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
  65         extends 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
 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:"),
 289             Label.RIGHT));
 290     tmp.add(name);
 291
 292     tmp = new Panel();
 293     panel.add(tmp);
 294     tmp.add(new Label(MessageManager.getString("label.group:"),
 295             Label.RIGHT));
 296     tmp.add(group);
 297
 298     tmp = new Panel();
 299     panel.add(tmp);
 300     tmp.add(new Label(MessageManager.getString("label.colour"),
 301             Label.RIGHT));
 302     tmp.add(colourPanel);
 303
 304     bigPanel.add(panel, BorderLayout.NORTH);
 305
 306     panel = new Panel();
 307     panel.add(new Label(MessageManager.getString("label.description:"),
 308             Label.RIGHT));
 309     panel.add(new ScrollPane().add(description));
 310
 311     if (!create)
 312     {
 313       bigPanel.add(panel, BorderLayout.SOUTH);
 314
 315       panel = new Panel();
 316       panel.add(new Label(MessageManager.getString("label.start"),
 317               Label.RIGHT));
 318       panel.add(start);
 319       panel.add(new Label(MessageManager.getString("label.end"),
 320               Label.RIGHT));
 321       panel.add(end);
 322       bigPanel.add(panel, BorderLayout.CENTER);
 323     }
 324     else
 325     {
 326       bigPanel.add(panel, BorderLayout.CENTER);
 327     }
 328
 329     /*
 330      * use defaults for type and group (and update them on Confirm) only
 331      * if feature type has not been supplied by the caller
 332      * (e.g. for Amend, or create features from Find)
 333      */
 334     SequenceFeature firstFeature = features.get(0);
 335     boolean useLastDefaults = firstFeature.getType() == null;
 336     String featureType = useLastDefaults ? lastFeatureAdded
 337             : firstFeature.getType();
 338     String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 339             : firstFeature.getFeatureGroup();
 340
 341     String title = create
 342             ? MessageManager.getString("label.create_new_sequence_features")
 343             : MessageManager.formatMessage("label.amend_delete_features",
 344                     new String[]
 345                     { sequences.get(0).getName() });
 346
 347     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 348             240);
 349
 350     dialog.setMainPanel(bigPanel);
 351
 352     name.setText(featureType);
 353     group.setText(featureGroup);
 354
 355     if (!create)
 356     {
 357       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 358       dialog.buttonPanel.add(deleteButton, 1);
 359       deleteButton.addActionListener(new ActionListener()
 360       {
 361         @Override
 362         public void actionPerformed(ActionEvent evt)
 363         {
 364           deleteFeature = true;
 365           dialog.setVisible(false);
 366         }
 367       });
 368     }
 369
 370     start.setText(firstFeature.getBegin() + "");
 371     end.setText(firstFeature.getEnd() + "");
 372     description.setText(firstFeature.getDescription());
 373     // lookup (or generate) the feature colour
 374     FeatureColourI fcol = getFeatureStyle(name.getText());
 375     // simply display the feature color in a box
 376     colourPanel.updateColor(fcol);
 377     dialog.setResizable(true);
 378     // TODO: render the graduated color in the box.
 379     colourPanel.addMouseListener(new MouseAdapter()
 380     {
 381       @Override
 382       public void mousePressed(MouseEvent evt)
 383       {
 384         if (!colourPanel.isGcol)
 385         {
 386           new UserDefinedColours(fr, ap.alignFrame);
 387         }
 388         else
 389         {
 390           new FeatureColourChooser(ap.alignFrame, name.getText());
 391           dialog.transferFocus();
 392         }
 393       }
 394     });
 395     dialog.setVisible(true);
 396
 397     FeaturesFile ffile = new FeaturesFile();
 398
 399     /*
 400      * only update default type and group if we used defaults
 401      */
 402     final String enteredType = name.getText().trim();
 403     final String enteredGroup = group.getText().trim();
 404     final String enteredDesc = description.getText().replace('\n', ' ');
 405
 406     if (dialog.accept && useLastDefaults)
 407     {
 408       lastFeatureAdded = enteredType;
 409       lastFeatureGroupAdded = enteredGroup;
 410     }
 411
 412     if (!create)
 413     {
 414       SequenceFeature sf = features.get(featureIndex);
 415       if (dialog.accept)
 416       {
 417         if (!colourPanel.isGcol)
 418         {
 419           // update colour - otherwise its already done.
