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.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 awt2swing.Button;
  35 import awt2swing.Choice;
  36 import java.awt.Color;
  37 import java.awt.Dimension;
  38 import java.awt.Font;
  39 import java.awt.Graphics;
  40 import java.awt.GridLayout;
  41 import awt2swing.Label;
  42 import awt2swing.Panel;
  43 import awt2swing.ScrollPane;
  44 import awt2swing.TextArea;
  45 import awt2swing.TextField;
  46 import java.awt.event.ActionEvent;
  47 import java.awt.event.ActionListener;
  48 import java.util.Hashtable;
  49
  50 /**
  51  * DOCUMENT ME!
  52  *
  53  * @author $author$
  54  * @version $Revision$
  55  */
  56 public class FeatureRenderer extends
  57         jalview.renderer.seqfeatures.FeatureRenderer
  58 {
  59
  60   // Holds web links for feature groups and feature types
  61   // in the form label|link
  62   Hashtable featureLinks = null;
  63
  64   /**
  65    * Creates a new FeatureRenderer object.
  66    *
  67    * @param av
  68    *          DOCUMENT ME!
  69    */
  70   public FeatureRenderer(AlignmentViewport av)
  71   {
  72     super();
  73     this.av = av;
  74
  75     setTransparencyAvailable(!System.getProperty("java.version")
  76             .startsWith("1.1"));
  77   }
  78
  79   static String lastFeatureAdded;
  80
  81   static String lastFeatureGroupAdded;
  82
  83   static String lastDescriptionAdded;
  84
  85   int featureIndex = 0;
  86
  87   boolean deleteFeature = false;
  88
  89   FeatureColourPanel colourPanel;
  90
  91   class FeatureColourPanel extends Panel
  92   {
  93     String label = "";
  94
  95     private Color maxCol;
  96
  97     private boolean isColourByLabel, isGcol;
  98
  99     /**
 100      * render a feature style in the amend feature dialog box
 101      */
 102     public void updateColor(Object newcol)
 103     {
 104
 105       Color bg, col = null;
 106       GraduatedColor gcol = null;
 107       String vlabel = "";
 108       if (newcol instanceof Color)
 109       {
 110         isGcol = false;
 111         col = (Color) newcol;
 112         gcol = null;
 113       }
 114       else if (newcol instanceof GraduatedColor)
 115       {
 116         isGcol = true;
 117         gcol = (GraduatedColor) newcol;
 118         col = null;
 119       }
 120       else
 121       {
 122         throw new Error(
 123                 MessageManager
 124                         .getString("error.invalid_colour_for_mycheckbox"));
 125       }
 126       if (col != null)
 127       {
 128         setBackground(bg = col);
 129       }
 130       else
 131       {
 132         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 133         {
 134           vlabel += " "
 135                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 136                           : "(<)");
 137         }
 138         if (isColourByLabel = gcol.isColourByLabel())
 139         {
 140           setBackground(bg = Color.white);
 141           vlabel += " (by Label)";
 142         }
 143         else
 144         {
 145           setBackground(bg = gcol.getMinColor());
 146           maxCol = gcol.getMaxColor();
 147         }
 148       }
 149       label = vlabel;
 150       setBackground(bg);
 151       repaint();
 152     }
 153
 154     FeatureColourPanel()
 155     {
 156       super(null);
 157     }
 158
 159     public void PaintComponent(Graphics g)
 160     {
 161       Dimension d = getSize();
 162       if (isGcol)
 163       {
 164         if (isColourByLabel)
 165         {
 166           g.setColor(Color.white);
 167           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 168           g.setColor(Color.black);
 169           Font f = new Font("Verdana", Font.PLAIN, 10);
 170           g.setFont(f);
 171           awt2swing.Util.drawString(g, MessageManager.getString("label.label"), 0, 0);
 172         }
 173         else
 174         {
 175           g.setColor(maxCol);
 176           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 177
 178         }
 179       }
 180     }
 181
 182   }
 183
 184   boolean amendFeatures(final SequenceI[] sequences,
 185           final SequenceFeature[] features, boolean newFeatures,
 186           final AlignmentPanel ap)
 187   {
 188     Panel bigPanel = new Panel(new BorderLayout());
 189     final TextField name = new TextField(16);
 190     final TextField source = new TextField(16);
 191     final TextArea description = new TextArea(3, 35);
 192     final TextField start = new TextField(8);
 193     final TextField end = new TextField(8);
 194     final Choice overlaps;
 195     Button deleteButton = new Button("Delete");
 196     deleteFeature = false;
 197
 198     colourPanel = new FeatureColourPanel();
 199     colourPanel.setSize(110, 15);
 200     final FeatureRenderer fr = this;
 201
 202     Panel panel = new Panel(new GridLayout(3, 1));
 203
 204     featureIndex = 0; // feature to be amended.
