src/jalview/appletgui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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.seqfeatures.FeaturesDisplayed;
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRenderer
  40 {
  41
  42   // Holds web links for feature groups and feature types
  43   // in the form label|link
  44   Hashtable featureLinks = null;
  45
  46   /**
  47    * Creates a new FeatureRenderer object.
  48    *
  49    * @param av
  50    *          DOCUMENT ME!
  51    */
  52   public FeatureRenderer(AlignViewport av)
  53   {
  54     super();
  55     this.av = av;
  56
  57     setTransparencyAvailable(!System.getProperty("java.version").startsWith("1.1"));
  58   }
  59
  60   static String lastFeatureAdded;
  61
  62   static String lastFeatureGroupAdded;
  63
  64   static String lastDescriptionAdded;
  65
  66   int featureIndex = 0;
  67
  68   boolean deleteFeature = false;
  69
  70   FeatureColourPanel colourPanel;
  71
  72   class FeatureColourPanel extends Panel
  73   {
  74     String label = "";
  75
  76     private Color maxCol;
  77
  78     private boolean isColourByLabel, isGcol;
  79
  80     /**
  81      * render a feature style in the amend feature dialog box
  82      */
  83     public void updateColor(Object newcol)
  84     {
  85
  86       Color bg, col = null;
  87       GraduatedColor gcol = null;
  88       String vlabel = "";
  89       if (newcol instanceof Color)
  90       {
  91         isGcol = false;
  92         col = (Color) newcol;
  93         gcol = null;
  94       }
  95       else if (newcol instanceof GraduatedColor)
  96       {
  97         isGcol = true;
  98         gcol = (GraduatedColor) newcol;
  99         col = null;
 100       }
 101       else
 102       {
 103         throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
 104       }
 105       if (col != null)
 106       {
 107         setBackground(bg = col);
 108       }
 109       else
 110       {
 111         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 112         {
 113           vlabel += " "
 114                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 115                           : "(<)");
 116         }
 117         if (isColourByLabel = gcol.isColourByLabel())
 118         {
 119           setBackground(bg = Color.white);
 120           vlabel += " (by Label)";
 121         }
 122         else
 123         {
 124           setBackground(bg = gcol.getMinColor());
 125           maxCol = gcol.getMaxColor();
 126         }
 127       }
 128       label = vlabel;
 129       setBackground(bg);
 130       repaint();
 131     }
 132
 133     FeatureColourPanel()
 134     {
 135       super(null);
 136     }
 137
 138     public void paint(Graphics g)
 139     {
 140       Dimension d = getSize();
 141       if (isGcol)
 142       {
 143         if (isColourByLabel)
 144         {
 145           g.setColor(Color.white);
 146           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 147           g.setColor(Color.black);
 148           Font f = new Font("Verdana", Font.PLAIN, 10);
 149           g.setFont(f);
 150           g.drawString(MessageManager.getString("label.label"), 0, 0);
 151         }
 152         else
 153         {
 154           g.setColor(maxCol);
 155           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 156
 157         }
 158       }
 159     }
 160
 161   }
 162
 163   boolean amendFeatures(final SequenceI[] sequences,
 164           final SequenceFeature[] features, boolean newFeatures,
 165           final AlignmentPanel ap)
 166   {
 167     Panel bigPanel = new Panel(new BorderLayout());
 168     final TextField name = new TextField(16);
 169     final TextField source = new TextField(16);
 170     final TextArea description = new TextArea(3, 35);
 171     final TextField start = new TextField(8);
 172     final TextField end = new TextField(8);
 173     final Choice overlaps;
 174     Button deleteButton = new Button("Delete");
 175     deleteFeature = false;
 176
 177     colourPanel = new FeatureColourPanel();
 178     colourPanel.setSize(110, 15);
 179     final FeatureRenderer fr = this;
 180
 181     Panel panel = new Panel(new GridLayout(3, 1));
 182
 183     featureIndex = 0; // feature to be amended.
