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