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
  41 import javax.swing.JColorChooser;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JLabel;
  44 import javax.swing.JOptionPane;
  45 import javax.swing.JPanel;
  46 import javax.swing.JScrollPane;
  47 import javax.swing.JSpinner;
  48 import javax.swing.JTextArea;
  49 import javax.swing.JTextField;
  50 import javax.swing.SwingConstants;
  51
  52 /**
  53  * DOCUMENT ME!
  54  *
  55  * @author $author$
  56  * @version $Revision$
  57  */
  58 public class FeatureRenderer extends
  59         jalview.renderer.seqfeatures.FeatureRenderer implements
  60         jalview.api.FeatureRenderer
  61 {
  62   Color resBoxColour;
  63
  64   AlignmentPanel ap;
  65
  66   /**
  67    * Creates a new FeatureRenderer object.
  68    *
  69    * @param av
  70    *          DOCUMENT ME!
  71    */
  72   public FeatureRenderer(AlignmentPanel ap)
  73   {
  74     super();
  75     this.ap = ap;
  76     this.av = ap.av;
  77     if (ap != null && ap.getSeqPanel() != null
  78             && ap.getSeqPanel().seqCanvas != null
  79             && ap.getSeqPanel().seqCanvas.fr != null)
  80     {
  81       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  82     }
  83   }
  84
  85   // // /////////////
  86   // // Feature Editing Dialog
  87   // // Will be refactored in next release.
  88
  89   static String lastFeatureAdded;
  90
  91   static String lastFeatureGroupAdded;
  92
  93   static String lastDescriptionAdded;
  94
  95   Object oldcol, fcol;
  96
  97   int featureIndex = 0;
  98
  99   boolean amendFeatures(final SequenceI[] sequences,
 100           final SequenceFeature[] features, boolean newFeatures,
 101           final AlignmentPanel ap)
 102   {
 103
 104     featureIndex = 0;
 105
 106     final JPanel bigPanel = new JPanel(new BorderLayout());
 107     final JComboBox overlaps;
 108     final JTextField name = new JTextField(25);
 109     final JTextField source = new JTextField(25);
 110     final JTextArea description = new JTextArea(3, 25);
 111     final JSpinner start = new JSpinner();
 112     final JSpinner end = new JSpinner();
 113     start.setPreferredSize(new Dimension(80, 20));
 114     end.setPreferredSize(new Dimension(80, 20));
 115     final FeatureRenderer me = this;
 116     final JLabel colour = new JLabel();
 117     colour.setOpaque(true);
 118     // colour.setBorder(BorderFactory.createEtchedBorder());
 119     colour.setMaximumSize(new Dimension(30, 16));
 120     colour.addMouseListener(new MouseAdapter()
 121     {
 122       FeatureColourChooser fcc = null;
 123
 124       public void mousePressed(MouseEvent evt)
 125       {
 126         if (fcol instanceof Color)
 127         {
 128           Color col = JColorChooser.showDialog(Desktop.desktop,
 129                   MessageManager.getString("label.select_feature_colour"),
 130                   ((Color) fcol));
 131           if (col != null)
 132           {
 133             fcol = col;
 134             updateColourButton(bigPanel, colour, col);
 135           }
 136         }
 137         else
 138         {
 139
 140           if (fcc == null)
 141           {
 142             final String type = features[featureIndex].getType();
 143             fcc = new FeatureColourChooser(me, type);
 144             fcc.setRequestFocusEnabled(true);
 145             fcc.requestFocus();
 146
 147             fcc.addActionListener(new ActionListener()
 148             {
 149
 150               public void actionPerformed(ActionEvent e)
 151               {
 152                 fcol = fcc.getLastColour();
 153                 fcc = null;
 154                 setColour(type, fcol);
 155                 updateColourButton(bigPanel, colour, fcol);
 156               }
 157             });
 158
 159           }
 160         }
 161       }
 162     });
 163     JPanel tmp = new JPanel();
 164     JPanel panel = new JPanel(new GridLayout(3, 1));
 165
 166     // /////////////////////////////////////
 167     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 168     if (!newFeatures && features.length > 1)
 169     {
 170       panel = new JPanel(new GridLayout(4, 1));
 171       tmp = new JPanel();
 172       tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
 173       overlaps = new JComboBox();
 174       for (int i = 0; i < features.length; i++)
 175       {
