src/jalview/appletgui/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.appletgui;
  22
  23 import jalview.datamodel.SearchResults;
  24 import jalview.datamodel.SequenceFeature;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.schemes.GraduatedColor;
  28 import jalview.util.MessageManager;
  29 import jalview.viewmodel.AlignmentViewport;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Button;
  33 import java.awt.Choice;
  34 import java.awt.Color;
  35 import java.awt.Dimension;
  36 import java.awt.Font;
  37 import java.awt.Graphics;
  38 import java.awt.GridLayout;
  39 import java.awt.Label;
  40 import java.awt.Panel;
  41 import java.awt.ScrollPane;
  42 import java.awt.TextArea;
  43 import java.awt.TextField;
  44 import java.awt.event.ActionEvent;
  45 import java.awt.event.ActionListener;
  46
  47 /**
  48  * DOCUMENT ME!
  49  *
  50  * @author $author$
  51  * @version $Revision$
  52  */
  53 public class FeatureRenderer extends
  54         jalview.renderer.seqfeatures.FeatureRenderer
  55 {
  56   /**
  57    * Creates a new FeatureRenderer object.
  58    *
  59    * @param av
  60    *          DOCUMENT ME!
  61    */
  62   public FeatureRenderer(AlignmentViewport av)
  63   {
  64     super();
  65     this.av = av;
  66
  67     setTransparencyAvailable(!System.getProperty("java.version")
  68             .startsWith("1.1"));
  69   }
  70
  71   static String lastFeatureAdded;
  72
  73   static String lastFeatureGroupAdded;
  74
  75   static String lastDescriptionAdded;
  76
  77   int featureIndex = 0;
  78
  79   boolean deleteFeature = false;
  80
  81   FeatureColourPanel colourPanel;
  82
  83   class FeatureColourPanel extends Panel
  84   {
  85     String label = "";
  86
  87     private Color maxCol;
  88
  89     private boolean isColourByLabel, isGcol;
  90
  91     /**
  92      * render a feature style in the amend feature dialog box
  93      */
  94     public void updateColor(Object newcol)
  95     {
  96
  97       Color bg, col = null;
  98       GraduatedColor gcol = null;
  99       String vlabel = "";
 100       if (newcol instanceof Color)
 101       {
 102         isGcol = false;
 103         col = (Color) newcol;
 104         gcol = null;
 105       }
 106       else if (newcol instanceof GraduatedColor)
 107       {
 108         isGcol = true;
 109         gcol = (GraduatedColor) newcol;
 110         col = null;
 111       }
 112       else
 113       {
 114         throw new Error(
 115                 MessageManager
 116                         .getString("error.invalid_colour_for_mycheckbox"));
 117       }
 118       if (col != null)
 119       {
 120         setBackground(bg = col);
 121       }
 122       else
 123       {
 124         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 125         {
 126           vlabel += " "
 127                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 128                           : "(<)");
 129         }
 130         if (isColourByLabel = gcol.isColourByLabel())
 131         {
 132           setBackground(bg = Color.white);
 133           vlabel += " (by Label)";
 134         }
 135         else
 136         {
 137           setBackground(bg = gcol.getMinColor());
 138           maxCol = gcol.getMaxColor();
 139         }
 140       }
 141       label = vlabel;
 142       setBackground(bg);
 143       repaint();
 144     }
 145
 146     FeatureColourPanel()
 147     {
 148       super(null);
 149     }
 150
 151     @Override
 152     public void paint(Graphics g)
 153     {
 154       Dimension d = getSize();
 155       if (isGcol)
 156       {
 157         if (isColourByLabel)
 158         {
 159           g.setColor(Color.white);
 160           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 161           g.setColor(Color.black);
 162           Font f = new Font("Verdana", Font.PLAIN, 10);
 163           g.setFont(f);
 164           g.drawString(MessageManager.getString("label.label"), 0, 0);
 165         }
 166         else
 167         {
 168           g.setColor(maxCol);
 169           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 170
 171         }
 172       }
 173     }
 174
 175   }
 176
 177   boolean amendFeatures(final SequenceI[] sequences,
 178           final SequenceFeature[] features, boolean newFeatures,
 179           final AlignmentPanel ap)
 180   {
 181     Panel bigPanel = new Panel(new BorderLayout());
 182     final TextField name = new TextField(16);
 183     final TextField source = new TextField(16);
 184     final TextArea description = new TextArea(3, 35);
 185     final TextField start = new TextField(8);
 186     final TextField end = new TextField(8);
 187     final Choice overlaps;
 188     Button deleteButton = new Button("Delete");
 189     deleteFeature = false;
 190
 191     colourPanel = new FeatureColourPanel();
 192     colourPanel.setSize(110, 15);
 193     final FeatureRenderer fr = this;
 194
 195     Panel panel = new Panel(new GridLayout(3, 1));
 196
 197     featureIndex = 0; // feature to be amended.
