unused/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.io.FeaturesFile;
  27 import jalview.schemes.AnnotationColourGradient;
  28 import jalview.schemes.GraduatedColor;
  29 import jalview.schemes.UserColourScheme;
  30 import jalview.util.MessageManager;
  31 import jalview.viewmodel.AlignmentViewport;
  32
  33 import java.awt.BorderLayout;
  34 import javax.swing.JButton;
  35 import java.awt.Color;
  36 import java.awt.Dimension;
  37 import java.awt.Font;
  38 import java.awt.Graphics;
  39 import java.awt.GridLayout;
  40 import javax.swing.JLabel;
  41 import javax.swing.JPanel;
  42 import javax.swing.JScrollPane;
  43 import javax.swing.JTextArea;
  44 import javax.swing.JTextField;
  45 import java.awt.event.ActionEvent;
  46 import java.awt.event.ActionListener;
  47 import java.util.Hashtable;
  48
  49 /**
  50  * DOCUMENT ME!
  51  *
  52  * @author $author$
  53  * @version $Revision$
  54  */
  55 public class FeatureRenderer extends
  56         jalview.renderer.seqfeatures.FeatureRenderer
  57 {
  58
  59   // Holds web links for feature groups and feature types
  60   // in the form label|link
  61   Hashtable featureLinks = null;
  62
  63   /**
  64    * Creates a new FeatureRenderer object.
  65    *
  66    * @param av
  67    *          DOCUMENT ME!
  68    */
  69   public FeatureRenderer(AlignmentViewport av)
  70   {
  71     super();
  72     this.av = av;
  73
  74     setTransparencyAvailable(!System.getProperty("java.version")
  75             .startsWith("1.1"));
  76   }
  77
  78   static String lastFeatureAdded;
  79
  80   static String lastFeatureGroupAdded;
  81
  82   static String lastDescriptionAdded;
  83
  84   int featureIndex = 0;
  85
  86   boolean deleteFeature = false;
  87
  88   FeatureColourPanel colourPanel;
  89
  90   class FeatureColourPanel extends JPanel
  91   {
  92     String label = "";
  93
  94     private Color maxCol;
  95
  96     private boolean isColourByLabel, isGcol;
  97
  98     /**
  99      * render a feature style in the amend feature dialog box
 100      */
 101     public void updateColor(Object newcol)
 102     {
 103
 104       Color bg, col = null;
 105       GraduatedColor gcol = null;
 106       String vlabel = "";
 107       if (newcol instanceof Color)
 108       {
 109         isGcol = false;
 110         col = (Color) newcol;
 111         gcol = null;
 112       }
 113       else if (newcol instanceof GraduatedColor)
 114       {
 115         isGcol = true;
 116         gcol = (GraduatedColor) newcol;
 117         col = null;
 118       }
 119       else
 120       {
 121         throw new Error(
 122                 MessageManager
 123                         .getString("error.invalid_colour_for_mycheckbox"));
 124       }
 125       if (col != null)
 126       {
 127         setBackground(bg = col);
 128       }
 129       else
 130       {
 131         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 132         {
 133           vlabel += " "
 134                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 135                           : "(<)");
 136         }
 137         if (isColourByLabel = gcol.isColourByLabel())
 138         {
 139           setBackground(bg = Color.white);
 140           vlabel += " (by Label)";
 141         }
 142         else
 143         {
 144           setBackground(bg = gcol.getMinColor());
 145           maxCol = gcol.getMaxColor();
 146         }
 147       }
 148       label = vlabel;
 149       setBackground(bg);
 150       repaint();
 151     }
 152
 153     FeatureColourPanel()
 154     {
 155       super(null);
 156     }
 157
 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     JPanel bigPanel = new JPanel(new BorderLayout());
 188     final JTextField name = new JTextField(16);
 189     final JTextField source = new JTextField(16);
 190     final JTextArea description = new JTextArea(3, 35);
 191     final JTextField start = new JTextField(8);
 192     final JTextField end = new JTextField(8);
 193     final Choice overlaps;
 194     JButton deleteButton = new JButton("Delete");
 195     deleteFeature = false;
 196
 197     colourPanel = new FeatureColourPanel();
 198     colourPanel.setSize(110, 15);
 199     final FeatureRenderer fr = this;
 200
 201     JPanel panel = new JPanel(new GridLayout(3, 1));
 202
 203     featureIndex = 0; // feature to be amended.
