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 import java.util.Map;
  47
  48 /**
  49  * DOCUMENT ME!
  50  *
  51  * @author $author$
  52  * @version $Revision$
  53  */
  54 public class FeatureRenderer extends
  55         jalview.renderer.seqfeatures.FeatureRenderer
  56 {
  57
  58   // Holds web links for feature groups and feature types
  59   // in the form label|link
  60   Map<String, String> featureLinks = null;
  61
  62   /**
  63    * Creates a new FeatureRenderer object.
  64    *
  65    * @param av
  66    *          DOCUMENT ME!
  67    */
  68   public FeatureRenderer(AlignmentViewport av)
  69   {
  70     super();
  71     this.av = av;
  72
  73     setTransparencyAvailable(!System.getProperty("java.version")
  74             .startsWith("1.1"));
  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(Object newcol)
 101     {
 102
 103       Color bg, col = null;
 104       GraduatedColor gcol = null;
 105       String vlabel = "";
 106       if (newcol instanceof Color)
 107       {
 108         isGcol = false;
 109         col = (Color) newcol;
 110         gcol = null;
 111       }
 112       else if (newcol instanceof GraduatedColor)
 113       {
 114         isGcol = true;
 115         gcol = (GraduatedColor) newcol;
 116         col = null;
 117       }
 118       else
 119       {
 120         throw new Error(
 121                 MessageManager
 122                         .getString("error.invalid_colour_for_mycheckbox"));
 123       }
 124       if (col != null)
 125       {
 126         setBackground(bg = col);
 127       }
 128       else
 129       {
 130         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 131         {
 132           vlabel += " "
 133                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 134                           : "(<)");
 135         }
 136         if (isColourByLabel = gcol.isColourByLabel())
 137         {
 138           setBackground(bg = Color.white);
 139           vlabel += " (by Label)";
 140         }
 141         else
 142         {
 143           setBackground(bg = gcol.getMinColor());
 144           maxCol = gcol.getMaxColor();
 145         }
 146       }
 147       label = vlabel;
 148       setBackground(bg);
 149       repaint();
 150     }
 151
 152     FeatureColourPanel()
 153     {
 154       super(null);
 155     }
 156
 157     @Override
 158     public void paint(Graphics g)
 159     {
 160       Dimension d = getSize();
 161       if (isGcol)
 162       {
 163         if (isColourByLabel)
 164         {
 165           g.setColor(Color.white);
 166           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 167           g.setColor(Color.black);
 168           Font f = new Font("Verdana", Font.PLAIN, 10);
 169           g.setFont(f);
 170           g.drawString(MessageManager.getString("label.label"), 0, 0);
 171         }
 172         else
 173         {
 174           g.setColor(maxCol);
 175           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 176
 177         }
 178       }
 179     }
 180
 181   }
 182
 183   boolean amendFeatures(final SequenceI[] sequences,
 184           final SequenceFeature[] features, boolean newFeatures,
 185           final AlignmentPanel ap)
 186   {
 187     Panel bigPanel = new Panel(new BorderLayout());
 188     final TextField name = new TextField(16);
 189     final TextField source = new TextField(16);
 190     final TextArea description = new TextArea(3, 35);
 191     final TextField start = new TextField(8);
 192     final TextField end = new TextField(8);
 193     final Choice overlaps;
 194     Button deleteButton = new Button("Delete");
 195     deleteFeature = false;
 196
 197     colourPanel = new FeatureColourPanel();
 198     colourPanel.setSize(110, 15);
 199     final FeatureRenderer fr = this;
 200
 201     Panel panel = new Panel(new GridLayout(3, 1));
 202
 203     featureIndex = 0; // feature to be amended.
