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 import java.util.HashMap;
  46
  47 import javax.swing.JColorChooser;
  48 import javax.swing.JComboBox;
  49 import javax.swing.JLabel;
  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
  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               + ":"));
 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             SearchResultsI 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(ColorUtils
 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:"),
 229             JLabel.RIGHT));
 230     tmp.add(name);
 231
 232     tmp = new JPanel();
 233     panel.add(tmp);
 234     tmp.add(new JLabel(MessageManager.getString("label.group:"),
 235             JLabel.RIGHT));
 236     tmp.add(source);
 237
 238     tmp = new JPanel();
 239     panel.add(tmp);
 240     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 241             JLabel.RIGHT));
 242     tmp.add(colour);
 243     colour.setPreferredSize(new Dimension(150, 15));
 244     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 245     colour.setForeground(Color.black);
 246     colour.setHorizontalAlignment(SwingConstants.CENTER);
 247     colour.setVerticalAlignment(SwingConstants.CENTER);
 248     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 249     colour.setVerticalTextPosition(SwingConstants.CENTER);
 250     bigPanel.add(panel, BorderLayout.NORTH);
 251
 252     panel = new JPanel();
 253     panel.add(new JLabel(MessageManager.getString("label.description:"),
 254             JLabel.RIGHT));
 255     description.setFont(JvSwingUtils.getTextAreaFont());
 256     description.setLineWrap(true);
 257     panel.add(new JScrollPane(description));
 258
 259     if (!newFeatures)
 260     {
 261       bigPanel.add(panel, BorderLayout.SOUTH);
 262
 263       panel = new JPanel();
 264       panel.add(new JLabel(MessageManager.getString("label.start"),
 265               JLabel.RIGHT));
 266       panel.add(start);
 267       panel.add(new JLabel(MessageManager.getString("label.end"),
 268               JLabel.RIGHT));
 269       panel.add(end);
 270       bigPanel.add(panel, BorderLayout.CENTER);
 271     }
 272     else
 273     {
 274       bigPanel.add(panel, BorderLayout.CENTER);
 275     }
 276
 277     if (lastFeatureAdded == null)
 278     {
 279       if (features[0].type != null)
 280       {
 281         lastFeatureAdded = features[0].type;
 282       }
 283       else
 284       {
 285         lastFeatureAdded = "feature_1";
 286       }
 287     }
 288
 289     if (lastFeatureGroupAdded == null)
 290     {
 291       if (features[0].featureGroup != null)
 292       {
 293         lastFeatureGroupAdded = features[0].featureGroup;
 294       }
 295       else
 296       {
 297         lastFeatureGroupAdded = "Jalview";
 298       }
 299     }
 300
 301     if (newFeatures)
 302     {
 303       name.setText(lastFeatureAdded);
 304       source.setText(lastFeatureGroupAdded);
 305     }
 306     else
 307     {
 308       name.setText(features[0].getType());
 309       source.setText(features[0].getFeatureGroup());
 310     }
 311
 312     start.setValue(new Integer(features[0].getBegin()));
 313     end.setValue(new Integer(features[0].getEnd()));
 314     description.setText(features[0].getDescription());
 315     updateColourButton(bigPanel, colour,
 316             (oldcol = fcol = getFeatureStyle(name.getText())));
 317     Object[] options;
 318     if (!newFeatures)
 319     {
 320       options = new Object[] { "Amend", "Delete", "Cancel" };
 321     }
 322     else
 323     {
 324       options = new Object[] { "OK", "Cancel" };
 325     }
 326
 327     String title = newFeatures ? MessageManager
 328             .getString("label.create_new_sequence_features")
 329             : MessageManager.formatMessage("label.amend_delete_features",
 330                     new String[] { sequences[0].getName() });
 331
 332     int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
 333             bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
 334             JvOptionPane.QUESTION_MESSAGE, null, options,
 335             MessageManager.getString("action.ok"));
 336
 337     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 338
 339     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
 340     {
 341       lastFeatureAdded = name.getText().trim();
 342       lastFeatureGroupAdded = source.getText().trim();