 176         overlaps.addItem(features[i].getType() + "/"
 177                 + features[i].getBegin() + "-" + features[i].getEnd()
 178                 + " (" + features[i].getFeatureGroup() + ")");
 179       }
 180
 181       tmp.add(overlaps);
 182
 183       overlaps.addItemListener(new ItemListener()
 184       {
 185         public void itemStateChanged(ItemEvent e)
 186         {
 187           int index = overlaps.getSelectedIndex();
 188           if (index != -1)
 189           {
 190             featureIndex = index;
 191             name.setText(features[index].getType());
 192             description.setText(features[index].getDescription());
 193             source.setText(features[index].getFeatureGroup());
 194             start.setValue(new Integer(features[index].getBegin()));
 195             end.setValue(new Integer(features[index].getEnd()));
 196
 197             SearchResults highlight = new SearchResults();
 198             highlight.addResult(sequences[0], features[index].getBegin(),
 199                     features[index].getEnd());
 200
 201             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 202
 203           }
 204           Object col = getFeatureStyle(name.getText());
 205           if (col == null)
 206           {
 207             col = new jalview.schemes.UserColourScheme()
 208                     .createColourFromName(name.getText());
 209           }
 210           oldcol = fcol = col;
 211           updateColourButton(bigPanel, colour, col);
 212         }
 213       });
 214
 215       panel.add(tmp);
 216     }
 217     // ////////
 218     // ////////////////////////////////////
 219
 220     tmp = new JPanel();
 221     panel.add(tmp);
 222     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
 223     tmp.add(name);
 224
 225     tmp = new JPanel();
 226     panel.add(tmp);
 227     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
 228             JLabel.RIGHT));
 229     tmp.add(source);
 230
 231     tmp = new JPanel();
 232     panel.add(tmp);
 233     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 234             JLabel.RIGHT));
 235     tmp.add(colour);
 236     colour.setPreferredSize(new Dimension(150, 15));
 237     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 238     colour.setForeground(Color.black);
 239     colour.setHorizontalAlignment(SwingConstants.CENTER);
 240     colour.setVerticalAlignment(SwingConstants.CENTER);
 241     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 242     colour.setVerticalTextPosition(SwingConstants.CENTER);
 243     bigPanel.add(panel, BorderLayout.NORTH);
 244
 245     panel = new JPanel();
 246     panel.add(new JLabel(MessageManager.getString("label.description"),
 247             JLabel.RIGHT));
 248     description.setFont(JvSwingUtils.getTextAreaFont());
 249     description.setLineWrap(true);
 250     panel.add(new JScrollPane(description));
 251
 252     if (!newFeatures)
 253     {
 254       bigPanel.add(panel, BorderLayout.SOUTH);
 255
 256       panel = new JPanel();
 257       panel.add(new JLabel(MessageManager.getString("label.start"),
 258               JLabel.RIGHT));
 259       panel.add(start);
 260       panel.add(new JLabel(MessageManager.getString("label.end"),
 261               JLabel.RIGHT));
 262       panel.add(end);
 263       bigPanel.add(panel, BorderLayout.CENTER);
 264     }
 265     else
 266     {
 267       bigPanel.add(panel, BorderLayout.CENTER);
 268     }
 269
 270     if (lastFeatureAdded == null)
 271     {
 272       if (features[0].type != null)
 273       {
 274         lastFeatureAdded = features[0].type;
 275       }
 276       else
 277       {
 278         lastFeatureAdded = "feature_1";
 279       }
 280     }
 281
 282     if (lastFeatureGroupAdded == null)
 283     {
 284       if (features[0].featureGroup != null)
 285       {
 286         lastFeatureGroupAdded = features[0].featureGroup;
 287       }
 288       else
 289       {
 290         lastFeatureGroupAdded = "Jalview";
 291       }
 292     }
 293
 294     if (newFeatures)
 295     {
 296       name.setText(lastFeatureAdded);
 297       source.setText(lastFeatureGroupAdded);
 298     }
 299     else
 300     {
 301       name.setText(features[0].getType());
 302       source.setText(features[0].getFeatureGroup());
 303     }
 304
 305     start.setValue(new Integer(features[0].getBegin()));
