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.api.FeatureColourI;
  24 import jalview.datamodel.SearchResults;
  25 import jalview.datamodel.SearchResultsI;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.io.FeaturesFile;
  29 import jalview.schemes.FeatureColour;
  30 import jalview.util.ColorUtils;
  31 import jalview.util.MessageManager;
  32 import jalview.viewmodel.AlignmentViewport;
  33
  34 import java.awt.BorderLayout;
  35 import java.awt.Button;
  36 import java.awt.Choice;
  37 import java.awt.Color;
  38 import java.awt.Dimension;
  39 import java.awt.FlowLayout;
  40 import java.awt.Font;
  41 import java.awt.Frame;
  42 import java.awt.Graphics;
  43 import java.awt.GridLayout;
  44 import java.awt.Label;
  45 import java.awt.Panel;
  46 import java.awt.ScrollPane;
  47 import java.awt.TextArea;
  48 import java.awt.TextField;
  49 import java.awt.event.ActionEvent;
  50 import java.awt.event.ActionListener;
  51 import java.awt.event.MouseAdapter;
  52 import java.awt.event.MouseEvent;
  53 import java.awt.event.TextEvent;
  54 import java.awt.event.TextListener;
  55 import java.util.Hashtable;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class FeatureRenderer extends
  64         jalview.renderer.seqfeatures.FeatureRenderer
  65 {
  66   /*
  67    * creating a new feature defaults to the type and group as
  68    * the last one created
  69    */
  70   static String lastFeatureAdded = "feature_1";
  71
  72   static String lastFeatureGroupAdded = "Jalview";
  73
  74   // Holds web links for feature groups and feature types
  75   // in the form label|link
  76   Hashtable featureLinks = null;
  77
  78   /**
  79    * Creates a new FeatureRenderer object.
  80    *
  81    * @param av
  82    */
  83   public FeatureRenderer(AlignmentViewport av)
  84   {
  85     super(av);
  86
  87   }
  88
  89   int featureIndex = 0;
  90
  91   boolean deleteFeature = false;
  92
  93   FeatureColourPanel colourPanel;
  94
  95   class FeatureColourPanel extends Panel
  96   {
  97     String label = "";
  98
  99     private Color maxCol;
 100
 101     private boolean isColourByLabel, isGcol;
 102
 103     /**
 104      * render a feature style in the amend feature dialog box
 105      */
 106     public void updateColor(FeatureColourI newcol)
 107     {
 108       Color bg = null;
 109       String vlabel = "";
 110       if (newcol.isSimpleColour())
 111       {
 112         bg = newcol.getColour();
 113         setBackground(bg);
 114       }
 115       else
 116       {
 117         if (newcol.isAboveThreshold())
 118         {
 119           vlabel += " (>)";
 120         }
 121         else if (newcol.isBelowThreshold())
 122         {
 123           vlabel += " (<)";
 124         }
 125
 126         if (isColourByLabel = newcol.isColourByLabel())
 127         {
 128           setBackground(bg = Color.white);
 129           vlabel += " (by Label)";
 130         }
 131         else
 132         {
 133           setBackground(bg = newcol.getMinColour());
 134           maxCol = newcol.getMaxColour();
 135         }
 136       }
 137       label = vlabel;
 138       setBackground(bg);
 139       repaint();
 140     }
 141
 142     FeatureColourPanel()
 143     {
 144       super(null);
 145     }
 146
 147     @Override
 148     public void paint(Graphics g)
 149     {
 150       Dimension d = getSize();
 151       if (isGcol)
 152       {
 153         if (isColourByLabel)
 154         {
 155           g.setColor(Color.white);
 156           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 157           g.setColor(Color.black);
 158           Font f = new Font("Verdana", Font.PLAIN, 10);
 159           g.setFont(f);
 160           g.drawString(MessageManager.getString("label.label"), 0, 0);
 161         }
 162         else
 163         {
 164           g.setColor(maxCol);
 165           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 166
 167         }
 168       }
 169     }
 170
 171   }
 172
 173   /**
 174    * Shows a dialog allowing the user to create, or amend or delete, sequence
 175    * features. If null in the supplied feature(s), feature type and group
 176    * default to those for the last feature created (with initial defaults of
 177    * "feature_1" and "Jalview").
 178    *
 179    * @param sequences
 180    * @param features
 181    * @param create
 182    * @param ap
 183    * @return
 184    */
 185   boolean amendFeatures(final SequenceI[] sequences,
 186           final SequenceFeature[] features, boolean create,
 187           final AlignmentPanel ap)
 188   {
 189     final Panel bigPanel = new Panel(new BorderLayout());
 190     final TextField name = new TextField(16);
 191     final TextField group = new TextField(16);
 192     final TextArea description = new TextArea(3, 35);
 193     final TextField start = new TextField(8);
 194     final TextField end = new TextField(8);
 195     final Choice overlaps;
 196     Button deleteButton = new Button("Delete");
 197     deleteFeature = false;
 198
 199     name.addTextListener(new TextListener()
 200     {
 201       @Override
 202       public void textValueChanged(TextEvent e)
 203       {
 204         warnIfTypeHidden(ap.alignFrame, name.getText());
 205       }
 206     });
 207     group.addTextListener(new TextListener()
 208     {
 209       @Override
 210       public void textValueChanged(TextEvent e)
 211       {
 212         warnIfGroupHidden(ap.alignFrame, group.getText());
 213       }
 214     });
 215     colourPanel = new FeatureColourPanel();
 216     colourPanel.setSize(110, 15);
 217     final FeatureRenderer fr = this;
 218
 219     Panel panel = new Panel(new GridLayout(3, 1));
 220
 221     featureIndex = 0; // feature to be amended.
