src/jalview/appletgui/AlignFrame.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.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureRenderer;
  29 import jalview.api.FeatureSettingsControllerI;
  30 import jalview.api.SequenceStructureBinding;
  31 import jalview.bin.JalviewLite;
  32 import jalview.commands.CommandI;
  33 import jalview.commands.EditCommand;
  34 import jalview.commands.EditCommand.Action;
  35 import jalview.commands.OrderCommand;
  36 import jalview.commands.RemoveGapColCommand;
  37 import jalview.commands.RemoveGapsCommand;
  38 import jalview.commands.SlideSequencesCommand;
  39 import jalview.commands.TrimRegionCommand;
  40 import jalview.datamodel.Alignment;
  41 import jalview.datamodel.AlignmentAnnotation;
  42 import jalview.datamodel.AlignmentI;
  43 import jalview.datamodel.AlignmentOrder;
  44 import jalview.datamodel.ColumnSelection;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceGroup;
  48 import jalview.datamodel.SequenceI;
  49 import jalview.io.AnnotationFile;
  50 import jalview.io.AppletFormatAdapter;
  51 import jalview.io.FeaturesFile;
  52 import jalview.io.TCoffeeScoreFile;
  53 import jalview.schemes.Blosum62ColourScheme;
  54 import jalview.schemes.BuriedColourScheme;
  55 import jalview.schemes.ClustalxColourScheme;
  56 import jalview.schemes.ColourSchemeI;
  57 import jalview.schemes.HelixColourScheme;
  58 import jalview.schemes.HydrophobicColourScheme;
  59 import jalview.schemes.NucleotideColourScheme;
  60 import jalview.schemes.PIDColourScheme;
  61 import jalview.schemes.PurinePyrimidineColourScheme;
  62 import jalview.schemes.RNAHelicesColourChooser;
  63 import jalview.schemes.StrandColourScheme;
  64 import jalview.schemes.TCoffeeColourScheme;
  65 import jalview.schemes.TaylorColourScheme;
  66 import jalview.schemes.TurnColourScheme;
  67 import jalview.schemes.ZappoColourScheme;
  68 import jalview.structure.StructureSelectionManager;
  69 import jalview.structures.models.AAStructureBindingModel;
  70 import jalview.util.MappingUtils;
  71 import jalview.util.MessageManager;
  72 import jalview.viewmodel.AlignmentViewport;
  73
  74 import java.awt.BorderLayout;
  75 import java.awt.Canvas;
  76 import java.awt.CheckboxMenuItem;
  77 import java.awt.Color;
  78 import java.awt.FlowLayout;
  79 import java.awt.Font;
  80 import java.awt.FontMetrics;
  81 import java.awt.Frame;
  82 import java.awt.Graphics;
  83 import java.awt.Label;
  84 import java.awt.Menu;
  85 import java.awt.MenuBar;
  86 import java.awt.MenuItem;
  87 import java.awt.Panel;
  88 import java.awt.event.ActionEvent;
  89 import java.awt.event.ActionListener;
  90 import java.awt.event.FocusEvent;
  91 import java.awt.event.FocusListener;
  92 import java.awt.event.ItemEvent;
  93 import java.awt.event.ItemListener;
  94 import java.awt.event.KeyEvent;
  95 import java.awt.event.KeyListener;
  96 import java.awt.event.WindowAdapter;
  97 import java.awt.event.WindowEvent;
  98 import java.io.IOException;
  99 import java.net.URL;
 100 import java.net.URLEncoder;
 101 import java.util.Arrays;
 102 import java.util.Deque;
 103 import java.util.HashMap;
 104 import java.util.Hashtable;
 105 import java.util.List;
 106 import java.util.Map;
 107 import java.util.StringTokenizer;
 108 import java.util.Vector;
 109
 110 import org.jmol.viewer.Viewer;
 111
 112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 113         ItemListener, KeyListener, AlignViewControllerGuiI
 114 {
 115   public AlignViewControllerI avc;
 116
 117   public AlignmentPanel alignPanel;
 118
 119   public AlignViewport viewport;
 120
 121   // width and height may be overridden by applet parameters
 122   int frameWidth = 700;
 123
 124   int frameHeight = 500;
 125
 126   String jalviewServletURL;
 127
 128   /*
 129    * Flag for showing autocalculated consensus above or below other consensus
 130    * rows
 131    */
 132   private boolean showAutoCalculatedAbove;
 133
 134   private SequenceAnnotationOrder annotationSortOrder;
 135
 136   /**
 137    * Constructor that creates the frame and adds it to the display.
 138    *
 139    * @param al
 140    * @param applet
 141    * @param title
 142    * @param embedded
 143    */
 144   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 145           boolean embedded)
 146   {
 147     this(al, applet, title, embedded, true);
 148   }
 149
 150   /**
 151    * Constructor that optionally allows the frame to be displayed or only
 152    * created.
 153    *
 154    * @param al
 155    * @param applet
 156    * @param title
 157    * @param embedded
 158    * @param addToDisplay
 159    */
 160   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 161           boolean embedded, boolean addToDisplay)
 162   {
 163     this(al, null, null, applet, title, embedded, addToDisplay);
 164   }
 165
 166   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 167           ColumnSelection columnSelection, JalviewLite applet,
 168           String title, boolean embedded)
 169   {
 170     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 171   }
 172
 173   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 174           ColumnSelection columnSelection, JalviewLite applet,
 175           String title, boolean embedded, boolean addToDisplay)
 176   {
 177     if (applet != null)
 178     {
 179       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 180     }
 181
 182     try
 183     {
 184       jbInit();
 185     } catch (Exception ex)
 186     {
 187       ex.printStackTrace();
 188     }
 189     // need to get window geometry before we calculate alignment layout
 190     if (applet != null)
 191     {
 192       String param;
 193       try
 194       {
 195         param = applet.getParameter("windowWidth");
 196         if (param != null)
 197         {
 198           int width = Integer.parseInt(param);
 199           frameWidth = width;
 200         }
 201         param = applet.getParameter("windowHeight");
 202         if (param != null)
 203         {
 204           int height = Integer.parseInt(param);
 205           frameHeight = height;
 206         }
 207       } catch (Exception ex)
 208       {
 209       }
 210     }
 211     viewport = new AlignViewport(al, applet);
 212
 213     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 214     {
 215       viewport.hideSequence(hiddenSeqs);
 216     }
 217     if (columnSelection != null)
 218     {
 219       viewport.setColumnSelection(columnSelection);
 220     }
 221
 222     alignPanel = new AlignmentPanel(this, viewport);
 223     avc = new jalview.controller.AlignViewController(this, viewport,
 224             alignPanel);
 225     viewport.updateConservation(alignPanel);
 226     viewport.updateConsensus(alignPanel);
 227
 228     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 229     followMouseOverFlag.setState(viewport.isFollowHighlight());
 230     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 231     showGroupConservation.setState(viewport.isShowGroupConservation());
 232     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 233     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 234     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 235     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 236     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 237     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 238     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 239     showAlignmentAnnotations.setState(true);
 240     showSequenceAnnotations.setState(false);
 241
 242     seqLimits.setState(viewport.getShowJVSuffix());
 243
 244     if (applet != null)
 245     {
 246       String param = applet.getParameter("sortBy");
 247       if (param != null)
 248       {
 249         if (param.equalsIgnoreCase("Id"))
 250         {
 251           sortIDMenuItem_actionPerformed();
 252         }
 253         else if (param.equalsIgnoreCase("Pairwise Identity"))
 254         {
 255           sortPairwiseMenuItem_actionPerformed();
 256         }
 257         else if (param.equalsIgnoreCase("Length"))
 258         {
 259           sortLengthMenuItem_actionPerformed();
 260         }
 261       }
 262
 263       param = applet.getParameter("wrap");
 264       if (param != null)
 265       {
 266         if (param.equalsIgnoreCase("true"))
 267         {
 268           wrapMenuItem.setState(true);
 269           wrapMenuItem_actionPerformed();
 270         }
 271       }
 272       param = applet.getParameter("centrecolumnlabels");
 273       if (param != null)
 274       {
 275         centreColumnLabelFlag.setState(true);
 276         centreColumnLabelFlag_stateChanged();
 277       }
 278
 279     }
 280     if (viewport.getAlignment().isNucleotide())
 281     {
 282       viewport.updateStrucConsensus(alignPanel);
 283       if (viewport.getAlignment().hasRNAStructure())
 284       {
 285         RNAHelixColour.setEnabled(true);
 286       }
 287       else
 288       {
 289         RNAHelixColour.setEnabled(false);
 290       }
 291     }
 292     else
 293     {
 294       RNAHelixColour.setEnabled(false);
 295       purinePyrimidineColour.setEnabled(false);
 296     }
 297     // Some JVMS send keyevents to Top frame or lowest panel,
 298     // Havent worked out why yet. So add to both this frame and seqCanvas for
 299     // now
 300     this.addKeyListener(this);
 301     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 302     alignPanel.idPanel.idCanvas.addKeyListener(this);
 303     alignPanel.scalePanel.addKeyListener(this);
 304     alignPanel.annotationPanel.addKeyListener(this);
 305     alignPanel.annotationPanelHolder.addKeyListener(this);
 306     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 307     alignPanel.alabels.addKeyListener(this);
 308
 309     setAnnotationsVisibility();
 310
 311     if (addToDisplay)
 312     {
 313       addToDisplay(embedded);
 314     }
 315   }
 316
 317   /**
 318    * @param embedded
 319    */
 320   public void addToDisplay(boolean embedded)
 321   {
 322     createAlignFrameWindow(embedded);
 323     validate();
 324     alignPanel.adjustAnnotationHeight();
 325     alignPanel.paintAlignment(true);
 326   }
 327
 328   public AlignViewport getAlignViewport()
 329   {
 330     return viewport;
 331   }
 332
 333   public SeqCanvas getSeqcanvas()
 334   {
 335     return alignPanel.seqPanel.seqCanvas;
 336   }
 337
 338   /**
 339    * Load a features file onto the alignment
 340    *
 341    * @param file
 342    *          file URL, content, or other resolvable path
 343    * @param type
 344    *          is protocol for accessing data referred to by file
 345    */
 346
 347   public boolean parseFeaturesFile(String file, String type)
 348   {
 349     return parseFeaturesFile(file, type, true);
 350   }
 351
 352   /**
 353    * Load a features file onto the alignment
 354    *
 355    * @param file
 356    *          file URL, content, or other resolvable path
 357    * @param type
 358    *          is protocol for accessing data referred to by file
 359    * @param autoenabledisplay
 360    *          when true, display features flag will be automatically enabled if
 361    *          features are loaded
 362    * @return true if data parsed as a features file
 363    */
 364   public boolean parseFeaturesFile(String file, String type,
 365           boolean autoenabledisplay)
 366   {
 367     // TODO: test if importing a features file onto an alignment which already
 368     // has features with links overwrites the original links.
 369
 370     Hashtable featureLinks = new Hashtable();
 371     boolean featuresFile = false;
 372     try
 373     {
 374       featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
 375               .getAlignment(), alignPanel.seqPanel.seqCanvas
 376               .getFeatureRenderer().getFeatureColours(), featureLinks,
 377               true, viewport.applet.getDefaultParameter("relaxedidmatch",
 378                       false));
 379     } catch (Exception ex)
 380     {
 381       ex.printStackTrace();
 382     }
 383
 384     if (featuresFile)
 385     {
 386       if (featureLinks.size() > 0)
 387       {
 388         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 389       }
 390       if (autoenabledisplay)
 391       {
 392         viewport.setShowSequenceFeatures(true);
 393         sequenceFeatures.setState(true);
 394       }
 395       if (alignPanel.seqPanel.seqCanvas.fr != null)
 396       {
 397         // update the min/max ranges where necessary
 398         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 399       }
 400       if (viewport.featureSettings != null)
 401       {
 402         viewport.featureSettings.refreshTable();
 403       }
 404       alignPanel.paintAlignment(true);
 405       statusBar.setText(MessageManager
 406               .getString("label.successfully_added_features_alignment"));
 407     }
 408     return featuresFile;
 409   }
 410
 411   @Override
 412   public void keyPressed(KeyEvent evt)
 413   {
 414     if (viewport.cursorMode
 415             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 416                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 417                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 418             && Character.isDigit(evt.getKeyChar()))
 419     {
 420       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 421     }
 422
 423     switch (evt.getKeyCode())
 424     {
 425     case 27: // escape key
 426       deselectAllSequenceMenuItem_actionPerformed();
 427
 428       alignPanel.alabels.cancelDrag();
 429       break;
 430     case KeyEvent.VK_X:
 431       if (evt.isControlDown() || evt.isMetaDown())
 432       {
 433         cut_actionPerformed();
 434       }
 435       break;
 436     case KeyEvent.VK_C:
 437       if (viewport.cursorMode && !evt.isControlDown())
 438       {
 439         alignPanel.seqPanel.setCursorColumn();
 440       }
 441       if (evt.isControlDown() || evt.isMetaDown())
 442       {
 443         copy_actionPerformed();
 444       }
 445       break;
 446     case KeyEvent.VK_V:
 447       if (evt.isControlDown())
 448       {
 449         paste(evt.isShiftDown());
 450       }
 451       break;
 452     case KeyEvent.VK_A:
 453       if (evt.isControlDown() || evt.isMetaDown())
 454       {
 455         selectAllSequenceMenuItem_actionPerformed();
 456       }
 457       break;
 458     case KeyEvent.VK_DOWN:
 459       if (viewport.cursorMode)
 460       {
 461         alignPanel.seqPanel.moveCursor(0, 1);
 462       }
 463       else
 464       {
 465         moveSelectedSequences(false);
 466       }
 467       break;
 468
 469     case KeyEvent.VK_UP:
 470       if (viewport.cursorMode)
 471       {
 472         alignPanel.seqPanel.moveCursor(0, -1);
 473       }
 474       else
 475       {
 476         moveSelectedSequences(true);
 477       }
 478       break;
 479
 480     case KeyEvent.VK_LEFT:
 481       if (evt.isAltDown() || !viewport.cursorMode)
 482       {
 483         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 484       }
 485       else
 486       {
 487         alignPanel.seqPanel.moveCursor(-1, 0);
 488       }
 489       break;
 490
 491     case KeyEvent.VK_RIGHT:
 492       if (evt.isAltDown() || !viewport.cursorMode)
 493       {
 494         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 495       }
 496       else
 497       {
 498         alignPanel.seqPanel.moveCursor(1, 0);
 499       }
 500       break;
 501
 502     case KeyEvent.VK_SPACE:
 503       if (viewport.cursorMode)
 504       {
 505         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 506                 || evt.isShiftDown() || evt.isAltDown());
 507       }
 508       break;
 509
 510     case KeyEvent.VK_DELETE:
 511     case KeyEvent.VK_BACK_SPACE:
 512       if (viewport.cursorMode)
 513       {
 514         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 515                 || evt.isShiftDown() || evt.isAltDown());
 516       }
 517       else
 518       {
 519         cut_actionPerformed();
 520         alignPanel.seqPanel.seqCanvas.repaint();
 521       }
 522       break;
 523
 524     case KeyEvent.VK_S:
 525       if (viewport.cursorMode)
 526       {
 527         alignPanel.seqPanel.setCursorRow();
 528       }
 529       break;
 530     case KeyEvent.VK_P:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.setCursorPosition();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_ENTER:
 538     case KeyEvent.VK_COMMA:
 539       if (viewport.cursorMode)
 540       {
 541         alignPanel.seqPanel.setCursorRowAndColumn();
 542       }
 543       break;
 544
 545     case KeyEvent.VK_Q:
 546       if (viewport.cursorMode)
 547       {
 548         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 549       }
 550       break;
 551     case KeyEvent.VK_M:
 552       if (viewport.cursorMode)
 553       {
 554         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 555       }
 556       break;
 557
 558     case KeyEvent.VK_F2:
 559       viewport.cursorMode = !viewport.cursorMode;
 560       statusBar.setText(MessageManager.formatMessage(
 561               "label.keyboard_editing_mode",
 562               new String[] { (viewport.cursorMode ? "on" : "off") }));
 563       if (viewport.cursorMode)
 564       {
 565         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 566         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 567       }
 568       break;
 569
 570     case KeyEvent.VK_F:
 571       if (evt.isControlDown())
 572       {
 573         findMenuItem_actionPerformed();
 574       }
 575       break;
 576
 577     case KeyEvent.VK_H:
 578     {
 579       boolean toggleSeqs = !evt.isControlDown();
 580       boolean toggleCols = !evt.isShiftDown();
 581       toggleHiddenRegions(toggleSeqs, toggleCols);
 582       break;
 583     }
 584
 585     case KeyEvent.VK_PAGE_UP:
 586       if (viewport.getWrapAlignment())
 587       {
 588         alignPanel.scrollUp(true);
 589       }
 590       else
 591       {
 592         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 593                 - viewport.endSeq + viewport.startSeq);
 594       }
 595       break;
 596
 597     case KeyEvent.VK_PAGE_DOWN:
 598       if (viewport.getWrapAlignment())
 599       {
 600         alignPanel.scrollUp(false);
 601       }
 602       else
 603       {
 604         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 605                 + viewport.endSeq - viewport.startSeq);
 606       }
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if ((viewport.getColumnSelection() != null
 712               && viewport.getColumnSelection().getSelected() != null && viewport
 713               .getColumnSelection().getSelected().size() > 0)
 714               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 715                       .getEndRes()))
 716       {
 717         // now invert the sequence set, if required - empty selection implies
 718         // that no hiding is required.
