src/jalview/gui/FeatureEditor.java

   1 package jalview.gui;
   2
   3 import jalview.api.FeatureColourI;
   4 import jalview.datamodel.SearchResults;
   5 import jalview.datamodel.SearchResultsI;
   6 import jalview.datamodel.SequenceFeature;
   7 import jalview.datamodel.SequenceI;
   8 import jalview.gui.JalviewColourChooser.ColourChooserListener;
   9 import jalview.io.FeaturesFile;
  10 import jalview.schemes.FeatureColour;
  11 import jalview.util.ColorUtils;
  12 import jalview.util.MessageManager;
  13 import jalview.util.dialogrunner.RunResponse;
  14
  15 import java.awt.BorderLayout;
  16 import java.awt.Color;
  17 import java.awt.Dimension;
  18 import java.awt.Font;
  19 import java.awt.GridLayout;
  20 import java.awt.event.ActionEvent;
  21 import java.awt.event.ActionListener;
  22 import java.awt.event.ItemEvent;
  23 import java.awt.event.ItemListener;
  24 import java.awt.event.MouseAdapter;
  25 import java.awt.event.MouseEvent;
  26 import java.util.ArrayList;
  27 import java.util.List;
  28
  29 import javax.swing.JComboBox;
  30 import javax.swing.JLabel;
  31 import javax.swing.JPanel;
  32 import javax.swing.JScrollPane;
  33 import javax.swing.JSpinner;
  34 import javax.swing.JTextArea;
  35 import javax.swing.JTextField;
  36 import javax.swing.SwingConstants;
  37 import javax.swing.event.DocumentEvent;
  38 import javax.swing.event.DocumentListener;
  39
  40 /**
  41  * Provides a dialog allowing the user to add new features, or amend or delete
  42  * existing features
  43  */
  44 public class FeatureEditor
  45 {
  46   /*
  47    * defaults for creating a new feature are the last created
  48    * feature type and group
  49    */
  50   static String lastFeatureAdded = "feature_1";
  51
  52   static String lastFeatureGroupAdded = "Jalview";
  53
  54   /*
  55    * the sequence(s) with features to be created / amended
  56    */
  57   final List<SequenceI> sequences;
  58
  59   /*
  60    * the features (or template features) to be created / amended
  61    */
  62   final List<SequenceFeature> features;
  63
  64   /*
  65    * true if the dialog is to create a new feature, false if
  66    * for amend or delete of existing feature(s)
  67    */
  68   final boolean forCreate;
  69
  70   /*
  71    * index into the list of features
  72    */
  73   int featureIndex;
  74
  75   FeatureColourI oldColour;
  76
  77   FeatureColourI featureColour;
  78
  79   FeatureRenderer fr;
  80
  81   AlignmentPanel ap;
  82
  83   Object[] options;
  84
  85   JTextField name;
  86
  87   JTextField group;
  88
  89   JTextArea description;
  90
  91   JSpinner start;
  92
  93   JSpinner end;
  94
  95   JPanel mainPanel;
  96
  97   /**
  98    * Constructor
  99    *
 100    * @param alignPanel
 101    * @param seqs
 102    * @param feats
 103    * @param create
 104    *          if true create a new feature, else amend or delete an existing
 105    *          feature
 106    */
 107   public FeatureEditor(AlignmentPanel alignPanel, List<SequenceI> seqs,
 108           List<SequenceFeature> feats, boolean create)
 109   {
 110     ap = alignPanel;
 111     fr = alignPanel.getSeqPanel().seqCanvas.fr;
 112     sequences = seqs;
 113     features = feats;
 114     this.forCreate = create;
 115
 116     init();
 117   }
 118
 119   /**
 120    * Initialise the layout and controls
 121    */
 122   protected void init()
 123   {
 124     featureIndex = 0;
 125
 126     mainPanel = new JPanel(new BorderLayout());
 127
 128     name = new JTextField(25);
 129     name.getDocument().addDocumentListener(new DocumentListener()
 130     {
 131       @Override
 132       public void insertUpdate(DocumentEvent e)
 133       {
 134         warnIfTypeHidden(mainPanel, name.getText());
 135       }
 136
 137       @Override
 138       public void removeUpdate(DocumentEvent e)
 139       {
 140         warnIfTypeHidden(mainPanel, name.getText());
 141       }
 142
 143       @Override
 144       public void changedUpdate(DocumentEvent e)
 145       {
 146         warnIfTypeHidden(mainPanel, name.getText());
 147       }
 148     });
 149
 150     group = new JTextField(25);
 151     group.getDocument().addDocumentListener(new DocumentListener()
 152     {
 153       @Override
 154       public void insertUpdate(DocumentEvent e)
 155       {
 156         warnIfGroupHidden(mainPanel, group.getText());
 157       }
 158
 159       @Override
 160       public void removeUpdate(DocumentEvent e)
 161       {
 162         warnIfGroupHidden(mainPanel, group.getText());
 163       }
 164
 165       @Override
 166       public void changedUpdate(DocumentEvent e)
 167       {
 168         warnIfGroupHidden(mainPanel, group.getText());
 169       }
 170     });
 171
 172     description = new JTextArea(3, 25);
 173     start = new JSpinner();
 174     end = new JSpinner();
 175     start.setPreferredSize(new Dimension(80, 20));