 204     Panel tmp;
 205
 206     // /////////////////////////////////////
 207     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 208     if (!newFeatures && features.length > 1)
 209     {
 210       panel = new Panel(new GridLayout(4, 1));
 211       tmp = new Panel();
 212       tmp.add(new Label("Select Feature: "));
 213       overlaps = new Choice();
 214       for (int i = 0; i < features.length; i++)
 215       {
 216         String item = features[i].getType() + "/" + features[i].getBegin()
 217                 + "-" + features[i].getEnd();
 218
 219         if (features[i].getFeatureGroup() != null)
 220         {
 221           item += " (" + features[i].getFeatureGroup() + ")";
 222         }
 223
 224         overlaps.addItem(item);
 225       }
 226
 227       tmp.add(overlaps);
 228
 229       overlaps.addItemListener(new java.awt.event.ItemListener()
 230       {
 231         @Override
 232         public void itemStateChanged(java.awt.event.ItemEvent e)
 233         {
 234           int index = overlaps.getSelectedIndex();
 235           if (index != -1)
 236           {
 237             featureIndex = index;
 238             name.setText(features[index].getType());
 239             description.setText(features[index].getDescription());
 240             source.setText(features[index].getFeatureGroup());
 241             start.setText(features[index].getBegin() + "");
 242             end.setText(features[index].getEnd() + "");
 243
 244             SearchResults highlight = new SearchResults();
 245             highlight.addResult(sequences[0], features[index].getBegin(),
 246                     features[index].getEnd());
 247
 248             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 249
 250           }
 251           Object col = getFeatureStyle(name.getText());
 252           if (col == null)
 253           {
 254             col = new jalview.schemes.UserColourScheme()
 255                     .createColourFromName(name.getText());
 256           }
 257
 258           colourPanel.updateColor(col);
 259         }
 260       });
 261
 262       panel.add(tmp);
 263     }
 264     // ////////
 265     // ////////////////////////////////////
 266
 267     tmp = new Panel();
 268     panel.add(tmp);
 269     tmp.add(new Label("Name: ", Label.RIGHT));
 270     tmp.add(name);
 271
 272     tmp = new Panel();
 273     panel.add(tmp);
 274     tmp.add(new Label("Group: ", Label.RIGHT));
 275     tmp.add(source);
 276
 277     tmp = new Panel();
 278     panel.add(tmp);
 279     tmp.add(new Label("Colour: ", Label.RIGHT));
 280     tmp.add(colourPanel);
 281
 282     bigPanel.add(panel, BorderLayout.NORTH);
 283
 284     panel = new Panel();
 285     panel.add(new Label("Description: ", Label.RIGHT));
 286     panel.add(new ScrollPane().add(description));
 287
 288     if (!newFeatures)
 289     {
 290       bigPanel.add(panel, BorderLayout.SOUTH);
 291
 292       panel = new Panel();
 293       panel.add(new Label(" Start:", Label.RIGHT));
 294       panel.add(start);
 295       panel.add(new Label("  End:", 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 (lastFeatureAdded == null)
 305     {
 306       if (features[0].type != null)
 307       {
 308         lastFeatureAdded = features[0].type;
 309       }
 310       else
 311       {
 312         lastFeatureAdded = "feature_1";
 313       }
 314     }
 315
 316     if (lastFeatureGroupAdded == null)
 317     {
 318       if (features[0].featureGroup != null)
 319       {
 320         lastFeatureGroupAdded = features[0].featureGroup;
 321       }
 322       else
 323       {
 324         lastFeatureAdded = "Jalview";
 325       }
 326     }
 327
 328     String title = newFeatures ? MessageManager
 329             .getString("label.create_new_sequence_features")
 330             : MessageManager.formatMessage("label.amend_delete_features",
 331                     new String[] { sequences[0].getName() });
 332
 333     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 334             240);
 335
 336     dialog.setMainPanel(bigPanel);
 337
 338     if (newFeatures)
 339     {
 340       name.setText(lastFeatureAdded);
 341       source.setText(lastFeatureGroupAdded);
 342     }
 343     else
 344     {
 345       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 346       dialog.buttonPanel.add(deleteButton, 1);
 347       deleteButton.addActionListener(new ActionListener()
 348       {
 349         @Override
 350         public void actionPerformed(ActionEvent evt)
 351         {
 352           deleteFeature = true;
 353           dialog.setVisible(false);
 354         }
 355       });
 356       name.setText(features[0].getType());
 357       source.setText(features[0].getFeatureGroup());
 358     }
 359
 360     start.setText(features[0].getBegin() + "");
 361     end.setText(features[0].getEnd() + "");
 362     description.setText(features[0].getDescription());
 363     Color col = getColour(name.getText());
 364     if (col == null)
 365     {
 366       col = new jalview.schemes.UserColourScheme()
 367               .createColourFromName(name.getText());
 368     }
 369     Object fcol = getFeatureStyle(name.getText());
 370     // simply display the feature color in a box
 371     colourPanel.updateColor(fcol);
 372     dialog.setResizable(true);
 373     // TODO: render the graduated color in the box.