 719         if (sg != null)
 720         {
 721           invertSequenceMenuItem_actionPerformed();
 722           sg = viewport.getSelectionGroup();
 723           toggleSeqs = true;
 724
 725         }
 726         viewport.expandColSelection(sg, true);
 727         // finally invert the column selection and get the new sequence
 728         // selection and indicate it should be hidden.
 729         invertColSel_actionPerformed();
 730         toggleCols = true;
 731       }
 732     }
 733
 734     if (toggleSeqs)
 735     {
 736       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 737       {
 738         hide = true;
 739         viewport.hideAllSelectedSeqs();
 740       }
 741       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 742               .size() > 0))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.getColumnSelection().getSelected().size() > 0)
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762     }
 763   }
 764
 765   @Override
 766   public void keyReleased(KeyEvent evt)
 767   {
 768   }
 769
 770   @Override
 771   public void keyTyped(KeyEvent evt)
 772   {
 773   }
 774
 775   @Override
 776   public void itemStateChanged(ItemEvent evt)
 777   {
 778     final Object source = evt.getSource();
 779     if (source == displayNonconservedMenuItem)
 780     {
 781       displayNonconservedMenuItem_actionPerformed();
 782     }
 783     else if (source == colourTextMenuItem)
 784     {
 785       colourTextMenuItem_actionPerformed();
 786     }
 787     else if (source == wrapMenuItem)
 788     {
 789       wrapMenuItem_actionPerformed();
 790     }
 791     else if (source == scaleAbove)
 792     {
 793       viewport.setScaleAboveWrapped(scaleAbove.getState());
 794     }
 795     else if (source == scaleLeft)
 796     {
 797       viewport.setScaleLeftWrapped(scaleLeft.getState());
 798     }
 799     else if (source == scaleRight)
 800     {
 801       viewport.setScaleRightWrapped(scaleRight.getState());
 802     }
 803     else if (source == seqLimits)
 804     {
 805       seqLimits_itemStateChanged();
 806     }
 807     else if (source == viewBoxesMenuItem)
 808     {
 809       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 810     }
 811     else if (source == viewTextMenuItem)
 812     {
 813       viewport.setShowText(viewTextMenuItem.getState());
 814     }
 815     else if (source == renderGapsMenuItem)
 816     {
 817       viewport.setRenderGaps(renderGapsMenuItem.getState());
 818     }
 819     else if (source == annotationPanelMenuItem)
 820     {
 821       boolean showAnnotations = annotationPanelMenuItem.getState();
 822       showAlignmentAnnotations.setEnabled(showAnnotations);
 823       showSequenceAnnotations.setEnabled(showAnnotations);
 824       viewport.setShowAnnotation(showAnnotations);
 825       alignPanel.setAnnotationVisible(showAnnotations);
 826     }
 827     else if (source == sequenceFeatures)
 828     {
 829       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 830       alignPanel.seqPanel.seqCanvas.repaint();
 831     }
 832     else if (source == showAlignmentAnnotations)
 833     {
 834       setAnnotationsVisibility();
 835     }
 836     else if (source == showSequenceAnnotations)
 837     {
 838       setAnnotationsVisibility();
 839     }
 840     else if (source == sortAnnBySequence)
 841     {
 842       boolean newState = sortAnnBySequence.getState();
 843       sortAnnByLabel.setState(false);
 844       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 845               : SequenceAnnotationOrder.NONE);
 846       setViewportAnnotationOrder();
 847     }
 848     else if (source == sortAnnByLabel)
 849     {
 850       boolean newState = sortAnnByLabel.getState();
 851       sortAnnBySequence.setState(false);
 852       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 853               : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == showAutoFirst)
 857     {
 858       showAutoLast.setState(!showAutoFirst.getState());
 859       setShowAutoCalculatedAbove(showAutoFirst.getState());
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == showAutoLast)
 863     {
 864       showAutoFirst.setState(!showAutoLast.getState());
 865       setShowAutoCalculatedAbove(showAutoFirst.getState());
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == conservationMenuItem)
 869     {
 870       conservationMenuItem_actionPerformed();
 871     }
 872     else if (source == abovePIDThreshold)
 873     {
 874       abovePIDThreshold_actionPerformed();
 875     }
 876     else if (source == applyToAllGroups)
 877     {
 878       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 879     }
 880     else if (source == autoCalculate)
 881     {
 882       viewport.autoCalculateConsensus = autoCalculate.getState();
 883     }
 884     else if (source == sortByTree)
 885     {
 886       viewport.sortByTree = sortByTree.getState();
 887     }
 888     else if (source == this.centreColumnLabelFlag)
 889     {
 890       centreColumnLabelFlag_stateChanged();
 891     }
 892     else if (source == this.followMouseOverFlag)
 893     {
 894       mouseOverFlag_stateChanged();
 895     }
 896     else if (source == showGroupConsensus)
 897     {
 898       showGroupConsensus_actionPerformed();
 899     }
 900     else if (source == showGroupConservation)
 901     {
 902       showGroupConservation_actionPerformed();
 903     }
 904     else if (source == showSequenceLogo)
 905     {
 906       showSequenceLogo_actionPerformed();
 907     }
 908     else if (source == normSequenceLogo)
 909     {
 910       normSequenceLogo_actionPerformed();
 911     }
 912     else if (source == showConsensusHistogram)
 913     {
 914       showConsensusHistogram_actionPerformed();
 915     }
 916     else if (source == applyAutoAnnotationSettings)
 917     {
 918       applyAutoAnnotationSettings_actionPerformed();
 919     }
 920     alignPanel.paintAlignment(true);
 921   }
 922
 923   /**
 924    * Set the visibility state of sequence-related and/or alignment-related
 925    * annotations depending on checkbox selections, and repaint.
 926    *
 927    * @param visible
 928    */
 929   private void setAnnotationsVisibility()
 930   {
 931     boolean showForAlignment = showAlignmentAnnotations.getState();
 932     boolean showForSequences = showSequenceAnnotations.getState();
 933     for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934             .getAlignmentAnnotation())
 935     {
 936       boolean visible = (aa.sequenceRef == null ? showForAlignment
 937               : showForSequences);
 938       aa.visible = visible;
 939     }
 940     alignPanel.validateAnnotationDimensions(true);
 941     validate();
 942     repaint();
 943   }
 944
 945   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 946   {
 947     this.annotationSortOrder = order;
 948   }
 949
 950   /**
 951    * Set flags on the viewport that control annotation ordering
 952    */
 953   private void setViewportAnnotationOrder()
 954   {
 955     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 956     this.alignPanel.av
 957             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 958   }
 959
 960   private void setShowAutoCalculatedAbove(boolean showAbove)
 961   {
 962     this.showAutoCalculatedAbove = showAbove;
 963   }
 964
 965   private void mouseOverFlag_stateChanged()
 966   {
 967     viewport.setFollowHighlight(followMouseOverFlag.getState());
 968     // TODO: could kick the scrollTo mechanism to reset view for current
 969     // searchresults.
 970   }
 971
 972   private void centreColumnLabelFlag_stateChanged()
 973   {
 974     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 975     this.alignPanel.annotationPanel.repaint();
 976   }
 977
 978   @Override
 979   public void actionPerformed(ActionEvent evt)
 980   {
 981     viewport.applet.currentAlignFrame = this;
 982
 983     Object source = evt.getSource();
 984
 985     if (source == inputText)
 986     {
 987       inputText_actionPerformed();
 988     }
 989     else if (source == loadTree)
 990     {
 991       loadTree_actionPerformed();
 992     }
 993     else if (source == loadApplication)
 994     {
 995       launchFullApplication();
 996     }
 997     else if (source == loadAnnotations)
 998     {
 999       loadAnnotations();
1000     }
1001     else if (source == outputAnnotations)
1002     {
1003       outputAnnotations(true);
1004     }
1005     else if (source == outputFeatures)
1006     {
1007       outputFeatures(true, "Jalview");
1008     }
1009     else if (source == closeMenuItem)
1010     {
1011       closeMenuItem_actionPerformed();
1012     }
1013     else if (source == copy)
1014     {
1015       copy_actionPerformed();
1016     }
1017     else if (source == undoMenuItem)
1018     {
1019       undoMenuItem_actionPerformed();
1020     }
1021     else if (source == redoMenuItem)
1022     {
1023       redoMenuItem_actionPerformed();
1024     }
1025     else if (source == inputText)
1026     {
1027       inputText_actionPerformed();
1028     }
1029     else if (source == closeMenuItem)
1030     {
1031       closeMenuItem_actionPerformed();
1032     }
1033     else if (source == undoMenuItem)
1034     {
1035       undoMenuItem_actionPerformed();
1036     }
1037     else if (source == redoMenuItem)
1038     {
1039       redoMenuItem_actionPerformed();
1040     }
1041     else if (source == copy)
1042     {
1043       copy_actionPerformed();
1044     }
1045     else if (source == pasteNew)
1046     {
1047       pasteNew_actionPerformed();
1048     }
1049     else if (source == pasteThis)
1050     {
1051       pasteThis_actionPerformed();
1052     }
1053     else if (source == cut)
1054     {
1055       cut_actionPerformed();
1056     }
1057     else if (source == delete)
1058     {
1059       delete_actionPerformed();
1060     }
1061     else if (source == grpsFromSelection)
1062     {
1063       makeGrpsFromSelection_actionPerformed();
1064     }
1065     else if (source == deleteGroups)
1066     {
1067       deleteGroups_actionPerformed();
1068     }
1069     else if (source == selectAllSequenceMenuItem)
1070     {
1071       selectAllSequenceMenuItem_actionPerformed();
1072     }
1073     else if (source == deselectAllSequenceMenuItem)
1074     {
1075       deselectAllSequenceMenuItem_actionPerformed();
1076     }
1077     else if (source == invertSequenceMenuItem)
1078     {
1079       invertSequenceMenuItem_actionPerformed();
1080     }
1081     else if (source == invertColSel)
1082     {
1083       viewport.invertColumnSelection();
1084       alignPanel.paintAlignment(true);
1085     }
1086     else if (source == remove2LeftMenuItem)
1087     {
1088       trimAlignment(true);
1089     }
1090     else if (source == remove2RightMenuItem)
1091     {
1092       trimAlignment(false);
1093     }
1094     else if (source == removeGappedColumnMenuItem)
1095     {
1096       removeGappedColumnMenuItem_actionPerformed();
1097     }
1098     else if (source == removeAllGapsMenuItem)
1099     {
1100       removeAllGapsMenuItem_actionPerformed();
1101     }
1102     else if (source == findMenuItem)
1103     {
1104       findMenuItem_actionPerformed();
1105     }
1106     else if (source == font)
1107     {
1108       new FontChooser(alignPanel);
1109     }
1110     else if (source == newView)
1111     {
1112       newView(null);
1113     }
1114     else if (source == showColumns)
1115     {
1116       viewport.showAllHiddenColumns();
1117       alignPanel.paintAlignment(true);
1118     }
1119     else if (source == showSeqs)
1120     {
1121       viewport.showAllHiddenSeqs();
1122       alignPanel.paintAlignment(true);
1123     }
1124     else if (source == hideColumns)
1125     {
1126       viewport.hideSelectedColumns();
1127       alignPanel.paintAlignment(true);
1128     }
1129     else if (source == hideSequences
1130             && viewport.getSelectionGroup() != null)
1131     {
1132       viewport.hideAllSelectedSeqs();
1133       alignPanel.paintAlignment(true);
1134     }
1135     else if (source == hideAllButSelection)
1136     {
1137       toggleHiddenRegions(false, false);
1138       alignPanel.paintAlignment(true);
1139     }
1140     else if (source == hideAllSelection)
1141     {
1142       SequenceGroup sg = viewport.getSelectionGroup();
1143       viewport.expandColSelection(sg, false);
1144       viewport.hideAllSelectedSeqs();
1145       viewport.hideSelectedColumns();
1146       alignPanel.paintAlignment(true);
1147     }
1148     else if (source == showAllHidden)
1149     {
1150       viewport.showAllHiddenColumns();
1151       viewport.showAllHiddenSeqs();
1152       alignPanel.paintAlignment(true);
1153     }
1154     else if (source == showGroupConsensus)
1155     {
1156       showGroupConsensus_actionPerformed();
1157     }
1158     else if (source == showGroupConservation)
1159     {
1160       showGroupConservation_actionPerformed();
1161     }
1162     else if (source == showSequenceLogo)
1163     {
1164       showSequenceLogo_actionPerformed();
1165     }
1166     else if (source == normSequenceLogo)
1167     {
1168       normSequenceLogo_actionPerformed();
1169     }
1170     else if (source == showConsensusHistogram)
1171     {
1172       showConsensusHistogram_actionPerformed();
1173     }
1174     else if (source == applyAutoAnnotationSettings)
1175     {
1176       applyAutoAnnotationSettings_actionPerformed();
1177     }
1178     else if (source == featureSettings)
1179     {
1180       new FeatureSettings(alignPanel);
1181     }
1182     else if (source == alProperties)
1183     {
1184       StringBuffer contents = new jalview.io.AlignmentProperties(
1185               viewport.getAlignment()).formatAsString();
1186       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1187       cap.setText(contents.toString());
1188       Frame frame = new Frame();
1189       frame.add(cap);
1190       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1191               "label.alignment_properties", new String[] { getTitle() }),
1192               400, 250);
1193     }
1194     else if (source == overviewMenuItem)
1195     {