 204     JPanel tmp;
 205
 206     // /////////////////////////////////////
 207     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 208     if (!newFeatures && features.length > 1)
 209     {
 210       panel = new JPanel(new GridLayout(4, 1));
 211       tmp = new JPanel();
 212       tmp.add(new JLabel("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         public void itemStateChanged(java.awt.event.ItemEvent e)
 232         {
 233           int index = overlaps.getSelectedIndex();
 234           if (index != -1)
 235           {
 236             featureIndex = index;
 237             name.setText(features[index].getType());
 238             description.setText(features[index].getDescription());
 239             source.setText(features[index].getFeatureGroup());
 240             start.setText(features[index].getBegin() + "");
 241             end.setText(features[index].getEnd() + "");
 242
 243             SearchResults highlight = new SearchResults();
 244             highlight.addResult(sequences[0], features[index].getBegin(),
 245                     features[index].getEnd());
 246
 247             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 248
 249           }
 250           Object col = getFeatureStyle(name.getText());
 251           if (col == null)
 252           {
 253             col = new UserColourScheme().createColourFromName(name
 254                     .getText());
 255           }
 256
 257           colourPanel.updateColor(col);
 258         }
 259       });
 260
 261       panel.add(tmp);
 262     }
 263     // ////////
 264     // ////////////////////////////////////
 265
 266     tmp = new JPanel();
 267     panel.add(tmp);
 268     tmp.add(new JLabel("Name: ", JLabel.RIGHT));
 269     tmp.add(name);
 270
 271     tmp = new JPanel();
 272     panel.add(tmp);
 273     tmp.add(new JLabel("Group: ", JLabel.RIGHT));
 274     tmp.add(source);
 275
 276     tmp = new JPanel();
 277     panel.add(tmp);
 278     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
 279     tmp.add(colourPanel);
 280
 281     bigPanel.add(panel, BorderLayout.NORTH);
 282
 283     panel = new JPanel();
 284     panel.add(new JLabel("Description: ", JLabel.RIGHT));
 285     panel.add(new JScrollPane().add(description));
 286
 287     if (!newFeatures)
 288     {
 289       bigPanel.add(panel, BorderLayout.SOUTH);
 290
 291       panel = new JPanel();
 292       panel.add(new JLabel(" Start:", JLabel.RIGHT));
 293       panel.add(start);
 294       panel.add(new JLabel("  End:", JLabel.RIGHT));
 295       panel.add(end);
 296       bigPanel.add(panel, BorderLayout.CENTER);
 297     }
 298     else
 299     {
 300       bigPanel.add(panel, BorderLayout.CENTER);
 301     }
 302
 303     if (lastFeatureAdded == null)
 304     {
 305       if (features[0].type != null)
 306       {
 307         lastFeatureAdded = features[0].type;
 308       }
 309       else
 310       {
 311         lastFeatureAdded = "feature_1";
 312       }
 313     }
 314
 315     if (lastFeatureGroupAdded == null)
 316     {
 317       if (features[0].featureGroup != null)
 318       {
 319         lastFeatureGroupAdded = features[0].featureGroup;
 320       }
 321       else
 322       {
 323         lastFeatureAdded = "Jalview";
 324       }
 325     }
 326
 327     String title = newFeatures ? MessageManager
 328             .getString("label.create_new_sequence_features")
 329             : MessageManager.formatMessage("label.amend_delete_features",
 330                     new String[]
 331                     { 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         public void actionPerformed(ActionEvent evt)
 350         {
 351           deleteFeature = true;
 352           dialog.setVisible(false);
 353         }
 354       });
 355       name.setText(features[0].getType());
 356       source.setText(features[0].getFeatureGroup());
 357     }
 358
 359     start.setText(features[0].getBegin() + "");
 360     end.setText(features[0].getEnd() + "");
 361     description.setText(features[0].getDescription());
 362     Color col = getColour(name.getText());
 363     if (col == null)
 364     {
 365       col = new UserColourScheme()
 366               .createColourFromName(name.getText());
 367     }
 368     Object fcol = getFeatureStyle(name.getText());
 369     // simply display the feature color in a box
 370     colourPanel.updateColor(fcol);
 371     dialog.setResizable(true);
 372     // TODO: render the graduated color in the box.