 176     end.setPreferredSize(new Dimension(80, 20));
 177     final JLabel colour = new JLabel();
 178     colour.setOpaque(true);
 179     colour.setMaximumSize(new Dimension(30, 16));
 180     colour.addMouseListener(new MouseAdapter()
 181     {
 182       @Override
 183       public void mousePressed(MouseEvent evt)
 184       {
 185         if (featureColour.isSimpleColour())
 186         {
 187           /*
 188            * open colour chooser on click in colour panel
 189            */
 190           String title = MessageManager
 191                   .getString("label.select_feature_colour");
 192           ColourChooserListener listener = new ColourChooserListener()
 193           {
 194             @Override
 195             public void colourSelected(Color c)
 196             {
 197               featureColour = new FeatureColour(c);
 198               updateColourButton(mainPanel, colour, featureColour);
 199             };
 200           };
 201           JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
 202                   title, featureColour.getColour(), listener);
 203         }
 204         else
 205         {
 206           /*
 207            * variable colour dialog - on OK, refetch the updated
 208            * feature colour and update this display
 209            */
 210           final String ft = features.get(featureIndex).getType();
 211           final String type = ft == null ? lastFeatureAdded : ft;
 212           FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
 213           fcc.setRequestFocusEnabled(true);
 214           fcc.requestFocus();
 215           fcc.addActionListener(new ActionListener()
 216           {
 217             @Override
 218             public void actionPerformed(ActionEvent e)
 219             {
 220               featureColour = fr.getFeatureStyle(ft);
 221               fr.setColour(type, featureColour);
 222               updateColourButton(mainPanel, colour, featureColour);
 223             }
 224           });
 225         }
 226       }
 227     });
 228     JPanel gridPanel = new JPanel(new GridLayout(3, 1));
 229
 230     if (!forCreate && features.size() > 1)
 231     {
 232       /*
 233        * more than one feature at selected position -
 234        * add a drop-down to choose the feature to amend
 235        * space pad text if necessary to make entries distinct
 236        */
 237       gridPanel = new JPanel(new GridLayout(4, 1));
 238       JPanel choosePanel = new JPanel();
 239       choosePanel.add(new JLabel(
 240               MessageManager.getString("label.select_feature") + ":"));
 241       final JComboBox<String> overlaps = new JComboBox<>();
 242       List<String> added = new ArrayList<>();
 243       for (SequenceFeature sf : features)
 244       {
 245         String text = String.format("%s/%d-%d (%s)", sf.getType(),
 246                 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
 247         while (added.contains(text))
 248         {
 249           text += " ";
 250         }
 251         overlaps.addItem(text);
 252         added.add(text);
 253       }
 254       choosePanel.add(overlaps);
 255
 256       overlaps.addItemListener(new ItemListener()
 257       {
 258         @Override
 259         public void itemStateChanged(ItemEvent e)
 260         {
 261           int index = overlaps.getSelectedIndex();
 262           if (index != -1)
 263           {
 264             featureIndex = index;
 265             SequenceFeature sf = features.get(index);
 266             name.setText(sf.getType());
 267             description.setText(sf.getDescription());
 268             group.setText(sf.getFeatureGroup());
 269             start.setValue(new Integer(sf.getBegin()));
 270             end.setValue(new Integer(sf.getEnd()));
 271
 272             SearchResultsI highlight = new SearchResults();
 273             highlight.addResult(sequences.get(0), sf.getBegin(),
 274                     sf.getEnd());
 275
 276             ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
 277           }
 278           FeatureColourI col = fr.getFeatureStyle(name.getText());
 279           if (col == null)
 280           {
 281             col = new FeatureColour(
 282                     ColorUtils.createColourFromName(name.getText()));
 283           }
 284           oldColour = featureColour = col;
 285           updateColourButton(mainPanel, colour, col);
 286         }
 287       });
 288
 289       gridPanel.add(choosePanel);
 290     }
 291
 292     JPanel namePanel = new JPanel();
 293     gridPanel.add(namePanel);
 294     namePanel.add(new JLabel(MessageManager.getString("label.name:"),
 295             JLabel.RIGHT));
 296     namePanel.add(name);
 297
 298     JPanel groupPanel = new JPanel();
 299     gridPanel.add(groupPanel);
 300     groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
 301             JLabel.RIGHT));
