src/jalview/gui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   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 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 jalview.renderer.seqfeatures.FeatureRenderer implements jalview.api.FeatureRenderer
  59 {
  60   Color resBoxColour;
  61
  62   AlignmentPanel ap;
  63
  64   /**
  65    * Creates a new FeatureRenderer object.
  66    *
  67    * @param av
  68    *          DOCUMENT ME!
  69    */
  70   public FeatureRenderer(AlignmentPanel ap)
  71   {
  72     super();
  73     this.ap = ap;
  74     this.av = ap.av;
  75     if (ap != null && ap.getSeqPanel() != null && ap.getSeqPanel().seqCanvas != null
  76             && ap.getSeqPanel().seqCanvas.fr != null)
  77     {
  78       transferSettings(ap.getSeqPanel().seqCanvas.fr);
  79     }
  80   }
  81
  82   // // /////////////
  83   // // Feature Editing Dialog
  84   // // Will be refactored in next release.
  85
  86   static String lastFeatureAdded;
  87
  88   static String lastFeatureGroupAdded;
  89
  90   static String lastDescriptionAdded;
  91
  92   Object oldcol, fcol;
  93
  94   int featureIndex = 0;
  95
  96   boolean amendFeatures(final SequenceI[] sequences,
  97           final SequenceFeature[] features, boolean newFeatures,
  98           final AlignmentPanel ap)
  99   {
 100
 101     featureIndex = 0;
 102
 103     final JPanel bigPanel = new JPanel(new BorderLayout());
 104     final JComboBox overlaps;
 105     final JTextField name = new JTextField(25);
 106     final JTextField source = new JTextField(25);
 107     final JTextArea description = new JTextArea(3, 25);
 108     final JSpinner start = new JSpinner();
 109     final JSpinner end = new JSpinner();
 110     start.setPreferredSize(new Dimension(80, 20));
 111     end.setPreferredSize(new Dimension(80, 20));
 112     final FeatureRenderer me = this;
 113     final JLabel colour = new JLabel();
 114     colour.setOpaque(true);
 115     // colour.setBorder(BorderFactory.createEtchedBorder());
 116     colour.setMaximumSize(new Dimension(30, 16));
 117     colour.addMouseListener(new MouseAdapter()
 118     {
 119       FeatureColourChooser fcc = null;
 120
 121       public void mousePressed(MouseEvent evt)
 122       {
 123         if (fcol instanceof Color)
 124         {
 125           Color col = JColorChooser.showDialog(Desktop.desktop,
 126                   MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
 127           if (col != null)
 128           {
 129             fcol = col;
 130             updateColourButton(bigPanel, colour, col);
 131           }
 132         }
 133         else
 134         {
 135
 136           if (fcc == null)
 137           {
 138             final String type = features[featureIndex].getType();
 139             fcc = new FeatureColourChooser(me, type);
 140             fcc.setRequestFocusEnabled(true);
 141             fcc.requestFocus();
 142
 143             fcc.addActionListener(new ActionListener()
 144             {
 145
 146               public void actionPerformed(ActionEvent e)
 147               {
 148                 fcol = fcc.getLastColour();
 149                 fcc = null;
 150                 setColour(type, fcol);
 151                 updateColourButton(bigPanel, colour, fcol);
 152               }
 153             });
 154
 155           }
 156         }
 157       }
 158     });
 159     JPanel tmp = new JPanel();
 160     JPanel panel = new JPanel(new GridLayout(3, 1));
 161
 162     // /////////////////////////////////////
 163     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 164     if (!newFeatures && features.length > 1)
 165     {
 166       panel = new JPanel(new GridLayout(4, 1));
 167       tmp = new JPanel();
 168       tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
 169       overlaps = new JComboBox();
 170       for (int i = 0; i < features.length; i++)
 171       {
 172         overlaps.addItem(features[i].getType() + "/"
 173                 + features[i].getBegin() + "-" + features[i].getEnd()
 174                 + " (" + features[i].getFeatureGroup() + ")");
 175       }
 176
 177       tmp.add(overlaps);
 178