 198     Panel tmp;
 199
 200     // /////////////////////////////////////
 201     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 202     if (!newFeatures && features.length > 1)
 203     {
 204       panel = new Panel(new GridLayout(4, 1));
 205       tmp = new Panel();
 206       tmp.add(new Label("Select Feature: "));
 207       overlaps = new Choice();
 208       for (int i = 0; i < features.length; i++)
 209       {
 210         String item = features[i].getType() + "/" + features[i].getBegin()
 211                 + "-" + features[i].getEnd();
 212
 213         if (features[i].getFeatureGroup() != null)
 214         {
 215           item += " (" + features[i].getFeatureGroup() + ")";
 216         }
 217
 218         overlaps.addItem(item);
 219       }
 220
 221       tmp.add(overlaps);
 222
 223       overlaps.addItemListener(new java.awt.event.ItemListener()
 224       {
 225         @Override
 226         public void itemStateChanged(java.awt.event.ItemEvent e)
 227         {
 228           int index = overlaps.getSelectedIndex();
 229           if (index != -1)
 230           {
 231             featureIndex = index;
 232             name.setText(features[index].getType());
 233             description.setText(features[index].getDescription());
 234             source.setText(features[index].getFeatureGroup());
 235             start.setText(features[index].getBegin() + "");
 236             end.setText(features[index].getEnd() + "");
 237
 238             SearchResults highlight = new SearchResults();
 239             highlight.addResult(sequences[0], features[index].getBegin(),
 240                     features[index].getEnd());
 241
 242             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 243
 244           }
 245           Object col = getFeatureStyle(name.getText());
 246           if (col == null)
 247           {
 248             col = new jalview.schemes.UserColourScheme()
 249                     .createColourFromName(name.getText());
 250           }
 251
 252           colourPanel.updateColor(col);
 253         }
 254       });
 255
 256       panel.add(tmp);
 257     }
 258     // ////////
 259     // ////////////////////////////////////
 260
 261     tmp = new Panel();
 262     panel.add(tmp);
 263     tmp.add(new Label("Name: ", Label.RIGHT));
 264     tmp.add(name);
 265
 266     tmp = new Panel();
 267     panel.add(tmp);
 268     tmp.add(new Label("Group: ", Label.RIGHT));
 269     tmp.add(source);
 270
 271     tmp = new Panel();
 272     panel.add(tmp);
 273     tmp.add(new Label("Colour: ", Label.RIGHT));
 274     tmp.add(colourPanel);
 275
 276     bigPanel.add(panel, BorderLayout.NORTH);
 277
 278     panel = new Panel();
 279     panel.add(new Label("Description: ", Label.RIGHT));
 280     panel.add(new ScrollPane().add(description));
 281
 282     if (!newFeatures)
 283     {
 284       bigPanel.add(panel, BorderLayout.SOUTH);
 285
 286       panel = new Panel();
 287       panel.add(new Label(" Start:", Label.RIGHT));
 288       panel.add(start);
 289       panel.add(new Label("  End:", Label.RIGHT));
 290       panel.add(end);
 291       bigPanel.add(panel, BorderLayout.CENTER);
 292     }
 293     else
 294     {
 295       bigPanel.add(panel, BorderLayout.CENTER);
 296     }
 297
 298     if (lastFeatureAdded == null)
 299     {
 300       if (features[0].type != null)
 301       {
 302         lastFeatureAdded = features[0].type;
 303       }
 304       else
 305       {
 306         lastFeatureAdded = "feature_1";
 307       }
 308     }
 309
 310     if (lastFeatureGroupAdded == null)
 311     {
 312       if (features[0].featureGroup != null)
 313       {
 314         lastFeatureGroupAdded = features[0].featureGroup;
 315       }
 316       else
 317       {
 318         lastFeatureAdded = "Jalview";
 319       }
 320     }
 321
 322     String title = newFeatures ? MessageManager
 323             .getString("label.create_new_sequence_features")
 324             : MessageManager.formatMessage("label.amend_delete_features",
 325                     new String[] { sequences[0].getName() });
 326
 327     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 328             240);
 329
 330     dialog.setMainPanel(bigPanel);
 331
 332     if (newFeatures)
 333     {
 334       name.setText(lastFeatureAdded);
 335       source.setText(lastFeatureGroupAdded);
 336     }
 337     else
 338     {
 339       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 340       dialog.buttonPanel.add(deleteButton, 1);
 341       deleteButton.addActionListener(new ActionListener()
 342       {
 343         @Override
 344         public void actionPerformed(ActionEvent evt)
 345         {
 346           deleteFeature = true;
 347           dialog.setVisible(false);
 348         }
 349       });
 350       name.setText(features[0].getType());
 351       source.setText(features[0].getFeatureGroup());
 352     }
 353
 354     start.setText(features[0].getBegin() + "");
 355     end.setText(features[0].getEnd() + "");
 356     description.setText(features[0].getDescription());
 357     Color col = getColour(name.getText());
 358     if (col == null)
 359     {
 360       col = new jalview.schemes.UserColourScheme()
 361               .createColourFromName(name.getText());
 362     }
 363     Object fcol = getFeatureStyle(name.getText());
 364     // simply display the feature color in a box
 365     colourPanel.updateColor(fcol);
 366     dialog.setResizable(true);
 367     // TODO: render the graduated color in the box.
