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