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.JOptionPane;
  50 import javax.swing.JPanel;
  51 import javax.swing.JScrollPane;
  52 import javax.swing.JSpinner;
  53 import javax.swing.JTextArea;
  54 import javax.swing.JTextField;
  55 import javax.swing.SwingConstants;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class FeatureRenderer extends
  64         jalview.renderer.seqfeatures.FeatureRenderer implements
  65         jalview.api.FeatureRenderer
  66 {
  67   Color resBoxColour;
  68
  69   AlignmentPanel ap;
  70
  71   /**
  72    * Creates a new FeatureRenderer object.
  73    *
  74    * @param av
  75    *          DOCUMENT ME!
  76    */
  77   public FeatureRenderer(AlignmentPanel ap)
  78   {
  79     super(ap.av);
  80     this.ap = ap;
  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               + ":"));
 179       overlaps = new JComboBox();
 180       for (int i = 0; i < features.length; i++)
 181       {
 182         overlaps.addItem(features[i].getType() + "/"
 183                 + features[i].getBegin() + "-" + features[i].getEnd()
 184                 + " (" + features[i].getFeatureGroup() + ")");
 185       }
 186
 187       tmp.add(overlaps);
 188
 189       overlaps.addItemListener(new ItemListener()
 190       {
 191         @Override
 192         public void itemStateChanged(ItemEvent e)
 193         {
 194           int index = overlaps.getSelectedIndex();
 195           if (index != -1)
 196           {
 197             featureIndex = index;
 198             name.setText(features[index].getType());
 199             description.setText(features[index].getDescription());
 200             source.setText(features[index].getFeatureGroup());
 201             start.setValue(new Integer(features[index].getBegin()));
 202             end.setValue(new Integer(features[index].getEnd()));
 203
 204             SearchResultsI highlight = new SearchResults();
 205             highlight.addResult(sequences[0], features[index].getBegin(),
 206                     features[index].getEnd());
 207
 208             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 209
 210           }
 211           FeatureColourI col = getFeatureStyle(name.getText());
 212           if (col == null)
 213           {
 214             col = new FeatureColour(ColorUtils
 215                     .createColourFromName(name.getText()));
 216           }
 217           oldcol = fcol = col;
 218           updateColourButton(bigPanel, colour, col);
 219         }
 220       });
 221
 222       panel.add(tmp);
 223     }
 224     // ////////
 225     // ////////////////////////////////////
 226
 227     tmp = new JPanel();
 228     panel.add(tmp);
 229     tmp.add(new JLabel(MessageManager.getString("label.name:"),
 230             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 = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 334             bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 335             JvOptionPane.QUESTION_MESSAGE, null, options,
 336             MessageManager.getString("action.ok"));
 337
 338     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 339
 340     if (reply == JvOptionPane.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 == JvOptionPane.NO_OPTION)
 360       {
 361         sequences[0].getDatasetSequence().deleteFeature(sf);
 362       }
 363       else if (reply == JvOptionPane.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 == JvOptionPane.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 col
 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(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 }