src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.FeatureRenderer;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.EditCommand.Action;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.ColumnSelection;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.io.AnnotationFile;
  46 import jalview.io.AppletFormatAdapter;
  47 import jalview.io.FeaturesFile;
  48 import jalview.io.TCoffeeScoreFile;
  49 import jalview.schemes.Blosum62ColourScheme;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.ClustalxColourScheme;
  52 import jalview.schemes.ColourSchemeI;
  53 import jalview.schemes.HelixColourScheme;
  54 import jalview.schemes.HydrophobicColourScheme;
  55 import jalview.schemes.NucleotideColourScheme;
  56 import jalview.schemes.PIDColourScheme;
  57 import jalview.schemes.PurinePyrimidineColourScheme;
  58 import jalview.schemes.RNAHelicesColourChooser;
  59 import jalview.schemes.RNAInteractionColourScheme;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.structures.models.AAStructureBindingModel;
  67 import jalview.util.MessageManager;
  68
  69 import java.awt.BorderLayout;
  70 import java.awt.Canvas;
  71 import java.awt.CheckboxMenuItem;
  72 import java.awt.Color;
  73 import java.awt.Font;
  74 import java.awt.FontMetrics;
  75 import java.awt.Frame;
  76 import java.awt.Graphics;
  77 import java.awt.Label;
  78 import java.awt.Menu;
  79 import java.awt.MenuBar;
  80 import java.awt.MenuItem;
  81 import java.awt.event.ActionEvent;
  82 import java.awt.event.ActionListener;
  83 import java.awt.event.FocusEvent;
  84 import java.awt.event.FocusListener;
  85 import java.awt.event.ItemEvent;
  86 import java.awt.event.ItemListener;
  87 import java.awt.event.KeyEvent;
  88 import java.awt.event.KeyListener;
  89 import java.awt.event.WindowAdapter;
  90 import java.awt.event.WindowEvent;
  91 import java.io.IOException;
  92 import java.net.URL;
  93 import java.net.URLEncoder;
  94 import java.util.Arrays;
  95 import java.util.Hashtable;
  96 import java.util.List;
  97 import java.util.Map;
  98 import java.util.StringTokenizer;
  99 import java.util.Vector;
 100
 101 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 102         ItemListener, KeyListener, AlignViewControllerGuiI
 103 {
 104   public AlignViewControllerI avc;
 105
 106   public AlignmentPanel alignPanel;
 107
 108   public AlignViewport viewport;
 109
 110   int DEFAULT_WIDTH = 700;
 111
 112   int DEFAULT_HEIGHT = 500;
 113
 114   String jalviewServletURL;
 115
 116   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 117           String title, boolean embedded)
 118   {
 119     if (applet != null)
 120     {
 121       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 122     }
 123
 124     try
 125     {
 126       jbInit();
 127     } catch (Exception ex)
 128     {
 129       ex.printStackTrace();
 130     }
 131     // need to get window geometry before we calculate alignment layout
 132     if (applet != null)
 133     {
 134       String param;
 135       try
 136       {
 137         param = applet.getParameter("windowWidth");
 138         if (param != null)
 139         {
 140           int width = Integer.parseInt(param);
 141           DEFAULT_WIDTH = width;
 142         }
 143         param = applet.getParameter("windowHeight");
 144         if (param != null)
 145         {
 146           int height = Integer.parseInt(param);
 147           DEFAULT_HEIGHT = height;
 148         }
 149       } catch (Exception ex)
 150       {
 151       }
 152     }
 153     viewport = new AlignViewport(al, applet);
 154     alignPanel = new AlignmentPanel(this, viewport);
 155     avc = new jalview.controller.AlignViewController(this, viewport,
 156             alignPanel);
 157     viewport.updateConservation(alignPanel);
 158     viewport.updateConsensus(alignPanel);
 159
 160     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 161     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 162     followMouseOverFlag.setState(viewport.getFollowHighlight());
