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.datamodel.SearchResults;
  24 import jalview.datamodel.SequenceFeature;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.schemes.GraduatedColor;
  28 import jalview.util.MessageManager;
  29 import jalview.viewmodel.AlignmentViewport;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Button;
  33 import java.awt.Choice;
  34 import java.awt.Color;
  35 import java.awt.Dimension;
  36 import java.awt.Font;
  37 import java.awt.Graphics;
  38 import java.awt.GridLayout;
  39 import java.awt.Label;
  40 import java.awt.Panel;
  41 import java.awt.ScrollPane;
  42 import java.awt.TextArea;
  43 import java.awt.TextField;
  44 import java.awt.event.ActionEvent;
  45 import java.awt.event.ActionListener;
  46
  47 /**
  48  * DOCUMENT ME!
  49  *
  50  * @author $author$
  51  * @version $Revision$
  52  */
  53 public class FeatureRenderer extends
  54         jalview.renderer.seqfeatures.FeatureRenderer
  55 {
  56   /**
  57    * Creates a new FeatureRenderer object.
  58    *
  59    * @param av
  60    *          DOCUMENT ME!
  61    */
  62   public FeatureRenderer(AlignmentViewport av)
  63   {
  64     super(av);
  65
  66     setTransparencyAvailable(!System.getProperty("java.version")
  67             .startsWith("1.1"));
  68   }
  69
  70   static String lastFeatureAdded;
  71
  72   static String lastFeatureGroupAdded;
  73
  74   static String lastDescriptionAdded;
  75
  76   int featureIndex = 0;
  77
  78   boolean deleteFeature = false;
  79
  80   FeatureColourPanel colourPanel;
  81
  82   class FeatureColourPanel extends Panel
  83   {
  84     String label = "";
  85
  86     private Color maxCol;
  87
  88     private boolean isColourByLabel, isGcol;
  89
  90     /**
  91      * render a feature style in the amend feature dialog box
  92      */
  93     public void updateColor(Object newcol)
  94     {
  95
  96       Color bg, col = null;
  97       GraduatedColor gcol = null;
  98       String vlabel = "";
  99       if (newcol instanceof Color)
 100       {
 101         isGcol = false;
 102         col = (Color) newcol;
 103         gcol = null;
 104       }
 105       else if (newcol instanceof GraduatedColor)
 106       {
 107         isGcol = true;
 108         gcol = (GraduatedColor) newcol;
 109         col = null;
 110       }
 111       else
 112       {
 113         throw new Error(
 114                 MessageManager
 115                         .getString("error.invalid_colour_for_mycheckbox"));
 116       }
 117       if (col != null)
 118       {
 119         setBackground(bg = col);
 120       }
 121       else
 122       {
 123         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 124         {
 125           vlabel += " "
 126                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 127                           : "(<)");
 128         }
 129         if (isColourByLabel = gcol.isColourByLabel())
 130         {
 131           setBackground(bg = Color.white);
 132           vlabel += " (by Label)";
 133         }
 134         else
 135         {
 136           setBackground(bg = gcol.getMinColor());
 137           maxCol = gcol.getMaxColor();
 138         }
 139       }
 140       label = vlabel;
 141       setBackground(bg);
 142       repaint();
 143     }
 144
 145     FeatureColourPanel()
 146     {
 147       super(null);
 148     }
 149
 150     @Override
 151     public void paint(Graphics g)
 152     {
 153       Dimension d = getSize();
 154       if (isGcol)
 155       {
 156         if (isColourByLabel)
 157         {
 158           g.setColor(Color.white);
 159           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 160           g.setColor(Color.black);
 161           Font f = new Font("Verdana", Font.PLAIN, 10);
 162           g.setFont(f);
 163           g.drawString(MessageManager.getString("label.label"), 0, 0);
 164         }
 165         else
 166         {
 167           g.setColor(maxCol);
 168           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 169
 170         }
 171       }
 172     }
 173
 174   }
 175
 176   boolean amendFeatures(final SequenceI[] sequences,
 177           final SequenceFeature[] features, boolean newFeatures,
 178           final AlignmentPanel ap)
 179   {
 180     Panel bigPanel = new Panel(new BorderLayout());
 181     final TextField name = new TextField(16);
 182     final TextField source = new TextField(16);
 183     final TextArea description = new TextArea(3, 35);
 184     final TextField start = new TextField(8);
 185     final TextField end = new TextField(8);
 186     final Choice overlaps;
 187     Button deleteButton = new Button("Delete");
 188     deleteFeature = false;
 189
 190     colourPanel = new FeatureColourPanel();
 191     colourPanel.setSize(110, 15);
 192     final FeatureRenderer fr = this;
 193
 194     Panel panel = new Panel(new GridLayout(3, 1));
 195
 196     featureIndex = 0; // feature to be amended.
