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();
  74     this.av = av;
  75
  76     setTransparencyAvailable(!System.getProperty("java.version")
  77             .startsWith("1.1"));
  78   }
  79
  80   static String lastFeatureAdded;
  81
  82   static String lastFeatureGroupAdded;
  83
  84   static String lastDescriptionAdded;
  85
  86   int featureIndex = 0;
  87
  88   boolean deleteFeature = false;
  89
  90   FeatureColourPanel colourPanel;
  91
  92   class FeatureColourPanel extends Panel
  93   {
  94     String label = "";
  95
  96     private Color maxCol;
  97
  98     private boolean isColourByLabel, isGcol;
  99
 100     /**
 101      * render a feature style in the amend feature dialog box
 102      */
 103     public void updateColor(FeatureColourI newcol)
 104     {
 105       Color bg = null;
 106       String vlabel = "";
 107       if (newcol.isSimpleColour())
 108       {
 109         bg = newcol.getColour();
 110         setBackground(bg);
 111       }
 112       else
 113       {
 114         if (newcol.isAboveThreshold())
 115         {
 116           vlabel += " (>)";
 117         }
 118         else if (newcol.isBelowThreshold())
 119         {
 120           vlabel += " (<)";
 121         }
 122
 123         if (isColourByLabel = newcol.isColourByLabel())
 124         {
 125           setBackground(bg = Color.white);
 126           vlabel += " (by Label)";
 127         }
 128         else
 129         {
 130           setBackground(bg = newcol.getMinColour());
 131           maxCol = newcol.getMaxColour();
 132         }
 133       }
 134       label = vlabel;
 135       setBackground(bg);
 136       repaint();
 137     }
 138
 139     FeatureColourPanel()
 140     {
 141       super(null);
 142     }
 143
 144     @Override
 145     public void paint(Graphics g)
 146     {
 147       Dimension d = getSize();
 148       if (isGcol)
 149       {
 150         if (isColourByLabel)
 151         {
 152           g.setColor(Color.white);
 153           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 154           g.setColor(Color.black);
 155           Font f = new Font("Verdana", Font.PLAIN, 10);
 156           g.setFont(f);
 157           g.drawString(MessageManager.getString("label.label"), 0, 0);
 158         }
 159         else
 160         {
 161           g.setColor(maxCol);
 162           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 163
 164         }
 165       }
 166     }
 167
 168   }
 169
 170   boolean amendFeatures(final SequenceI[] sequences,
 171           final SequenceFeature[] features, boolean newFeatures,
 172           final AlignmentPanel ap)
 173   {
 174     Panel bigPanel = new Panel(new BorderLayout());
 175     final TextField name = new TextField(16);
 176     final TextField source = new TextField(16);
 177     final TextArea description = new TextArea(3, 35);
 178     final TextField start = new TextField(8);
 179     final TextField end = new TextField(8);
 180     final Choice overlaps;
 181     Button deleteButton = new Button("Delete");
 182     deleteFeature = false;
 183
 184     colourPanel = new FeatureColourPanel();
 185     colourPanel.setSize(110, 15);
 186     final FeatureRenderer fr = this;
 187
 188     Panel panel = new Panel(new GridLayout(3, 1));
 189
 190     featureIndex = 0; // feature to be amended.
 191     Panel tmp;
 192
 193     // /////////////////////////////////////
 194     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 195     if (!newFeatures && features.length > 1)
 196     {
 197       panel = new Panel(new GridLayout(4, 1));
 198       tmp = new Panel();
 199       tmp.add(new Label("Select Feature: "));
 200       overlaps = new Choice();
 201       for (int i = 0; i < features.length; i++)
 202       {
 203         String item = features[i].getType() + "/" + features[i].getBegin()
 204                 + "-" + features[i].getEnd();
 205
 206         if (features[i].getFeatureGroup() != null)
 207         {
 208           item += " (" + features[i].getFeatureGroup() + ")";
 209         }
 210
 211         overlaps.addItem(item);
 212       }
 213
 214       tmp.add(overlaps);
 215
 216       overlaps.addItemListener(new java.awt.event.ItemListener()
 217       {
 218         @Override
 219         public void itemStateChanged(java.awt.event.ItemEvent e)
 220         {
 221           int index = overlaps.getSelectedIndex();
 222           if (index != -1)
 223           {
 224             featureIndex = index;
 225             name.setText(features[index].getType());
 226             description.setText(features[index].getDescription());
 227             source.setText(features[index].getFeatureGroup());
 228             start.setText(features[index].getBegin() + "");
 229             end.setText(features[index].getEnd() + "");
 230
 231             SearchResults highlight = new SearchResults();
 232             highlight.addResult(sequences[0], features[index].getBegin(),
 233                     features[index].getEnd());
 234
 235             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 236
 237           }
 238           FeatureColourI col = getFeatureStyle(name.getText());
 239           if (col == null)
 240           {
 241             Color generatedColour = UserColourScheme
 242                     .createColourFromName(name.getText());
 243             col = new FeatureColour(generatedColour);
 244           }
 245
 246           colourPanel.updateColor(col);
 247         }
 248       });
 249
 250       panel.add(tmp);
 251     }
 252     // ////////
 253     // ////////////////////////////////////
 254
 255     tmp = new Panel();
 256     panel.add(tmp);
 257     tmp.add(new Label("Name: ", Label.RIGHT));
 258     tmp.add(name);
 259
 260     tmp = new Panel();
 261     panel.add(tmp);
 262     tmp.add(new Label("Group: ", Label.RIGHT));
 263     tmp.add(source);
 264
 265     tmp = new Panel();
 266     panel.add(tmp);
 267     tmp.add(new Label("Colour: ", Label.RIGHT));
 268     tmp.add(colourPanel);
 269
 270     bigPanel.add(panel, BorderLayout.NORTH);
 271
 272     panel = new Panel();
 273     panel.add(new Label("Description: ", Label.RIGHT));
 274     panel.add(new ScrollPane().add(description));
 275
 276     if (!newFeatures)
 277     {
 278       bigPanel.add(panel, BorderLayout.SOUTH);
 279
 280       panel = new Panel();
 281       panel.add(new Label(" Start:", Label.RIGHT));
 282       panel.add(start);
 283       panel.add(new Label("  End:", 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 }