 184     Panel tmp;
 185
 186     // /////////////////////////////////////
 187     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 188     if (!newFeatures && features.length > 1)
 189     {
 190       panel = new Panel(new GridLayout(4, 1));
 191       tmp = new Panel();
 192       tmp.add(new Label("Select Feature: "));
 193       overlaps = new Choice();
 194       for (int i = 0; i < features.length; i++)
 195       {
 196         String item = features[i].getType() + "/" + features[i].getBegin()
 197                 + "-" + features[i].getEnd();
 198
 199         if (features[i].getFeatureGroup() != null)
 200           item += " (" + features[i].getFeatureGroup() + ")";
 201
 202         overlaps.addItem(item);
 203       }
 204
 205       tmp.add(overlaps);
 206
 207       overlaps.addItemListener(new java.awt.event.ItemListener()
 208       {
 209         public void itemStateChanged(java.awt.event.ItemEvent e)
 210         {
 211           int index = overlaps.getSelectedIndex();
 212           if (index != -1)
 213           {
 214             featureIndex = index;
 215             name.setText(features[index].getType());
 216             description.setText(features[index].getDescription());
 217             source.setText(features[index].getFeatureGroup());
 218             start.setText(features[index].getBegin() + "");
 219             end.setText(features[index].getEnd() + "");
 220
 221             SearchResults highlight = new SearchResults();
 222             highlight.addResult(sequences[0], features[index].getBegin(),
 223                     features[index].getEnd());
 224
 225             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 226
 227           }
 228           Object col = getFeatureStyle(name.getText());
 229           if (col == null)
 230           {
 231             col = new jalview.schemes.UserColourScheme()
 232                     .createColourFromName(name.getText());
 233           }
 234
 235           colourPanel.updateColor(col);
 236         }
 237       });
 238
 239       panel.add(tmp);
 240     }
 241     // ////////
 242     // ////////////////////////////////////
 243
 244     tmp = new Panel();
 245     panel.add(tmp);
 246     tmp.add(new Label("Name: ", Label.RIGHT));
 247     tmp.add(name);
 248
 249     tmp = new Panel();
 250     panel.add(tmp);
 251     tmp.add(new Label("Group: ", Label.RIGHT));
 252     tmp.add(source);
 253
 254     tmp = new Panel();
 255     panel.add(tmp);
 256     tmp.add(new Label("Colour: ", Label.RIGHT));
 257     tmp.add(colourPanel);
 258
 259     bigPanel.add(panel, BorderLayout.NORTH);
 260
 261     panel = new Panel();
 262     panel.add(new Label("Description: ", Label.RIGHT));
 263     panel.add(new ScrollPane().add(description));
 264
 265     if (!newFeatures)
 266     {
 267       bigPanel.add(panel, BorderLayout.SOUTH);
 268
 269       panel = new Panel();
 270       panel.add(new Label(" Start:", Label.RIGHT));
 271       panel.add(start);
 272       panel.add(new Label("  End:", Label.RIGHT));
 273       panel.add(end);
 274       bigPanel.add(panel, BorderLayout.CENTER);
 275     }
 276     else
 277     {
 278       bigPanel.add(panel, BorderLayout.CENTER);
 279     }
 280
 281     if (lastFeatureAdded == null)
 282     {
 283       if (features[0].type != null)
 284       {
 285         lastFeatureAdded = features[0].type;
 286       }
 287       else
 288       {
 289         lastFeatureAdded = "feature_1";
 290       }
 291     }
 292
 293     if (lastFeatureGroupAdded == null)
 294     {
 295       if (features[0].featureGroup != null)
 296       {
 297         lastFeatureGroupAdded = features[0].featureGroup;
 298       }
 299       else
 300       {
 301         lastFeatureAdded = "Jalview";
 302       }
 303     }
 304
 305     String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
 306             : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 307
 308     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 309             240);
 310
 311     dialog.setMainPanel(bigPanel);
 312
 313     if (newFeatures)
 314     {
 315       name.setText(lastFeatureAdded);
 316       source.setText(lastFeatureGroupAdded);
 317     }
 318     else
 319     {
 320       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 321       dialog.buttonPanel.add(deleteButton, 1);
 322       deleteButton.addActionListener(new ActionListener()
 323       {
 324         public void actionPerformed(ActionEvent evt)
 325         {
 326           deleteFeature = true;
 327           dialog.setVisible(false);
 328         }
 329       });
 330       name.setText(features[0].getType());
 331       source.setText(features[0].getFeatureGroup());
 332     }
 333
 334     start.setText(features[0].getBegin() + "");
 335     end.setText(features[0].getEnd() + "");
 336     description.setText(features[0].getDescription());
 337     Color col = getColour(name.getText());
 338     if (col == null)
 339     {
 340       col = new jalview.schemes.UserColourScheme()
 341               .createColourFromName(name.getText());
 342     }
 343     Object fcol = getFeatureStyle(name.getText());
 344     // simply display the feature color in a box
 345     colourPanel.updateColor(fcol);
 346     dialog.setResizable(true);
 347     // TODO: render the graduated color in the box.
