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.Hashtable;
  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   Hashtable 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     public void paint(Graphics g)
 158     {
 159       Dimension d = getSize();
 160       if (isGcol)
 161       {
 162         if (isColourByLabel)
 163         {
 164           g.setColor(Color.white);
 165           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 166           g.setColor(Color.black);
 167           Font f = new Font("Verdana", Font.PLAIN, 10);
 168           g.setFont(f);
 169           g.drawString(MessageManager.getString("label.label"), 0, 0);
 170         }
 171         else
 172         {
 173           g.setColor(maxCol);
 174           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 175
 176         }
 177       }
 178     }
 179
 180   }
 181
 182   boolean amendFeatures(final SequenceI[] sequences,
 183           final SequenceFeature[] features, boolean newFeatures,
 184           final AlignmentPanel ap)
 185   {
 186     Panel bigPanel = new Panel(new BorderLayout());
 187     final TextField name = new TextField(16);
 188     final TextField source = new TextField(16);
 189     final TextArea description = new TextArea(3, 35);
 190     final TextField start = new TextField(8);
 191     final TextField end = new TextField(8);
 192     final Choice overlaps;
 193     Button deleteButton = new Button("Delete");
 194     deleteFeature = false;
 195
 196     colourPanel = new FeatureColourPanel();
 197     colourPanel.setSize(110, 15);
 198     final FeatureRenderer fr = this;
 199
 200     Panel panel = new Panel(new GridLayout(3, 1));
 201
 202     featureIndex = 0; // feature to be amended.
 203     Panel tmp;
 204
 205     // /////////////////////////////////////
 206     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 207     if (!newFeatures && features.length > 1)
 208     {
 209       panel = new Panel(new GridLayout(4, 1));
 210       tmp = new Panel();
 211       tmp.add(new Label("Select Feature: "));
 212       overlaps = new Choice();
 213       for (int i = 0; i < features.length; i++)
 214       {
 215         String item = features[i].getType() + "/" + features[i].getBegin()
 216                 + "-" + features[i].getEnd();
 217
 218         if (features[i].getFeatureGroup() != null)
 219         {
 220           item += " (" + features[i].getFeatureGroup() + ")";
 221         }
 222
 223         overlaps.addItem(item);
 224       }
 225
 226       tmp.add(overlaps);
 227
 228       overlaps.addItemListener(new java.awt.event.ItemListener()
 229       {
 230         public void itemStateChanged(java.awt.event.ItemEvent e)
 231         {
 232           int index = overlaps.getSelectedIndex();
 233           if (index != -1)
 234           {
 235             featureIndex = index;
 236             name.setText(features[index].getType());
 237             description.setText(features[index].getDescription());
 238             source.setText(features[index].getFeatureGroup());
 239             start.setText(features[index].getBegin() + "");
 240             end.setText(features[index].getEnd() + "");
 241
 242             SearchResults highlight = new SearchResults();
 243             highlight.addResult(sequences[0], features[index].getBegin(),
 244                     features[index].getEnd());
 245
 246             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 247
 248           }
 249           Object col = getFeatureStyle(name.getText());
 250           if (col == null)
 251           {
 252             col = new jalview.schemes.UserColourScheme()
 253                     .createColourFromName(name.getText());
 254           }
 255
 256           colourPanel.updateColor(col);
 257         }
 258       });
 259
 260       panel.add(tmp);
 261     }
 262     // ////////
 263     // ////////////////////////////////////
 264
 265     tmp = new Panel();
 266     panel.add(tmp);
 267     tmp.add(new Label("Name: ", Label.RIGHT));
 268     tmp.add(name);
 269
 270     tmp = new Panel();
 271     panel.add(tmp);
 272     tmp.add(new Label("Group: ", Label.RIGHT));
 273     tmp.add(source);
 274
 275     tmp = new Panel();
 276     panel.add(tmp);
 277     tmp.add(new Label("Colour: ", Label.RIGHT));
 278     tmp.add(colourPanel);
 279
 280     bigPanel.add(panel, BorderLayout.NORTH);
 281
 282     panel = new Panel();
 283     panel.add(new Label("Description: ", Label.RIGHT));
 284     panel.add(new ScrollPane().add(description));
 285
 286     if (!newFeatures)
 287     {
 288       bigPanel.add(panel, BorderLayout.SOUTH);
 289
 290       panel = new Panel();
 291       panel.add(new Label(" Start:", Label.RIGHT));
 292       panel.add(start);
 293       panel.add(new Label("  End:", Label.RIGHT));
 294       panel.add(end);
 295       bigPanel.add(panel, BorderLayout.CENTER);
 296     }
 297     else
 298     {
 299       bigPanel.add(panel, BorderLayout.CENTER);
 300     }
 301
 302     if (lastFeatureAdded == null)
 303     {
 304       if (features[0].type != null)
 305       {
 306         lastFeatureAdded = features[0].type;
 307       }
 308       else
 309       {
 310         lastFeatureAdded = "feature_1";
 311       }
 312     }
 313
 314     if (lastFeatureGroupAdded == null)
 315     {
 316       if (features[0].featureGroup != null)
 317       {