 222     Panel tmp;
 223
 224     // /////////////////////////////////////
 225     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 226     if (!create && features.length > 1)
 227     {
 228       panel = new Panel(new GridLayout(4, 1));
 229       tmp = new Panel();
 230       tmp.add(new Label("Select Feature: "));
 231       overlaps = new Choice();
 232       for (int i = 0; i < features.length; i++)
 233       {
 234         String item = features[i].getType() + "/" + features[i].getBegin()
 235                 + "-" + features[i].getEnd();
 236
 237         if (features[i].getFeatureGroup() != null)
 238         {
 239           item += " (" + features[i].getFeatureGroup() + ")";
 240         }
 241
 242         overlaps.addItem(item);
 243       }
 244
 245       tmp.add(overlaps);
 246
 247       overlaps.addItemListener(new java.awt.event.ItemListener()
 248       {
 249         @Override
 250         public void itemStateChanged(java.awt.event.ItemEvent e)
 251         {
 252           int index = overlaps.getSelectedIndex();
 253           if (index != -1)
 254           {
 255             featureIndex = index;
 256             name.setText(features[index].getType());
 257             description.setText(features[index].getDescription());
 258             group.setText(features[index].getFeatureGroup());
 259             start.setText(features[index].getBegin() + "");
 260             end.setText(features[index].getEnd() + "");
 261
 262             SearchResultsI highlight = new SearchResults();
 263             highlight.addResult(sequences[0], features[index].getBegin(),
 264                     features[index].getEnd());
 265
 266             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 267
 268           }
 269           FeatureColourI col = getFeatureStyle(name.getText());
 270           if (col == null)
 271           {
 272             Color generatedColour = ColorUtils
 273                     .createColourFromName(name.getText());
 274             col = new FeatureColour(generatedColour);
 275           }
 276
 277           colourPanel.updateColor(col);
 278         }
 279       });
 280
 281       panel.add(tmp);
 282     }
 283     // ////////
 284     // ////////////////////////////////////
 285
 286     tmp = new Panel();
 287     panel.add(tmp);
 288     tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT));
 289     tmp.add(name);
 290
 291     tmp = new Panel();
 292     panel.add(tmp);
 293     tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT));
 294     tmp.add(group);
 295
 296     tmp = new Panel();
 297     panel.add(tmp);
 298     tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT));
 299     tmp.add(colourPanel);
 300
 301     bigPanel.add(panel, BorderLayout.NORTH);
 302
 303     panel = new Panel();
 304     panel.add(new Label(MessageManager.getString("label.description:"),
 305             Label.RIGHT));
 306     panel.add(new ScrollPane().add(description));
 307
 308     if (!create)
 309     {
 310       bigPanel.add(panel, BorderLayout.SOUTH);
 311
 312       panel = new Panel();
 313       panel.add(new Label(MessageManager.getString("label.start"),
 314               Label.RIGHT));
 315       panel.add(start);
 316       panel.add(new Label(MessageManager.getString("label.end"),
 317               Label.RIGHT));
 318       panel.add(end);
 319       bigPanel.add(panel, BorderLayout.CENTER);
 320     }
 321     else
 322     {
 323       bigPanel.add(panel, BorderLayout.CENTER);
 324     }
 325
 326     /*
 327      * use defaults for type and group (and update them on Confirm) only
 328      * if feature type has not been supplied by the caller
 329      * (e.g. for Amend, or create features from Find)
 330      */
 331     boolean useLastDefaults = features[0].getType() == null;
 332     String featureType = useLastDefaults ? lastFeatureAdded : features[0]
 333             .getType();
 334     String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 335             : features[0].getFeatureGroup();
 336
 337     String title = create ? MessageManager
 338             .getString("label.create_new_sequence_features")
 339             : MessageManager.formatMessage("label.amend_delete_features",
 340                     new String[] { sequences[0].getName() });
 341
 342     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 343             240);
 344
 345     dialog.setMainPanel(bigPanel);
 346
 347     name.setText(featureType);
 348     group.setText(featureGroup);
 349
 350     if (!create)
 351     {
 352       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 353       dialog.buttonPanel.add(deleteButton, 1);
 354       deleteButton.addActionListener(new ActionListener()
 355       {
 356         @Override
 357         public void actionPerformed(ActionEvent evt)
 358         {
 359           deleteFeature = true;
 360           dialog.setVisible(false);
 361         }
 362       });
 363     }
 364
 365     start.setText(features[0].getBegin() + "");
 366     end.setText(features[0].getEnd() + "");
 367     description.setText(features[0].getDescription());
 368     // lookup (or generate) the feature colour
 369     FeatureColourI 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 MouseAdapter()
 375     {
 376       @Override
 377       public void mousePressed(MouseEvent evt)
 378       {
 379         if (!colourPanel.isGcol)
 380         {
 381           new UserDefinedColours(fr, ap.alignFrame);
 382         }
 383         else
 384         {
 385           new FeatureColourChooser(ap.alignFrame, name.getText());
 386           dialog.transferFocus();
 387         }
 388       }
 389     });
 390     dialog.setVisible(true);
 391
 392     FeaturesFile ffile = new FeaturesFile();
 393
 394     /*
 395      * only update default type and group if we used defaults
 396      */
 397     final String enteredType = name.getText().trim();
 398     final String enteredGroup = group.getText().trim();
 399     final String enteredDesc = description.getText().replace('\n', ' ');
 400
 401     if (dialog.accept && useLastDefaults)
 402     {
 403       lastFeatureAdded = enteredType;
 404       lastFeatureGroupAdded = enteredGroup;
 405     }
 406
 407     if (!create)
 408     {
 409       SequenceFeature sf = features[featureIndex];
 410       if (dialog.accept)
 411       {
 412         if (!colourPanel.isGcol)
 413         {
 414           // update colour - otherwise its already done.