 197     Panel tmp;
 198
 199     // /////////////////////////////////////
 200     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 201     if (!newFeatures && features.length > 1)
 202     {
 203       panel = new Panel(new GridLayout(4, 1));
 204       tmp = new Panel();
 205       tmp.add(new Label("Select Feature: "));
 206       overlaps = new Choice();
 207       for (int i = 0; i < features.length; i++)
 208       {
 209         String item = features[i].getType() + "/" + features[i].getBegin()
 210                 + "-" + features[i].getEnd();
 211
 212         if (features[i].getFeatureGroup() != null)
 213         {
 214           item += " (" + features[i].getFeatureGroup() + ")";
 215         }
 216
 217         overlaps.addItem(item);
 218       }
 219
 220       tmp.add(overlaps);
 221
 222       overlaps.addItemListener(new java.awt.event.ItemListener()
 223       {
 224         @Override
 225         public void itemStateChanged(java.awt.event.ItemEvent e)
 226         {
 227           int index = overlaps.getSelectedIndex();
 228           if (index != -1)
 229           {
 230             featureIndex = index;
 231             name.setText(features[index].getType());
 232             description.setText(features[index].getDescription());
 233             source.setText(features[index].getFeatureGroup());
 234             start.setText(features[index].getBegin() + "");
 235             end.setText(features[index].getEnd() + "");
 236
 237             SearchResults highlight = new SearchResults();
 238             highlight.addResult(sequences[0], features[index].getBegin(),
 239                     features[index].getEnd());
 240
 241             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 242
 243           }
 244           Object col = getFeatureStyle(name.getText());
 245           if (col == null)
 246           {
 247             col = new jalview.schemes.UserColourScheme()
 248                     .createColourFromName(name.getText());
 249           }
 250
 251           colourPanel.updateColor(col);
 252         }
 253       });
 254
 255       panel.add(tmp);
 256     }
 257     // ////////
 258     // ////////////////////////////////////
 259
 260     tmp = new Panel();
 261     panel.add(tmp);
 262     tmp.add(new Label("Name: ", Label.RIGHT));
 263     tmp.add(name);
 264
 265     tmp = new Panel();
 266     panel.add(tmp);
 267     tmp.add(new Label("Group: ", Label.RIGHT));
 268     tmp.add(source);
 269
 270     tmp = new Panel();
 271     panel.add(tmp);
 272     tmp.add(new Label("Colour: ", Label.RIGHT));
 273     tmp.add(colourPanel);
 274
 275     bigPanel.add(panel, BorderLayout.NORTH);
 276
 277     panel = new Panel();
 278     panel.add(new Label("Description: ", Label.RIGHT));
 279     panel.add(new ScrollPane().add(description));
 280
 281     if (!newFeatures)
 282     {
 283       bigPanel.add(panel, BorderLayout.SOUTH);
 284
 285       panel = new Panel();
 286       panel.add(new Label(" Start:", Label.RIGHT));
 287       panel.add(start);
 288       panel.add(new Label("  End:", Label.RIGHT));
 289       panel.add(end);
 290       bigPanel.add(panel, BorderLayout.CENTER);
 291     }
 292     else
 293     {
 294       bigPanel.add(panel, BorderLayout.CENTER);
 295     }
 296
 297     if (lastFeatureAdded == null)
 298     {
 299       if (features[0].type != null)
 300       {
 301         lastFeatureAdded = features[0].type;
 302       }
 303       else
 304       {
 305         lastFeatureAdded = "feature_1";
 306       }
 307     }
 308
 309     if (lastFeatureGroupAdded == null)
 310     {
 311       if (features[0].featureGroup != null)
 312       {
 313         lastFeatureGroupAdded = features[0].featureGroup;
 314       }
 315       else
 316       {
 317         lastFeatureAdded = "Jalview";
 318       }
 319     }
 320
 321     String title = newFeatures ? MessageManager
 322             .getString("label.create_new_sequence_features")
 323             : MessageManager.formatMessage("label.amend_delete_features",
 324                     new String[] { sequences[0].getName() });
 325
 326     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 327             240);
 328
 329     dialog.setMainPanel(bigPanel);
 330
 331     if (newFeatures)
 332     {
 333       name.setText(lastFeatureAdded);
 334       source.setText(lastFeatureGroupAdded);
 335     }
 336     else
 337     {
 338       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 339       dialog.buttonPanel.add(deleteButton, 1);
 340       deleteButton.addActionListener(new ActionListener()
 341       {
 342         @Override
 343         public void actionPerformed(ActionEvent evt)
 344         {
 345           deleteFeature = true;
 346           dialog.setVisible(false);
 347         }
 348       });
 349       name.setText(features[0].getType());
 350       source.setText(features[0].getFeatureGroup());
 351     }
 352
 353     start.setText(features[0].getBegin() + "");
 354     end.setText(features[0].getEnd() + "");
 355     description.setText(features[0].getDescription());
 356     Color col = getColour(name.getText());
 357     if (col == null)
 358     {
 359       col = new jalview.schemes.UserColourScheme()
 360               .createColourFromName(name.getText());
 361     }
 362     Object fcol = getFeatureStyle(name.getText());
 363     // simply display the feature color in a box
 364     colourPanel.updateColor(fcol);
 365     dialog.setResizable(true);
 366     // TODO: render the graduated color in the box.
