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 import java.util.List;
  57
  58 /**
  59  * DOCUMENT ME!
  60  *
  61  * @author $author$
  62  * @version $Revision$
  63  */
  64 public class FeatureRenderer extends
  65         jalview.renderer.seqfeatures.FeatureRenderer
  66 {
  67   /*
  68    * creating a new feature defaults to the type and group as
  69    * the last one created
  70    */
  71   static String lastFeatureAdded = "feature_1";
  72
  73   static String lastFeatureGroupAdded = "Jalview";
  74
  75   // Holds web links for feature groups and feature types
  76   // in the form label|link
  77   Hashtable featureLinks = null;
  78
  79   /**
  80    * Creates a new FeatureRenderer object.
  81    *
  82    * @param av
  83    */
  84   public FeatureRenderer(AlignmentViewport av)
  85   {
  86     super(av);
  87
  88   }
  89
  90   int featureIndex = 0;
  91
  92   boolean deleteFeature = false;
  93
  94   FeatureColourPanel colourPanel;
  95
  96   class FeatureColourPanel extends Panel
  97   {
  98     String label = "";
  99
 100     private Color maxCol;
 101
 102     private boolean isColourByLabel, isGcol;
 103
 104     /**
 105      * render a feature style in the amend feature dialog box
 106      */
 107     public void updateColor(FeatureColourI newcol)
 108     {
 109       Color bg = null;
 110       String vlabel = "";
 111       if (newcol.isSimpleColour())
 112       {
 113         bg = newcol.getColour();
 114         setBackground(bg);
 115       }
 116       else
 117       {
 118         if (newcol.isAboveThreshold())
 119         {
 120           vlabel += " (>)";
 121         }
 122         else if (newcol.isBelowThreshold())
 123         {
 124           vlabel += " (<)";
 125         }
 126
 127         if (isColourByLabel = newcol.isColourByLabel())
 128         {
 129           setBackground(bg = Color.white);
 130           vlabel += " (by Label)";
 131         }
 132         else
 133         {
 134           setBackground(bg = newcol.getMinColour());
 135           maxCol = newcol.getMaxColour();
 136         }
 137       }
 138       label = vlabel;
 139       setBackground(bg);
 140       repaint();
 141     }
 142
 143     FeatureColourPanel()
 144     {
 145       super(null);
 146     }
 147
 148     @Override
 149     public void paint(Graphics g)
 150     {
 151       Dimension d = getSize();
 152       if (isGcol)
 153       {
 154         if (isColourByLabel)
 155         {
 156           g.setColor(Color.white);
 157           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 158           g.setColor(Color.black);
 159           Font f = new Font("Verdana", Font.PLAIN, 10);
 160           g.setFont(f);
 161           g.drawString(MessageManager.getString("label.label"), 0, 0);
 162         }
 163         else
 164         {
 165           g.setColor(maxCol);
 166           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 167
 168         }
 169       }
 170     }
 171
 172   }
 173
 174   /**
 175    * Shows a dialog allowing the user to create, or amend or delete, sequence
 176    * features. If null in the supplied feature(s), feature type and group
 177    * default to those for the last feature created (with initial defaults of
 178    * "feature_1" and "Jalview").
 179    *
 180    * @param sequences
 181    * @param features
 182    * @param create
 183    * @param ap
 184    * @return
 185    */
 186   boolean amendFeatures(final List<SequenceI> sequences,
 187           final List<SequenceFeature> features, boolean create,
 188           final AlignmentPanel ap)
 189   {
 190     final Panel bigPanel = new Panel(new BorderLayout());
 191     final TextField name = new TextField(16);
 192     final TextField group = new TextField(16);
 193     final TextArea description = new TextArea(3, 35);
 194     final TextField start = new TextField(8);
 195     final TextField end = new TextField(8);
 196     final Choice overlaps;
 197     Button deleteButton = new Button("Delete");
 198     deleteFeature = false;
 199
 200     name.addTextListener(new TextListener()
 201     {
 202       @Override
 203       public void textValueChanged(TextEvent e)
 204       {
 205         warnIfTypeHidden(ap.alignFrame, name.getText());
 206       }
 207     });
 208     group.addTextListener(new TextListener()
 209     {
 210       @Override
 211       public void textValueChanged(TextEvent e)
 212       {
 213         warnIfGroupHidden(ap.alignFrame, group.getText());
 214       }
 215     });
 216     colourPanel = new FeatureColourPanel();
 217     colourPanel.setSize(110, 15);
 218     final FeatureRenderer fr = this;
 219
 220     Panel panel = new Panel(new GridLayout(3, 1));
 221
 222     featureIndex = 0; // feature to be amended.