 415           setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
 416         }
 417         int newBegin = sf.begin;
 418         int newEnd = sf.end;
 419         try
 420         {
 421           newBegin = Integer.parseInt(start.getText());
 422           newEnd = Integer.parseInt(end.getText());
 423         } catch (NumberFormatException ex)
 424         {
 425           //
 426         }
 427
 428         /*
 429          * replace the feature by deleting it and adding a new one
 430          * (to ensure integrity of SequenceFeatures data store)
 431          */
 432         sequences[0].deleteFeature(sf);
 433         SequenceFeature newSf = new SequenceFeature(sf, newBegin, newEnd,
 434                 enteredGroup, sf.getScore());
 435         newSf.setDescription(enteredDesc);
 436         ffile.parseDescriptionHTML(newSf, false);
 437         // amend features dialog only updates one sequence at a time
 438         sequences[0].addSequenceFeature(newSf);
 439         boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
 440                 .equals(sf.featureGroup));
 441
 442         ffile.parseDescriptionHTML(sf, false);
 443         if (typeOrGroupChanged)
 444         {
 445           featuresAdded();
 446         }
 447       }
 448       if (deleteFeature)
 449       {
 450         sequences[0].deleteFeature(sf);
 451         // ensure Feature Settings reflects removal of feature / group
 452         featuresAdded();
 453       }
 454     }
 455     else
 456     {
 457       /*
 458        * adding feature(s)
 459        */
 460       if (dialog.accept && name.getText().length() > 0)
 461       {
 462         for (int i = 0; i < sequences.length; i++)
 463         {
 464           SequenceFeature sf = features[i];
 465           SequenceFeature sf2 = new SequenceFeature(enteredType,
 466                   enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
 467           ffile.parseDescriptionHTML(sf2, false);
 468           sequences[i].addSequenceFeature(sf2);
 469         }
 470
 471         Color newColour = colourPanel.getBackground();
 472         // setColour(lastFeatureAdded, fcol);
 473
 474         setColour(enteredType, new FeatureColour(newColour)); // was fcol
 475         featuresAdded();
 476       }
 477       else
 478       {
 479         // no update to the alignment
 480         return false;
 481       }
 482     }
 483     // refresh the alignment and the feature settings dialog
 484     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 485     {
 486       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 487     }
 488     // findAllFeatures();
 489
 490     ap.paintAlignment(true);
 491
 492     return true;
 493   }
 494
 495   protected void warnIfGroupHidden(Frame frame, String group)
 496   {
 497     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 498     {
 499       String msg = MessageManager.formatMessage("label.warning_hidden",
 500               MessageManager.getString("label.group"), group);
 501       showWarning(frame, msg);
 502     }
 503   }
 504
 505   protected void warnIfTypeHidden(Frame frame, String type)
 506   {
 507     if (getRenderOrder().contains(type))
 508     {
 509       if (!showFeatureOfType(type))
 510       {
 511         String msg = MessageManager.formatMessage("label.warning_hidden",
 512                 MessageManager.getString("label.feature_type"), type);
 513         showWarning(frame, msg);
 514       }
 515     }
 516   }
 517
 518   /**
 519    * @param frame
 520    * @param msg
 521    */
 522   protected void showWarning(Frame frame, String msg)
 523   {
 524     JVDialog d = new JVDialog(frame, "", true, 350, 200);
 525     Panel mp = new Panel();
 526     d.ok.setLabel(MessageManager.getString("action.ok"));
 527     d.cancel.setVisible(false);
 528     mp.setLayout(new FlowLayout());
 529     mp.add(new Label(msg));
 530     d.setMainPanel(mp);
 531     d.setVisible(true);
 532   }
 533 }