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