 367     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 368     {
 369       @Override
 370       public void mousePressed(java.awt.event.MouseEvent evt)
 371       {
 372         if (!colourPanel.isGcol)
 373         {
 374           new UserDefinedColours(fr, ap.alignFrame);
 375         }
 376         else
 377         {
 378           FeatureColourChooser fcc = new FeatureColourChooser(
 379                   ap.alignFrame, name.getText());
 380           dialog.transferFocus();
 381         }
 382       }
 383     });
 384     dialog.setVisible(true);
 385
 386     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 387
 388     if (dialog.accept)
 389     {
 390       // This ensures that the last sequence
 391       // is refreshed and new features are rendered
 392       lastSeq = null;
 393       lastFeatureAdded = name.getText().trim();
 394       lastFeatureGroupAdded = source.getText().trim();
 395       lastDescriptionAdded = description.getText().replace('\n', ' ');
 396     }
 397
 398     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 399     {
 400       lastFeatureGroupAdded = null;
 401     }
 402
 403     if (!newFeatures)
 404     {
 405
 406       SequenceFeature sf = features[featureIndex];
 407       if (dialog.accept)
 408       {
 409         sf.type = lastFeatureAdded;
 410         sf.featureGroup = lastFeatureGroupAdded;
 411         sf.description = lastDescriptionAdded;
 412         if (!colourPanel.isGcol)
 413         {
 414           // update colour - otherwise its already done.
 415           setColour(sf.type, colourPanel.getBackground());
 416         }
 417         try
 418         {
 419           sf.begin = Integer.parseInt(start.getText());
 420           sf.end = Integer.parseInt(end.getText());
 421         } catch (NumberFormatException ex)
 422         {
 423         }
 424
 425         ffile.parseDescriptionHTML(sf, false);
 426         setVisible(lastFeatureAdded); // if user edited name then make sure new
 427                                       // type is visible
 428       }
 429       if (deleteFeature)
 430       {
 431         sequences[0].deleteFeature(sf);
 432       }
 433
 434     }
 435     else
 436     {
 437       if (dialog.accept && name.getText().length() > 0)
 438       {
 439         for (int i = 0; i < sequences.length; i++)
 440         {
 441           features[i].type = lastFeatureAdded;
 442           features[i].featureGroup = lastFeatureGroupAdded;
 443           features[i].description = lastDescriptionAdded;
 444           sequences[i].addSequenceFeature(features[i]);
 445           ffile.parseDescriptionHTML(features[i], false);
 446         }
 447
 448         Color newColour = colourPanel.getBackground();
 449         // setColour(lastFeatureAdded, fcol);
 450
 451         if (lastFeatureGroupAdded != null)
 452         {
 453           setGroupVisibility(lastFeatureGroupAdded, true);
 454         }
 455         setColour(lastFeatureAdded, newColour); // was fcol
 456         setVisible(lastFeatureAdded);
 457         findAllFeatures(false); // different to original applet behaviour ?
 458         // findAllFeatures();
 459       }
 460       else
 461       {
 462         // no update to the alignment
 463         return false;
 464       }
 465     }
 466     // refresh the alignment and the feature settings dialog
 467     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 468     {
 469       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 470     }
 471     // findAllFeatures();
 472
 473     ap.paintAlignment(true);
 474
 475     return true;
 476   }
 477 }