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.schemes.FeatureColour;
  29 import jalview.util.ColorUtils;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Font;
  36 import java.awt.GridLayout;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.ItemEvent;
  40 import java.awt.event.ItemListener;
  41 import java.awt.event.MouseAdapter;
  42 import java.awt.event.MouseEvent;
  43 import java.util.Arrays;
  44 import java.util.Comparator;
  45
  46 import javax.swing.JColorChooser;
  47 import javax.swing.JComboBox;
  48 import javax.swing.JLabel;
  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
  64 {
  65   Color resBoxColour;
  66
  67   AlignmentPanel ap;
  68
  69   /**
  70    * Creates a new FeatureRenderer object.
  71    *
  72    * @param av
  73    *          DOCUMENT ME!
  74    */
  75   public FeatureRenderer(AlignmentPanel ap)
  76   {
  77     super(ap.av);
  78     this.ap = ap;
  79     if (ap != null && ap.getSeqPanel() != null
  80             && ap.getSeqPanel().seqCanvas != null
  81             && ap.getSeqPanel().seqCanvas.fr != null)
  82     {
  83       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  84     }
  85   }
  86
  87   // // /////////////
  88   // // Feature Editing Dialog
  89   // // Will be refactored in next release.
  90
  91   static String lastFeatureAdded;
  92
  93   static String lastFeatureGroupAdded;
  94
  95   static String lastDescriptionAdded;
  96
  97   FeatureColourI oldcol, fcol;
  98
  99   int featureIndex = 0;
 100
 101   boolean amendFeatures(final SequenceI[] sequences,
 102           final SequenceFeature[] features, boolean newFeatures,
 103           final AlignmentPanel ap)
 104   {
 105
 106     featureIndex = 0;
 107
 108     final JPanel bigPanel = new JPanel(new BorderLayout());
 109     final JComboBox overlaps;
 110     final JTextField name = new JTextField(25);
 111     final JTextField source = new JTextField(25);
 112     final JTextArea description = new JTextArea(3, 25);
 113     final JSpinner start = new JSpinner();
 114     final JSpinner end = new JSpinner();
 115     start.setPreferredSize(new Dimension(80, 20));
 116     end.setPreferredSize(new Dimension(80, 20));
 117     final FeatureRenderer me = this;
 118     final JLabel colour = new JLabel();
 119     colour.setOpaque(true);
 120     // colour.setBorder(BorderFactory.createEtchedBorder());
 121     colour.setMaximumSize(new Dimension(30, 16));
 122     colour.addMouseListener(new MouseAdapter()
 123     {
 124       FeatureColourChooser fcc = null;
 125
 126       @Override
 127       public void mousePressed(MouseEvent evt)
 128       {
 129         if (fcol.isSimpleColour())
 130         {
 131           Color col = JColorChooser.showDialog(Desktop.desktop,
 132                   MessageManager.getString("label.select_feature_colour"),
 133                   fcol.getColour());
 134           if (col != null)
 135           {
 136             fcol = new FeatureColour(col);
 137             updateColourButton(bigPanel, colour, new FeatureColour(col));
 138           }
 139         }
 140         else
 141         {
 142           if (fcc == null)
 143           {
 144             final String type = features[featureIndex].getType();
 145             fcc = new FeatureColourChooser(me, type);
 146             fcc.setRequestFocusEnabled(true);
 147             fcc.requestFocus();
 148
 149             fcc.addActionListener(new ActionListener()
 150             {
 151
 152               @Override
 153               public void actionPerformed(ActionEvent e)
 154               {
 155                 fcol = fcc.getLastColour();
 156                 fcc = null;
 157                 setColour(type, fcol);
 158                 updateColourButton(bigPanel, colour, fcol);
 159               }
 160             });
 161
 162           }
 163         }
 164       }
 165     });
 166     JPanel tmp = new JPanel();
 167     JPanel panel = new JPanel(new GridLayout(3, 1));
 168
 169     // /////////////////////////////////////
 170     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 171     if (!newFeatures && features.length > 1)
 172     {
 173       panel = new JPanel(new GridLayout(4, 1));
 174       tmp = new JPanel();
 175       tmp.add(new JLabel(MessageManager.getString("label.select_feature")
 176               + ":"));
 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             SearchResultsI 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(ColorUtils
 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:"),
 228             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 = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 332             bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 333             JvOptionPane.QUESTION_MESSAGE, null, options,
 334             MessageManager.getString("action.ok"));
 335
 336     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 337
 338     if (reply == JvOptionPane.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 == JvOptionPane.NO_OPTION)
 358       {
 359         sequences[0].getDatasetSequence().deleteFeature(sf);
 360       }
 361       else if (reply == JvOptionPane.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 == JvOptionPane.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 }