 368     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 369     {
 370       @Override
 371       public void mousePressed(java.awt.event.MouseEvent evt)
 372       {
 373         if (!colourPanel.isGcol)
 374         {
 375           new UserDefinedColours(fr, ap.alignFrame);
 376         }
 377         else
 378         {
 379           FeatureColourChooser fcc = new FeatureColourChooser(
 380                   ap.alignFrame, name.getText());
 381           dialog.transferFocus();
 382         }
 383       }
 384     });
 385     dialog.setVisible(true);
 386
 387     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 388
 389     if (dialog.accept)
 390     {
 391       // This ensures that the last sequence
 392       // is refreshed and new features are rendered
 393       lastSeq = null;
 394       lastFeatureAdded = name.getText().trim();
 395       lastFeatureGroupAdded = source.getText().trim();
 396       lastDescriptionAdded = description.getText().replace('\n', ' ');
 397     }
 398
 399     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 400     {
 401       lastFeatureGroupAdded = null;
 402     }
 403
 404     if (!newFeatures)
 405     {
 406
 407       SequenceFeature sf = features[featureIndex];
 408       if (dialog.accept)
 409       {
 410         sf.type = lastFeatureAdded;
 411         sf.featureGroup = lastFeatureGroupAdded;
 412         sf.description = lastDescriptionAdded;
 413         if (!colourPanel.isGcol)
 414         {
 415           // update colour - otherwise its already done.
 416           setColour(sf.type, colourPanel.getBackground());
 417         }
 418         try
 419         {
 420           sf.begin = Integer.parseInt(start.getText());
 421           sf.end = Integer.parseInt(end.getText());
 422         } catch (NumberFormatException ex)
 423         {
 424         }
 425
 426         ffile.parseDescriptionHTML(sf, false);
 427         setVisible(lastFeatureAdded); // if user edited name then make sure new
 428                                       // type is visible
 429       }
 430       if (deleteFeature)
 431       {
 432         sequences[0].deleteFeature(sf);
 433       }
 434
 435     }
 436     else
 437     {
 438       if (dialog.accept && name.getText().length() > 0)
 439       {
 440         for (int i = 0; i < sequences.length; i++)
 441         {
 442           features[i].type = lastFeatureAdded;
 443           features[i].featureGroup = lastFeatureGroupAdded;
 444           features[i].description = lastDescriptionAdded;
 445           sequences[i].addSequenceFeature(features[i]);
 446           ffile.parseDescriptionHTML(features[i], false);
 447         }
 448
 449         Color newColour = colourPanel.getBackground();
 450         // setColour(lastFeatureAdded, fcol);
 451
 452         if (lastFeatureGroupAdded != null)
 453         {
 454           setGroupVisibility(lastFeatureGroupAdded, true);
 455         }
 456         setColour(lastFeatureAdded, newColour); // was fcol
 457         setVisible(lastFeatureAdded);
 458         findAllFeatures(false); // different to original applet behaviour ?
 459         // findAllFeatures();
 460       }
 461       else
 462       {
 463         // no update to the alignment
 464         return false;
 465       }
 466     }
 467     // refresh the alignment and the feature settings dialog
 468     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 469     {
 470       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 471     }
 472     // findAllFeatures();
 473
 474     ap.paintAlignment(true);
 475
 476     return true;
 477   }
 478 }