1196       overviewMenuItem_actionPerformed();
1197     }
1198     else if (source == noColourmenuItem)
1199     {
1200       changeColour(null);
1201     }
1202     else if (source == clustalColour)
1203     {
1204       abovePIDThreshold.setState(false);
1205       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1206     }
1207     else if (source == zappoColour)
1208     {
1209       changeColour(new ZappoColourScheme());
1210     }
1211     else if (source == taylorColour)
1212     {
1213       changeColour(new TaylorColourScheme());
1214     }
1215     else if (source == hydrophobicityColour)
1216     {
1217       changeColour(new HydrophobicColourScheme());
1218     }
1219     else if (source == helixColour)
1220     {
1221       changeColour(new HelixColourScheme());
1222     }
1223     else if (source == strandColour)
1224     {
1225       changeColour(new StrandColourScheme());
1226     }
1227     else if (source == turnColour)
1228     {
1229       changeColour(new TurnColourScheme());
1230     }
1231     else if (source == buriedColour)
1232     {
1233       changeColour(new BuriedColourScheme());
1234     }
1235     else if (source == nucleotideColour)
1236     {
1237       changeColour(new NucleotideColourScheme());
1238     }
1239     else if (source == purinePyrimidineColour)
1240     {
1241       changeColour(new PurinePyrimidineColourScheme());
1242     }
1243     // else if (source == RNAInteractionColour)
1244     // {
1245     // changeColour(new RNAInteractionColourScheme());
1246     // }
1247     else if (source == RNAHelixColour)
1248     {
1249       new RNAHelicesColourChooser(viewport, alignPanel);
1250     }
1251     else if (source == modifyPID)
1252     {
1253       modifyPID_actionPerformed();
1254     }
1255     else if (source == modifyConservation)
1256     {
1257       modifyConservation_actionPerformed();
1258     }
1259     else if (source == userDefinedColour)
1260     {
1261       new UserDefinedColours(alignPanel, null);
1262     }
1263     else if (source == PIDColour)
1264     {
1265       changeColour(new PIDColourScheme());
1266     }
1267     else if (source == BLOSUM62Colour)
1268     {
1269       changeColour(new Blosum62ColourScheme());
1270     }
1271     else if (source == tcoffeeColour)
1272     {
1273       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1274     }
1275     else if (source == annotationColour)
1276     {
1277       new AnnotationColourChooser(viewport, alignPanel);
1278     }
1279     else if (source == annotationColumnSelection)
1280     {
1281       new AnnotationColumnChooser(viewport, alignPanel);
1282     }
1283     else if (source == sortPairwiseMenuItem)
1284     {
1285       sortPairwiseMenuItem_actionPerformed();
1286     }
1287     else if (source == sortIDMenuItem)
1288     {
1289       sortIDMenuItem_actionPerformed();
1290     }
1291     else if (source == sortLengthMenuItem)
1292     {
1293       sortLengthMenuItem_actionPerformed();
1294     }
1295     else if (source == sortGroupMenuItem)
1296     {
1297       sortGroupMenuItem_actionPerformed();
1298     }
1299     else if (source == removeRedundancyMenuItem)
1300     {
1301       removeRedundancyMenuItem_actionPerformed();
1302     }
1303     else if (source == pairwiseAlignmentMenuItem)
1304     {
1305       pairwiseAlignmentMenuItem_actionPerformed();
1306     }
1307     else if (source == PCAMenuItem)
1308     {
1309       PCAMenuItem_actionPerformed();
1310     }
1311     else if (source == averageDistanceTreeMenuItem)
1312     {
1313       averageDistanceTreeMenuItem_actionPerformed();
1314     }
1315     else if (source == neighbourTreeMenuItem)
1316     {
1317       neighbourTreeMenuItem_actionPerformed();
1318     }
1319     else if (source == njTreeBlosumMenuItem)
1320     {
1321       njTreeBlosumMenuItem_actionPerformed();
1322     }
1323     else if (source == avDistanceTreeBlosumMenuItem)
1324     {
1325       avTreeBlosumMenuItem_actionPerformed();
1326     }
1327     else if (source == documentation)
1328     {
1329       documentation_actionPerformed();
1330     }
1331     else if (source == about)
1332     {
1333       about_actionPerformed();
1334     }
1335
1336   }
1337
1338   public void inputText_actionPerformed()
1339   {
1340     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1341     Frame frame = new Frame();
1342     frame.add(cap);
1343     jalview.bin.JalviewLite.addFrame(frame,
1344             MessageManager.getString("label.input_cut_paste"), 500, 500);
1345   }
1346
1347   protected void outputText_actionPerformed(ActionEvent e)
1348   {
1349     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350     Frame frame = new Frame();
1351     frame.add(cap);
1352     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1353             "label.alignment_output_command",
1354             new Object[] { e.getActionCommand() }), 600, 500);
1355
1356     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1357     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1358             e.getActionCommand(), viewport.getAlignment(),
1359             viewport.getShowJVSuffix()));
1360   }
1361
1362   public void loadAnnotations()
1363   {
1364     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1365     cap.setText(MessageManager
1366             .getString("label.paste_features_annotations_Tcoffee_here"));
1367     cap.setAnnotationImport();
1368     Frame frame = new Frame();
1369     frame.add(cap);
1370     jalview.bin.JalviewLite.addFrame(frame,
1371             MessageManager.getString("action.paste_annotations"), 400, 300);
1372
1373   }
1374
1375   public String outputAnnotations(boolean displayTextbox)
1376   {
1377     String annotation = new AnnotationFile()
1378             .printAnnotationsForView(viewport);
1379
1380     if (displayTextbox)
1381     {
1382       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1383       Frame frame = new Frame();
1384       frame.add(cap);
1385       jalview.bin.JalviewLite.addFrame(frame,
1386               MessageManager.getString("label.annotations"), 600, 500);
1387       cap.setText(annotation);
1388     }
1389
1390     return annotation;
1391   }
1392
1393   private Map<String, Object> getDisplayedFeatureCols()
1394   {
1395     if (alignPanel.getFeatureRenderer() != null
1396             && viewport.getFeaturesDisplayed() != null)
1397     {
1398       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1399
1400     }
1401     return null;
1402   }
1403
1404   public String outputFeatures(boolean displayTextbox, String format)
1405   {
1406     String features;
1407     if (format.equalsIgnoreCase("Jalview"))
1408     {
1409       features = new FeaturesFile().printJalviewFormat(viewport
1410               .getAlignment().getSequencesArray(),
1411               getDisplayedFeatureCols());
1412     }
1413     else
1414     {
1415       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1416               .getSequencesArray(), getDisplayedFeatureCols());
1417     }
1418
1419     if (displayTextbox)
1420     {
1421       boolean frimport = false;
1422       if (features == null || features.equals("No Features Visible"))
1423       {
1424         features = "# No features visible - paste some and import them here.";
1425         frimport = true;
1426       }
1427
1428       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1429       if (frimport)
1430       {
1431         cap.setAnnotationImport();
1432       }
1433       Frame frame = new Frame();
1434       frame.add(cap);
1435       jalview.bin.JalviewLite.addFrame(frame,
1436               MessageManager.getString("label.features"), 600, 500);
1437       cap.setText(features);
1438     }
1439     else
1440     {
1441       if (features == null)
1442       {
1443         features = "";
1444       }
1445     }
1446
1447     return features;
1448   }
1449
1450   void launchFullApplication()
1451   {
1452     StringBuffer url = new StringBuffer(jalviewServletURL);
1453
1454     // allow servlet parameters to be passed in applet parameter
1455     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1456             : "?";
1457     url.append(firstSep);
1458
1459     url.append("open="
1460             + appendProtocol(viewport.applet.getParameter("file")));
1461
1462     if (viewport.applet.getParameter("features") != null)
1463     {
1464       url.append("&features=");
1465       url.append(appendProtocol(viewport.applet.getParameter("features")));
1466     }
1467
1468     if (viewport.applet.getParameter("annotations") != null)
1469     {
1470       url.append("&annotations=");
1471       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1472     }
1473
1474     if (viewport.applet.getParameter("jnetfile") != null)
1475     {
1476       url.append("&annotations=");
1477       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1478     }
1479
1480     if (viewport.applet.getParameter("defaultColour") != null)
1481     {
1482       url.append("&colour="
1483               + removeWhiteSpace(viewport.applet
1484                       .getParameter("defaultColour")));
1485     }
1486
1487     if (viewport.applet.getParameter("userDefinedColour") != null)
1488     {
1489       url.append("&colour="
1490               + removeWhiteSpace(viewport.applet
1491                       .getParameter("userDefinedColour")));
1492     }
1493     if (viewport.applet.getParameter("tree") != null)
1494     {
1495       url.append("&tree="
1496               + appendProtocol(viewport.applet.getParameter("tree")));
1497     }
1498     if (viewport.applet.getParameter("treeFile") != null)
1499     {
1500       url.append("&tree="
1501               + appendProtocol(viewport.applet.getParameter("treeFile")));
1502     }
1503
1504     showURL(url.toString(), "FULL_APP");
1505   }
1506
1507   String removeWhiteSpace(String colour)
1508   {
1509     StringBuffer sb = new StringBuffer();
1510     for (int i = 0; i < colour.length(); i++)
1511     {
1512       if (Character.isWhitespace(colour.charAt(i)))
1513       {
1514         sb.append("%20");
1515       }
1516       else
1517       {
1518         sb.append(colour.charAt(i));
1519       }
1520     }
1521
1522     return sb.toString();
1523   }
1524
1525   String appendProtocol(String url)
1526   {
1527     try
1528     {
1529       new URL(url);
1530       url = URLEncoder.encode(url);
1531     }
1532     /*
1533      * When we finally deprecate 1.1 compatibility, we can start to use
1534      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1535      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1536      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1537      * ex.printStackTrace(); }
1538      */
1539     catch (java.net.MalformedURLException ex)
1540     {
1541       url = viewport.applet.getCodeBase() + url;
1542     }
1543     return url;
1544   }
1545
1546   public void closeMenuItem_actionPerformed()
1547   {
1548     PaintRefresher.RemoveComponent(alignPanel);
1549     if (alignPanel.seqPanel != null
1550             && alignPanel.seqPanel.seqCanvas != null)
1551     {
1552       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1553     }
1554     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1555     {
1556       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1557     }
1558
1559     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1560     {
1561       System.exit(0);
1562     }
1563     else
1564     {
1565     }
1566     viewport = null;
1567     alignPanel = null;
1568     this.dispose();
1569   }
1570
1571   /**
1572    * TODO: JAL-1104
1573    */
1574   void updateEditMenuBar()
1575   {
1576
1577     if (viewport.getHistoryList().size() > 0)
1578     {
1579       undoMenuItem.setEnabled(true);
1580       CommandI command = viewport.getHistoryList().peek();
1581       undoMenuItem.setLabel(MessageManager.formatMessage(
1582               "label.undo_command",
1583               new Object[] { command.getDescription() }));
1584     }
1585     else
1586     {
1587       undoMenuItem.setEnabled(false);
1588       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1589     }
1590
1591     if (viewport.getRedoList().size() > 0)
1592     {
1593       redoMenuItem.setEnabled(true);
1594
1595       CommandI command = viewport.getRedoList().peek();
1596       redoMenuItem.setLabel(MessageManager.formatMessage(
1597               "label.redo_command",
1598               new Object[] { command.getDescription() }));
1599     }
1600     else
1601     {
1602       redoMenuItem.setEnabled(false);
1603       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1604     }
1605   }
1606
1607   /**
1608    * TODO: JAL-1104
1609    */
1610   @Override
1611   public void addHistoryItem(CommandI command)
1612   {
1613     if (command.getSize() > 0)
1614     {
1615       viewport.addToHistoryList(command);
1616       viewport.clearRedoList();
1617       updateEditMenuBar();
1618       viewport.updateHiddenColumns();
1619     }
1620   }
1621
1622   /**
1623    * TODO: JAL-1104 DOCUMENT ME!
1624    *
1625    * @param e
1626    *          DOCUMENT ME!
1627    */
1628   protected void undoMenuItem_actionPerformed()
1629   {
1630     if (viewport.getHistoryList().isEmpty())
1631     {
1632       return;
1633     }
1634
1635     CommandI command = viewport.getHistoryList().pop();
1636     viewport.addToRedoList(command);
1637     command.undoCommand(null);
1638
1639     AlignmentViewport originalSource = getOriginatingSource(command);
1640     // JBPNote Test
1641     if (originalSource != viewport)
1642     {
1643       System.err
1644               .println("Warning: Viewport object mismatch whilst undoing");
1645     }
1646     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1647                                           // viewport.getColumnSelection().getHiddenColumns()
1648                                           // != null;
1649     updateEditMenuBar();
1650     originalSource.firePropertyChange("alignment", null, originalSource
1651             .getAlignment().getSequences());
1652   }
1653
1654   /**
1655    * TODO: JAL-1104 DOCUMENT ME!
1656    *
1657    * @param e
1658    *          DOCUMENT ME!