 302     groupPanel.add(group);
 303
 304     JPanel colourPanel = new JPanel();
 305     gridPanel.add(colourPanel);
 306     colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
 307             JLabel.RIGHT));
 308     colourPanel.add(colour);
 309     colour.setPreferredSize(new Dimension(150, 15));
 310     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
 311     colour.setForeground(Color.black);
 312     colour.setHorizontalAlignment(SwingConstants.CENTER);
 313     colour.setVerticalAlignment(SwingConstants.CENTER);
 314     colour.setHorizontalTextPosition(SwingConstants.CENTER);
 315     colour.setVerticalTextPosition(SwingConstants.CENTER);
 316     mainPanel.add(gridPanel, BorderLayout.NORTH);
 317
 318     JPanel descriptionPanel = new JPanel();
 319     descriptionPanel.add(new JLabel(
 320             MessageManager.getString("label.description:"), JLabel.RIGHT));
 321     description.setFont(JvSwingUtils.getTextAreaFont());
 322     description.setLineWrap(true);
 323     descriptionPanel.add(new JScrollPane(description));
 324
 325     if (!forCreate)
 326     {
 327       mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
 328
 329       JPanel startEndPanel = new JPanel();
 330       startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
 331               JLabel.RIGHT));
 332       startEndPanel.add(start);
 333       startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
 334               JLabel.RIGHT));
 335       startEndPanel.add(end);
 336       mainPanel.add(startEndPanel, BorderLayout.CENTER);
 337     }
 338     else
 339     {
 340       mainPanel.add(descriptionPanel, BorderLayout.CENTER);
 341     }
 342
 343     /*
 344      * default feature type and group to that of the first feature supplied,
 345      * or to the last feature created if not supplied (null value)
 346      */
 347     SequenceFeature firstFeature = features.get(0);
 348     boolean useLastDefaults = firstFeature.getType() == null;
 349     final String featureType = useLastDefaults ? lastFeatureAdded
 350             : firstFeature.getType();
 351     final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
 352             : firstFeature.getFeatureGroup();
 353     name.setText(featureType);
 354     group.setText(featureGroup);
 355
 356     start.setValue(new Integer(firstFeature.getBegin()));
 357     end.setValue(new Integer(firstFeature.getEnd()));
 358     description.setText(firstFeature.getDescription());
 359     featureColour = fr.getFeatureStyle(featureType);
 360     oldColour = featureColour;
 361     updateColourButton(mainPanel, colour, oldColour);
 362     if (forCreate)
 363     {
 364       options = new Object[] { MessageManager.getString("action.ok"),
 365           MessageManager.getString("action.cancel") };
 366     }
 367     else
 368     {
 369       options = new Object[] { MessageManager.getString("label.amend"),
 370           MessageManager.getString("action.delete"),
 371           MessageManager.getString("action.cancel") };
 372     }
 373   }
 374
 375   /**
 376    * Presents a dialog allowing the user to add new features, or amend or delete
 377    * an existing feature. Currently this can be on
 378    * <ul>
 379    * <li>double-click on a sequence - Amend/Delete features at position</li>
 380    * <li>Create sequence feature from pop-up menu on selected region</li>
 381    * <li>Create features for pattern matches from Find</li>
 382    * </ul>
 383    * If the supplied feature type is null, show (and update on confirm) the type
 384    * and group of the last new feature created (with initial defaults of
 385    * "feature_1" and "Jalview").
 386    */
 387   public void showDialog()
 388   {
 389     RunResponse okAction = forCreate ? getCreateAction() : getAmendAction();
 390     RunResponse deleteAction = getDeleteAction();
 391     Runnable cancelAction = getCancelAction();
 392
 393     String title = forCreate
 394             ? MessageManager.getString("label.create_new_sequence_features")
 395             : MessageManager.formatMessage("label.amend_delete_features",
 396                     new String[]
 397                     { sequences.get(0).getName() });
 398
 399     JvOptionPane.newOptionDialog(Desktop.desktop).response(okAction)
 400             .response(deleteAction).defaultResponse(cancelAction)
 401             .showInternalDialog(mainPanel, title,
 402                     JvOptionPane.YES_NO_CANCEL_OPTION,
 403                     JvOptionPane.QUESTION_MESSAGE, null, options,
 404                     MessageManager.getString("action.ok"));
 405   }
 406
 407   /**
 408    * Answers an action to run on Cancel in the dialog. This is just to remove
 409    * any feature highlighting from the display. Changes in the dialog are not
 410    * applied until it is dismissed with OK, Amend or Delete, so there are no
 411    * updates to reset on Cancel.
