     panel = new JPanel();
 255     panel.add(new JLabel(MessageManager.getString("label.description:"),
 256             JLabel.RIGHT));
 257     description.setFont(JvSwingUtils.getTextAreaFont());
 258     description.setLineWrap(true);
 259     panel.add(new JScrollPane(description));
 260
 261     if (!newFeatures)
 262     {
 263       bigPanel.add(panel, BorderLayout.SOUTH);
 264
 265       panel = new JPanel();
 266       panel.add(new JLabel(MessageManager.getString("label.start"),
 267               JLabel.RIGHT));
 268       panel.add(start);
 269       panel.add(new JLabel(MessageManager.getString("label.end"),
 270               JLabel.RIGHT));
 271       panel.add(end);
 272       bigPanel.add(panel, BorderLayout.CENTER);
 273     }
 274     else
 275     {
 276       bigPanel.add(panel, BorderLayout.CENTER);
 277     }
 278
 279     if (lastFeatureAdded == null)
 280     {
 281       if (features[0].type != null)
 282       {
 283         lastFeatureAdded = features[0].type;
 284       }
 285       else
 286       {
 287         lastFeatureAdded = "feature_1";
 288       }
 289     }
 290
 291     if (lastFeatureGroupAdded == null)
 292     {
 293       if (features[0].featureGroup != null)
 294       {
 295         lastFeatureGroupAdded = features[0].featureGroup;
 296       }
 297       else
 298       {
 299         lastFeatureGroupAdded = "Jalview";
 300       }
 301     }
 302
 303     if (newFeatures)
 304     {
 305       name.setText(lastFeatureAdded);
 306       source.setText(lastFeatureGroupAdded);
 307     }
 308     else
 309     {
 310       name.setText(features[0].getType());
 311       source.setText(features[0].getFeatureGroup());
 312     }
 313
 314     start.setValue(new Integer(features[0].getBegin()));
 315     end.setValue(new Integer(features[0].getEnd()));
 316     description.setText(features[0].getDescription());
 317     updateColourButton(bigPanel, colour,
 318             (oldcol = fcol = getFeatureStyle(name.getText())));
 319     Object[] options;
 320     if (!newFeatures)
 321     {
 322       options = new Object[] { "Amend", "Delete", "Cancel" };
 323     }
 324     else
 325     {
 326       options = new Object[] { "OK", "Cancel" };
 327     }
 328
 329     String title = newFeatures ? MessageManager
 330             .getString("label.create_new_sequence_features")
 331             : MessageManager.formatMessage("label.amend_delete_features",
 332                     new String[] { sequences[0].getName() });
 333
 334     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 335             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 336             JOptionPane.QUESTION_MESSAGE, null, options,
 337             MessageManager.getString("action.ok"));
 338
 339     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 340
 341     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 342     {
 343       // This ensures that the last sequence
 344       // is refreshed and new features are rendered
 345       lastSeq = null;
 346       lastFeatureAdded = name.getText().trim();
 347       lastFeatureGroupAdded = source.getText().trim();
 348       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 349       // TODO: determine if the null feature group is valid
 350       if (lastFeatureGroupAdded.length() < 1)
 351       {
 352         lastFeatureGroupAdded = null;
 353       }
 354     }
 355
 356     if (!newFeatures)
 357     {
 358       SequenceFeature sf = features[featureIndex];
 359
 360       if (reply == JOptionPane.NO_OPTION)
 361       {
 362         sequences[0].getDatasetSequence().deleteFeature(sf);
 363       }
 364       else if (reply == JOptionPane.YES_OPTION)
 365       {
 366         sf.type = lastFeatureAdded;
 367         sf.featureGroup = lastFeatureGroupAdded;
 368         sf.description = lastDescriptionAdded;
 369
 370         setColour(sf.type, fcol);
 371         getFeaturesDisplayed().setVisible(sf.type);
 372
 373         try
 374         {
 375           sf.begin = ((Integer) start.getValue()).intValue();
 376           sf.end = ((Integer) end.getValue()).intValue();
 377         } catch (NumberFormatException ex)
 378         {
 379         }
 380
 381         ffile.parseDescriptionHTML(sf, false);
 382       }
 383     }
 384     else
 385     // NEW FEATURES ADDED
 386     {
 387       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 388       {
 389         for (int i = 0; i < sequences.length; i++)
 390         {
 391           features[i].type = lastFeatureAdded;
 392           // fix for JAL-1538 - always set feature group here
 393           features[i].featureGroup = lastFeatureGroupAdded;
 394           features[i].description = lastDescriptionAdded;
 395           sequences[i].addSequenceFeature(features[i]);
 396           ffile.parseDescriptionHTML(features[i], false);
 397         }
 398
 399         if (lastFeatureGroupAdded != null)
 400         {
 401           setGroupVisibility(lastFeatureGroupAdded, true);
 402         }
 403         setColour(lastFeatureAdded, fcol);
 404         setVisible(lastFeatureAdded);
 405
 406         findAllFeatures(false);
 407
 408         ap.paintAlignment(true);
 409
 410         return true;
 411       }
 412       else
 413       {
 414         return false;
 415       }
 416     }
 417
 418     ap.paintAlignment(true);
 419
 420     return true;
 421   }
 422
 423   /**
 424    * update the amend feature button dependent on the given style
 425    *
 426    * @param bigPanel
 427    * @param colour
 428    * @param col
 429 <<<<<<< HEAD
 430 =======
 431    * @param col
 432 >>>>>>> refs/heads/develop
 433    */
 434   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 435           FeatureColourI col)
 436   {
 437     colour.removeAll();
 438     colour.setIcon(null);
 439     colour.setToolTipText(null);
 440     colour.setText("");
 441
 442     if (col.isSimpleColour())
 443     {
 444       colour.setBackground(ColorUtils.getColor(col.getColour()));
 445     }
 446     else
 447     {
 448       colour.setBackground(bigPanel.getBackground());
 449       colour.setForeground(Color.black);
 450       FeatureSettings.renderGraduatedColor(colour, col);
 451     }
 452   }
 453
 454   /**
 455    * Orders features in render precedence (last in order is last to render, so
 456    * displayed on top of other features)
 457    *
 458    * @param order
 459    */
 460   public void orderFeatures(Comparator<String> order)
 461   {
 462     Arrays.sort(renderOrder, order);
 463   }
 464 }