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.datamodel.SearchResults;
  24 import jalview.datamodel.SequenceFeature;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.schemes.GraduatedColor;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Color;
  31 import java.awt.Dimension;
  32 import java.awt.Font;
  33 import java.awt.GridLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.awt.event.MouseAdapter;
  39 import java.awt.event.MouseEvent;
  40 import java.util.Arrays;
  41 import java.util.Comparator;
  42
  43 import javax.swing.JColorChooser;
  44 import javax.swing.JComboBox;
  45 import javax.swing.JLabel;
  46 import javax.swing.JOptionPane;
  47 import javax.swing.JPanel;
  48 import javax.swing.JScrollPane;
  49 import javax.swing.JSpinner;
  50 import javax.swing.JTextArea;
  51 import javax.swing.JTextField;
  52 import javax.swing.SwingConstants;
  53
  54 /**
  55  * DOCUMENT ME!
  56  *
  57  * @author $author$
  58  * @version $Revision$
  59  */
  60 public class FeatureRenderer extends
  61         jalview.renderer.seqfeatures.FeatureRenderer implements
  62         jalview.api.FeatureRenderer
  63 {
  64   Color resBoxColour;
  65
  66   AlignmentPanel ap;
  67
  68   /**
  69    * Creates a new FeatureRenderer object.
  70    *
  71    * @param av
  72    *          DOCUMENT ME!
  73    */
  74   public FeatureRenderer(AlignmentPanel ap)
  75   {
  76     super(ap.av);
  77     this.ap = ap;
  78     if (ap != null && ap.getSeqPanel() != null
  79             && ap.getSeqPanel().seqCanvas != null
  80             && ap.getSeqPanel().seqCanvas.fr != null)
  81     {
  82       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  83     }
  84   }
  85
  86   // // /////////////
  87   // // Feature Editing Dialog
  88   // // Will be refactored in next release.
  89
  90   static String lastFeatureAdded;
  91
  92   static String lastFeatureGroupAdded;
  93
  94   static String lastDescriptionAdded;
  95
  96   Object oldcol, fcol;
  97
  98   int featureIndex = 0;
  99
 100   boolean amendFeatures(final SequenceI[] sequences,
 101           final SequenceFeature[] features, boolean newFeatures,
 102           final AlignmentPanel ap)
 103   {
 104
 105     featureIndex = 0;
 106
 107     final JPanel bigPanel = new JPanel(new BorderLayout());
 108     final JComboBox overlaps;
 109     final JTextField name = new JTextField(25);
 110     final JTextField source = new JTextField(25);
 111     final JTextArea description = new JTextArea(3, 25);
 112     final JSpinner start = new JSpinner();
 113     final JSpinner end = new JSpinner();
 114     start.setPreferredSize(new Dimension(80, 20));
 115     end.setPreferredSize(new Dimension(80, 20));
 116     final FeatureRenderer me = this;
 117     final JLabel colour = new JLabel();
 118     colour.setOpaque(true);
 119     // colour.setBorder(BorderFactory.createEtchedBorder());
 120     colour.setMaximumSize(new Dimension(30, 16));
 121     colour.addMouseListener(new MouseAdapter()
 122     {
 123       FeatureColourChooser fcc = null;
 124
 125       @Override
 126       public void mousePressed(MouseEvent evt)
 127       {
 128         if (fcol instanceof Color)
 129         {
 130           Color col = JColorChooser.showDialog(Desktop.desktop,
 131                   MessageManager.getString("label.select_feature_colour"),
 132                   ((Color) fcol));
 133           if (col != null)
 134           {
 135             fcol = col;
 136             updateColourButton(bigPanel, colour, col);
 137           }
 138         }
 139         else
 140         {
 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       overlaps = new JComboBox();
 177       for (int i = 0; i < features.length; i++)
 178       {
 179         overlaps.addItem(features[i].getType() + "/"
 180                 + features[i].getBegin() + "-" + features[i].getEnd()
 181                 + " (" + features[i].getFeatureGroup() + ")");
 182       }
 183
 184       tmp.add(overlaps);
 185
 186       overlaps.addItemListener(new ItemListener()
 187       {
 188         @Override
 189         public void itemStateChanged(ItemEvent e)
 190         {
 191           int index = overlaps.getSelectedIndex();
 192           if (index != -1)
 193           {
 194             featureIndex = index;
 195             name.setText(features[index].getType());
 196             description.setText(features[index].getDescription());
 197             source.setText(features[index].getFeatureGroup());
 198             start.setValue(new Integer(features[index].getBegin()));
 199             end.setValue(new Integer(features[index].getEnd()));
 200
 201             SearchResults highlight = new SearchResults();
 202             highlight.addResult(sequences[0], features[index].getBegin(),
 203                     features[index].getEnd());
 204
 205             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 206
 207           }
 208           Object col = getFeatureStyle(name.getText());
 209           if (col == null)
 210           {
 211             col = new jalview.schemes.UserColourScheme()
 212                     .createColourFromName(name.getText());
 213           }
 214           oldcol = fcol = col;
 215           updateColourButton(bigPanel, colour, col);
 216         }
 217       });
 218
 219       panel.add(tmp);
 220     }
 221     // ////////
 222     // ////////////////////////////////////
 223
 224     tmp = new JPanel();
 225     panel.add(tmp);
 226     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
 227     tmp.add(name);
 228
 229     tmp = new JPanel();
 230     panel.add(tmp);
 231     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
 232             JLabel.RIGHT));
 233     tmp.add(source);
 234
 235     tmp = new JPanel();
 236     panel.add(tmp);
 237     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 238             JLabel.RIGHT));
 239     tmp.add(colour);
 240     colour.setPreferredSize(new Dimension(150, 15));
 241     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 242     colour.setForeground(Color.black);