 348     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 349     {
 350       public void mousePressed(java.awt.event.MouseEvent evt)
 351       {
 352         if (!colourPanel.isGcol)
 353         {
 354           new UserDefinedColours(fr, ap.alignFrame);
 355         }
 356         else
 357         {
 358           FeatureColourChooser fcc = new FeatureColourChooser(
 359                   ap.alignFrame, name.getText());
 360           dialog.transferFocus();
 361         }
 362       }
 363     });
 364     dialog.setVisible(true);
 365
 366     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 367
 368     if (dialog.accept)
 369     {
 370       // This ensures that the last sequence
 371       // is refreshed and new features are rendered
 372       lastSeq = null;
 373       lastFeatureAdded = name.getText().trim();
 374       lastFeatureGroupAdded = source.getText().trim();
 375       lastDescriptionAdded = description.getText().replace('\n', ' ');
 376     }
 377
 378     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 379       lastFeatureGroupAdded = null;
 380
 381     if (!newFeatures)
 382     {
 383
 384       SequenceFeature sf = features[featureIndex];
 385       if (dialog.accept)
 386       {
 387         sf.type = lastFeatureAdded;
 388         sf.featureGroup = lastFeatureGroupAdded;
 389         sf.description = lastDescriptionAdded;
 390         if (!colourPanel.isGcol)
 391         {
 392           // update colour - otherwise its already done.
 393           setColour(sf.type, colourPanel.getBackground());
 394         }
 395         try
 396         {
 397           sf.begin = Integer.parseInt(start.getText());
 398           sf.end = Integer.parseInt(end.getText());
 399         } catch (NumberFormatException ex)
 400         {
 401         }
 402
 403         ffile.parseDescriptionHTML(sf, false);
 404         setVisible(lastFeatureAdded); // if user edited name then make sure new type is visible
 405       }
 406       if (deleteFeature)
 407       {
 408         sequences[0].deleteFeature(sf);
 409       }
 410
 411     }
 412     else
 413     {
 414       if (dialog.accept && name.getText().length() > 0)
 415       {
 416         for (int i = 0; i < sequences.length; i++)
 417         {
 418           features[i].type = lastFeatureAdded;
 419           features[i].featureGroup = lastFeatureGroupAdded;
 420           features[i].description = lastDescriptionAdded;
 421           sequences[i].addSequenceFeature(features[i]);
 422           ffile.parseDescriptionHTML(features[i], false);
 423         }
 424
 425         col = colourPanel.getBackground();
 426         // setColour(lastFeatureAdded, fcol);
 427
 428         if (lastFeatureGroupAdded != null)
 429         {
 430           setGroupVisibility(lastFeatureGroupAdded, true);
 431         }
 432         setColour(lastFeatureAdded, fcol);
 433         setVisible(lastFeatureAdded);
 434         findAllFeatures(false); // different to original applet behaviour ?
 435         // findAllFeatures();
 436       }
 437       else
 438       {
 439         // no update to the alignment
 440         return false;
 441       }
 442     }
 443     // refresh the alignment and the feature settings dialog
 444     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 445     {
 446       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 447     }
 448     // findAllFeatures();
 449
 450     ap.paintAlignment(true);
 451
 452     return true;
 453   }
 454 }