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.FeatureColour;
  28 import jalview.schemes.UserColourScheme;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.Dimension;
  34 import java.awt.Font;
  35 import java.awt.GridLayout;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.ItemEvent;
  39 import java.awt.event.ItemListener;
  40 import java.awt.event.MouseAdapter;
  41 import java.awt.event.MouseEvent;
  42 import java.util.Arrays;
  43 import java.util.Comparator;
  44
  45 import javax.swing.JColorChooser;
  46 import javax.swing.JComboBox;
  47 import javax.swing.JLabel;
  48 import javax.swing.JOptionPane;
  49 import javax.swing.JPanel;
  50 import javax.swing.JScrollPane;
  51 import javax.swing.JSpinner;
  52 import javax.swing.JTextArea;
  53 import javax.swing.JTextField;
  54 import javax.swing.SwingConstants;
  55
  56 /**
  57  * DOCUMENT ME!
  58  *
  59  * @author $author$
  60  * @version $Revision$
  61  */
  62 public class FeatureRenderer extends
  63         jalview.renderer.seqfeatures.FeatureRenderer implements
  64         jalview.api.FeatureRenderer
  65 {
  66   Color resBoxColour;
  67
  68   AlignmentPanel ap;
  69
  70   /**
  71    * Creates a new FeatureRenderer object.
  72    *
  73    * @param av
  74    *          DOCUMENT ME!
  75    */
  76   public FeatureRenderer(AlignmentPanel ap)
  77   {
  78     super();
  79     this.ap = ap;
  80     this.av = ap.av;
  81     if (ap != null && ap.getSeqPanel() != null
  82             && ap.getSeqPanel().seqCanvas != null
  83             && ap.getSeqPanel().seqCanvas.fr != null)
  84     {
  85       transferSettings(ap.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   boolean amendFeatures(final SequenceI[] sequences,
 104           final SequenceFeature[] features, boolean newFeatures,
 105           final AlignmentPanel ap)
 106   {
 107
 108     featureIndex = 0;
 109
 110     final JPanel bigPanel = new JPanel(new BorderLayout());
 111     final JComboBox overlaps;
 112     final JTextField name = new JTextField(25);
 113     final JTextField source = new JTextField(25);
 114     final JTextArea description = new JTextArea(3, 25);
 115     final JSpinner start = new JSpinner();
 116     final JSpinner end = new JSpinner();
 117     start.setPreferredSize(new Dimension(80, 20));
 118     end.setPreferredSize(new Dimension(80, 20));
 119     final FeatureRenderer me = this;
 120     final JLabel colour = new JLabel();
 121     colour.setOpaque(true);
 122     // colour.setBorder(BorderFactory.createEtchedBorder());
 123     colour.setMaximumSize(new Dimension(30, 16));
 124     colour.addMouseListener(new MouseAdapter()
 125     {
 126       FeatureColourChooser fcc = null;
 127
 128       @Override
 129       public void mousePressed(MouseEvent evt)
 130       {
 131         if (fcol.isSimpleColour())
 132         {
 133           Color col = JColorChooser.showDialog(Desktop.desktop,
 134                   MessageManager.getString("label.select_feature_colour"),
 135                   fcol.getColour());
 136           if (col != null)
 137           {
 138             fcol = new FeatureColour(col);
 139             updateColourButton(bigPanel, colour, new FeatureColour(col));
 140           }
 141         }
 142         else
 143         {
 144           if (fcc == null)
 145           {
 146             final String type = features[featureIndex].getType();
 147             fcc = new FeatureColourChooser(me, type);
 148             fcc.setRequestFocusEnabled(true);
 149             fcc.requestFocus();
 150
 151             fcc.addActionListener(new ActionListener()
 152             {
 153
 154               @Override
 155               public void actionPerformed(ActionEvent e)
 156               {
 157                 fcol = fcc.getLastColour();
 158                 fcc = null;
 159                 setColour(type, fcol);
 160                 updateColourButton(bigPanel, colour, fcol);
 161               }
 162             });
 163
 164           }
 165         }
 166       }
 167     });
 168     JPanel tmp = new JPanel();
 169     JPanel panel = new JPanel(new GridLayout(3, 1));
 170
 171     // /////////////////////////////////////
 172     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 173     if (!newFeatures && features.length > 1)
 174     {
 175       panel = new JPanel(new GridLayout(4, 1));
 176       tmp = new JPanel();
 177       tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
 178       overlaps = new JComboBox();
 179       for (int i = 0; i < features.length; i++)