 373     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 374     {
 375       public void mousePressed(java.awt.event.MouseEvent evt)
 376       {
 377         if (!colourPanel.isGcol)
 378         {
 379           new UserDefinedColours(fr, ap.alignFrame);
 380         }
 381         else
 382         {
 383           FeatureColourChooser fcc = new FeatureColourChooser(
 384                   ap.alignFrame, name.getText());
 385           dialog.transferFocus();
 386         }
 387       }
 388     });
 389     dialog.setVisible(true);
 390
 391     FeaturesFile ffile = new FeaturesFile();
 392
 393     if (dialog.accept)
 394     {
 395       // This ensures that the last sequence
 396       // is refreshed and new features are rendered
 397       lastSeq = null;
 398       lastFeatureAdded = name.getText().trim();
 399       lastFeatureGroupAdded = source.getText().trim();
 400       lastDescriptionAdded = description.getText().replace('\n', ' ');
 401     }
 402
 403     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 404     {
 405       lastFeatureGroupAdded = null;
 406     }
 407
 408     if (!newFeatures)
 409     {
 410
 411       SequenceFeature sf = features[featureIndex];
 412       if (dialog.accept)
 413       {
 414         sf.type = lastFeatureAdded;
 415         sf.featureGroup = lastFeatureGroupAdded;
 416         sf.description = lastDescriptionAdded;
 417         if (!colourPanel.isGcol)
 418         {
 419           // update colour - otherwise its already done.
 420           setColour(sf.type, colourPanel.getBackground());
 421         }
 422         try
 423         {
 424           sf.begin = Integer.parseInt(start.getText());
 425           sf.end = Integer.parseInt(end.getText());
 426         } catch (NumberFormatException ex)
 427         {
 428         }
 429
 430         ffile.parseDescriptionHTML(sf, false);
 431         setVisible(lastFeatureAdded); // if user edited name then make sure new
 432                                       // type is visible
 433       }
 434       if (deleteFeature)
 435       {
 436         sequences[0].deleteFeature(sf);
 437       }
 438
 439     }
 440     else
 441     {
 442       if (dialog.accept && name.getText().length() > 0)
 443       {
 444         for (int i = 0; i < sequences.length; i++)
 445         {
 446           features[i].type = lastFeatureAdded;
 447           features[i].featureGroup = lastFeatureGroupAdded;
 448           features[i].description = lastDescriptionAdded;
 449           sequences[i].addSequenceFeature(features[i]);
 450           ffile.parseDescriptionHTML(features[i], false);
 451         }
 452
 453         Color newColour = colourPanel.getBackground();
 454         // setColour(lastFeatureAdded, fcol);
 455
 456         if (lastFeatureGroupAdded != null)
 457         {
 458           setGroupVisibility(lastFeatureGroupAdded, true);
 459         }
 460         setColour(lastFeatureAdded, newColour); // was fcol
 461         setVisible(lastFeatureAdded);
 462         findAllFeatures(false); // different to original applet behaviour ?
 463         // findAllFeatures();
 464       }
 465       else
 466       {
 467         // no update to the alignment
 468         return false;
 469       }
 470     }
 471     // refresh the alignment and the feature settings dialog
 472     if (((AlignViewport) av).featureSettings != null)
 473     {
 474       ((AlignViewport) av).featureSettings.refreshTable();
 475     }
 476     // findAllFeatures();
 477
 478     ap.paintAlignment(true);
 479
 480     return true;
 481   }
 482 }