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