 318         lastFeatureGroupAdded = features[0].featureGroup;
 319       }
 320       else
 321       {
 322         lastFeatureAdded = "Jalview";
 323       }
 324     }
 325
 326     String title = newFeatures ? MessageManager
 327             .getString("label.create_new_sequence_features")
 328             : MessageManager.formatMessage("label.amend_delete_features",
 329                     new String[] { sequences[0].getName() });
 330
 331     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 332             240);
 333
 334     dialog.setMainPanel(bigPanel);
 335
 336     if (newFeatures)
 337     {
 338       name.setText(lastFeatureAdded);
 339       source.setText(lastFeatureGroupAdded);
 340     }
 341     else
 342     {
 343       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 344       dialog.buttonPanel.add(deleteButton, 1);
 345       deleteButton.addActionListener(new ActionListener()
 346       {
 347         public void actionPerformed(ActionEvent evt)
 348         {
 349           deleteFeature = true;
 350           dialog.setVisible(false);
 351         }
 352       });
 353       name.setText(features[0].getType());
 354       source.setText(features[0].getFeatureGroup());
 355     }
 356
 357     start.setText(features[0].getBegin() + "");
 358     end.setText(features[0].getEnd() + "");
 359     description.setText(features[0].getDescription());
 360     Color col = getColour(name.getText());
 361     if (col == null)
 362     {
 363       col = new jalview.schemes.UserColourScheme()
 364               .createColourFromName(name.getText());
 365     }
 366     Object fcol = getFeatureStyle(name.getText());
 367     // simply display the feature color in a box
 368     colourPanel.updateColor(fcol);
 369     dialog.setResizable(true);
 370     // TODO: render the graduated color in the box.
 371     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 372     {
 373       public void mousePressed(java.awt.event.MouseEvent evt)
 374       {
 375         if (!colourPanel.isGcol)
 376         {
 377           new UserDefinedColours(fr, ap.alignFrame);
 378         }
 379         else
 380         {
 381           FeatureColourChooser fcc = new FeatureColourChooser(
 382                   ap.alignFrame, name.getText());
 383           dialog.transferFocus();
 384         }
 385       }
 386     });
 387     dialog.setVisible(true);
 388
 389     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 390
 391     if (dialog.accept)
 392     {
 393       // This ensures that the last sequence
 394       // is refreshed and new features are rendered
 395       lastSeq = null;
 396       lastFeatureAdded = name.getText().trim();
 397       lastFeatureGroupAdded = source.getText().trim();
 398       lastDescriptionAdded = description.getText().replace('\n', ' ');
 399     }
 400
 401     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 402     {
 403       lastFeatureGroupAdded = null;
 404     }
 405
 406     if (!newFeatures)
 407     {
 408
 409       SequenceFeature sf = features[featureIndex];
 410       if (dialog.accept)
 411       {
 412         sf.type = lastFeatureAdded;
 413         sf.featureGroup = lastFeatureGroupAdded;
 414         sf.description = lastDescriptionAdded;
 415         if (!colourPanel.isGcol)
 416         {
 417           // update colour - otherwise its already done.
 418           setColour(sf.type, colourPanel.getBackground());
 419         }
 420         try
 421         {
 422           sf.begin = Integer.parseInt(start.getText());
 423           sf.end = Integer.parseInt(end.getText());
 424         } catch (NumberFormatException ex)
 425         {
 426         }
 427
 428         ffile.parseDescriptionHTML(sf, false);
 429         setVisible(lastFeatureAdded); // if user edited name then make sure new
 430                                       // type is visible
 431       }
 432       if (deleteFeature)
 433       {
 434         sequences[0].deleteFeature(sf);
 435       }
 436
 437     }
 438     else
 439     {
 440       if (dialog.accept && name.getText().length() > 0)
 441       {
 442         for (int i = 0; i < sequences.length; i++)
 443         {
 444           features[i].type = lastFeatureAdded;
 445           features[i].featureGroup = lastFeatureGroupAdded;
 446           features[i].description = lastDescriptionAdded;
 447           sequences[i].addSequenceFeature(features[i]);
 448           ffile.parseDescriptionHTML(features[i], false);
 449         }
 450
 451         Color newColour = colourPanel.getBackground();
 452         // setColour(lastFeatureAdded, fcol);
 453
 454         if (lastFeatureGroupAdded != null)
 455         {
 456           setGroupVisibility(lastFeatureGroupAdded, true);
 457         }
 458         setColour(lastFeatureAdded, newColour); // was fcol
 459         setVisible(lastFeatureAdded);
 460         findAllFeatures(false); // different to original applet behaviour ?
 461         // findAllFeatures();
 462       }
 463       else
 464       {
 465         // no update to the alignment
 466         return false;
 467       }
 468     }
 469     // refresh the alignment and the feature settings dialog
 470     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 471     {
 472       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 473     }
 474     // findAllFeatures();
 475
 476     ap.paintAlignment(true);
 477
 478     return true;
 479   }
 480 }