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