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