 205     Panel tmp;
 206
 207     // /////////////////////////////////////
 208     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 209     if (!newFeatures && features.length > 1)
 210     {
 211       panel = new Panel(new GridLayout(4, 1));
 212       tmp = new Panel();
 213       tmp.add(new Label("Select Feature: "));
 214       overlaps = new Choice();
 215       for (int i = 0; i < features.length; i++)
 216       {
 217         String item = features[i].getType() + "/" + features[i].getBegin()
 218                 + "-" + features[i].getEnd();
 219
 220         if (features[i].getFeatureGroup() != null)
 221         {
 222           item += " (" + features[i].getFeatureGroup() + ")";
 223         }
 224
 225         overlaps.addItem(item);
 226       }
 227
 228       tmp.add(overlaps);
 229
 230       overlaps.addItemListener(new java.awt.event.ItemListener()
 231       {
 232         public void itemStateChanged(java.awt.event.ItemEvent e)
 233         {
 234           int index = overlaps.getSelectedIndex();
 235           if (index != -1)
 236           {
 237             featureIndex = index;
 238             name.setText(features[index].getType());
 239             description.setText(features[index].getDescription());
 240             source.setText(features[index].getFeatureGroup());
 241             start.setText(features[index].getBegin() + "");
 242             end.setText(features[index].getEnd() + "");
 243
 244             SearchResults highlight = new SearchResults();
 245             highlight.addResult(sequences[0], features[index].getBegin(),
 246                     features[index].getEnd());
 247
 248             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 249
 250           }
 251           Object col = getFeatureStyle(name.getText());
 252           if (col == null)
 253           {
 254             col = new UserColourScheme().createColourFromName(name
 255                     .getText());
 256           }
 257
 258           colourPanel.updateColor(col);
 259         }
 260       });
 261
 262       panel.add(tmp);
 263     }
 264     // ////////
 265     // ////////////////////////////////////
 266
 267     tmp = new Panel();
 268     panel.add(tmp);
 269     tmp.add(new Label("Name: ", Label.RIGHT));
 270     tmp.add(name);
 271
 272     tmp = new Panel();
 273     panel.add(tmp);
 274     tmp.add(new Label("Group: ", Label.RIGHT));
 275     tmp.add(source);
 276
 277     tmp = new Panel();
 278     panel.add(tmp);
 279     tmp.add(new Label("Colour: ", Label.RIGHT));
 280     tmp.add(colourPanel);
 281
 282     bigPanel.add(panel, BorderLayout.NORTH);
 283
 284     panel = new Panel();
 285     panel.add(new Label("Description: ", Label.RIGHT));
 286     panel.add(new ScrollPane().add(description));
 287
 288     if (!newFeatures)
 289     {
 290       bigPanel.add(panel, BorderLayout.SOUTH);
 291
 292       panel = new Panel();
 293       panel.add(new Label(" Start:", Label.RIGHT));
 294       panel.add(start);
 295       panel.add(new Label("  End:", Label.RIGHT));
 296       panel.add(end);
 297       bigPanel.add(panel, BorderLayout.CENTER);
 298     }
 299     else
 300     {
 301       bigPanel.add(panel, BorderLayout.CENTER);
 302     }
 303
 304     if (lastFeatureAdded == null)
 305     {
 306       if (features[0].type != null)
 307       {
 308         lastFeatureAdded = features[0].type;
 309       }
 310       else
 311       {
 312         lastFeatureAdded = "feature_1";
 313       }
 314     }
 315
 316     if (lastFeatureGroupAdded == null)
 317     {
 318       if (features[0].featureGroup != null)
 319       {
 320         lastFeatureGroupAdded = features[0].featureGroup;
 321       }
 322       else
 323       {
 324         lastFeatureAdded = "Jalview";
 325       }
 326     }
 327
 328     String title = newFeatures ? MessageManager
 329             .getString("label.create_new_sequence_features")
 330             : MessageManager.formatMessage("label.amend_delete_features",
 331                     new String[]
 332                     { sequences[0].getName() });
 333
 334     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 335             240);
 336
 337     dialog.setMainPanel(bigPanel);
 338
 339     if (newFeatures)
 340     {
 341       name.setText(lastFeatureAdded);
 342       source.setText(lastFeatureGroupAdded);
 343     }
 344     else
 345     {
 346       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 347       dialog.buttonPanel.add(deleteButton, 1);
 348       deleteButton.addActionListener(new ActionListener()
 349       {
 350         public void actionPerformed(ActionEvent evt)
 351         {
 352           deleteFeature = true;
 353           dialog.setVisible(false);
 354         }
 355       });
 356       name.setText(features[0].getType());
 357       source.setText(features[0].getFeatureGroup());
 358     }
 359
 360     start.setText(features[0].getBegin() + "");
 361     end.setText(features[0].getEnd() + "");
 362     description.setText(features[0].getDescription());
 363     Color col = getColour(name.getText());
 364     if (col == null)
 365     {
 366       col = new UserColourScheme()
 367               .createColourFromName(name.getText());
 368     }
 369     Object fcol = getFeatureStyle(name.getText());
 370     // simply display the feature color in a box
 371     colourPanel.updateColor(fcol);
 372     dialog.setResizable(true);
 373     // TODO: render the graduated color in the box.