 412    *
 413    * @return
 414    */
 415   protected Runnable getCancelAction()
 416   {
 417     Runnable defaultResponse = new Runnable()
 418     {
 419       public void run()
 420       {
 421         ap.highlightSearchResults(null);
 422         ap.paintAlignment(false, false);
 423       }
 424     };
 425     return defaultResponse;
 426   }
 427
 428   /**
 429    * Returns the action to be run on OK in the dialog when creating one or more
 430    * sequence features. Note these may have a pre-supplied feature type (such as
 431    * a Find pattern), or none, in which case the feature type and group default
 432    * to those last added through this dialog. The action includes refreshing the
 433    * Feature Settings panel (if it is open), to show any new feature type, or
 434    * amended colour for an existing type.
 435    *
 436    * @return
 437    */
 438   protected RunResponse getCreateAction()
 439   {
 440     RunResponse okAction = new RunResponse(JvOptionPane.OK_OPTION)
 441     {
 442       boolean useLastDefaults = features.get(0).getType() == null;
 443
 444       public void run()
 445       {
 446         final String enteredType = name.getText().trim();
 447         final String enteredGroup = group.getText().trim();
 448         final String enteredDescription = description.getText()
 449                 .replaceAll("\n", " ");
 450         if (enteredType.length() > 0)
 451         {
 452           /*
 453            * update default values only if creating using default values
 454            */
 455           if (useLastDefaults)
 456           {
 457             lastFeatureAdded = enteredType;
 458             lastFeatureGroupAdded = enteredGroup;
 459             // TODO: determine if the null feature group is valid
 460             if (lastFeatureGroupAdded.length() < 1)
 461             {
 462               lastFeatureGroupAdded = null;
 463             }
 464           }
 465         }
 466
 467         if (enteredType.length() > 0)
 468         {
 469           for (int i = 0; i < sequences.size(); i++)
 470           {
 471             SequenceFeature sf = features.get(i);
 472             SequenceFeature sf2 = new SequenceFeature(enteredType,
 473                     enteredDescription, sf.getBegin(), sf.getEnd(),
 474                     enteredGroup);
 475             new FeaturesFile().parseDescriptionHTML(sf2, false);
 476             sequences.get(i).addSequenceFeature(sf2);
 477           }
 478
 479           fr.setColour(enteredType, featureColour);
 480           fr.featuresAdded();
 481
 482           repaintPanel();
 483         }
 484       }
 485     };
 486     return okAction;
 487   }
 488
 489   /**
 490    * Answers the action to run on Delete in the dialog. Note this includes
 491    * refreshing the Feature Settings (if open) in case the only instance of a
 492    * feature type or group has been deleted.
 493    *
 494    * @return
 495    */
 496   protected RunResponse getDeleteAction()
 497   {
 498     RunResponse deleteAction = new RunResponse(JvOptionPane.NO_OPTION)
 499     {
 500       public void run()
 501       {
 502         SequenceFeature sf = features.get(featureIndex);
 503         sequences.get(0).getDatasetSequence().deleteFeature(sf);
 504         fr.featuresAdded();
 505         ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
 506         ap.paintAlignment(true, true);
 507       }
 508     };
 509     return deleteAction;
 510   }
 511
 512   /**
 513    * update the amend feature button dependent on the given style
 514    *
 515    * @param bigPanel
 516    * @param col
 517    * @param col
 518    */
 519   protected void updateColourButton(JPanel bigPanel, JLabel colour,
 520           FeatureColourI col)
 521   {
 522     colour.removeAll();
 523     colour.setIcon(null);
 524     colour.setText("");
 525
 526     if (col.isSimpleColour())
 527     {
 528       colour.setToolTipText(null);
 529       colour.setBackground(col.getColour());
 530     }
 531     else
 532     {
 533       colour.setBackground(bigPanel.getBackground());
 534       colour.setForeground(Color.black);
 535       colour.setToolTipText(FeatureSettings.getColorTooltip(col, false));
 536       FeatureSettings.renderGraduatedColor(colour, col);
 537     }
 538   }
 539
 540   /**
 541    * Show a warning message if the entered group is one that is currently hidden
 542    *
 543    * @param panel
 544    * @param group
 545    */
 546   protected void warnIfGroupHidden(JPanel panel, String group)
 547   {
 548     if (!fr.isGroupVisible(group))
 549     {
 550       String msg = MessageManager.formatMessage("label.warning_hidden",
