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.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   /**
 169    * Shows a dialog allowing the user to create, or amend or delete, sequence
 170    * features.
 171    *
 172    * @param sequences
 173    * @param features
 174    * @param create
 175    * @param ap
 176    * @param featureType
 177    * @return
 178    */
 179   boolean amendFeatures(final SequenceI[] sequences,
 180           final SequenceFeature[] features, boolean create,
 181           final AlignmentPanel ap, String featureType)
 182   {
 183     Panel bigPanel = new Panel(new BorderLayout());
 184     final TextField name = new TextField(16);
 185     final TextField source = new TextField(16);
 186     final TextArea description = new TextArea(3, 35);
 187     final TextField start = new TextField(8);
 188     final TextField end = new TextField(8);
 189     final Choice overlaps;
 190     Button deleteButton = new Button("Delete");
 191     deleteFeature = false;
 192
 193     colourPanel = new FeatureColourPanel();
 194     colourPanel.setSize(110, 15);
 195     final FeatureRenderer fr = this;
 196
 197     Panel panel = new Panel(new GridLayout(3, 1));
 198
 199     featureIndex = 0; // feature to be amended.
 200     Panel tmp;
 201
 202     // /////////////////////////////////////
 203     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 204     if (!create && features.length > 1)
 205     {
 206       panel = new Panel(new GridLayout(4, 1));
 207       tmp = new Panel();
 208       tmp.add(new Label("Select Feature: "));
 209       overlaps = new Choice();
 210       for (int i = 0; i < features.length; i++)
 211       {
 212         String item = features[i].getType() + "/" + features[i].getBegin()
 213                 + "-" + features[i].getEnd();
 214
 215         if (features[i].getFeatureGroup() != null)
 216         {
 217           item += " (" + features[i].getFeatureGroup() + ")";
 218         }
 219
 220         overlaps.addItem(item);
 221       }
 222
 223       tmp.add(overlaps);
 224
 225       overlaps.addItemListener(new java.awt.event.ItemListener()
 226       {
 227         @Override
 228         public void itemStateChanged(java.awt.event.ItemEvent e)
 229         {
 230           int index = overlaps.getSelectedIndex();
 231           if (index != -1)
 232           {
 233             featureIndex = index;
 234             name.setText(features[index].getType());
 235             description.setText(features[index].getDescription());
 236             source.setText(features[index].getFeatureGroup());
 237             start.setText(features[index].getBegin() + "");
 238             end.setText(features[index].getEnd() + "");
 239
 240             SearchResultsI highlight = new SearchResults();
 241             highlight.addResult(sequences[0], features[index].getBegin(),
 242                     features[index].getEnd());
 243
 244             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 245
 246           }
 247           FeatureColourI col = getFeatureStyle(name.getText());
 248           if (col == null)
 249           {
 250             Color generatedColour = ColorUtils
 251                     .createColourFromName(name.getText());
 252             col = new FeatureColour(generatedColour);
 253           }
 254
 255           colourPanel.updateColor(col);
 256         }
 257       });
 258
 259       panel.add(tmp);
 260     }
 261     // ////////
 262     // ////////////////////////////////////
 263
 264     tmp = new Panel();
 265     panel.add(tmp);
 266     tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
 267     tmp.add(name);
 268
 269     tmp = new Panel();
 270     panel.add(tmp);
 271     tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
 272     tmp.add(source);
 273
 274     tmp = new Panel();
 275     panel.add(tmp);
 276     tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
 277     tmp.add(colourPanel);
 278
 279     bigPanel.add(panel, BorderLayout.NORTH);
 280
 281     panel = new Panel();
 282     panel.add(new Label(MessageManager.getString("label.description:"),
 283             Label.RIGHT));
 284     panel.add(new ScrollPane().add(description));
 285
 286     if (!create)
 287     {
 288       bigPanel.add(panel, BorderLayout.SOUTH);
 289
 290       panel = new Panel();
 291       panel.add(new Label(MessageManager.getString("label.start"),
 292               Label.RIGHT));
 293       panel.add(start);
 294       panel.add(new Label(MessageManager.getString("label.end"),
 295               Label.RIGHT));
 296       panel.add(end);
 297       bigPanel.add(panel, BorderLayout.CENTER);
 298     }
 299     else
 300     {
 301       bigPanel.add(panel, BorderLayout.CENTER);
 302     }
 303
 304     if (featureType != null)
 305     {
 306       lastFeatureAdded = featureType;
 307     }
 308     else
 309     {
 310       if (lastFeatureAdded == null)
 311       {
 312         if (features[0].type != null)
 313         {
 314           lastFeatureAdded = features[0].type;
 315         }
 316         else
 317         {
 318           lastFeatureAdded = "feature_1";
 319         }
 320       }
 321     }
 322
 323     if (lastFeatureGroupAdded == null)