 243     colour.setHorizontalAlignment(SwingConstants.CENTER);
 244     colour.setVerticalAlignment(SwingConstants.CENTER);
 245     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 246     colour.setVerticalTextPosition(SwingConstants.CENTER);
 247     bigPanel.add(panel, BorderLayout.NORTH);
 248
 249     panel = new JPanel();
 250     panel.add(new JLabel(MessageManager.getString("label.description"),
 251             JLabel.RIGHT));
 252     description.setFont(JvSwingUtils.getTextAreaFont());
 253     description.setLineWrap(true);
 254     panel.add(new JScrollPane(description));
 255
 256     if (!newFeatures)
 257     {
 258       bigPanel.add(panel, BorderLayout.SOUTH);
 259
 260       panel = new JPanel();
 261       panel.add(new JLabel(MessageManager.getString("label.start"),
 262               JLabel.RIGHT));
 263       panel.add(start);
 264       panel.add(new JLabel(MessageManager.getString("label.end"),
 265               JLabel.RIGHT));
 266       panel.add(end);
 267       bigPanel.add(panel, BorderLayout.CENTER);
 268     }
 269     else
 270     {
 271       bigPanel.add(panel, BorderLayout.CENTER);
 272     }
 273
 274     if (lastFeatureAdded == null)
 275     {
 276       if (features[0].type != null)
 277       {
 278         lastFeatureAdded = features[0].type;
 279       }
 280       else
 281       {
 282         lastFeatureAdded = "feature_1";
 283       }
 284     }
 285
 286     if (lastFeatureGroupAdded == null)
 287     {
 288       if (features[0].featureGroup != null)
 289       {
 290         lastFeatureGroupAdded = features[0].featureGroup;
 291       }
 292       else
 293       {
 294         lastFeatureGroupAdded = "Jalview";
 295       }
 296     }
 297
 298     if (newFeatures)
 299     {
 300       name.setText(lastFeatureAdded);
 301       source.setText(lastFeatureGroupAdded);
 302     }
 303     else
 304     {
 305       name.setText(features[0].getType());
 306       source.setText(features[0].getFeatureGroup());
 307     }
 308
 309     start.setValue(new Integer(features[0].getBegin()));
 310     end.setValue(new Integer(features[0].getEnd()));
 311     description.setText(features[0].getDescription());
 312     updateColourButton(bigPanel, colour,
 313             (oldcol = fcol = getFeatureStyle(name.getText())));
 314     Object[] options;
 315     if (!newFeatures)
 316     {
 317       options = new Object[] { "Amend", "Delete", "Cancel" };
 318     }
 319     else
 320     {
 321       options = new Object[] { "OK", "Cancel" };
 322     }
 323
 324     String title = newFeatures ? MessageManager
 325             .getString("label.create_new_sequence_features")
 326             : MessageManager.formatMessage("label.amend_delete_features",
 327                     new String[] { sequences[0].getName() });
 328
 329     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 330             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 331             JOptionPane.QUESTION_MESSAGE, null, options,
 332             MessageManager.getString("action.ok"));
 333
 334     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 335
 336     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 337     {
 338       // This ensures that the last sequence
 339       // is refreshed and new features are rendered
 340       lastSeq = null;
 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 == JOptionPane.NO_OPTION)
 356       {
 357         sequences[0].getDatasetSequence().deleteFeature(sf);
 358       }
 359       else if (reply == JOptionPane.YES_OPTION)
 360       {
 361         sf.type = lastFeatureAdded;
 362         sf.featureGroup = lastFeatureGroupAdded;
 363         sf.description = lastDescriptionAdded;
 364
 365         setColour(sf.type, fcol);
 366         getFeaturesDisplayed().setVisible(sf.type);
 367
 368         try
 369         {
 370           sf.begin = ((Integer) start.getValue()).intValue();
 371           sf.end = ((Integer) end.getValue()).intValue();
 372         } catch (NumberFormatException ex)
 373         {
 374         }
 375
 376         ffile.parseDescriptionHTML(sf, false);
 377       }
 378     }
 379     else
 380     // NEW FEATURES ADDED
 381     {
 382       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 383       {
 384         for (int i = 0; i < sequences.length; i++)
 385         {
 386           features[i].type = lastFeatureAdded;
 387           // fix for JAL-1538 - always set feature group here
 388           features[i].featureGroup = lastFeatureGroupAdded;
 389           features[i].description = lastDescriptionAdded;
 390           sequences[i].addSequenceFeature(features[i]);
 391           ffile.parseDescriptionHTML(features[i], false);
 392         }
 393
 394         if (lastFeatureGroupAdded != null)
 395         {
 396           setGroupVisibility(lastFeatureGroupAdded, true);
 397         }
 398         setColour(lastFeatureAdded, fcol);
 399         setVisible(lastFeatureAdded);
 400
 401         findAllFeatures(false);
 402
 403         ap.paintAlignment(true);
 404
 405         return true;
 406       }
 407       else
 408       {
 409         return false;
 410       }
 411     }
 412
 413     ap.paintAlignment(true);
 414
 415     return true;
 416   }
 417
 418   /**
 419    * update the amend feature button dependent on the given style
 420    *
 421    * @param bigPanel
 422    * @param col
 423    * @param col2
 424    */
 425   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 426           Object col2)
 427   {
 428     colour.removeAll();
 429     colour.setIcon(null);
 430     colour.setToolTipText(null);
 431     colour.setText("");
 432
 433     if (col2 instanceof Color)
 434     {
 435       colour.setBackground((Color) col2);
 436     }
 437     else
 438     {
 439       colour.setBackground(bigPanel.getBackground());
 440       colour.setForeground(Color.black);
 441       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
 442       // colour.setForeground(colour.getBackground());
 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 }