 163     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 164     showGroupConservation.setState(viewport.isShowGroupConservation());
 165     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 166     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 167     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 168     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 169
 170     seqLimits.setState(viewport.getShowJVSuffix());
 171
 172     if (applet != null)
 173     {
 174       String param = applet.getParameter("sortBy");
 175       if (param != null)
 176       {
 177         if (param.equalsIgnoreCase("Id"))
 178         {
 179           sortIDMenuItem_actionPerformed();
 180         }
 181         else if (param.equalsIgnoreCase("Pairwise Identity"))
 182         {
 183           sortPairwiseMenuItem_actionPerformed();
 184         }
 185         else if (param.equalsIgnoreCase("Length"))
 186         {
 187           sortLengthMenuItem_actionPerformed();
 188         }
 189       }
 190
 191       param = applet.getParameter("wrap");
 192       if (param != null)
 193       {
 194         if (param.equalsIgnoreCase("true"))
 195         {
 196           wrapMenuItem.setState(true);
 197           wrapMenuItem_actionPerformed();
 198         }
 199       }
 200       param = applet.getParameter("centrecolumnlabels");
 201       if (param != null)
 202       {
 203         centreColumnLabelFlag.setState(true);
 204         centreColumnLabelFlag_stateChanged();
 205       }
 206
 207     }
 208     if (viewport.getAlignment().isNucleotide())
 209     {
 210       viewport.updateStrucConsensus(alignPanel);
 211       if (viewport.getAlignment().hasRNAStructure())
 212       {
 213         RNAHelixColour.setEnabled(true);
 214       }
 215       else
 216       {
 217         RNAHelixColour.setEnabled(false);
 218       }
 219     }
 220     else
 221     {
 222       RNAHelixColour.setEnabled(false);
 223       purinePyrimidineColour.setEnabled(false);
 224     }
 225     // Some JVMS send keyevents to Top frame or lowest panel,
 226     // Havent worked out why yet. So add to both this frame and seqCanvas for
 227     // now
 228     this.addKeyListener(this);
 229     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 230     alignPanel.idPanel.idCanvas.addKeyListener(this);
 231     alignPanel.scalePanel.addKeyListener(this);
 232     alignPanel.annotationPanel.addKeyListener(this);
 233     alignPanel.annotationPanelHolder.addKeyListener(this);
 234     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 235     alignPanel.alabels.addKeyListener(this);
 236     createAlignFrameWindow(embedded, title);
 237
 238     validate();
 239     alignPanel.adjustAnnotationHeight();
 240     alignPanel.paintAlignment(true);
 241   }
 242
 243   public AlignViewport getAlignViewport()
 244   {
 245     return viewport;
 246   }
 247
 248   public SeqCanvas getSeqcanvas()
 249   {
 250     return alignPanel.seqPanel.seqCanvas;
 251   }
 252
 253   /**
 254    * Load a features file onto the alignment
 255    *
 256    * @param file
 257    *          file URL, content, or other resolvable path
 258    * @param type
 259    *          is protocol for accessing data referred to by file
 260    */
 261
 262   public boolean parseFeaturesFile(String file, String type)
 263   {
 264     return parseFeaturesFile(file, type, true);
 265   }
 266
 267   /**
 268    * Load a features file onto the alignment
 269    *
 270    * @param file
 271    *          file URL, content, or other resolvable path
 272    * @param type
 273    *          is protocol for accessing data referred to by file
 274    * @param autoenabledisplay
 275    *          when true, display features flag will be automatically enabled if
 276    *          features are loaded
 277    * @return true if data parsed as a features file
 278    */
 279   public boolean parseFeaturesFile(String file, String type,
 280           boolean autoenabledisplay)
 281   {
 282     // TODO: test if importing a features file onto an alignment which already
 283     // has features with links overwrites the original links.