1659    */
1660   protected void redoMenuItem_actionPerformed()
1661   {
1662     if (viewport.getRedoList().isEmpty())
1663     {
1664       return;
1665     }
1666
1667     CommandI command = viewport.getRedoList().pop();
1668     viewport.addToHistoryList(command);
1669     command.doCommand(null);
1670
1671     AlignmentViewport originalSource = getOriginatingSource(command);
1672     // JBPNote Test
1673     if (originalSource != viewport)
1674     {
1675       System.err
1676               .println("Warning: Viewport object mismatch whilst re-doing");
1677     }
1678     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1679                                           // viewport.getColumnSelection().getHiddenColumns()
1680                                           // != null;
1681
1682     updateEditMenuBar();
1683     originalSource.firePropertyChange("alignment", null, originalSource
1684             .getAlignment().getSequences());
1685   }
1686
1687   AlignmentViewport getOriginatingSource(CommandI command)
1688   {
1689     AlignmentViewport originalSource = null;
1690     // For sequence removal and addition, we need to fire
1691     // the property change event FROM the viewport where the
1692     // original alignment was altered
1693     AlignmentI al = null;
1694     if (command instanceof EditCommand)
1695     {
1696       EditCommand editCommand = (EditCommand) command;
1697       al = editCommand.getAlignment();
1698       Vector comps = (Vector) PaintRefresher.components.get(viewport
1699               .getSequenceSetId());
1700       for (int i = 0; i < comps.size(); i++)
1701       {
1702         if (comps.elementAt(i) instanceof AlignmentPanel)
1703         {
1704           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1705           {
1706             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1707             break;
1708           }
1709         }
1710       }
1711     }
1712
1713     if (originalSource == null)
1714     {
1715       // The original view is closed, we must validate
1716       // the current view against the closed view first
1717       if (al != null)
1718       {
1719         PaintRefresher.validateSequences(al, viewport.getAlignment());
1720       }
1721
1722       originalSource = viewport;
1723     }
1724
1725     return originalSource;
1726   }
1727
1728   /**
1729    * Move the currently selected sequences up or down one position in the
1730    * alignment
1731    *
1732    * @param up
1733    */
1734   public void moveSelectedSequences(boolean up)
1735   {
1736     SequenceGroup sg = viewport.getSelectionGroup();
1737     if (sg == null)
1738     {
1739       return;
1740     }
1741     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1742             up ? null : viewport.getHiddenRepSequences(), up);
1743     alignPanel.paintAlignment(true);
1744
1745     /*
1746      * Also move cDNA/protein complement sequences
1747      */
1748     AlignViewportI complement = viewport.getCodingComplement();
1749     if (complement != null)
1750     {
1751       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1752               viewport, complement);
1753       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1754               up ? null : complement.getHiddenRepSequences(), up);
1755       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1756     }
1757   }
1758
1759   synchronized void slideSequences(boolean right, int size)
1760   {
1761     List<SequenceI> sg = new Vector<SequenceI>();
1762     if (viewport.cursorMode)
1763     {
1764       sg.add(viewport.getAlignment().getSequenceAt(
1765               alignPanel.seqPanel.seqCanvas.cursorY));
1766     }
1767     else if (viewport.getSelectionGroup() != null
1768             && viewport.getSelectionGroup().getSize() != viewport
1769                     .getAlignment().getHeight())
1770     {
1771       sg = viewport.getSelectionGroup().getSequences(
1772               viewport.getHiddenRepSequences());
1773     }
1774
1775     if (sg.size() < 1)
1776     {
1777       return;
1778     }
1779
1780     Vector<SequenceI> invertGroup = new Vector();
1781
1782     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1783     {
1784       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1785       {
1786         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1787       }
1788     }
1789
1790     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1791
1792     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1793             .size()]);
1794     for (int i = 0; i < invertGroup.size(); i++)
1795     {
1796       seqs2[i] = invertGroup.elementAt(i);
1797     }
1798
1799     SlideSequencesCommand ssc;
1800     if (right)
1801     {
1802       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1803               size, viewport.getGapCharacter());
1804     }
1805     else
1806     {
1807       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1808               size, viewport.getGapCharacter());
1809     }
1810
1811     int groupAdjustment = 0;
1812     if (ssc.getGapsInsertedBegin() && right)
1813     {
1814       if (viewport.cursorMode)
1815       {
1816         alignPanel.seqPanel.moveCursor(size, 0);
1817       }
1818       else
1819       {
1820         groupAdjustment = size;
1821       }
1822     }
1823     else if (!ssc.getGapsInsertedBegin() && !right)
1824     {
1825       if (viewport.cursorMode)
1826       {
1827         alignPanel.seqPanel.moveCursor(-size, 0);
1828       }
1829       else
1830       {
1831         groupAdjustment = -size;
1832       }
1833     }
1834
1835     if (groupAdjustment != 0)
1836     {
1837       viewport.getSelectionGroup().setStartRes(
1838               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1839       viewport.getSelectionGroup().setEndRes(
1840               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1841     }
1842
1843     boolean appendHistoryItem = false;
1844     Deque<CommandI> historyList = viewport.getHistoryList();
1845     if (historyList != null && historyList.size() > 0
1846             && historyList.peek() instanceof SlideSequencesCommand)
1847     {
1848       appendHistoryItem = ssc
1849               .appendSlideCommand((SlideSequencesCommand) historyList
1850                       .peek());
1851     }
1852
1853     if (!appendHistoryItem)
1854     {
1855       addHistoryItem(ssc);
1856     }
1857
1858     repaint();
1859   }
1860
1861   static StringBuffer copiedSequences;
1862
1863   static Vector copiedHiddenColumns;
1864
1865   protected void copy_actionPerformed()
1866   {
1867     if (viewport.getSelectionGroup() == null)
1868     {
1869       return;
1870     }
1871
1872     SequenceGroup sg = viewport.getSelectionGroup();
1873     copiedSequences = new StringBuffer();
1874     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1875     for (int i = 0; i < sg.getSize(); i++)
1876     {
1877       SequenceI seq = sg.getSequenceAt(i);
1878       int index = viewport.getAlignment().findIndex(seq);
1879       orderedSeqs.put(index, seq);
1880     }
1881
1882     int index = 0, startRes, endRes;
1883     char ch;
1884
1885     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1886     {
1887       copiedHiddenColumns = new Vector();
1888       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1889       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1890       {
1891         copiedHiddenColumns.addElement(new int[] {
1892             region[0] - hiddenOffset, region[1] - hiddenOffset });
1893       }
1894     }
1895     else
1896     {
1897       copiedHiddenColumns = null;
1898     }
1899
1900     for (int i = 0; i < sg.getSize(); i++)
1901     {
1902       SequenceI seq = null;
1903
1904       while (seq == null)
1905       {
1906         if (orderedSeqs.containsKey(index))
1907         {
1908           seq = orderedSeqs.get(index);
1909           index++;
1910           break;
1911         }
1912         else
1913         {
1914           index++;
1915         }
1916       }
1917
1918       // FIND START RES
1919       // Returns residue following index if gap
1920       startRes = seq.findPosition(sg.getStartRes());
1921
1922       // FIND END RES
1923       // Need to find the residue preceeding index if gap
1924       endRes = 0;
1925
1926       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1927       {
1928         ch = seq.getCharAt(j);
1929         if (!jalview.util.Comparison.isGap((ch)))
1930         {
1931           endRes++;
1932         }
1933       }
1934
1935       if (endRes > 0)
1936       {
1937         endRes += seq.getStart() - 1;
1938       }
1939
1940       copiedSequences.append(seq.getName()
1941               + "\t"
1942               + startRes
1943               + "\t"
1944               + endRes
1945               + "\t"
1946               + seq.getSequenceAsString(sg.getStartRes(),
1947                       sg.getEndRes() + 1) + "\n");
1948     }
1949
1950   }
1951
1952   protected void pasteNew_actionPerformed()
1953   {
1954     paste(true);
1955   }
1956
1957   protected void pasteThis_actionPerformed()
1958   {
1959     paste(false);
1960   }
1961
1962   void paste(boolean newAlignment)
1963   {
1964     try
1965     {
1966
1967       if (copiedSequences == null)
1968       {
1969         return;
1970       }
1971
1972       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1973       Vector seqs = new Vector();
1974       while (st.hasMoreElements())
1975       {
1976         String name = st.nextToken();
1977         int start = Integer.parseInt(st.nextToken());
1978         int end = Integer.parseInt(st.nextToken());
1979         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1980       }
1981       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1982       for (int i = 0; i < seqs.size(); i++)
1983       {
1984         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1985       }
1986
1987       if (newAlignment)
1988       {
1989         String newtitle = MessageManager
1990                 .getString("label.copied_sequences");
1991         if (getTitle().startsWith(
1992                 MessageManager.getString("label.copied_sequences")))
1993         {
1994           newtitle = getTitle();
1995         }
1996         else
1997         {
1998           newtitle = newtitle.concat(MessageManager.formatMessage(
1999                   "label.from_msname", new String[] { getTitle() }));
2000         }
2001         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2002                 viewport.applet, newtitle, false);
2003         if (copiedHiddenColumns != null)
2004         {
2005           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2006           {
2007             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2008             af.viewport.hideColumns(region[0], region[1]);
2009           }
2010         }
2011
2012         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2013                 frameHeight);
2014       }
2015       else
2016       {
2017         addSequences(newSeqs);
2018       }
2019
2020     } catch (Exception ex)
2021     {
2022     } // could be anything being pasted in here
2023
2024   }
2025
2026   void addSequences(SequenceI[] seqs)
2027   {
2028     for (int i = 0; i < seqs.length; i++)
2029     {
2030       viewport.getAlignment().addSequence(seqs[i]);
2031     }
2032
2033     // !newAlignment
2034     addHistoryItem(new EditCommand(
2035             MessageManager.getString("label.add_sequences"), Action.PASTE,
2036             seqs, 0, viewport.getAlignment().getWidth(),
2037             viewport.getAlignment()));
2038
2039     viewport.setEndSeq(viewport.getAlignment().getHeight());
2040     viewport.getAlignment().getWidth();
2041     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2042             .getSequences());
2043
2044   }
2045
2046   protected void cut_actionPerformed()
2047   {
2048     copy_actionPerformed();
2049     delete_actionPerformed();
2050   }
2051
2052   protected void delete_actionPerformed()
2053   {
2054
2055     SequenceGroup sg = viewport.getSelectionGroup();
2056     if (sg == null)
2057     {
2058       return;
2059     }
2060
2061     Vector seqs = new Vector();
2062     SequenceI seq;
2063     for (int i = 0; i < sg.getSize(); i++)
2064     {
2065       seq = sg.getSequenceAt(i);
2066       seqs.addElement(seq);
2067     }
2068
2069     /*
2070      * If the cut affects all sequences, warn, remove highlighted columns
2071      */
2072     if (sg.getSize() == viewport.getAlignment().getHeight())
2073     {
2074       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2075               .getAlignment().getWidth()) ? true : false;
2076       if (isEntireAlignWidth)
2077       {
2078         String title = MessageManager.getString("label.delete_all");
2079         Panel infoPanel = new Panel();
2080         infoPanel.setLayout(new FlowLayout());
2081         infoPanel
2082                 .add(new Label(MessageManager.getString("warn.delete_all")));
2083
2084         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2085         dialog.setMainPanel(infoPanel);
2086         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2087         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2088         dialog.setVisible(true);
2089
2090         if (!dialog.accept)
2091         {
2092           return;
2093         }
2094       }
2095       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2096               sg.getEndRes() + 1);
2097     }
2098
2099     SequenceI[] cut = new SequenceI[seqs.size()];
2100     for (int i = 0; i < seqs.size(); i++)
2101     {
2102       cut[i] = (SequenceI) seqs.elementAt(i);
2103     }
2104
2105     /*
2106      * //ADD HISTORY ITEM
2107      */
2108     addHistoryItem(new EditCommand(
2109             MessageManager.getString("label.cut_sequences"), Action.CUT,
2110             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2111             viewport.getAlignment()));
2112
2113     viewport.setSelectionGroup(null);
2114     viewport.getAlignment().deleteGroup(sg);
2115
2116     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2117             .getSequences());
2118
2119     if (viewport.getAlignment().getHeight() < 1)
2120     {
2121       this.setVisible(false);
2122     }
2123     viewport.sendSelection();
2124   }
2125
2126   /**
2127    * group consensus toggled
2128    *
2129    */
2130   protected void showGroupConsensus_actionPerformed()
2131   {
2132     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2133     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2134
2135   }
2136
2137   /**
2138    * group conservation toggled.
2139    */
2140   protected void showGroupConservation_actionPerformed()
2141   {
2142     viewport.setShowGroupConservation(showGroupConservation.getState());
2143     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144   }
2145
2146   /*
2147    * (non-Javadoc)
2148    *
2149    * @see
2150    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2151    * .event.ActionEvent)
2152    */
2153   protected void showConsensusHistogram_actionPerformed()
2154   {
2155     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2156     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157   }
2158
2159   /*
2160    * (non-Javadoc)
2161    *
2162    * @see
2163    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2164    * .event.ActionEvent)
2165    */
2166   protected void showSequenceLogo_actionPerformed()
2167   {
2168     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2169     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170   }
2171
2172   protected void normSequenceLogo_actionPerformed()
2173   {
2174     showSequenceLogo.setState(true);
2175     viewport.setShowSequenceLogo(true);
2176     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2177     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2178   }
2179
2180   protected void applyAutoAnnotationSettings_actionPerformed()
2181   {
2182     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183   }
2184
2185   protected void makeGrpsFromSelection_actionPerformed()
2186   {
2187     if (avc.makeGroupsFromSelection())
2188     {
2189       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2190       alignPanel.updateAnnotation();
2191       alignPanel.paintAlignment(true);
2192     }
2193   }
2194
2195   protected void createGroup_actionPerformed()
2196   {
2197     avc.createGroup();
2198   }
2199
2200   protected void unGroup_actionPerformed()
2201   {
2202     if (avc.unGroup())
2203     {
2204       alignPanel.alignmentChanged();
2205     }
2206   }
2207
2208   protected void deleteGroups_actionPerformed()
2209   {
2210     if (avc.deleteGroups())
2211     {
2212       alignPanel.alignmentChanged();
2213     }
2214   }
2215
2216   public void selectAllSequenceMenuItem_actionPerformed()
2217   {
2218     SequenceGroup sg = new SequenceGroup();
2219     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2220     {
2221       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2222     }
2223     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2224     viewport.setSelectionGroup(sg);
2225     alignPanel.paintAlignment(true);
2226     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2227     viewport.sendSelection();
2228   }
2229
2230   public void deselectAllSequenceMenuItem_actionPerformed()
2231   {
2232     if (viewport.cursorMode)
2233     {
2234       alignPanel.seqPanel.keyboardNo1 = null;
2235       alignPanel.seqPanel.keyboardNo2 = null;
2236     }
2237     viewport.setSelectionGroup(null);
2238     viewport.getColumnSelection().clear();
2239     viewport.setSelectionGroup(null);
2240     alignPanel.idPanel.idCanvas.searchResults = null;