 374     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 375     {
 376       public void mousePressed(java.awt.event.MouseEvent evt)
 377       {
 378         if (!colourPanel.isGcol)
 379         {
 380           new UserDefinedColours(fr, ap.alignFrame);
 381         }
 382         else
 383         {
 384           FeatureColourChooser fcc = new FeatureColourChooser(
 385                   ap.alignFrame, name.getText());
 386           dialog.transferFocus();
 387         }
 388       }
 389     });
 390     dialog.setVisible(true);
 391
 392     FeaturesFile ffile = new FeaturesFile();
 393
 394     if (dialog.accept)
 395     {
 396       // This ensures that the last sequence
 397       // is refreshed and new features are rendered
 398       lastSeq = null;
 399       lastFeatureAdded = name.getText().trim();
 400       lastFeatureGroupAdded = source.getText().trim();
 401       lastDescriptionAdded = description.getText().replace('\n', ' ');
 402     }
 403
 404     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 405     {
 406       lastFeatureGroupAdded = null;
 407     }
 408
 409     if (!newFeatures)
 410     {
 411
 412       SequenceFeature sf = features[featureIndex];
 413       if (dialog.accept)
 414       {
 415         sf.type = lastFeatureAdded;
 416         sf.featureGroup = lastFeatureGroupAdded;
 417         sf.description = lastDescriptionAdded;
 418         if (!colourPanel.isGcol)
 419         {
 420           // update colour - otherwise its already done.
 421           setColour(sf.type, colourPanel.getBackground());
 422         }
 423         try
 424         {
 425           sf.begin = Integer.parseInt(start.getText());
 426           sf.end = Integer.parseInt(end.getText());
 427         } catch (NumberFormatException ex)
 428         {
 429         }
 430
 431         ffile.parseDescriptionHTML(sf, false);
 432         setVisible(lastFeatureAdded); // if user edited name then make sure new
 433                                       // type is visible
 434       }
 435       if (deleteFeature)
 436       {
 437         sequences[0].deleteFeature(sf);
 438       }
 439
 440     }
 441     else
 442     {
 443       if (dialog.accept && name.getText().length() > 0)
 444       {
 445         for (int i = 0; i < sequences.length; i++)
 446         {
 447           features[i].type = lastFeatureAdded;
 448           features[i].featureGroup = lastFeatureGroupAdded;
 449           features[i].description = lastDescriptionAdded;
 450           sequences[i].addSequenceFeature(features[i]);
 451           ffile.parseDescriptionHTML(features[i], false);
 452         }
 453
 454         Color newColour = colourPanel.getBackground();
 455         // setColour(lastFeatureAdded, fcol);
 456
 457         if (lastFeatureGroupAdded != null)
 458         {
 459           setGroupVisibility(lastFeatureGroupAdded, true);
 460         }
 461         setColour(lastFeatureAdded, newColour); // was fcol
 462         setVisible(lastFeatureAdded);
 463         findAllFeatures(false); // different to original applet behaviour ?
 464         // findAllFeatures();
 465       }
 466       else
 467       {
 468         // no update to the alignment
 469         return false;
 470       }
 471     }
 472     // refresh the alignment and the feature settings dialog
 473     if (((AlignViewport) av).featureSettings != null)
 474     {
 475       ((AlignViewport) av).featureSettings.refreshTable();
 476     }
 477     // findAllFeatures();
 478
 479     ap.paintAlignment(true);
 480
 481     return true;
 482   }
 483 }