 284
 285     Hashtable featureLinks = new Hashtable();
 286     boolean featuresFile = false;
 287     try
 288     {
 289       featuresFile = new jalview.io.FeaturesFile(file, type)
 290               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 291                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 292                       true, viewport.applet.getDefaultParameter(
 293                               "relaxedidmatch", false));
 294     } catch (Exception ex)
 295     {
 296       ex.printStackTrace();
 297     }
 298
 299     if (featuresFile)
 300     {
 301       if (featureLinks.size() > 0)
 302       {
 303         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 304       }
 305       if (autoenabledisplay)
 306       {
 307         viewport.setShowSequenceFeatures(true);
 308         sequenceFeatures.setState(true);
 309       }
 310       if (alignPanel.seqPanel.seqCanvas.fr != null)
 311       {
 312         // update the min/max ranges where necessary
 313         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 314       }
 315       if (viewport.featureSettings != null)
 316       {
 317         viewport.featureSettings.refreshTable();
 318       }
 319       alignPanel.paintAlignment(true);
 320       statusBar.setText(MessageManager
 321               .getString("label.successfully_added_features_alignment"));
 322     }
 323     return featuresFile;
 324   }
 325
 326   @Override
 327   public void keyPressed(KeyEvent evt)
 328   {
 329     if (viewport.cursorMode
 330             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 331                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 332                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 333             && Character.isDigit(evt.getKeyChar()))
 334     {
 335       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 336     }
 337
 338     switch (evt.getKeyCode())
 339     {
 340     case 27: // escape key
 341       deselectAllSequenceMenuItem_actionPerformed();
 342
 343       alignPanel.alabels.cancelDrag();
 344       break;
 345     case KeyEvent.VK_X:
 346       if (evt.isControlDown() || evt.isMetaDown())
 347       {
 348         cut_actionPerformed();
 349       }
 350       break;
 351     case KeyEvent.VK_C:
 352       if (viewport.cursorMode && !evt.isControlDown())
 353       {
 354         alignPanel.seqPanel.setCursorColumn();
 355       }
 356       if (evt.isControlDown() || evt.isMetaDown())
 357       {
 358         copy_actionPerformed();
 359       }
 360       break;
 361     case KeyEvent.VK_V:
 362       if (evt.isControlDown())
 363       {
 364         paste(evt.isShiftDown());
 365       }
 366       break;
 367     case KeyEvent.VK_A:
 368       if (evt.isControlDown() || evt.isMetaDown())
 369       {
 370         selectAllSequenceMenuItem_actionPerformed();
 371       }
 372       break;
 373     case KeyEvent.VK_DOWN:
 374       if (viewport.cursorMode)
 375       {
 376         alignPanel.seqPanel.moveCursor(0, 1);
 377       }
 378       else
 379       {
 380         moveSelectedSequences(false);
 381       }
 382       break;
 383
 384     case KeyEvent.VK_UP:
 385       if (viewport.cursorMode)
 386       {
 387         alignPanel.seqPanel.moveCursor(0, -1);
 388       }
 389       else
 390       {
 391         moveSelectedSequences(true);
 392       }
 393       break;
 394
 395     case KeyEvent.VK_LEFT:
 396       if (evt.isAltDown() || !viewport.cursorMode)
 397       {
 398         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 399       }
 400       else
 401       {
 402         alignPanel.seqPanel.moveCursor(-1, 0);
 403       }
 404       break;
 405
 406     case KeyEvent.VK_RIGHT:
 407       if (evt.isAltDown() || !viewport.cursorMode)
 408       {
 409         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 410       }
 411       else
 412       {
 413         alignPanel.seqPanel.moveCursor(1, 0);
 414       }
 415       break;
 416
 417     case KeyEvent.VK_SPACE:
 418       if (viewport.cursorMode)
 419       {
 420         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 421                 || evt.isShiftDown() || evt.isAltDown());
 422       }
 423       break;
 424
 425     case KeyEvent.VK_DELETE:
 426     case KeyEvent.VK_BACK_SPACE:
 427       if (viewport.cursorMode)
 428       {
 429         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 430                 || evt.isShiftDown() || evt.isAltDown());
 431       }
 432       else
 433       {
 434         cut_actionPerformed();
 435         alignPanel.seqPanel.seqCanvas.repaint();
 436       }
 437       break;
 438
 439     case KeyEvent.VK_S:
 440       if (viewport.cursorMode)
 441       {
 442         alignPanel.seqPanel.setCursorRow();
 443       }
 444       break;
 445     case KeyEvent.VK_P:
 446       if (viewport.cursorMode)
 447       {
 448         alignPanel.seqPanel.setCursorPosition();
 449       }
 450       break;