2241     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2242     alignPanel.paintAlignment(true);
2243     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2244     viewport.sendSelection();
2245   }
2246
2247   public void invertSequenceMenuItem_actionPerformed()
2248   {
2249     SequenceGroup sg = viewport.getSelectionGroup();
2250     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2251     {
2252       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2253     }
2254
2255     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2256     viewport.sendSelection();
2257   }
2258
2259   public void invertColSel_actionPerformed()
2260   {
2261     viewport.invertColumnSelection();
2262     alignPanel.paintAlignment(true);
2263     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2264     viewport.sendSelection();
2265   }
2266
2267   void trimAlignment(boolean trimLeft)
2268   {
2269     ColumnSelection colSel = viewport.getColumnSelection();
2270     int column;
2271
2272     if (colSel.size() > 0)
2273     {
2274       if (trimLeft)
2275       {
2276         column = colSel.getMin();
2277       }
2278       else
2279       {
2280         column = colSel.getMax();
2281       }
2282
2283       SequenceI[] seqs;
2284       if (viewport.getSelectionGroup() != null)
2285       {
2286         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2287                 viewport.getHiddenRepSequences());
2288       }
2289       else
2290       {
2291         seqs = viewport.getAlignment().getSequencesArray();
2292       }
2293
2294       TrimRegionCommand trimRegion;
2295       if (trimLeft)
2296       {
2297         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2298                 column, viewport.getAlignment());
2299         viewport.setStartRes(0);
2300       }
2301       else
2302       {
2303         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2304                 column, viewport.getAlignment());
2305       }
2306
2307       statusBar.setText(MessageManager.formatMessage(
2308               "label.removed_columns",
2309               new String[] { Integer.valueOf(trimRegion.getSize())
2310                       .toString() }));
2311       addHistoryItem(trimRegion);
2312
2313       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2314       {
2315         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2316                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2317         {
2318           viewport.getAlignment().deleteGroup(sg);
2319         }
2320       }
2321
2322       viewport.firePropertyChange("alignment", null, viewport
2323               .getAlignment().getSequences());
2324     }
2325   }
2326
2327   public void removeGappedColumnMenuItem_actionPerformed()
2328   {
2329     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2330
2331     SequenceI[] seqs;
2332     if (viewport.getSelectionGroup() != null)
2333     {
2334       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335               viewport.getHiddenRepSequences());
2336       start = viewport.getSelectionGroup().getStartRes();
2337       end = viewport.getSelectionGroup().getEndRes();
2338     }
2339     else
2340     {
2341       seqs = viewport.getAlignment().getSequencesArray();
2342     }
2343
2344     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2345             "Remove Gapped Columns", seqs, start, end,
2346             viewport.getAlignment());
2347
2348     addHistoryItem(removeGapCols);
2349
2350     statusBar.setText(MessageManager.formatMessage(
2351             "label.removed_empty_columns",
2352             new String[] { Integer.valueOf(removeGapCols.getSize())
2353                     .toString() }));
2354
2355     // This is to maintain viewport position on first residue
2356     // of first sequence
2357     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2358     int startRes = seq.findPosition(viewport.startRes);
2359     // ShiftList shifts;
2360     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2361     // edit.alColumnChanges=shifts.getInverse();
2362     // if (viewport.hasHiddenColumns)
2363     // viewport.getColumnSelection().compensateForEdits(shifts);
2364     viewport.setStartRes(seq.findIndex(startRes) - 1);
2365     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2366             .getSequences());
2367
2368   }
2369
2370   public void removeAllGapsMenuItem_actionPerformed()
2371   {
2372     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2373
2374     SequenceI[] seqs;
2375     if (viewport.getSelectionGroup() != null)
2376     {
2377       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2378               viewport.getHiddenRepSequences());
2379       start = viewport.getSelectionGroup().getStartRes();
2380       end = viewport.getSelectionGroup().getEndRes();
2381     }
2382     else
2383     {
2384       seqs = viewport.getAlignment().getSequencesArray();
2385     }
2386
2387     // This is to maintain viewport position on first residue
2388     // of first sequence
2389     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2390     int startRes = seq.findPosition(viewport.startRes);
2391
2392     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2393             viewport.getAlignment()));
2394
2395     viewport.setStartRes(seq.findIndex(startRes) - 1);
2396
2397     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2398             .getSequences());
2399
2400   }
2401
2402   public void findMenuItem_actionPerformed()
2403   {
2404     new Finder(alignPanel);
2405   }
2406
2407   /**
2408    * create a new view derived from the current view
2409    *
2410    * @param viewtitle
2411    * @return frame for the new view
2412    */
2413   public AlignFrame newView(String viewtitle)
2414   {
2415     AlignmentI newal;
2416     if (viewport.hasHiddenRows())
2417     {
2418       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2419               .getFullAlignment().getSequencesArray());
2420     }
2421     else
2422     {
2423       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2424     }
2425
2426     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2427     {
2428       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2429       {
2430         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2431         {
2432           newal.addAnnotation(viewport.getAlignment()
2433                   .getAlignmentAnnotation()[i]);
2434         }
2435       }
2436     }
2437
2438     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2439
2440     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2441     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2442     PaintRefresher.Register(newaf.alignPanel,
2443             newaf.alignPanel.av.getSequenceSetId());
2444
2445     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2446             newaf.alignPanel.av.getSequenceSetId());
2447     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2448             newaf.alignPanel.av.getSequenceSetId());
2449
2450     Vector comps = (Vector) PaintRefresher.components.get(viewport
2451             .getSequenceSetId());
2452     int viewSize = -1;
2453     for (int i = 0; i < comps.size(); i++)
2454     {
2455       if (comps.elementAt(i) instanceof AlignmentPanel)
2456       {
2457         viewSize++;
2458       }
2459     }
2460
2461     String title = new String(this.getTitle());
2462     if (viewtitle != null)
2463     {
2464       title = viewtitle + " ( " + title + ")";
2465     }
2466     else
2467     {
2468       if (title.indexOf("(View") > -1)
2469       {
2470         title = title.substring(0, title.indexOf("(View"));
2471       }
2472       title += "(View " + viewSize + ")";
2473     }
2474
2475     newaf.setTitle(title.toString());
2476
2477     newaf.viewport.setHistoryList(viewport.getHistoryList());
2478     newaf.viewport.setRedoList(viewport.getRedoList());
2479     return newaf;
2480   }
2481
2482   /**
2483    *
2484    * @return list of feature groups on the view
2485    */
2486   public String[] getFeatureGroups()
2487   {
2488     FeatureRenderer fr = null;
2489     if (alignPanel != null
2490             && (fr = alignPanel.getFeatureRenderer()) != null)
2491     {
2492       List<String> gps = fr.getFeatureGroups();
2493       String[] _gps = gps.toArray(new String[gps.size()]);
2494       return _gps;
2495     }
2496     return null;
2497   }
2498
2499   /**
2500    * get sequence feature groups that are hidden or shown
2501    *
2502    * @param visible
2503    *          true is visible
2504    * @return list
2505    */
2506   public String[] getFeatureGroupsOfState(boolean visible)
2507   {
2508     FeatureRenderer fr = null;
2509     if (alignPanel != null
2510             && (fr = alignPanel.getFeatureRenderer()) != null)
2511     {
2512       List<String> gps = fr.getGroups(visible);
2513       String[] _gps = gps.toArray(new String[gps.size()]);
2514       return _gps;
2515     }
2516     return null;
2517   }
2518
2519   /**
2520    * Change the display state for the given feature groups
2521    *
2522    * @param groups
2523    *          list of group strings
2524    * @param state
2525    *          visible or invisible
2526    */
2527   public void setFeatureGroupState(String[] groups, boolean state)
2528   {
2529     FeatureRenderer fr = null;
2530     this.sequenceFeatures.setState(true);
2531     viewport.setShowSequenceFeatures(true);
2532     if (alignPanel != null
2533             && (fr = alignPanel.getFeatureRenderer()) != null)
2534     {
2535
2536       fr.setGroupVisibility(Arrays.asList(groups), state);
2537       alignPanel.seqPanel.seqCanvas.repaint();
2538       if (alignPanel.overviewPanel != null)
2539       {
2540         alignPanel.overviewPanel.updateOverviewImage();
2541       }
2542     }
2543   }
2544
2545   public void seqLimits_itemStateChanged()
2546   {
2547     viewport.setShowJVSuffix(seqLimits.getState());
2548     alignPanel.fontChanged();
2549     alignPanel.paintAlignment(true);
2550   }
2551
2552   protected void colourTextMenuItem_actionPerformed()
2553   {
2554     viewport.setColourText(colourTextMenuItem.getState());
2555     alignPanel.paintAlignment(true);
2556   }
2557
2558   protected void displayNonconservedMenuItem_actionPerformed()
2559   {
2560     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2561     alignPanel.paintAlignment(true);
2562   }
2563
2564   protected void wrapMenuItem_actionPerformed()
2565   {
2566     viewport.setWrapAlignment(wrapMenuItem.getState());
2567     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2568     scaleAbove.setEnabled(wrapMenuItem.getState());
2569     scaleLeft.setEnabled(wrapMenuItem.getState());
2570     scaleRight.setEnabled(wrapMenuItem.getState());
2571     alignPanel.paintAlignment(true);
2572   }
2573
2574   public void overviewMenuItem_actionPerformed()
2575   {
2576     if (alignPanel.overviewPanel != null)
2577     {
2578       return;
2579     }
2580
2581     Frame frame = new Frame();
2582     OverviewPanel overview = new OverviewPanel(alignPanel);
2583     frame.add(overview);
2584     // +50 must allow for applet frame window
2585     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2586             "label.overview_params", new String[] { this.getTitle() }),
2587             overview.getPreferredSize().width,
2588             overview.getPreferredSize().height + 50);
2589
2590     frame.pack();
2591     final AlignmentPanel ap = alignPanel;
2592     frame.addWindowListener(new WindowAdapter()
2593     {
2594       @Override
2595       public void windowClosing(WindowEvent e)
2596       {
2597         if (ap != null)
2598         {
2599           ap.setOverviewPanel(null);
2600         }
2601       };
2602     });
2603
2604     alignPanel.setOverviewPanel(overview);
2605
2606   }
2607
2608   @Override
2609   public void changeColour(ColourSchemeI cs)
2610   {
2611
2612     if (cs != null)
2613     {
2614       if (viewport.getAbovePIDThreshold())
2615       {
2616         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2617                 cs, "Background"));
2618       }
2619
2620       if (viewport.getConservationSelected())
2621       {
2622         cs.setConservationApplied(true);
2623         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2624                 cs, "Background"));
2625       }
2626       else
2627       {
2628         cs.setConservationApplied(false);
2629       }
2630     }
2631     viewport.setGlobalColourScheme(cs);
2632
2633     alignPanel.paintAlignment(true);
2634   }
2635
2636   protected void modifyPID_actionPerformed()
2637   {
2638     if (viewport.getAbovePIDThreshold()
2639             && viewport.getGlobalColourScheme() != null)
2640     {
2641       SliderPanel.setPIDSliderSource(alignPanel,
2642               viewport.getGlobalColourScheme(), "Background");
2643       SliderPanel.showPIDSlider();
2644     }
2645   }
2646
2647   protected void modifyConservation_actionPerformed()
2648   {
2649     if (viewport.getConservationSelected()
2650             && viewport.getGlobalColourScheme() != null)
2651     {
2652       SliderPanel.setConservationSlider(alignPanel,
2653               viewport.getGlobalColourScheme(), "Background");
2654       SliderPanel.showConservationSlider();
2655     }
2656   }
2657
2658   protected void conservationMenuItem_actionPerformed()
2659   {
2660     viewport.setConservationSelected(conservationMenuItem.getState());
2661
2662     viewport.setAbovePIDThreshold(false);
2663     abovePIDThreshold.setState(false);
2664
2665     changeColour(viewport.getGlobalColourScheme());
2666
2667     modifyConservation_actionPerformed();
2668   }
2669
2670   public void abovePIDThreshold_actionPerformed()
2671   {
2672     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2673
2674     conservationMenuItem.setState(false);
2675     viewport.setConservationSelected(false);
2676
2677     changeColour(viewport.getGlobalColourScheme());
2678
2679     modifyPID_actionPerformed();
2680   }
2681
2682   public void sortPairwiseMenuItem_actionPerformed()
2683   {
2684     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2685     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2686             .getAlignment().getSequenceAt(0), null);
2687
2688     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2689             viewport.getAlignment()));
2690     alignPanel.paintAlignment(true);
2691   }
2692
2693   public void sortIDMenuItem_actionPerformed()
2694   {
2695     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2696     AlignmentSorter.sortByID(viewport.getAlignment());
2697     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2698             viewport.getAlignment()));
2699     alignPanel.paintAlignment(true);
2700   }
2701
2702   public void sortLengthMenuItem_actionPerformed()
2703   {
2704     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2705     AlignmentSorter.sortByLength(viewport.getAlignment());
2706     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2707             viewport.getAlignment()));
2708     alignPanel.paintAlignment(true);
2709   }
2710
2711   public void sortGroupMenuItem_actionPerformed()
2712   {
2713     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714     AlignmentSorter.sortByGroup(viewport.getAlignment());
2715     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2716             viewport.getAlignment()));
2717     alignPanel.paintAlignment(true);
2718
2719   }
2720
2721   public void removeRedundancyMenuItem_actionPerformed()
2722   {
2723     new RedundancyPanel(alignPanel);
2724   }
2725
2726   public void pairwiseAlignmentMenuItem_actionPerformed()
2727   {
2728     if (viewport.getSelectionGroup() != null
2729             && viewport.getSelectionGroup().getSize() > 1)
2730     {
2731       Frame frame = new Frame();
2732       frame.add(new PairwiseAlignPanel(alignPanel));
2733       jalview.bin.JalviewLite.addFrame(frame,
2734               MessageManager.getString("action.pairwise_alignment"), 600,
2735               500);
2736     }
2737   }
2738
2739   public void PCAMenuItem_actionPerformed()
2740   {
2741     // are the sequences aligned?
2742     if (!viewport.getAlignment().isAligned(false))
2743     {
2744       SequenceI current;
2745       int Width = viewport.getAlignment().getWidth();
2746
2747       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2748       {
2749         current = viewport.getAlignment().getSequenceAt(i);
2750
2751         if (current.getLength() < Width)
2752         {
2753           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2754         }
2755       }
2756       alignPanel.paintAlignment(true);
2757     }
2758
2759     if ((viewport.getSelectionGroup() != null
2760             && viewport.getSelectionGroup().getSize() < 4 && viewport
2761             .getSelectionGroup().getSize() > 0)
2762             || viewport.getAlignment().getHeight() < 4)
2763     {
2764       return;
2765     }
2766
2767     try
2768     {
2769       new PCAPanel(viewport);
2770     } catch (java.lang.OutOfMemoryError ex)
2771     {
2772     }
2773
2774   }
2775
2776   public void averageDistanceTreeMenuItem_actionPerformed()
2777   {
2778     NewTreePanel("AV", "PID", "Average distance tree using PID");
2779   }
2780
2781   public void neighbourTreeMenuItem_actionPerformed()
2782   {
2783     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2784   }
2785
2786   protected void njTreeBlosumMenuItem_actionPerformed()
2787   {
2788     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2789   }
2790
2791   protected void avTreeBlosumMenuItem_actionPerformed()
2792   {
2793     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2794   }
2795
2796   void NewTreePanel(String type, String pwType, String title)
2797   {
2798     // are the sequences aligned?