 306     end.setValue(new Integer(features[0].getEnd()));
 307     description.setText(features[0].getDescription());
 308     updateColourButton(bigPanel, colour,
 309             (oldcol = fcol = getFeatureStyle(name.getText())));
 310     Object[] options;
 311     if (!newFeatures)
 312     {
 313       options = new Object[] { "Amend", "Delete", "Cancel" };
 314     }
 315     else
 316     {
 317       options = new Object[] { "OK", "Cancel" };
 318     }
 319
 320     String title = newFeatures ? MessageManager
 321             .getString("label.create_new_sequence_features")
 322             : MessageManager.formatMessage("label.amend_delete_features",
 323                     new String[] { sequences[0].getName() });
 324
 325     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 326             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 327             JOptionPane.QUESTION_MESSAGE, null, options,
 328             MessageManager.getString("action.ok"));
 329
 330     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 331
 332     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 333     {
 334       // This ensures that the last sequence
 335       // is refreshed and new features are rendered
 336       lastSeq = null;
 337       lastFeatureAdded = name.getText().trim();
 338       lastFeatureGroupAdded = source.getText().trim();
 339       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 340       // TODO: determine if the null feature group is valid
 341       if (lastFeatureGroupAdded.length() < 1)
 342       {
 343         lastFeatureGroupAdded = null;
 344       }
 345     }
 346
 347     if (!newFeatures)
 348     {
 349       SequenceFeature sf = features[featureIndex];
 350
 351       if (reply == JOptionPane.NO_OPTION)
 352       {
 353         sequences[0].getDatasetSequence().deleteFeature(sf);
 354       }
 355       else if (reply == JOptionPane.YES_OPTION)
 356       {
 357         sf.type = lastFeatureAdded;
 358         sf.featureGroup = lastFeatureGroupAdded;
 359         sf.description = lastDescriptionAdded;
 360
 361         setColour(sf.type, fcol);
 362         getFeaturesDisplayed().setVisible(sf.type);
 363
 364         try
 365         {
 366           sf.begin = ((Integer) start.getValue()).intValue();
 367           sf.end = ((Integer) end.getValue()).intValue();
 368         } catch (NumberFormatException ex)
 369         {
 370         }
 371
 372         ffile.parseDescriptionHTML(sf, false);
 373       }
 374     }
 375     else
 376     // NEW FEATURES ADDED
 377     {
 378       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 379       {
 380         for (int i = 0; i < sequences.length; i++)
 381         {
 382           features[i].type = lastFeatureAdded;
 383           // fix for JAL-1538 - always set feature group here
 384           features[i].featureGroup = lastFeatureGroupAdded;
 385           features[i].description = lastDescriptionAdded;
 386           sequences[i].addSequenceFeature(features[i]);
 387           ffile.parseDescriptionHTML(features[i], false);
 388         }
 389
 390         if (lastFeatureGroupAdded != null)
 391         {
 392           setGroupVisibility(lastFeatureGroupAdded, true);
 393         }
 394         setColour(lastFeatureAdded, fcol);
 395         setVisible(lastFeatureAdded);
 396
 397         findAllFeatures(false);
 398
 399         ap.paintAlignment(true);
 400
 401         return true;
 402       }
 403       else
 404       {
 405         return false;
 406       }
 407     }
 408
 409     ap.paintAlignment(true);
 410
 411     return true;
 412   }
 413
 414   /**
 415    * update the amend feature button dependent on the given style
 416    *
 417    * @param bigPanel
 418    * @param col
 419    * @param col2
 420    */
 421   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 422           Object col2)
 423   {
 424     colour.removeAll();
 425     colour.setIcon(null);
 426     colour.setToolTipText(null);
 427     colour.setText("");
 428
 429     if (col2 instanceof Color)
 430     {
 431       colour.setBackground((Color) col2);
 432     }
 433     else
 434     {
 435       colour.setBackground(bigPanel.getBackground());
 436       colour.setForeground(Color.black);
 437       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
 438       // colour.setForeground(colour.getBackground());
 439     }
 440   }
 441 }