 324     {
 325       if (features[0].featureGroup != null)
 326       {
 327         lastFeatureGroupAdded = features[0].featureGroup;
 328       }
 329       else
 330       {
 331         lastFeatureAdded = "Jalview";
 332       }
 333     }
 334
 335     String title = create ? MessageManager
 336             .getString("label.create_new_sequence_features")
 337             : MessageManager.formatMessage("label.amend_delete_features",
 338                     new String[] { sequences[0].getName() });
 339
 340     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 341             240);
 342
 343     dialog.setMainPanel(bigPanel);
 344
 345     if (create)
 346     {
 347       name.setText(lastFeatureAdded);
 348       source.setText(lastFeatureGroupAdded);
 349     }
 350     else
 351     {
 352       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 353       dialog.buttonPanel.add(deleteButton, 1);
 354       deleteButton.addActionListener(new ActionListener()
 355       {
 356         @Override
 357         public void actionPerformed(ActionEvent evt)
 358         {
 359           deleteFeature = true;
 360           dialog.setVisible(false);
 361         }
 362       });
 363       name.setText(features[0].getType());
 364       source.setText(features[0].getFeatureGroup());
 365     }
 366
 367     start.setText(features[0].getBegin() + "");
 368     end.setText(features[0].getEnd() + "");
 369     description.setText(features[0].getDescription());
 370     // lookup (or generate) the feature colour
 371     FeatureColourI fcol = getFeatureStyle(name.getText());
 372     // simply display the feature color in a box
 373     colourPanel.updateColor(fcol);
 374     dialog.setResizable(true);
 375     // TODO: render the graduated color in the box.
 376     colourPanel.addMouseListener(new MouseAdapter()
 377     {
 378       @Override
 379       public void mousePressed(MouseEvent evt)
 380       {
 381         if (!colourPanel.isGcol)
 382         {
 383           new UserDefinedColours(fr, ap.alignFrame);
 384         }
 385         else
 386         {
 387           new FeatureColourChooser(ap.alignFrame, name.getText());
 388           dialog.transferFocus();
 389         }
 390       }
 391     });
 392     dialog.setVisible(true);
 393
 394     FeaturesFile ffile = new FeaturesFile();
 395
 396     if (dialog.accept)
 397     {
 398       lastFeatureAdded = name.getText().trim();
 399       lastFeatureGroupAdded = source.getText().trim();
 400       lastDescriptionAdded = description.getText().replace('\n', ' ');
 401     }
 402
 403     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 404     {
 405       lastFeatureGroupAdded = null;
 406     }
 407
 408     if (!create)
 409     {
 410
 411       SequenceFeature sf = features[featureIndex];
 412       if (dialog.accept)
 413       {
 414         sf.type = lastFeatureAdded;
 415         sf.featureGroup = lastFeatureGroupAdded;
 416         sf.description = lastDescriptionAdded;
 417         if (!colourPanel.isGcol)
 418         {
 419           // update colour - otherwise its already done.
 420           setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
 421         }
 422         try
 423         {
 424           sf.begin = Integer.parseInt(start.getText());
 425           sf.end = Integer.parseInt(end.getText());
 426         } catch (NumberFormatException ex)
 427         {
 428         }
 429
 430         ffile.parseDescriptionHTML(sf, false);
 431         setVisible(lastFeatureAdded); // if user edited name then make sure new
 432                                       // type is visible
 433       }
 434       if (deleteFeature)
 435       {
 436         sequences[0].deleteFeature(sf);
 437       }
 438
 439     }
 440     else
 441     {
 442       if (dialog.accept && name.getText().length() > 0)
 443       {
 444         for (int i = 0; i < sequences.length; i++)
 445         {
 446           features[i].type = lastFeatureAdded;
 447           features[i].featureGroup = lastFeatureGroupAdded;
 448           features[i].description = lastDescriptionAdded;
 449           sequences[i].addSequenceFeature(features[i]);
 450           ffile.parseDescriptionHTML(features[i], false);
 451         }
 452
 453         Color newColour = colourPanel.getBackground();
 454         // setColour(lastFeatureAdded, fcol);
 455
 456         if (lastFeatureGroupAdded != null)
 457         {
 458           setGroupVisibility(lastFeatureGroupAdded, true);
 459         }
 460         setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
 461         setVisible(lastFeatureAdded);
 462         findAllFeatures(false); // different to original applet behaviour ?
 463         // findAllFeatures();
 464       }
 465       else
 466       {
 467         // no update to the alignment
 468         return false;
 469       }
 470     }
 471     // refresh the alignment and the feature settings dialog
 472     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 473     {
 474       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 475     }
 476     // findAllFeatures();
 477
 478     ap.paintAlignment(true);
 479
 480     return true;
 481   }
 482 }