2799     if (!viewport.getAlignment().isAligned(false))
2800     {
2801       SequenceI current;
2802       int Width = viewport.getAlignment().getWidth();
2803
2804       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2805       {
2806         current = viewport.getAlignment().getSequenceAt(i);
2807
2808         if (current.getLength() < Width)
2809         {
2810           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2811         }
2812       }
2813       alignPanel.paintAlignment(true);
2814
2815     }
2816
2817     if ((viewport.getSelectionGroup() != null && viewport
2818             .getSelectionGroup().getSize() > 1)
2819             || (viewport.getAlignment().getHeight() > 1))
2820     {
2821       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2822
2823       addTreeMenuItem(tp, title);
2824
2825       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2826     }
2827   }
2828
2829   void loadTree_actionPerformed()
2830   {
2831     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2832     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2833     cap.setTreeImport();
2834     Frame frame = new Frame();
2835     frame.add(cap);
2836     jalview.bin.JalviewLite.addFrame(frame,
2837             MessageManager.getString("label.paste_newick_file"), 400, 300);
2838   }
2839
2840   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2841   {
2842     TreePanel tp = new TreePanel(alignPanel, treeFile,
2843             MessageManager.getString("label.load_tree_from_file"), tree);
2844     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2845     addTreeMenuItem(tp, treeFile);
2846   }
2847
2848   /**
2849    * sort the alignment using the given treePanel
2850    *
2851    * @param treePanel
2852    *          tree used to sort view
2853    * @param title
2854    *          string used for undo event name
2855    */
2856   public void sortByTree(TreePanel treePanel, String title)
2857   {
2858     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2859     AlignmentSorter
2860             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2861     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2862     // HistoryItem.SORT));
2863     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2864             "label.order_by_params", new String[] { title }), oldOrder,
2865             viewport.getAlignment()));
2866     alignPanel.paintAlignment(true);
2867   }
2868
2869   /**
2870    * Do any automatic reordering of the alignment and add the necessary bits to
2871    * the menu structure for the new tree
2872    *
2873    * @param treePanel
2874    * @param title
2875    */
2876   protected void addTreeMenuItem(final TreePanel treePanel,
2877           final String title)
2878   {
2879     final MenuItem item = new MenuItem(title);
2880     sortByTreeMenu.add(item);
2881     item.addActionListener(new java.awt.event.ActionListener()
2882     {
2883       @Override
2884       public void actionPerformed(ActionEvent evt)
2885       {
2886         sortByTree(treePanel, title); // treePanel.getTitle());
2887       }
2888     });
2889
2890     treePanel.addWindowListener(new WindowAdapter()
2891     {
2892       @Override
2893       public void windowOpened(WindowEvent e)
2894       {
2895         if (viewport.sortByTree)
2896         {
2897           sortByTree(treePanel, title);
2898         }
2899         super.windowOpened(e);
2900       }
2901
2902       @Override
2903       public void windowClosing(WindowEvent e)
2904       {
2905         sortByTreeMenu.remove(item);
2906       };
2907     });
2908   }
2909
2910   public boolean sortBy(AlignmentOrder alorder, String undoname)
2911   {
2912     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2913     if (viewport.applet.debug)
2914     {
2915       System.err.println("Sorting " + alorder.getOrder().size()
2916               + " in alignment '" + getTitle() + "'");
2917     }
2918     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2919     if (undoname != null)
2920     {
2921       addHistoryItem(new OrderCommand(undoname, oldOrder,
2922               viewport.getAlignment()));
2923     }
2924     alignPanel.paintAlignment(true);
2925     return true;
2926   }
2927
2928   protected void documentation_actionPerformed()
2929   {
2930     alignPanel.av.applet.openJalviewHelpUrl();
2931   }
2932
2933   protected void about_actionPerformed()
2934   {
2935
2936     class AboutPanel extends Canvas
2937     {
2938       String version;
2939
2940       String builddate;
2941
2942       public AboutPanel(String version, String builddate)
2943       {
2944         this.version = version;
2945         this.builddate = builddate;
2946       }
2947
2948       @Override
2949       public void paint(Graphics g)
2950       {
2951         g.setColor(Color.white);
2952         g.fillRect(0, 0, getSize().width, getSize().height);
2953         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2954         FontMetrics fm = g.getFontMetrics();
2955         int fh = fm.getHeight();
2956         int y = 5, x = 7;
2957         g.setColor(Color.black);
2958         // TODO: update this text for each release or centrally store it for
2959         // lite and application
2960         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2961         g.drawString(MessageManager.formatMessage(
2962                 "label.jalviewLite_release", new String[] { version }), x,
2963                 y += fh);
2964         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2965         g.drawString(MessageManager.formatMessage(
2966                 "label.jaview_build_date", new String[] { builddate }), x,
2967                 y += fh);
2968         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2969         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2970                 x, y += fh * 1.5);
2971         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2972                 x + 50, y += fh + 8);
2973         g.drawString(
2974                 MessageManager.getString("label.jalview_dev_managers"), x,
2975                 y += fh);
2976         g.drawString(MessageManager
2977                 .getString("label.jalview_distribution_lists"), x, y += fh);
2978         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2979                 x, y += fh + 8);
2980         g.drawString(
2981                 MessageManager.getString("label.jalview_cite_1_authors"),
2982                 x, y += fh);
2983         g.drawString(
2984                 MessageManager.getString("label.jalview_cite_1_title"), x,
2985                 y += fh);
2986         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2987                 x, y += fh);
2988       }
2989     }
2990
2991     Frame frame = new Frame();
2992     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2993             .getBuildDate()));
2994     jalview.bin.JalviewLite.addFrame(frame,
2995             MessageManager.getString("label.jalview"), 580, 220);
2996
2997   }
2998
2999   public void showURL(String url, String target)
3000   {
3001     if (viewport.applet == null)
3002     {
3003       System.out.println("Not running as applet - no browser available.");
3004     }
3005     else
3006     {
3007       viewport.applet.showURL(url, target);
3008     }
3009   }
3010
3011   // ////////////////////////////////////////////////////////////////////////////////
3012   // JBuilder Graphics here
3013
3014   MenuBar alignFrameMenuBar = new MenuBar();
3015
3016   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3017
3018   MenuItem loadApplication = new MenuItem(
3019           MessageManager.getString("label.view_full_application"));
3020
3021   MenuItem loadTree = new MenuItem(
3022           MessageManager.getString("label.load_associated_tree"));
3023
3024   MenuItem loadAnnotations = new MenuItem(
3025           MessageManager.getString("label.load_features_annotations"));
3026
3027   MenuItem outputFeatures = new MenuItem(
3028           MessageManager.getString("label.export_features"));
3029
3030   MenuItem outputAnnotations = new MenuItem(
3031           MessageManager.getString("label.export_annotations"));
3032
3033   MenuItem closeMenuItem = new MenuItem(
3034           MessageManager.getString("action.close"));
3035
3036   MenuItem selectAllSequenceMenuItem = new MenuItem(
3037           MessageManager.getString("action.select_all"));
3038
3039   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3040           MessageManager.getString("action.deselect_all"));
3041
3042   MenuItem invertSequenceMenuItem = new MenuItem(
3043           MessageManager.getString("action.invert_selection"));
3044
3045   MenuItem remove2LeftMenuItem = new MenuItem();
3046
3047   MenuItem remove2RightMenuItem = new MenuItem();
3048
3049   MenuItem removeGappedColumnMenuItem = new MenuItem();
3050
3051   MenuItem removeAllGapsMenuItem = new MenuItem();
3052
3053   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3054
3055   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3056
3057   MenuItem sortPairwiseMenuItem = new MenuItem();
3058
3059   MenuItem sortIDMenuItem = new MenuItem();
3060
3061   MenuItem sortLengthMenuItem = new MenuItem();
3062
3063   MenuItem sortGroupMenuItem = new MenuItem();
3064
3065   MenuItem removeRedundancyMenuItem = new MenuItem();
3066
3067   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3068
3069   MenuItem PCAMenuItem = new MenuItem();
3070
3071   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3072
3073   MenuItem neighbourTreeMenuItem = new MenuItem();
3074
3075   BorderLayout borderLayout1 = new BorderLayout();
3076
3077   public Label statusBar = new Label();
3078
3079   MenuItem clustalColour = new MenuItem();
3080
3081   MenuItem zappoColour = new MenuItem();
3082
3083   MenuItem taylorColour = new MenuItem();
3084
3085   MenuItem hydrophobicityColour = new MenuItem();
3086
3087   MenuItem helixColour = new MenuItem();
3088
3089   MenuItem strandColour = new MenuItem();
3090
3091   MenuItem turnColour = new MenuItem();
3092
3093   MenuItem buriedColour = new MenuItem();
3094
3095   MenuItem purinePyrimidineColour = new MenuItem();
3096
3097   // MenuItem RNAInteractionColour = new MenuItem();
3098
3099   MenuItem RNAHelixColour = new MenuItem();
3100
3101   MenuItem userDefinedColour = new MenuItem();
3102
3103   MenuItem PIDColour = new MenuItem();
3104
3105   MenuItem BLOSUM62Colour = new MenuItem();
3106
3107   MenuItem tcoffeeColour = new MenuItem();
3108
3109   MenuItem njTreeBlosumMenuItem = new MenuItem();
3110
3111   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3112
3113   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3114
3115   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3116
3117   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3118
3119   MenuItem alProperties = new MenuItem(
3120           MessageManager.getString("label.alignment_props"));
3121
3122   MenuItem overviewMenuItem = new MenuItem();
3123
3124   MenuItem undoMenuItem = new MenuItem();
3125
3126   MenuItem redoMenuItem = new MenuItem();
3127
3128   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3129
3130   MenuItem noColourmenuItem = new MenuItem();
3131
3132   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3133
3134   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3135
3136   MenuItem findMenuItem = new MenuItem();
3137
3138   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3139
3140   MenuItem nucleotideColour = new MenuItem();
3141
3142   MenuItem deleteGroups = new MenuItem();
3143
3144   MenuItem grpsFromSelection = new MenuItem();
3145
3146   MenuItem createGroup = new MenuItem();
3147
3148   MenuItem unGroup = new MenuItem();
3149
3150   MenuItem delete = new MenuItem();
3151
3152   MenuItem copy = new MenuItem();
3153
3154   MenuItem cut = new MenuItem();
3155
3156   Menu pasteMenu = new Menu();
3157
3158   MenuItem pasteNew = new MenuItem();
3159
3160   MenuItem pasteThis = new MenuItem();
3161
3162   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3163
3164   MenuItem font = new MenuItem();
3165
3166   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3167
3168   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3169
3170   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3171
3172   MenuItem modifyPID = new MenuItem();
3173
3174   MenuItem modifyConservation = new MenuItem();
3175
3176   CheckboxMenuItem autoCalculate = null;
3177
3178   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3179           "Sort Alignment With New Tree", true);
3180
3181   Menu sortByTreeMenu = new Menu();
3182
3183   MenuItem inputText = new MenuItem();
3184
3185   MenuItem documentation = new MenuItem();
3186
3187   MenuItem about = new MenuItem();
3188
3189   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3190
3191   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3192
3193   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3194
3195   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3196
3197   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3198
3199   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3200
3201   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3202
3203   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3204
3205   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3206
3207   /**
3208    * Initialise menus and other items
3209    *
3210    * @throws Exception
3211    */
3212   private void jbInit() throws Exception
3213   {
3214     setMenuBar(alignFrameMenuBar);
3215
3216     /*
3217      * Configure File menu items and actions
3218      */
3219     inputText
3220             .setLabel(MessageManager.getString("label.input_from_textbox"));
3221     inputText.addActionListener(this);
3222     Menu outputTextboxMenu = new Menu(
3223             MessageManager.getString("label.out_to_textbox"));
3224     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3225     {
3226
3227       MenuItem item = new MenuItem(
3228               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3229
3230       item.addActionListener(new java.awt.event.ActionListener()
3231       {
3232         @Override
3233         public void actionPerformed(ActionEvent e)
3234         {
3235           outputText_actionPerformed(e);
3236         }
3237       });
3238
3239       outputTextboxMenu.add(item);
3240     }
3241     closeMenuItem.addActionListener(this);
3242     loadApplication.addActionListener(this);
3243     loadTree.addActionListener(this);
3244     loadAnnotations.addActionListener(this);
3245     outputFeatures.addActionListener(this);
3246     outputAnnotations.addActionListener(this);
3247
3248     /*
3249      * Configure Edit menu items and actions
3250      */
3251     undoMenuItem.setEnabled(false);
3252     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3253     undoMenuItem.addActionListener(this);
3254     redoMenuItem.setEnabled(false);
3255     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3256     redoMenuItem.addActionListener(this);
3257     copy.setLabel(MessageManager.getString("action.copy"));
3258     copy.addActionListener(this);
3259     cut.setLabel(MessageManager.getString("action.cut"));
3260     cut.addActionListener(this);
3261     delete.setLabel(MessageManager.getString("action.delete"));
3262     delete.addActionListener(this);
3263     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3264     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3265     pasteNew.addActionListener(this);
3266     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3267     pasteThis.addActionListener(this);
3268     remove2LeftMenuItem.setLabel(MessageManager
3269             .getString("action.remove_left"));
3270     remove2LeftMenuItem.addActionListener(this);
3271     remove2RightMenuItem.setLabel(MessageManager
3272             .getString("action.remove_right"));
3273     remove2RightMenuItem.addActionListener(this);
3274     removeGappedColumnMenuItem.setLabel(MessageManager
3275             .getString("action.remove_empty_columns"));
3276     removeGappedColumnMenuItem.addActionListener(this);
3277     removeAllGapsMenuItem.setLabel(MessageManager
3278             .getString("action.remove_all_gaps"));
3279     removeAllGapsMenuItem.addActionListener(this);
3280     removeRedundancyMenuItem.setLabel(MessageManager
3281             .getString("action.remove_redundancy"));
3282     removeRedundancyMenuItem.addActionListener(this);
3283
3284     /*
3285      * Configure Select menu items and actions
3286      */
3287     findMenuItem.setLabel(MessageManager.getString("action.find"));
3288     findMenuItem.addActionListener(this);
3289     selectAllSequenceMenuItem.addActionListener(this);
3290     deselectAllSequenceMenuItem.addActionListener(this);
3291     invertSequenceMenuItem.setLabel(MessageManager
3292             .getString("action.invert_sequence_selection"));
3293     invertSequenceMenuItem.addActionListener(this);
3294     invertColSel.setLabel(MessageManager
3295             .getString("action.invert_column_selection"));
3296     invertColSel.addActionListener(this);
3297     deleteGroups.setLabel(MessageManager
3298             .getString("action.undefine_groups"));
3299     deleteGroups.addActionListener(this);
3300     grpsFromSelection.setLabel(MessageManager
3301             .getString("action.make_groups_selection"));
3302     grpsFromSelection.addActionListener(this);
3303     createGroup.setLabel(MessageManager.getString("action.create_group"));
3304     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3305     annotationColumnSelection.setLabel(MessageManager
3306             .getString("action.select_by_annotation"));
3307     annotationColumnSelection.addActionListener(this);
3308
3309     /*
3310      * Configure View menu items and actions
3311      */
3312     newView.setLabel(MessageManager.getString("action.new_view"));
3313     newView.addActionListener(this);
3314     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3315     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3316     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3317     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3318     hideColumns
3319             .setLabel(MessageManager.getString("label.selected_columns"));
3320     hideSequences.setLabel(MessageManager
3321             .getString("label.selected_sequences"));
3322     hideAllButSelection.setLabel(MessageManager
3323             .getString("label.all_but_selected_region"));
3324     hideAllSelection.setLabel(MessageManager
3325             .getString("label.selected_region"));
3326     showAllHidden.setLabel(MessageManager
3327             .getString("label.all_sequences_columns"));
3328     showColumns.addActionListener(this);
3329     showSeqs.addActionListener(this);
3330     hideColumns.addActionListener(this);
3331     hideSequences.addActionListener(this);
3332     hideAllButSelection.addActionListener(this);
3333     hideAllSelection.addActionListener(this);
3334     showAllHidden.addActionListener(this);
3335     featureSettings.setLabel(MessageManager
3336             .getString("action.feature_settings"));
3337     featureSettings.addActionListener(this);
3338     sequenceFeatures.setLabel(MessageManager
3339             .getString("label.show_sequence_features"));
3340     sequenceFeatures.addItemListener(this);
3341     sequenceFeatures.setState(false);
3342     followMouseOverFlag.setLabel(MessageManager
3343             .getString("label.automatic_scrolling"));
3344     followMouseOverFlag.addItemListener(this);
3345     alProperties.addActionListener(this);
3346     overviewMenuItem.setLabel(MessageManager
3347             .getString("label.overview_window"));
