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