 223     Panel tmp;
 224
 225     // /////////////////////////////////////
 226     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 227     if (!create && features.size() > 1)
 228     {
 229       panel = new Panel(new GridLayout(4, 1));
 230       tmp = new Panel();
 231       tmp.add(new Label("Select Feature: "));
 232       overlaps = new Choice();
 233       for (SequenceFeature sf : features)
 234       {
 235         String item = sf.getType() + "/" + sf.getBegin() + "-"
 236                 + sf.getEnd();
 237         if (sf.getFeatureGroup() != null)
 238         {
 239           item += " (" + sf.getFeatureGroup() + ")";
 240         }
 241         overlaps.addItem(item);
 242       }
 243
 244       tmp.add(overlaps);
 245
 246       overlaps.addItemListener(new java.awt.event.ItemListener()
 247       {
 248         @Override
 249         public void itemStateChanged(java.awt.event.ItemEvent e)
 250         {
 251           int index = overlaps.getSelectedIndex();
 252           if (index != -1)
 253           {
 254             featureIndex = index;
 255             SequenceFeature sf = features.get(index);
 256             name.setText(sf.getType());
 257             description.setText(sf.getDescription());
 258             group.setText(sf.getFeatureGroup());
 259             start.setText(sf.getBegin() + "");
 260             end.setText(sf.getEnd() + "");
 261
 262             SearchResultsI highlight = new SearchResults();
 263             highlight.addResult(sequences.get(0), sf.getBegin(),
 264                     sf.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.createColourFromName(name
 273                     .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     SequenceFeature firstFeature = features.get(0);
 332     boolean useLastDefaults = firstFeature.getType() == null;
 333     String featureType = useLastDefaults ? lastFeatureAdded : firstFeature
 334             .getType();
 335     String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 336             : firstFeature.getFeatureGroup();
 337
 338     String title = create ? MessageManager
 339             .getString("label.create_new_sequence_features")
 340             : MessageManager.formatMessage("label.amend_delete_features",
 341                     new String[] { sequences.get(0).getName() });
 342
 343     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 344             240);
 345
 346     dialog.setMainPanel(bigPanel);
 347
 348     name.setText(featureType);
 349     group.setText(featureGroup);
 350
 351     if (!create)
 352     {
 353       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 354       dialog.buttonPanel.add(deleteButton, 1);
 355       deleteButton.addActionListener(new ActionListener()
 356       {
 357         @Override
 358         public void actionPerformed(ActionEvent evt)
 359         {
 360           deleteFeature = true;
 361           dialog.setVisible(false);
 362         }
 363       });
 364     }
 365
 366     start.setText(firstFeature.getBegin() + "");
 367     end.setText(firstFeature.getEnd() + "");
 368     description.setText(firstFeature.getDescription());
 369     // lookup (or generate) the feature colour
 370     FeatureColourI fcol = getFeatureStyle(name.getText());
 371     // simply display the feature color in a box
 372     colourPanel.updateColor(fcol);
 373     dialog.setResizable(true);
 374     // TODO: render the graduated color in the box.