3348     overviewMenuItem.addActionListener(this);
3349
3350     /*
3351      * Configure Annotations menu items and actions
3352      */
3353     annotationPanelMenuItem.setLabel(MessageManager
3354             .getString("label.show_annotations"));
3355     annotationPanelMenuItem.addItemListener(this);
3356     showGroupConsensus.setLabel(MessageManager
3357             .getString("label.group_consensus"));
3358     showGroupConservation.setLabel(MessageManager
3359             .getString("label.group_conservation"));
3360     showConsensusHistogram.setLabel(MessageManager
3361             .getString("label.show_consensus_histogram"));
3362     showSequenceLogo.setLabel(MessageManager
3363             .getString("label.show_consensus_logo"));
3364     normSequenceLogo.setLabel(MessageManager
3365             .getString("label.norm_consensus_logo"));
3366     applyAutoAnnotationSettings.setLabel(MessageManager
3367             .getString("label.apply_all_groups"));
3368     applyAutoAnnotationSettings.setState(true);
3369     Menu autoAnnMenu = new Menu(
3370             MessageManager.getString("label.autocalculated_annotation"));
3371     showGroupConsensus.addItemListener(this);
3372     showGroupConservation.addItemListener(this);
3373     showConsensusHistogram.addItemListener(this);
3374     showSequenceLogo.addItemListener(this);
3375     normSequenceLogo.addItemListener(this);
3376     applyAutoAnnotationSettings.addItemListener(this);
3377     showAlignmentAnnotations = new CheckboxMenuItem(
3378             MessageManager.getString("label.show_all_al_annotations"));
3379     showSequenceAnnotations = new CheckboxMenuItem(
3380             MessageManager.getString("label.show_all_seq_annotations"));
3381     sortAnnBySequence = new CheckboxMenuItem(
3382             MessageManager.getString("label.sort_annotations_by_sequence"));
3383     sortAnnByLabel = new CheckboxMenuItem(
3384             MessageManager.getString("label.sort_annotations_by_label"));
3385     showAutoFirst = new CheckboxMenuItem(
3386             MessageManager.getString("label.show_first"));
3387     showAutoFirst.setState(false); // pending applet parameter
3388     setShowAutoCalculatedAbove(showAutoFirst.getState());
3389     showAutoLast = new CheckboxMenuItem(
3390             MessageManager.getString("label.show_last"));
3391     showAutoLast.setState(!showAutoFirst.getState());
3392     showAlignmentAnnotations.addItemListener(this);
3393     showSequenceAnnotations.addItemListener(this);
3394     sortAnnBySequence.addItemListener(this);
3395     sortAnnByLabel.addItemListener(this);
3396     showAutoFirst.addItemListener(this);
3397     showAutoLast.addItemListener(this);
3398
3399     /*
3400      * Configure Format menu items and actions
3401      */
3402     font.setLabel(MessageManager.getString("action.font"));
3403     font.addActionListener(this);
3404     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3405     scaleAbove.setState(true);
3406     scaleAbove.setEnabled(false);
3407     scaleAbove.addItemListener(this);
3408     scaleLeft.setEnabled(false);
3409     scaleLeft.setState(true);
3410     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3411     scaleLeft.addItemListener(this);
3412     scaleRight.setEnabled(false);
3413     scaleRight.setState(true);
3414     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3415     scaleRight.addItemListener(this);
3416     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3417     viewBoxesMenuItem.setState(true);
3418     viewBoxesMenuItem.addItemListener(this);
3419     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3420     viewTextMenuItem.setState(true);
3421     viewTextMenuItem.addItemListener(this);
3422     colourTextMenuItem.setLabel(MessageManager
3423             .getString("label.colour_text"));
3424     colourTextMenuItem.addItemListener(this);
3425     displayNonconservedMenuItem.setLabel(MessageManager
3426             .getString("label.show_non_conversed"));
3427     displayNonconservedMenuItem.addItemListener(this);
3428     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3429     wrapMenuItem.addItemListener(this);
3430     renderGapsMenuItem.setLabel(MessageManager
3431             .getString("action.show_gaps"));
3432     renderGapsMenuItem.setState(true);
3433     renderGapsMenuItem.addItemListener(this);
3434     centreColumnLabelFlag.setLabel(MessageManager
3435             .getString("label.centre_column_labels"));
3436     centreColumnLabelFlag.addItemListener(this);
3437     seqLimits.setState(true);
3438     seqLimits.setLabel(MessageManager
3439             .getString("label.show_sequence_limits"));
3440     seqLimits.addItemListener(this);
3441
3442     /*
3443      * Configure Colour menu items and actions
3444      */
3445     applyToAllGroups.setLabel(MessageManager
3446             .getString("label.apply_colour_to_all_groups"));
3447     applyToAllGroups.setState(true);
3448     applyToAllGroups.addItemListener(this);
3449     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3450     clustalColour.addActionListener(this);
3451     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3452     zappoColour.addActionListener(this);
3453     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3454     taylorColour.addActionListener(this);
3455     hydrophobicityColour.setLabel(MessageManager
3456             .getString("label.hydrophobicity"));
3457     hydrophobicityColour.addActionListener(this);
3458     helixColour
3459             .setLabel(MessageManager.getString("label.helix_propensity"));
3460     helixColour.addActionListener(this);
3461     strandColour.setLabel(MessageManager
3462             .getString("label.strand_propensity"));
3463     strandColour.addActionListener(this);
3464     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3465     turnColour.addActionListener(this);
3466     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3467     buriedColour.addActionListener(this);
3468     purinePyrimidineColour.setLabel(MessageManager
3469             .getString("label.purine_pyrimidine"));
3470     purinePyrimidineColour.addActionListener(this);
3471     // RNAInteractionColour.setLabel(MessageManager
3472     // .getString("label.rna_interaction"));
3473     // RNAInteractionColour.addActionListener(this);
3474     RNAHelixColour.setLabel(MessageManager
3475             .getString("action.by_rna_helixes"));
3476     RNAHelixColour.addActionListener(this);
3477     userDefinedColour.setLabel(MessageManager
3478             .getString("action.user_defined"));
3479     userDefinedColour.addActionListener(this);
3480     PIDColour.setLabel(MessageManager
3481             .getString("label.percentage_identity"));
3482     PIDColour.addActionListener(this);
3483     BLOSUM62Colour.setLabel(MessageManager
3484             .getString("label.blosum62_score"));
3485     BLOSUM62Colour.addActionListener(this);
3486     tcoffeeColour
3487             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3488     // it will be enabled only if a score file is provided
3489     tcoffeeColour.setEnabled(false);
3490     tcoffeeColour.addActionListener(this);
3491     conservationMenuItem.setLabel(MessageManager
3492             .getString("action.by_conservation"));
3493     conservationMenuItem.addItemListener(this);
3494     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3495     noColourmenuItem.addActionListener(this);
3496     abovePIDThreshold.setLabel(MessageManager
3497             .getString("label.above_identity_threshold"));
3498     abovePIDThreshold.addItemListener(this);
3499     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3500     nucleotideColour.addActionListener(this);
3501     modifyPID.setLabel(MessageManager
3502             .getString("label.modify_identity_thereshold"));
3503     modifyPID.addActionListener(this);
3504     modifyConservation.setLabel(MessageManager
3505             .getString("label.modify_conservation_thereshold"));
3506     modifyConservation.addActionListener(this);
3507     annotationColour.setLabel(MessageManager
3508             .getString("action.by_annotation"));
3509     annotationColour.addActionListener(this);
3510
3511     /*
3512      * Configure Calculate menu items and actions
3513      */
3514     sortPairwiseMenuItem.setLabel(MessageManager
3515             .getString("action.by_pairwise_id"));
3516     sortPairwiseMenuItem.addActionListener(this);
3517     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3518     sortIDMenuItem.addActionListener(this);
3519     sortLengthMenuItem.setLabel(MessageManager
3520             .getString("action.by_length"));
3521     sortLengthMenuItem.addActionListener(this);
3522     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3523     sortGroupMenuItem.addActionListener(this);
3524     pairwiseAlignmentMenuItem.setLabel(MessageManager
3525             .getString("action.pairwise_alignment"));
3526     pairwiseAlignmentMenuItem.addActionListener(this);
3527     PCAMenuItem.setLabel(MessageManager
3528             .getString("label.principal_component_analysis"));
3529     PCAMenuItem.addActionListener(this);
3530     autoCalculate = new CheckboxMenuItem(
3531             MessageManager.getString("label.autocalculate_consensus"), true);
3532     averageDistanceTreeMenuItem.setLabel(MessageManager
3533             .getString("label.average_distance_identity"));
3534     averageDistanceTreeMenuItem.addActionListener(this);
3535     neighbourTreeMenuItem.setLabel(MessageManager
3536             .getString("label.neighbour_joining_identity"));
3537     neighbourTreeMenuItem.addActionListener(this);
3538     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3539             .getString("label.average_distance_bloslum62"));
3540     avDistanceTreeBlosumMenuItem.addActionListener(this);
3541     njTreeBlosumMenuItem.setLabel(MessageManager
3542             .getString("label.neighbour_blosum62"));
3543     njTreeBlosumMenuItem.addActionListener(this);
3544     sortByTreeMenu.setLabel(MessageManager
3545             .getString("action.by_tree_order"));
3546     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3547     Menu calculateTreeMenu = new Menu(
3548             MessageManager.getString("action.calculate_tree"));
3549     autoCalculate.addItemListener(this);
3550     sortByTree.addItemListener(this);
3551
3552     /*
3553      * Configure Help menu items and actions
3554      */
3555     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3556     documentation.setLabel(MessageManager.getString("label.documentation"));
3557     documentation.addActionListener(this);
3558     about.setLabel(MessageManager.getString("label.about"));
3559     about.addActionListener(this);
3560
3561     /*
3562      * Add top level menus to frame
3563      */
3564     alignFrameMenuBar.add(fileMenu);
3565     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3566     alignFrameMenuBar.add(editMenu);
3567     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3568     alignFrameMenuBar.add(selectMenu);
3569     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3570     alignFrameMenuBar.add(viewMenu);
3571     Menu annotationsMenu = new Menu(
3572             MessageManager.getString("action.annotations"));
3573     alignFrameMenuBar.add(annotationsMenu);
3574     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3575     alignFrameMenuBar.add(formatMenu);
3576     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3577     alignFrameMenuBar.add(colourMenu);
3578     Menu calculateMenu = new Menu(
3579             MessageManager.getString("action.calculate"));
3580     alignFrameMenuBar.add(calculateMenu);
3581     alignFrameMenuBar.add(helpMenu);
3582
3583     /*
3584      * File menu
3585      */
3586     fileMenu.add(inputText);
3587     fileMenu.add(loadTree);
3588     fileMenu.add(loadAnnotations);
3589     fileMenu.addSeparator();
3590     fileMenu.add(outputTextboxMenu);
3591     fileMenu.add(outputFeatures);
3592     fileMenu.add(outputAnnotations);
3593     if (jalviewServletURL != null)
3594     {
3595       fileMenu.add(loadApplication);
3596     }
3597     fileMenu.addSeparator();
3598     fileMenu.add(closeMenuItem);
3599
3600     /*
3601      * Edit menu
3602      */
3603     editMenu.add(undoMenuItem);
3604     editMenu.add(redoMenuItem);
3605     editMenu.add(cut);
3606     editMenu.add(copy);
3607     pasteMenu.add(pasteNew);
3608     pasteMenu.add(pasteThis);
3609     editMenu.add(pasteMenu);
3610     editMenu.add(delete);
3611     editMenu.addSeparator();
3612     editMenu.add(remove2LeftMenuItem);
3613     editMenu.add(remove2RightMenuItem);
3614     editMenu.add(removeGappedColumnMenuItem);
3615     editMenu.add(removeAllGapsMenuItem);
3616     editMenu.add(removeRedundancyMenuItem);
3617
3618     /*
3619      * Select menu
3620      */
3621     selectMenu.add(findMenuItem);
3622     selectMenu.addSeparator();
3623     selectMenu.add(selectAllSequenceMenuItem);
3624     selectMenu.add(deselectAllSequenceMenuItem);
3625     selectMenu.add(invertSequenceMenuItem);
3626     selectMenu.add(invertColSel);
3627     selectMenu.add(createGroup);
3628     selectMenu.add(unGroup);
3629     selectMenu.add(grpsFromSelection);
3630     selectMenu.add(deleteGroups);
3631     selectMenu.add(annotationColumnSelection);
3632
3633     /*
3634      * View menu
3635      */
3636     viewMenu.add(newView);
3637     viewMenu.addSeparator();
3638     showMenu.add(showColumns);
3639     showMenu.add(showSeqs);
3640     showMenu.add(showAllHidden);
3641     viewMenu.add(showMenu);
3642     hideMenu.add(hideColumns);
3643     hideMenu.add(hideSequences);
3644     hideMenu.add(hideAllSelection);
3645     hideMenu.add(hideAllButSelection);
3646     viewMenu.add(hideMenu);
3647     viewMenu.addSeparator();
3648     viewMenu.add(followMouseOverFlag);
3649     viewMenu.addSeparator();
3650     viewMenu.add(sequenceFeatures);
3651     viewMenu.add(featureSettings);
3652     viewMenu.addSeparator();
3653     viewMenu.add(alProperties);
3654     viewMenu.addSeparator();
3655     viewMenu.add(overviewMenuItem);
3656
3657     /*
3658      * Annotations menu
3659      */
3660     annotationsMenu.add(annotationPanelMenuItem);
3661     annotationsMenu.addSeparator();
3662     annotationsMenu.add(showAlignmentAnnotations);
3663     annotationsMenu.add(showSequenceAnnotations);
3664     annotationsMenu.add(sortAnnBySequence);
3665     annotationsMenu.add(sortAnnByLabel);
3666     annotationsMenu.addSeparator();
3667     autoAnnMenu.add(showAutoFirst);
3668     autoAnnMenu.add(showAutoLast);
3669     autoAnnMenu.addSeparator();
3670     autoAnnMenu.add(applyAutoAnnotationSettings);
3671     autoAnnMenu.add(showConsensusHistogram);
3672     autoAnnMenu.add(showSequenceLogo);
3673     autoAnnMenu.add(normSequenceLogo);
3674     autoAnnMenu.addSeparator();
3675     autoAnnMenu.add(showGroupConservation);
3676     autoAnnMenu.add(showGroupConsensus);
3677     annotationsMenu.add(autoAnnMenu);
3678
3679     /*
3680      * Format menu
3681      */
3682     formatMenu.add(font);
3683     formatMenu.add(seqLimits);
3684     formatMenu.add(wrapMenuItem);
3685     formatMenu.add(scaleAbove);
3686     formatMenu.add(scaleLeft);
3687     formatMenu.add(scaleRight);
3688     formatMenu.add(viewBoxesMenuItem);
3689     formatMenu.add(viewTextMenuItem);
3690     formatMenu.add(colourTextMenuItem);
3691     formatMenu.add(displayNonconservedMenuItem);
3692     formatMenu.add(renderGapsMenuItem);
3693     formatMenu.add(centreColumnLabelFlag);
3694
3695     /*
3696      * Colour menu
3697      */
3698     colourMenu.add(applyToAllGroups);
3699     colourMenu.addSeparator();
3700     colourMenu.add(noColourmenuItem);
3701     colourMenu.add(clustalColour);
3702     colourMenu.add(BLOSUM62Colour);
3703     colourMenu.add(PIDColour);
3704     colourMenu.add(zappoColour);
3705     colourMenu.add(taylorColour);
3706     colourMenu.add(hydrophobicityColour);
3707     colourMenu.add(helixColour);
3708     colourMenu.add(strandColour);
3709     colourMenu.add(turnColour);
3710     colourMenu.add(buriedColour);
3711     colourMenu.add(nucleotideColour);
3712     colourMenu.add(purinePyrimidineColour);
3713     // colourMenu.add(RNAInteractionColour);
3714     colourMenu.add(tcoffeeColour);
3715     colourMenu.add(userDefinedColour);
3716     colourMenu.addSeparator();
3717     colourMenu.add(conservationMenuItem);
3718     colourMenu.add(modifyConservation);
3719     colourMenu.add(abovePIDThreshold);
3720     colourMenu.add(modifyPID);
3721     colourMenu.add(annotationColour);
3722     colourMenu.add(RNAHelixColour);
3723
3724     /*
3725      * Calculate menu
3726      */
3727     sortMenu.add(sortIDMenuItem);
3728     sortMenu.add(sortLengthMenuItem);
3729     sortMenu.add(sortByTreeMenu);
3730     sortMenu.add(sortGroupMenuItem);
3731     sortMenu.add(sortPairwiseMenuItem);
3732     calculateMenu.add(sortMenu);
3733     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3734     calculateTreeMenu.add(neighbourTreeMenuItem);
3735     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3736     calculateTreeMenu.add(njTreeBlosumMenuItem);
3737     calculateMenu.add(calculateTreeMenu);
3738     calculateMenu.addSeparator();
3739     calculateMenu.add(pairwiseAlignmentMenuItem);
3740     calculateMenu.add(PCAMenuItem);
3741     calculateMenu.add(autoCalculate);
3742     calculateMenu.add(sortByTree);
3743
3744     /*
3745      * Help menu
3746      */
3747     helpMenu.add(documentation);
3748     helpMenu.add(about);
3749
3750     /*
3751      * Status bar
3752      */
3753     statusBar.setBackground(Color.white);
3754     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3755     statusBar.setText(MessageManager.getString("label.status_bar"));
3756     this.add(statusBar, BorderLayout.SOUTH);
3757   }
3758
3759   @Override
3760   public void setStatus(String string)
3761   {
3762     statusBar.setText(string);
3763   };
3764
3765   MenuItem featureSettings = new MenuItem();
3766
3767   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3768
3769   MenuItem annotationColour = new MenuItem();
3770
3771   MenuItem annotationColumnSelection = new MenuItem();
3772
3773   MenuItem invertColSel = new MenuItem();
3774
3775   MenuItem showColumns = new MenuItem();
3776
3777   MenuItem showSeqs = new MenuItem();
3778
3779   MenuItem hideColumns = new MenuItem();
3780
3781   MenuItem hideSequences = new MenuItem();
3782
3783   MenuItem hideAllButSelection = new MenuItem();
3784
3785   MenuItem hideAllSelection = new MenuItem();
3786
3787   MenuItem showAllHidden = new MenuItem();
3788
3789   MenuItem newView = new MenuItem();
3790
3791   private CheckboxMenuItem showAlignmentAnnotations;
3792
3793   private CheckboxMenuItem showSequenceAnnotations;
3794
3795   private CheckboxMenuItem sortAnnBySequence;
3796
3797   private CheckboxMenuItem sortAnnByLabel;
3798
3799   private CheckboxMenuItem showAutoFirst;
3800
3801   private CheckboxMenuItem showAutoLast;
3802
3803   private SplitFrame splitFrame;
3804
3805   /**
3806    * Attach the alignFrame panels after embedding menus, if necessary. This used
3807    * to be called setEmbedded, but is now creates the dropdown menus in a
3808    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3809    *
3810    * @param reallyEmbedded
3811    *          true to attach the view to the applet area on the page rather than
3812    *          in a new window
3813    */
3814   public void createAlignFrameWindow(boolean reallyEmbedded)
3815   {
3816     if (reallyEmbedded)
3817     {
3818       embedAlignFrameInApplet(viewport.applet);
3819     }
3820     else
3821     {
3822       // //////
3823       // test and embed menu bar if necessary.