 180       {
 181         overlaps.addItem(features[i].getType() + "/"
 182                 + features[i].getBegin() + "-" + features[i].getEnd()
 183                 + " (" + features[i].getFeatureGroup() + ")");
 184       }
 185
 186       tmp.add(overlaps);
 187
 188       overlaps.addItemListener(new ItemListener()
 189       {
 190         @Override
 191         public void itemStateChanged(ItemEvent e)
 192         {
 193           int index = overlaps.getSelectedIndex();
 194           if (index != -1)
 195           {
 196             featureIndex = index;
 197             name.setText(features[index].getType());
 198             description.setText(features[index].getDescription());
 199             source.setText(features[index].getFeatureGroup());
 200             start.setValue(new Integer(features[index].getBegin()));
 201             end.setValue(new Integer(features[index].getEnd()));
 202
 203             SearchResults highlight = new SearchResults();
 204             highlight.addResult(sequences[0], features[index].getBegin(),
 205                     features[index].getEnd());
 206
 207             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 208
 209           }
 210           FeatureColourI col = getFeatureStyle(name.getText());
 211           if (col == null)
 212           {
 213             col = new FeatureColour(UserColourScheme
 214                     .createColourFromName(name.getText()));
 215           }
 216           oldcol = fcol = col;
 217           updateColourButton(bigPanel, colour, col);
 218         }
 219       });
 220
 221       panel.add(tmp);
 222     }
 223     // ////////
 224     // ////////////////////////////////////
 225
 226     tmp = new JPanel();
 227     panel.add(tmp);
 228     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
 229     tmp.add(name);
 230
 231     tmp = new JPanel();
 232     panel.add(tmp);
 233     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
 234             JLabel.RIGHT));
 235     tmp.add(source);
 236
 237     tmp = new JPanel();
 238     panel.add(tmp);
 239     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 240             JLabel.RIGHT));
 241     tmp.add(colour);
 242     colour.setPreferredSize(new Dimension(150, 15));
 243     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 244     colour.setForeground(Color.black);
 245     colour.setHorizontalAlignment(SwingConstants.CENTER);
 246     colour.setVerticalAlignment(SwingConstants.CENTER);
 247     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 248     colour.setVerticalTextPosition(SwingConstants.CENTER);
 249     bigPanel.add(panel, BorderLayout.NORTH);
 250
 251     panel = new JPanel();
 252     panel.add(new JLabel(MessageManager.getString("label.description"),
 253             JLabel.RIGHT));
 254     description.setFont(JvSwingUtils.getTextAreaFont());
 255     description.setLineWrap(true);
 256     panel.add(new JScrollPane(description));
 257
 258     if (!newFeatures)
 259     {
 260       bigPanel.add(panel, BorderLayout.SOUTH);
 261
 262       panel = new JPanel();
 263       panel.add(new JLabel(MessageManager.getString("label.start"),
 264               JLabel.RIGHT));
 265       panel.add(start);
 266       panel.add(new JLabel(MessageManager.getString("label.end"),
 267               JLabel.RIGHT));
 268       panel.add(end);
 269       bigPanel.add(panel, BorderLayout.CENTER);
 270     }
 271     else
 272     {
 273       bigPanel.add(panel, BorderLayout.CENTER);
 274     }
 275
 276     if (lastFeatureAdded == null)
 277     {
 278       if (features[0].type != null)
 279       {
 280         lastFeatureAdded = features[0].type;
 281       }
 282       else
 283       {
 284         lastFeatureAdded = "feature_1";
 285       }
 286     }
 287
 288     if (lastFeatureGroupAdded == null)
 289     {
 290       if (features[0].featureGroup != null)
 291       {
 292         lastFeatureGroupAdded = features[0].featureGroup;
 293       }
 294       else
 295       {
 296         lastFeatureGroupAdded = "Jalview";
 297       }
 298     }
 299
 300     if (newFeatures)
 301     {
 302       name.setText(lastFeatureAdded);
 303       source.setText(lastFeatureGroupAdded);
 304     }
 305     else
 306     {
 307       name.setText(features[0].getType());
 308       source.setText(features[0].getFeatureGroup());
 309     }
 310
 311     start.setValue(new Integer(features[0].getBegin()));
 312     end.setValue(new Integer(features[0].getEnd()));
 313     description.setText(features[0].getDescription());