 375     colourPanel.addMouseListener(new MouseAdapter()
 376     {
 377       @Override
 378       public void mousePressed(MouseEvent evt)
 379       {
 380         if (!colourPanel.isGcol)
 381         {
 382           new UserDefinedColours(fr, ap.alignFrame);
 383         }
 384         else
 385         {
 386           new FeatureColourChooser(ap.alignFrame, name.getText());
 387           dialog.transferFocus();
 388         }
 389       }
 390     });
 391     dialog.setVisible(true);
 392
 393     FeaturesFile ffile = new FeaturesFile();
 394
 395     /*
 396      * only update default type and group if we used defaults
 397      */
 398     String enteredType = name.getText().trim();
 399     if (dialog.accept && useLastDefaults)
 400     {
 401       lastFeatureAdded = enteredType;
 402       lastFeatureGroupAdded = group.getText().trim();
 403     }
 404
 405     if (!create)
 406     {
 407       SequenceFeature sf = features.get(featureIndex);
 408       if (dialog.accept)
 409       {
 410         sf.type = enteredType;
 411         sf.featureGroup = group.getText().trim();
 412         if (sf.featureGroup != null && sf.featureGroup.length() < 1)
 413         {
 414           sf.featureGroup = null;
 415         }
 416         sf.description = description.getText().replace('\n', ' ');
 417         if (!colourPanel.isGcol)
 418         {
 419           // update colour - otherwise its already done.
 420           setColour(sf.type, new FeatureColour(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         boolean typeOrGroupChanged = (!featureType.equals(sf.type) || !featureGroup
 431                 .equals(sf.featureGroup));
 432
 433         ffile.parseDescriptionHTML(sf, false);
 434         if (typeOrGroupChanged)
 435         {
 436           featuresAdded();
 437         }
 438       }
 439       if (deleteFeature)
 440       {
 441         sequences.get(0).deleteFeature(sf);
 442         // ensure Feature Settings reflects removal of feature / group
 443         featuresAdded();
 444       }
 445     }
 446     else
 447     {
 448       /*
 449        * adding feature(s)
 450        */
 451       if (dialog.accept && name.getText().length() > 0)
 452       {
 453         for (int i = 0; i < sequences.size(); i++)
 454         {
 455           features.get(i).type = enteredType;
 456           features.get(i).featureGroup = group.getText().trim();
 457           features.get(i).description = description.getText()
 458                   .replace('\n', ' ');
 459           sequences.get(i).addSequenceFeature(features.get(i));
 460           ffile.parseDescriptionHTML(features.get(i), false);
 461         }
 462
 463         Color newColour = colourPanel.getBackground();
 464         // setColour(lastFeatureAdded, fcol);
 465
 466         setColour(enteredType, new FeatureColour(newColour)); // was fcol
 467         featuresAdded();
 468       }
 469       else
 470       {
 471         // no update to the alignment
 472         return false;
 473       }
 474     }
 475     // refresh the alignment and the feature settings dialog
 476     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 477     {
 478       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 479     }
 480     // findAllFeatures();
 481
 482     ap.paintAlignment(true);
 483
 484     return true;
 485   }
 486
 487   protected void warnIfGroupHidden(Frame frame, String group)
 488   {
 489     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 490     {
 491       String msg = MessageManager.formatMessage("label.warning_hidden",
 492               MessageManager.getString("label.group"), group);
 493       showWarning(frame, msg);
 494     }
 495   }
 496
 497   protected void warnIfTypeHidden(Frame frame, String type)
 498   {
 499     if (getRenderOrder().contains(type))
 500     {
 501       if (!showFeatureOfType(type))
 502       {
 503         String msg = MessageManager.formatMessage("label.warning_hidden",
 504                 MessageManager.getString("label.feature_type"), type);
 505         showWarning(frame, msg);
 506       }
 507     }
 508   }
 509
 510   /**
 511    * @param frame
 512    * @param msg
 513    */
 514   protected void showWarning(Frame frame, String msg)
 515   {
 516     JVDialog d = new JVDialog(frame, "", true, 350, 200);
 517     Panel mp = new Panel();
 518     d.ok.setLabel(MessageManager.getString("action.ok"));
 519     d.cancel.setVisible(false);
 520     mp.setLayout(new FlowLayout());
 521     mp.add(new Label(msg));
 522     d.setMainPanel(mp);
 523     d.setVisible(true);
 524   }
 525 }