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