3824       //
3825       if (embedMenuIfNeeded(alignPanel))
3826       {
3827         /*
3828          * adjust for status bar height too. ? pointless as overridden by layout
3829          * manager
3830          */
3831         alignPanel.setSize(getSize().width,
3832                 getSize().height - statusBar.getHeight());
3833       }
3834       add(statusBar, BorderLayout.SOUTH);
3835       add(alignPanel, BorderLayout.CENTER);
3836       // and register with the applet so it can pass external API calls to us
3837       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3838               frameHeight);
3839     }
3840   }
3841
3842   /**
3843    * Add the components of this AlignFrame to the applet container.
3844    *
3845    * @param theApplet
3846    */
3847   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3848   {
3849     // ////
3850     // Explicitly build the embedded menu panel for the on-page applet
3851     //
3852     // view cannot be closed if its actually on the page
3853     fileMenu.remove(closeMenuItem);
3854     fileMenu.remove(3); // Remove Separator
3855     // construct embedded menu, using default font
3856     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3857     // and actually add the components to the applet area
3858     theApplet.setLayout(new BorderLayout());
3859     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3860     theApplet.add(statusBar, BorderLayout.SOUTH);
3861     // TODO should size be left to the layout manager?
3862     alignPanel.setSize(theApplet.getSize().width,
3863             theApplet.getSize().height - embeddedMenu.getHeight()
3864                     - statusBar.getHeight());
3865     theApplet.add(alignPanel, BorderLayout.CENTER);
3866     final AlignFrame me = this;
3867     theApplet.addFocusListener(new FocusListener()
3868     {
3869
3870       @Override
3871       public void focusLost(FocusEvent e)
3872       {
3873         if (theApplet.currentAlignFrame == me)
3874         {
3875           theApplet.currentAlignFrame = null;
3876         }
3877       }
3878
3879       @Override
3880       public void focusGained(FocusEvent e)
3881       {
3882         theApplet.currentAlignFrame = me;
3883       }
3884     });
3885     theApplet.validate();
3886   }
3887
3888   /**
3889    * create a new binding between structures in an existing jmol viewer instance
3890    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3891    * this does not open a new Jmol window, or modify the display of the
3892    * structures in the original jmol window. Note This method doesn't work
3893    * without an additional javascript library to exchange messages between the
3894    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3895    *
3896    * @param viewer
3897    *          JmolViewer instance
3898    * @param sequenceIds
3899    *          - sequence Ids to search for associations
3900    */
3901   public SequenceStructureBinding addStructureViewInstance(
3902           Object jmolviewer, String[] sequenceIds)
3903   {
3904     Viewer viewer = null;
3905     try
3906     {
3907       viewer = (Viewer) jmolviewer;
3908     } catch (ClassCastException ex)
3909     {
3910       System.err.println("Unsupported viewer object :"
3911               + jmolviewer.getClass());
3912     }
3913     if (viewer == null)
3914     {
3915       System.err.println("Can't use this object as a structure viewer:"
3916               + jmolviewer.getClass());
3917       return null;
3918     }
3919     SequenceI[] seqs = null;
3920     if (sequenceIds == null || sequenceIds.length == 0)
3921     {
3922       seqs = viewport.getAlignment().getSequencesArray();
3923     }
3924     else
3925     {
3926       Vector sqi = new Vector();
3927       AlignmentI al = viewport.getAlignment();
3928       for (int sid = 0; sid < sequenceIds.length; sid++)
3929       {
3930         SequenceI sq = al.findName(sequenceIds[sid]);
3931         if (sq != null)
3932         {
3933           sqi.addElement(sq);
3934         }
3935       }
3936       if (sqi.size() > 0)
3937       {
3938         seqs = new SequenceI[sqi.size()];
3939         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3940         {
3941           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3942         }
3943       }
3944       else
3945       {
3946         return null;
3947       }
3948     }
3949     AAStructureBindingModel jmv = null;
3950     // TODO: search for a jmv that involves viewer
3951     if (jmv == null)
3952     { // create a new viewer/jalview binding.
3953       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3954     }
3955     return jmv;
3956
3957   }
3958
3959   /**
3960    * bind a pdb file to a sequence in the current view
3961    *
3962    * @param sequenceId
3963    *          - sequenceId within the dataset.
3964    * @param pdbEntryString
3965    *          - the short name for the PDB file
3966    * @param pdbFile
3967    *          - pdb file - either a URL or a valid PDB file.
3968    * @return true if binding was as success TODO: consider making an exception
3969    *         structure for indicating when PDB parsing or sequenceId location
3970    *         fails.
3971    */
3972   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3973           String pdbFile)
3974   {
3975     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3976     boolean needtoadd = false;
3977     if (toaddpdb != null)
3978     {
3979       Vector pdbe = toaddpdb.getAllPDBEntries();
3980       PDBEntry pdbentry = null;
3981       if (pdbe != null && pdbe.size() > 0)
3982       {
3983         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3984         {
3985           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3986           if (!pdbentry.getId().equals(pdbEntryString)
3987                   && !pdbentry.getFile().equals(pdbFile))
3988           {
3989             pdbentry = null;
3990           }
3991           else
3992           {
3993             continue;
3994           }
3995         }
3996       }
3997       if (pdbentry == null)
3998       {
3999         pdbentry = new PDBEntry();
4000         pdbentry.setId(pdbEntryString);
4001         pdbentry.setFile(pdbFile);
4002         needtoadd = true; // add this new entry to sequence.
4003       }
4004       // resolve data source
4005       // TODO: this code should be a refactored to an io package
4006       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4007       if (protocol == null)
4008       {
4009         return false;
4010       }
4011       if (needtoadd)
4012       {
4013         // make a note of the access mode and add
4014         if (pdbentry.getProperty() == null)
4015         {
4016           pdbentry.setProperty(new Hashtable());
4017         }
4018         pdbentry.getProperty().put("protocol", protocol);
4019         toaddpdb.addPDBId(pdbentry);
4020         alignPanel.getStructureSelectionManager()
4021                 .registerPDBEntry(pdbentry);
4022       }
4023     }
4024     return true;
4025   }
4026
4027   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4028   {
4029     if (seqs != null)
4030     {
4031       Vector sequences = new Vector();
4032       for (int i = 0; i < seqs.length; i++)
4033       {
4034         if (seqs[i] != null)
4035         {
4036           sequences.addElement(new Object[] { seqs[i],
4037               (chains != null) ? chains[i] : null });
4038         }
4039       }
4040       seqs = new SequenceI[sequences.size()];
4041       chains = new String[sequences.size()];
4042       for (int i = 0, isize = sequences.size(); i < isize; i++)
4043       {
4044         Object[] oj = (Object[]) sequences.elementAt(i);
4045
4046         seqs[i] = (SequenceI) oj[0];
4047         chains[i] = (String) oj[1];
4048       }
4049     }
4050     return new Object[] { seqs, chains };
4051
4052   }
4053
4054   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4055           SequenceI[] seqs, String[] chains, String protocol)
4056   {
4057     // Scrub any null sequences from the array
4058     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4059     seqs = (SequenceI[]) sqch[0];
4060     chains = (String[]) sqch[1];
4061     if (seqs == null || seqs.length == 0)
4062     {
4063       System.err
4064               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4065     }
4066     if (protocol == null || protocol.trim().length() == 0
4067             || protocol.equals("null"))
4068     {
4069       protocol = (String) pdb.getProperty().get("protocol");
4070       if (protocol == null)
4071       {
4072         System.err.println("Couldn't work out protocol to open structure: "
4073                 + pdb.getId());
4074         return;
4075       }
4076     }
4077     if (applet.useXtrnalSviewer)
4078     {
4079       // register the association(s) and quit, don't create any windows.
4080       if (StructureSelectionManager.getStructureSelectionManager(applet)
4081               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4082       {
4083         System.err.println("Failed to map " + pdb.getFile() + " ("
4084                 + protocol + ") to any sequences");
4085       }
4086       return;
4087     }
4088     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4089     {
4090       // can only do alignments with Jmol
4091       // find the last jmol window assigned to this alignment
4092       jalview.appletgui.AppletJmol ajm = null, tajm;
4093       Vector jmols = applet
4094               .getAppletWindow(jalview.appletgui.AppletJmol.class);
4095       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4096       {
4097         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4098         if (tajm.ap.alignFrame == this)
4099         {
4100           ajm = tajm;
4101           break;
4102         }
4103       }
4104       if (ajm != null)
4105       {
4106         System.err
4107                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4108         // try and add the pdb structure
4109         // ajm.addS
4110         ajm = null;
4111       }
4112     }
4113     // otherwise, create a new window
4114     if (applet.jmolAvailable)
4115     {
4116       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4117               protocol);
4118       applet.lastFrameX += 40;
4119       applet.lastFrameY += 40;
4120     }
4121     else
4122     {
4123       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4124     }
4125
4126   }
4127
4128   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4129           SequenceI[][] seqs, String[][] chains, String[] protocols)
4130   {
4131     // TODO Auto-generated method stub
4132     System.err.println("Aligned Structure View: Not yet implemented.");
4133   }
4134
4135   /**
4136    * modify the current selection, providing the user has not made a selection
4137    * already.
4138    *
4139    * @param sel
4140    *          - sequences from this alignment
4141    * @param csel
4142    *          - columns to be selected on the alignment
4143    */
4144   public void select(SequenceGroup sel, ColumnSelection csel)
4145   {
4146     alignPanel.seqPanel.selection(sel, csel, null);
4147   }
4148
4149   public void scrollTo(int row, int column)
4150   {
4151     alignPanel.seqPanel.scrollTo(row, column);
4152   }
4153
4154   public void scrollToRow(int row)
4155   {
4156     alignPanel.seqPanel.scrollToRow(row);
4157   }
4158
4159   public void scrollToColumn(int column)
4160   {
4161     alignPanel.seqPanel.scrollToColumn(column);
4162   }
4163
4164   /**
4165    * @return the alignments unique ID.
4166    */
4167   public String getSequenceSetId()
4168   {
4169     return viewport.getSequenceSetId();
4170   }
4171
4172   /**
4173    * Load the (T-Coffee) score file from the specified url
4174    *
4175    * @param source
4176    *          File/URL/T-COFFEE score file contents
4177    * @throws IOException
4178    * @return true if alignment was annotated with data from source
4179    */
4180   public boolean loadScoreFile(String source) throws IOException
4181   {
4182
4183     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4184             AppletFormatAdapter.checkProtocol(source));
4185     if (!file.isValid())
4186     {
4187       // TODO: raise dialog for gui
4188       System.err.println("Problems parsing T-Coffee scores: "
4189               + file.getWarningMessage());
4190       System.err.println("Origin was:\n" + source);
4191       return false;
4192     }
4193
4194     /*
4195      * check that the score matrix matches the alignment dimensions
4196      */
4197     AlignmentI aln;
4198     if ((aln = viewport.getAlignment()) != null
4199             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4200                     .getWidth()))
4201     {
4202       // TODO: raise a dialog box here rather than bomb out.
4203       System.err
4204               .println("The scores matrix does not match the alignment dimensions");
4205
4206     }
4207
4208     // TODO add parameter to indicate if matching should be done
4209     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4210     {
4211       alignPanel.fontChanged();
4212       tcoffeeColour.setEnabled(true);
4213       // switch to this color
4214       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4215       return true;
4216     }
4217     else
4218     {
4219       System.err.println("Problems resolving T-Coffee scores:");
4220       if (file.getWarningMessage() != null)
4221       {
4222         System.err.println(file.getWarningMessage());
4223       }
4224     }
4225     return false;
4226   }
4227
4228   public SplitFrame getSplitFrame()
4229   {
4230     return this.splitFrame;
4231   }
4232
4233   public void setSplitFrame(SplitFrame sf)
4234   {
4235     this.splitFrame = sf;
4236   }
4237
4238   // may not need this
4239   @Override
4240   public void setShowSeqFeatures(boolean b)
4241   {
4242     // showSeqFeatures.setSelected(b);
4243     viewport.setShowSequenceFeatures(b);
4244
4245   }
4246
4247   @Override
4248   public void setMenusForViewport()
4249   {
4250     // setMenusFromViewport(viewport);
4251
4252   }
4253
4254   @Override
4255   public void refreshFeatureUI(boolean enableIfNecessary)
4256   {
4257     if (enableIfNecessary)
4258     {
4259       sequenceFeatures.setState(true);
4260       alignPanel.av.setShowSequenceFeatures(true);
4261     }
4262   }
4263
4264   @Override
4265   public FeatureSettingsControllerI getFeatureSettingsUI()
4266   {
4267     return alignPanel.av.featureSettings;
4268   }
4269
4270 }