 420           setColour(enteredType,
 421                   new FeatureColour(colourPanel.getBackground()));
 422         }
 423         int newBegin = sf.begin;
 424         int newEnd = sf.end;
 425         try
 426         {
 427           newBegin = Integer.parseInt(start.getText());
 428           newEnd = Integer.parseInt(end.getText());
 429         } catch (NumberFormatException ex)
 430         {
 431           //
 432         }
 433
 434         /*
 435          * replace the feature by deleting it and adding a new one
 436          * (to ensure integrity of SequenceFeatures data store)
 437          */
 438         sequences.get(0).deleteFeature(sf);
 439         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 440                 newBegin, newEnd, enteredGroup, sf.getScore());
 441         newSf.setDescription(enteredDesc);
 442         ffile.parseDescriptionHTML(newSf, false);
 443         // amend features dialog only updates one sequence at a time
 444         sequences.get(0).addSequenceFeature(newSf);
 445         boolean typeOrGroupChanged = (!featureType.equals(newSf.getType()) || !featureGroup
 446                 .equals(newSf.getFeatureGroup()));
 447
 448         ffile.parseDescriptionHTML(sf, false);
 449         if (typeOrGroupChanged)
 450         {
 451           featuresAdded();
 452         }
 453       }
 454       if (deleteFeature)
 455       {
 456         sequences.get(0).deleteFeature(sf);
 457         // ensure Feature Settings reflects removal of feature / group
 458         featuresAdded();
 459       }
 460     }
 461     else
 462     {
 463       /*
 464        * adding feature(s)
 465        */
 466       if (dialog.accept && name.getText().length() > 0)
 467       {
 468         for (int i = 0; i < sequences.size(); i++)
 469         {
 470           SequenceFeature sf = features.get(i);
 471           SequenceFeature sf2 = new SequenceFeature(enteredType,
 472                   enteredDesc, sf.getBegin(), sf.getEnd(), enteredGroup);
 473           ffile.parseDescriptionHTML(sf2, false);
 474           sequences.get(i).addSequenceFeature(sf2);
 475         }
 476
 477         Color newColour = colourPanel.getBackground();
 478         // setColour(lastFeatureAdded, fcol);
 479
 480         setColour(enteredType, new FeatureColour(newColour)); // was fcol
 481         featuresAdded();
 482       }
 483       else
 484       {
 485         // no update to the alignment
 486         return false;
 487       }
 488     }
 489     // refresh the alignment and the feature settings dialog
 490     if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
 491     {
 492       ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
 493     }
 494     // findAllFeatures();
 495
 496     ap.paintAlignment(true, true);
 497
 498     return true;
 499   }
 500
 501   protected void warnIfGroupHidden(Frame frame, String group)
 502   {
 503     if (featureGroups.containsKey(group) && !featureGroups.get(group))
 504     {
 505       String msg = MessageManager.formatMessage("label.warning_hidden",
 506               MessageManager.getString("label.group"), group);
 507       showWarning(frame, msg);
 508     }
 509   }
 510
 511   protected void warnIfTypeHidden(Frame frame, String type)
 512   {
 513     if (getRenderOrder().contains(type))
 514     {
 515       if (!showFeatureOfType(type))
 516       {
 517         String msg = MessageManager.formatMessage("label.warning_hidden",
 518                 MessageManager.getString("label.feature_type"), type);
 519         showWarning(frame, msg);
 520       }
 521     }
 522   }
 523
 524   /**
 525    * @param frame
 526    * @param msg
 527    */
 528   protected void showWarning(Frame frame, String msg)
 529   {
 530     JVDialog d = new JVDialog(frame, "", true, 350, 200);
 531     Panel mp = new Panel();
 532     d.ok.setLabel(MessageManager.getString("action.ok"));
 533     d.cancel.setVisible(false);
 534     mp.setLayout(new FlowLayout());
 535     mp.add(new Label(msg));
 536     d.setMainPanel(mp);
 537     d.setVisible(true);
 538   }
 539 }