src/jalview/gui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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 java.util.*;
  24 import java.awt.*;
  25 import java.awt.event.*;
  26 import java.awt.image.*;
  27 import java.beans.PropertyChangeListener;
  28
  29 import javax.swing.*;
  30
  31 import jalview.datamodel.*;
  32 import jalview.schemes.GraduatedColor;
  33 import jalview.util.MessageManager;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer
  42 {
  43   Color resBoxColour;
  44
  45   AlignmentPanel ap;
  46
  47   /**
  48    * Creates a new FeatureRenderer object.
  49    *
  50    * @param av
  51    *          DOCUMENT ME!
  52    */
  53   public FeatureRenderer(AlignmentPanel ap)
  54   {
  55     super();
  56     this.ap = ap;
  57     this.av = ap.av;
  58     if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
  59             && ap.getSeqPanel().seqCanvas.fr != null)
  60     {
  61       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  62     }
  63   }
  64
  65   // // /////////////
  66   // // Feature Editing Dialog
  67   // // Will be refactored in next release.
  68
  69   static String lastFeatureAdded;
  70
  71   static String lastFeatureGroupAdded;
  72
  73   static String lastDescriptionAdded;
  74
  75   Object oldcol, fcol;
  76
  77   int featureIndex = 0;
  78
  79   boolean amendFeatures(final SequenceI[] sequences,
  80           final SequenceFeature[] features, boolean newFeatures,
  81           final AlignmentPanel ap)
  82   {
  83
  84     featureIndex = 0;
  85
  86     final JPanel bigPanel = new JPanel(new BorderLayout());
  87     final JComboBox overlaps;
  88     final JTextField name = new JTextField(25);
  89     final JTextField source = new JTextField(25);
  90     final JTextArea description = new JTextArea(3, 25);
  91     final JSpinner start = new JSpinner();
  92     final JSpinner end = new JSpinner();
  93     start.setPreferredSize(new Dimension(80, 20));
  94     end.setPreferredSize(new Dimension(80, 20));
  95     final FeatureRenderer me = this;
  96     final JLabel colour = new JLabel();
  97     colour.setOpaque(true);
  98     // colour.setBorder(BorderFactory.createEtchedBorder());
  99     colour.setMaximumSize(new Dimension(30, 16));
 100     colour.addMouseListener(new MouseAdapter()
 101     {
 102       FeatureColourChooser fcc = null;
 103
 104       public void mousePressed(MouseEvent evt)
 105       {
 106         if (fcol instanceof Color)
 107         {
 108           Color col = JColorChooser.showDialog(Desktop.desktop,
 109                   MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
 110           if (col != null)
 111           {
 112             fcol = col;
 113             updateColourButton(bigPanel, colour, col);
 114           }
 115         }
 116         else
 117         {
 118
 119           if (fcc == null)
 120           {
 121             final String type = features[featureIndex].getType();
 122             fcc = new FeatureColourChooser(me, type);
 123             fcc.setRequestFocusEnabled(true);
 124             fcc.requestFocus();
 125
 126             fcc.addActionListener(new ActionListener()
 127             {
 128
 129               public void actionPerformed(ActionEvent e)
 130               {
 131                 fcol = fcc.getLastColour();
 132                 fcc = null;
 133                 setColour(type, fcol);
 134                 updateColourButton(bigPanel, colour, fcol);
 135               }
 136             });
 137
 138           }
 139         }
 140       }
 141     });
 142     JPanel tmp = new JPanel();
 143     JPanel panel = new JPanel(new GridLayout(3, 1));
 144
 145     // /////////////////////////////////////
 146     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 147     if (!newFeatures && features.length > 1)
 148     {
 149       panel = new JPanel(new GridLayout(4, 1));
 150       tmp = new JPanel();
 151       tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
 152       overlaps = new JComboBox();
 153       for (int i = 0; i < features.length; i++)
 154       {
 155         overlaps.addItem(features[i].getType() + "/"
 156                 + features[i].getBegin() + "-" + features[i].getEnd()