 179       overlaps.addItemListener(new ItemListener()
 180       {
 181         public void itemStateChanged(ItemEvent e)
 182         {
 183           int index = overlaps.getSelectedIndex();
 184           if (index != -1)
 185           {
 186             featureIndex = index;
 187             name.setText(features[index].getType());
 188             description.setText(features[index].getDescription());
 189             source.setText(features[index].getFeatureGroup());
 190             start.setValue(new Integer(features[index].getBegin()));
 191             end.setValue(new Integer(features[index].getEnd()));
 192
 193             SearchResults highlight = new SearchResults();
 194             highlight.addResult(sequences[0], features[index].getBegin(),
 195                     features[index].getEnd());
 196
 197             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 198
 199           }
 200           Object col = getFeatureStyle(name.getText());
 201           if (col == null)
 202           {
 203             col = new jalview.schemes.UserColourScheme()
 204                     .createColourFromName(name.getText());
 205           }
 206           oldcol = fcol = col;
 207           updateColourButton(bigPanel, colour, col);
 208         }
 209       });
 210
 211       panel.add(tmp);
 212     }
 213     // ////////
 214     // ////////////////////////////////////
 215
 216     tmp = new JPanel();
 217     panel.add(tmp);
 218     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
 219     tmp.add(name);
 220
 221     tmp = new JPanel();
 222     panel.add(tmp);
 223     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
 224             JLabel.RIGHT));
 225     tmp.add(source);
 226
 227     tmp = new JPanel();
 228     panel.add(tmp);
 229     tmp.add(new JLabel(MessageManager.getString("label.colour"),
 230             JLabel.RIGHT));
 231     tmp.add(colour);
 232     colour.setPreferredSize(new Dimension(150, 15));
 233     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 234     colour.setForeground(Color.black);
 235     colour.setHorizontalAlignment(SwingConstants.CENTER);
 236     colour.setVerticalAlignment(SwingConstants.CENTER);
 237     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 238     colour.setVerticalTextPosition(SwingConstants.CENTER);
 239     bigPanel.add(panel, BorderLayout.NORTH);
 240
 241     panel = new JPanel();
 242     panel.add(new JLabel(MessageManager.getString("label.description"),
 243             JLabel.RIGHT));
 244     description.setFont(JvSwingUtils.getTextAreaFont());
 245     description.setLineWrap(true);
 246     panel.add(new JScrollPane(description));
 247
 248     if (!newFeatures)
 249     {
 250       bigPanel.add(panel, BorderLayout.SOUTH);
 251
 252       panel = new JPanel();
 253       panel.add(new JLabel(MessageManager.getString("label.start"),
 254               JLabel.RIGHT));
 255       panel.add(start);
 256       panel.add(new JLabel(MessageManager.getString("label.end"),
 257               JLabel.RIGHT));
 258       panel.add(end);
 259       bigPanel.add(panel, BorderLayout.CENTER);
 260     }
 261     else
 262     {
 263       bigPanel.add(panel, BorderLayout.CENTER);
 264     }
 265
 266     if (lastFeatureAdded == null)
 267     {
 268       if (features[0].type != null)
 269       {
 270         lastFeatureAdded = features[0].type;
 271       }
 272       else
 273       {
 274         lastFeatureAdded = "feature_1";
 275       }
 276     }
 277
 278     if (lastFeatureGroupAdded == null)
 279     {
 280       if (features[0].featureGroup != null)
 281       {
 282         lastFeatureGroupAdded = features[0].featureGroup;
 283       }
 284       else
 285       {
 286         lastFeatureGroupAdded = "Jalview";
 287       }
 288     }
 289
 290     if (newFeatures)
 291     {
 292       name.setText(lastFeatureAdded);
 293       source.setText(lastFeatureGroupAdded);
 294     }
 295     else
 296     {
 297       name.setText(features[0].getType());
 298       source.setText(features[0].getFeatureGroup());
 299     }
 300
 301     start.setValue(new Integer(features[0].getBegin()));
 302     end.setValue(new Integer(features[0].getEnd()));