 343       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 344       // TODO: determine if the null feature group is valid
 345       if (lastFeatureGroupAdded.length() < 1)
 346       {
 347         lastFeatureGroupAdded = null;
 348       }
 349     }
 350
 351     if (!newFeatures)
 352     {
 353       SequenceFeature sf = features[featureIndex];
 354
 355       if (reply == JvOptionPane.NO_OPTION)
 356       {
 357         sequences[0].getDatasetSequence().deleteFeature(sf);
 358       }
 359       else if (reply == JvOptionPane.YES_OPTION)
 360       {
 361         String newType = lastFeatureAdded;
 362         String newFeatureGroup = lastFeatureGroupAdded;
 363         String newDescription = lastDescriptionAdded;
 364
 365         setColour(newType, fcol);
 366         getFeaturesDisplayed().setVisible(newType);
 367         int newBegin = sf.begin;
 368         int newEnd = sf.end;
 369         try
 370         {
 371           newBegin = ((Integer) start.getValue()).intValue();
 372           newEnd = ((Integer) end.getValue()).intValue();
 373         } catch (NumberFormatException ex)
 374         {
 375           // JSpinner doesn't accept invalid format data :-)
 376         }
 377
 378         /*
 379          * replace the feature by deleting it and adding a new one
 380          * (to ensure integrity of SequenceFeatures data store)
 381          */
 382         sequences[0].deleteFeature(sf);
 383         SequenceFeature newSf = new SequenceFeature(newType,
 384                 newDescription, newBegin, newEnd, sf.getScore(),
 385                 newFeatureGroup);
 386         // ensure any additional properties are copied
 387         if (sf.otherDetails != null)
 388         {
 389           newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
 390         }
 391         ffile.parseDescriptionHTML(newSf, false);
 392         // add any additional links not parsed from description
 393         if (sf.links != null)
 394         {
 395           for (String link : sf.links)
 396           {
 397             newSf.addLink(link);
 398           }
 399         }
 400         // amend features only gets one sequence to act on
 401         sequences[0].addSequenceFeature(newSf);
 402       }
 403     }
 404     else
 405     // NEW FEATURES ADDED
 406     {
 407       if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 408       {
 409         for (int i = 0; i < sequences.length; i++)
 410         {
 411           features[i].type = lastFeatureAdded;
 412           // fix for JAL-1538 - always set feature group here
 413           features[i].featureGroup = lastFeatureGroupAdded;
 414           features[i].description = lastDescriptionAdded;
 415           sequences[i].addSequenceFeature(features[i]);
 416           ffile.parseDescriptionHTML(features[i], false);
 417         }
 418
 419         if (lastFeatureGroupAdded != null)
 420         {
 421           setGroupVisibility(lastFeatureGroupAdded, true);
 422         }
 423         setColour(lastFeatureAdded, fcol);
 424         setVisible(lastFeatureAdded);
 425
 426         findAllFeatures(false);
 427
 428         ap.paintAlignment(true);
 429
 430         return true;
 431       }
 432       else
 433       {
 434         return false;
 435       }
 436     }
 437
 438     ap.paintAlignment(true);
 439
 440     return true;
 441   }
 442
 443   /**
 444    * update the amend feature button dependent on the given style
 445    *
 446    * @param bigPanel
 447    * @param col
 448    * @param col
 449    */
 450   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 451           FeatureColourI col)
 452   {
 453     colour.removeAll();
 454     colour.setIcon(null);
 455     colour.setToolTipText(null);
 456     colour.setText("");
 457
 458     if (col.isSimpleColour())
 459     {
 460       colour.setBackground(col.getColour());
 461     }
 462     else
 463     {
 464       colour.setBackground(bigPanel.getBackground());
 465       colour.setForeground(Color.black);
 466       FeatureSettings.renderGraduatedColor(colour, col);
 467     }
 468   }
 469
 470   /**
 471    * Orders features in render precedence (last in order is last to render, so
 472    * displayed on top of other features)
 473    *
 474    * @param order
 475    */
 476   public void orderFeatures(Comparator<String> order)
 477   {
 478     Arrays.sort(renderOrder, order);
 479   }
 480 }