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