 303     description.setText(features[0].getDescription());
 304     updateColourButton(bigPanel, colour,
 305             (oldcol = fcol = getFeatureStyle(name.getText())));
 306     Object[] options;
 307     if (!newFeatures)
 308     {
 309       options = new Object[]
 310       { "Amend", "Delete", "Cancel" };
 311     }
 312     else
 313     {
 314       options = new Object[]
 315       { "OK", "Cancel" };
 316     }
 317
 318     String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
 319             : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 320
 321     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
 322             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
 323             JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
 324
 325     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 326
 327     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
 328     {
 329       // This ensures that the last sequence
 330       // is refreshed and new features are rendered
 331       lastSeq = null;
 332       lastFeatureAdded = name.getText().trim();
 333       lastFeatureGroupAdded = source.getText().trim();
 334       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
 335       // TODO: determine if the null feature group is valid
 336       if (lastFeatureGroupAdded.length() < 1)
 337       {
 338         lastFeatureGroupAdded = null;
 339       }
 340     }
 341
 342     if (!newFeatures)
 343     {
 344       SequenceFeature sf = features[featureIndex];
 345
 346       if (reply == JOptionPane.NO_OPTION)
 347       {
 348         sequences[0].getDatasetSequence().deleteFeature(sf);
 349       }
 350       else if (reply == JOptionPane.YES_OPTION)
 351       {
 352         sf.type = lastFeatureAdded;
 353         sf.featureGroup = lastFeatureGroupAdded;
 354         sf.description = lastDescriptionAdded;
 355
 356         setColour(sf.type, fcol);
 357         getFeaturesDisplayed().setVisible(sf.type);
 358
 359         try
 360         {
 361           sf.begin = ((Integer) start.getValue()).intValue();
 362           sf.end = ((Integer) end.getValue()).intValue();
 363         } catch (NumberFormatException ex)
 364         {
 365         }
 366
 367         ffile.parseDescriptionHTML(sf, false);
 368       }
 369     }
 370     else
 371     // NEW FEATURES ADDED
 372     {
 373       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
 374       {
 375         for (int i = 0; i < sequences.length; i++)
 376         {
 377           features[i].type = lastFeatureAdded;
 378           // fix for JAL-1538 - always set feature group here
 379           features[i].featureGroup = lastFeatureGroupAdded;
 380           features[i].description = lastDescriptionAdded;
 381           sequences[i].addSequenceFeature(features[i]);
 382           ffile.parseDescriptionHTML(features[i], false);
 383         }
 384
 385         if (lastFeatureGroupAdded != null)
 386         {
 387           setGroupVisibility(lastFeatureGroupAdded, true);
 388         }
 389         setColour(lastFeatureAdded, fcol);
 390         setVisible(lastFeatureAdded);
 391
 392         findAllFeatures(false);
 393
 394         ap.paintAlignment(true);
 395
 396         return true;
 397       }
 398       else
 399       {
 400         return false;
 401       }
 402     }
 403
 404     ap.paintAlignment(true);
 405
 406     return true;
 407   }
 408
 409
 410   /**
 411    * update the amend feature button dependent on the given style
 412    *
 413    * @param bigPanel
 414    * @param col
 415    * @param col2
 416    */
 417   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 418           Object col2)
 419   {
 420     colour.removeAll();
 421     colour.setIcon(null);
 422     colour.setToolTipText(null);
 423     colour.setText("");
 424
 425     if (col2 instanceof Color)
 426     {
 427       colour.setBackground((Color) col2);
 428     }
 429     else
 430     {
 431       colour.setBackground(bigPanel.getBackground());
 432       colour.setForeground(Color.black);
 433       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
 434       // colour.setForeground(colour.getBackground());
 435     }
 436   }
 437 }