 551               MessageManager.getString("label.group"), group);
 552       JvOptionPane.showMessageDialog(panel, msg, "",
 553               JvOptionPane.OK_OPTION);
 554     }
 555   }
 556
 557   /**
 558    * Show a warning message if the entered type is one that is currently hidden
 559    *
 560    * @param panel
 561    * @param type
 562    */
 563   protected void warnIfTypeHidden(JPanel panel, String type)
 564   {
 565     if (fr.getRenderOrder().contains(type))
 566     {
 567       if (!fr.showFeatureOfType(type))
 568       {
 569         String msg = MessageManager.formatMessage("label.warning_hidden",
 570                 MessageManager.getString("label.feature_type"), type);
 571         JvOptionPane.showMessageDialog(panel, msg, "",
 572                 JvOptionPane.OK_OPTION);
 573       }
 574     }
 575   }
 576
 577   /**
 578    * On closing the dialog - ensure feature display is turned on, to show any
 579    * new features - remove highlighting of the last selected feature - repaint
 580    * the panel to show any changes
 581    */
 582   protected void repaintPanel()
 583   {
 584     ap.alignFrame.showSeqFeatures.setSelected(true);
 585     ap.av.setShowSequenceFeatures(true);
 586     ap.av.setSearchResults(null);
 587     ap.paintAlignment(true, true);
 588   }
 589
 590   /**
 591    * Returns the action to be run on OK in the dialog when amending a feature.
 592    * Note this may include refreshing the Feature Settings panel (if it is
 593    * open), if feature type, group or colour has changed (but not for
 594    * description or extent).
 595    *
 596    * @return
 597    */
 598   protected RunResponse getAmendAction()
 599   {
 600     RunResponse okAction = new RunResponse(JvOptionPane.OK_OPTION)
 601     {
 602       boolean useLastDefaults = features.get(0).getType() == null;
 603
 604       String featureType = name.getText();
 605
 606       String featureGroup = group.getText();
 607
 608       public void run()
 609       {
 610         final String enteredType = name.getText().trim();
 611         final String enteredGroup = group.getText().trim();
 612         final String enteredDescription = description.getText()
 613                 .replaceAll("\n", " ");
 614         if (enteredType.length() > 0)
 615
 616         {
 617           /*
 618            * update default values only if creating using default values
 619            */
 620           if (useLastDefaults)
 621           {
 622             lastFeatureAdded = enteredType;
 623             lastFeatureGroupAdded = enteredGroup;
 624             // TODO: determine if the null feature group is valid
 625             if (lastFeatureGroupAdded.length() < 1)
 626             {
 627               lastFeatureGroupAdded = null;
 628             }
 629           }
 630         }
 631
 632         SequenceFeature sf = features.get(featureIndex);
 633
 634         /*
 635          * Need to refresh Feature Settings if type, group or colour changed;
 636          * note we don't force the feature to be visible - the user has been
 637          * warned if a hidden feature type or group was entered
 638          */
 639         boolean refreshSettings = (!featureType.equals(enteredType)
 640                 || !featureGroup.equals(enteredGroup));
 641         refreshSettings |= (featureColour != oldColour);
 642         fr.setColour(enteredType, featureColour);
 643         int newBegin = sf.begin;
 644         int newEnd = sf.end;
 645         try
 646         {
 647           newBegin = ((Integer) start.getValue()).intValue();
 648           newEnd = ((Integer) end.getValue()).intValue();
 649         } catch (NumberFormatException ex)
 650         {
 651           // JSpinner doesn't accept invalid format data :-)
 652         }
 653
 654         /*
 655          * 'amend' the feature by deleting it and adding a new one
 656          * (to ensure integrity of SequenceFeatures data store)
 657          * note this dialog only updates one sequence at a time
 658          */
 659         sequences.get(0).deleteFeature(sf);
 660         SequenceFeature newSf = new SequenceFeature(sf, enteredType,
 661                 newBegin, newEnd, enteredGroup, sf.getScore());
 662         newSf.setDescription(enteredDescription);
 663         new FeaturesFile().parseDescriptionHTML(newSf, false);
 664         sequences.get(0).addSequenceFeature(newSf);
 665
 666         if (refreshSettings)
 667         {
 668           fr.featuresAdded();
 669         }
 670         repaintPanel();
 671       }
 672     };
 673     return okAction;
 674   }
 675
 676 }