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