 314     updateColourButton(bigPanel, colour,
 315             (oldcol = fcol = getFeatureStyle(name.getText())));
 316     Object[] options;
 317     if (!newFeatures)
 318     {
 319       options = new Object[] { "Amend", "Delete", "Cancel" };
 320     }
 321     else
 322     {
 323       options = new Object[] { "OK", "Cancel" };
 324     }
 325
 326     String title = newFeatures ? MessageManager
 327             .getString("label.create_new_sequence_features")
 328             : MessageManager.formatMessage("label.amend_delete_features",
 329                     new String[] { sequences[0].getName() });
 330
 331     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 332             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 333             JOptionPane.QUESTION_MESSAGE, null, options,
 334             MessageManager.getString("action.ok"));
 335
 336     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 337
 338     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 339     {
 340       // This ensures that the last sequence
 341       // is refreshed and new features are rendered
 342       lastSeq = null;
 343       lastFeatureAdded = name.getText().trim();
 344       lastFeatureGroupAdded = source.getText().trim();
 345       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 346       // TODO: determine if the null feature group is valid
 347       if (lastFeatureGroupAdded.length() < 1)
 348       {
 349         lastFeatureGroupAdded = null;
 350       }
 351     }
 352
 353     if (!newFeatures)
 354     {
 355       SequenceFeature sf = features[featureIndex];
 356
 357       if (reply == JOptionPane.NO_OPTION)
 358       {
 359         sequences[0].getDatasetSequence().deleteFeature(sf);
 360       }
 361       else if (reply == JOptionPane.YES_OPTION)
 362       {
 363         sf.type = lastFeatureAdded;
 364         sf.featureGroup = lastFeatureGroupAdded;
 365         sf.description = lastDescriptionAdded;
 366
 367         setColour(sf.type, fcol);
 368         getFeaturesDisplayed().setVisible(sf.type);
 369
 370         try
 371         {
 372           sf.begin = ((Integer) start.getValue()).intValue();
 373           sf.end = ((Integer) end.getValue()).intValue();
 374         } catch (NumberFormatException ex)
 375         {
 376         }
 377
 378         ffile.parseDescriptionHTML(sf, false);
 379       }
 380     }
 381     else
 382     // NEW FEATURES ADDED
 383     {
 384       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 385       {
 386         for (int i = 0; i < sequences.length; i++)
 387         {
 388           features[i].type = lastFeatureAdded;
 389           // fix for JAL-1538 - always set feature group here
 390           features[i].featureGroup = lastFeatureGroupAdded;
 391           features[i].description = lastDescriptionAdded;
 392           sequences[i].addSequenceFeature(features[i]);
 393           ffile.parseDescriptionHTML(features[i], false);
 394         }
 395
 396         if (lastFeatureGroupAdded != null)
 397         {
 398           setGroupVisibility(lastFeatureGroupAdded, true);
 399         }
 400         setColour(lastFeatureAdded, fcol);
 401         setVisible(lastFeatureAdded);
 402
 403         findAllFeatures(false);
 404
 405         ap.paintAlignment(true);
 406
 407         return true;
 408       }
 409       else
 410       {
 411         return false;
 412       }
 413     }
 414
 415     ap.paintAlignment(true);
 416
 417     return true;
 418   }
 419
 420   /**
 421    * update the amend feature button dependent on the given style
 422    *
 423    * @param bigPanel
 424    * @param col
 425    * @param col
 426    */
 427   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 428           FeatureColourI col)
 429   {
 430     colour.removeAll();
 431     colour.setIcon(null);
 432     colour.setToolTipText(null);
 433     colour.setText("");
 434
 435     if (col.isSimpleColour())
 436     {
 437       colour.setBackground(col.getColour());
 438     }
 439     else
 440     {
 441       colour.setBackground(bigPanel.getBackground());
 442       colour.setForeground(Color.black);
 443       FeatureSettings.renderGraduatedColor(colour, col);
 444     }
 445   }
 446
 447   /**
 448    * Orders features in render precedence (last in order is last to render, so
 449    * displayed on top of other features)
 450    *
 451    * @param order
 452    */
 453   public void orderFeatures(Comparator<String> order)
 454   {
 455     Arrays.sort(renderOrder, order);
 456   }
 457 }