 157                 + " (" + features[i].getFeatureGroup() + ")");
 158       }
 159
 160       tmp.add(overlaps);
 161
 162       overlaps.addItemListener(new ItemListener()
 163       {
 164         public void itemStateChanged(ItemEvent e)
 165         {
 166           int index = overlaps.getSelectedIndex();
 167           if (index != -1)
 168           {
 169             featureIndex = index;
 170             name.setText(features[index].getType());
 171             description.setText(features[index].getDescription());
 172             source.setText(features[index].getFeatureGroup());
 173             start.setValue(new Integer(features[index].getBegin()));
 174             end.setValue(new Integer(features[index].getEnd()));
 175
 176             SearchResults highlight = new SearchResults();
 177             highlight.addResult(sequences[0], features[index].getBegin(),
 178                     features[index].getEnd());
 179
 180             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 181
 182           }
 183           Object col = getFeatureStyle(name.getText());
 184           if (col == null)
 185           {
 186             col = new jalview.schemes.UserColourScheme()
 187                     .createColourFromName(name.getText());
 188           }
 189           oldcol = fcol = col;
 190           updateColourButton(bigPanel, colour, col);
 191         }
 192       });
 193
 194       panel.add(tmp);
 195     }
 196     // ////////
 197     // ////////////////////////////////////
 198
 199     tmp = new JPanel();
 200     panel.add(tmp);
 201     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
 202     tmp.add(name);
 203
 204     tmp = new JPanel();
 205     panel.add(tmp);
 206     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
 207             JLabel.RIGHT));
 208     tmp.add(source);
 209
 210     tmp = new JPanel();
 211     panel.add(tmp);
 212     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 213             JLabel.RIGHT));
 214     tmp.add(colour);
 215     colour.setPreferredSize(new Dimension(150, 15));
 216     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 217     colour.setForeground(Color.black);
 218     colour.setHorizontalAlignment(SwingConstants.CENTER);
 219     colour.setVerticalAlignment(SwingConstants.CENTER);
 220     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 221     colour.setVerticalTextPosition(SwingConstants.CENTER);
 222     bigPanel.add(panel, BorderLayout.NORTH);
 223
 224     panel = new JPanel();
 225     panel.add(new JLabel(MessageManager.getString("label.description"),
 226             JLabel.RIGHT));
 227     description.setFont(JvSwingUtils.getTextAreaFont());
 228     description.setLineWrap(true);
 229     panel.add(new JScrollPane(description));
 230
 231     if (!newFeatures)
 232     {
 233       bigPanel.add(panel, BorderLayout.SOUTH);
 234
 235       panel = new JPanel();
 236       panel.add(new JLabel(MessageManager.getString("label.start"),
 237               JLabel.RIGHT));
 238       panel.add(start);
 239       panel.add(new JLabel(MessageManager.getString("label.end"),
 240               JLabel.RIGHT));
 241       panel.add(end);
 242       bigPanel.add(panel, BorderLayout.CENTER);
 243     }
 244     else
 245     {
 246       bigPanel.add(panel, BorderLayout.CENTER);
 247     }
 248
 249     if (lastFeatureAdded == null)
 250     {
 251       if (features[0].type != null)
 252       {
 253         lastFeatureAdded = features[0].type;
 254       }
 255       else
 256       {
 257         lastFeatureAdded = "feature_1";
 258       }
 259     }
 260
 261     if (lastFeatureGroupAdded == null)
 262     {
 263       if (features[0].featureGroup != null)
 264       {
 265         lastFeatureGroupAdded = features[0].featureGroup;
 266       }
 267       else
 268       {
 269         lastFeatureGroupAdded = "Jalview";
 270       }
 271     }
 272
 273     if (newFeatures)
 274     {
 275       name.setText(lastFeatureAdded);
 276       source.setText(lastFeatureGroupAdded);
 277     }
 278     else
 279     {
 280       name.setText(features[0].getType());
 281       source.setText(features[0].getFeatureGroup());
 282     }
 283
 284     start.setValue(new Integer(features[0].getBegin()));