 374     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 375     {
 376       @Override
 377       public void mousePressed(java.awt.event.MouseEvent evt)
 378       {
 379         if (!colourPanel.isGcol)
 380         {
 381           new UserDefinedColours(fr, ap.alignFrame);
 382         }
 383         else
 384         {
 385           FeatureColourChooser fcc = new FeatureColourChooser(
 386                   ap.alignFrame, name.getText());
 387           dialog.transferFocus();
 388         }
 389       }
 390     });
 391     dialog.setVisible(true);
 392
 393     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 394
 395     if (dialog.accept)
 396     {
 397       // This ensures that the last sequence
 398       // is refreshed and new features are rendered
 399       lastSeq = null;
 400       lastFeatureAdded = name.getText().trim();
 401       lastFeatureGroupAdded = source.getText().trim();
 402       lastDescriptionAdded = description.getText().replace('\n', ' ');
 403     }
 404
 405     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 406     {
 407       lastFeatureGroupAdded = null;
 408     }
 409
 410     if (!newFeatures)
 411     {
 412
 413       SequenceFeature sf = features[featureIndex];
 414       if (dialog.accept)
 415       {
 416         sf.type = lastFeatureAdded;
 417         sf.featureGroup = lastFeatureGroupAdded;
 418         sf.description = lastDescriptionAdded;
 419         if (!colourPanel.isGcol)
 420         {
 421           // update colour - otherwise its already done.
 422           setColour(sf.type, colourPanel.getBackground());
 423         }
 424         try
 425         {
 426           sf.begin = Integer.parseInt(start.getText());
 427           sf.end = Integer.parseInt(end.getText());
 428         } catch (NumberFormatException ex)
 429         {
 430         }
 431
 432         ffile.parseDescriptionHTML(sf, false);
 433         setVisible(lastFeatureAdded); // if user edited name then make sure new
 434                                       // type is visible
 435       }
 436       if (deleteFeature)
 437       {
 438         sequences[0].deleteFeature(sf);
 439       }
 440
 441     }
 442     else
 443     {
 444       if (dialog.accept && name.getText().length() > 0)
 445       {
 446         for (int i = 0; i < sequences.length; i++)
 447         {
 448           features[i].type = lastFeatureAdded;
 449           features[i].featureGroup = lastFeatureGroupAdded;
 450           features[i].description = lastDescriptionAdded;
 451           sequences[i].addSequenceFeature(features[i]);
 452           ffile.parseDescriptionHTML(features[i], false);
 453         }
 454
 455         Color newColour = colourPanel.getBackground();
 456         // setColour(lastFeatureAdded, fcol);
 457
 458         if (lastFeatureGroupAdded != null)
 459         {
 460           setGroupVisibility(lastFeatureGroupAdded, true);
 461         }
 462         setColour(lastFeatureAdded, newColour); // was fcol
 463         setVisible(lastFeatureAdded);
 464         findAllFeatures(false); // different to original applet behaviour ?
 465         // findAllFeatures();
 466       }
 467       else
 468       {
 469         // no update to the alignment
 470         return false;
 471       }
 472     }
 473     // refresh the alignment and the feature settings dialog
 474     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 475     {
 476       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 477     }
 478     // findAllFeatures();
 479
 480     ap.paintAlignment(true);
 481
 482     return true;
 483   }
 484 }