 285     end.setValue(new Integer(features[0].getEnd()));
 286     description.setText(features[0].getDescription());
 287     updateColourButton(bigPanel, colour,
 288             (oldcol = fcol = getFeatureStyle(name.getText())));
 289     Object[] options;
 290     if (!newFeatures)
 291     {
 292       options = new Object[]
 293       { "Amend", "Delete", "Cancel" };
 294     }
 295     else
 296     {
 297       options = new Object[]
 298       { "OK", "Cancel" };
 299     }
 300
 301     String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
 302             : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 303
 304     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 305             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 306             JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
 307
 308     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 309
 310     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 311     {
 312       // This ensures that the last sequence
 313       // is refreshed and new features are rendered
 314       lastSeq = null;
 315       lastFeatureAdded = name.getText().trim();
 316       lastFeatureGroupAdded = source.getText().trim();
 317       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 318       // TODO: determine if the null feature group is valid
 319       if (lastFeatureGroupAdded.length() < 1)
 320         lastFeatureGroupAdded = null;
 321     }
 322
 323     if (!newFeatures)
 324     {
 325       SequenceFeature sf = features[featureIndex];
 326
 327       if (reply == JOptionPane.NO_OPTION)
 328       {
 329         sequences[0].getDatasetSequence().deleteFeature(sf);
 330       }
 331       else if (reply == JOptionPane.YES_OPTION)
 332       {
 333         sf.type = lastFeatureAdded;
 334         sf.featureGroup = lastFeatureGroupAdded;
 335         sf.description = lastDescriptionAdded;
 336
 337         setColour(sf.type, fcol);
 338         getFeaturesDisplayed().setVisible(sf.type);
 339
 340         try
 341         {
 342           sf.begin = ((Integer) start.getValue()).intValue();
 343           sf.end = ((Integer) end.getValue()).intValue();
 344         } catch (NumberFormatException ex)
 345         {
 346         }
 347
 348         ffile.parseDescriptionHTML(sf, false);
 349       }
 350     }
 351     else
 352     // NEW FEATURES ADDED
 353     {
 354       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 355       {
 356         for (int i = 0; i < sequences.length; i++)
 357         {
 358           features[i].type = lastFeatureAdded;
 359           // fix for JAL-1538 - always set feature group here
 360           features[i].featureGroup = lastFeatureGroupAdded;
 361           features[i].description = lastDescriptionAdded;
 362           sequences[i].addSequenceFeature(features[i]);
 363           ffile.parseDescriptionHTML(features[i], false);
 364         }
 365
 366
 367         if (lastFeatureGroupAdded != null)
 368         {
 369           setGroupVisibility(lastFeatureGroupAdded, true);
 370         }
 371         setColour(lastFeatureAdded, fcol);
 372         setVisible(lastFeatureAdded);
 373
 374         findAllFeatures(false);
 375
 376         ap.paintAlignment(true);
 377
 378         return true;
 379       }
 380       else
 381       {
 382         return false;
 383       }
 384     }
 385
 386     ap.paintAlignment(true);
 387
 388     return true;
 389   }
 390
 391
 392   /**
 393    * update the amend feature button dependent on the given style
 394    *
 395    * @param bigPanel
 396    * @param col
 397    * @param col2
 398    */
 399   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 400           Object col2)
 401   {
 402     colour.removeAll();
 403     colour.setIcon(null);
 404     colour.setToolTipText(null);
 405     colour.setText("");
 406
 407     if (col2 instanceof Color)
 408     {
 409       colour.setBackground((Color) col2);
 410     }
 411     else
 412     {
 413       colour.setBackground(bigPanel.getBackground());
 414       colour.setForeground(Color.black);
 415       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
 416       // colour.setForeground(colour.getBackground());
 417     }
 418   }
 419 }