 451
 452     case KeyEvent.VK_ENTER:
 453     case KeyEvent.VK_COMMA:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.setCursorRowAndColumn();
 457       }
 458       break;
 459
 460     case KeyEvent.VK_Q:
 461       if (viewport.cursorMode)
 462       {
 463         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 464       }
 465       break;
 466     case KeyEvent.VK_M:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_F2:
 474       viewport.cursorMode = !viewport.cursorMode;
 475       statusBar.setText(MessageManager.formatMessage(
 476               "label.keyboard_editing_mode", new String[]
 477               { (viewport.cursorMode ? "on" : "off") }));
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 481         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 482       }
 483       break;
 484
 485     case KeyEvent.VK_F:
 486       if (evt.isControlDown())
 487       {
 488         findMenuItem_actionPerformed();
 489       }
 490       break;
 491
 492     case KeyEvent.VK_H:
 493     {
 494       boolean toggleSeqs = !evt.isControlDown();
 495       boolean toggleCols = !evt.isShiftDown();
 496       toggleHiddenRegions(toggleSeqs, toggleCols);
 497       break;
 498     }
 499
 500     case KeyEvent.VK_PAGE_UP:
 501       if (viewport.getWrapAlignment())
 502       {
 503         alignPanel.scrollUp(true);
 504       }
 505       else
 506       {
 507         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 508                 - viewport.endSeq + viewport.startSeq);
 509       }
 510       break;
 511
 512     case KeyEvent.VK_PAGE_DOWN:
 513       if (viewport.getWrapAlignment())
 514       {
 515         alignPanel.scrollUp(false);
 516       }
 517       else
 518       {
 519         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 520                 + viewport.endSeq - viewport.startSeq);
 521       }
 522       break;
 523
 524     case KeyEvent.VK_Z:
 525       if (evt.isControlDown())
 526       {
 527         undoMenuItem_actionPerformed();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_Y:
 532       if (evt.isControlDown())
 533       {
 534         redoMenuItem_actionPerformed();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_L:
 539       if (evt.isControlDown())
 540       {
 541         trimAlignment(true);
 542       }
 543       break;
 544
 545     case KeyEvent.VK_R:
 546       if (evt.isControlDown())
 547       {
 548         trimAlignment(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_E:
 553       if (evt.isControlDown())
 554       {
 555         if (evt.isShiftDown())
 556         {
 557           this.removeAllGapsMenuItem_actionPerformed();
 558         }
 559         else
 560         {
 561           removeGappedColumnMenuItem_actionPerformed();
 562         }
 563       }
 564       break;
 565     case KeyEvent.VK_I:
 566       if (evt.isControlDown())
 567       {
 568         if (evt.isAltDown())
 569         {
 570           invertColSel_actionPerformed();
 571         }
 572         else
 573         {
 574           invertSequenceMenuItem_actionPerformed();
 575         }
 576       }
 577       break;
 578
 579     case KeyEvent.VK_G:
 580       if (evt.isControlDown())
 581       {
 582         if (evt.isShiftDown())
 583         {
 584           this.unGroup_actionPerformed();
 585         }
 586         else
 587         {
 588           this.createGroup_actionPerformed();
 589         }
 590       }
 591       break;
 592
 593     case KeyEvent.VK_U:
 594       if (evt.isControlDown())
 595       {
 596         this.deleteGroups_actionPerformed();
 597       }
 598       break;
 599
 600     case KeyEvent.VK_T:
 601       if (evt.isControlDown())
 602       {
 603         newView(null);
 604       }
 605       break;
 606
 607     }
 608     alignPanel.paintAlignment(true);
 609   }
 610
 611   /**
 612    * called by key handler and the hide all/show all menu items
 613    *
 614    * @param toggleSeqs
 615    * @param toggleCols
 616    */
 617   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 618   {
 619     boolean hide = false;
 620     SequenceGroup sg = viewport.getSelectionGroup();
 621     if (!toggleSeqs && !toggleCols)
 622     {
 623       // Hide everything by the current selection - this is a hack - we do the
 624       // invert and then hide
 625       // first check that there will be visible columns after the invert.
 626       if ((viewport.getColumnSelection() != null
 627               && viewport.getColumnSelection().getSelected() != null && viewport
 628               .getColumnSelection().getSelected().size() > 0)
 629               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 630                       .getEndRes()))
 631       {
 632         // now invert the sequence set, if required - empty selection implies
 633         // that no hiding is required.
 634         if (sg != null)
 635         {
 636           invertSequenceMenuItem_actionPerformed();
 637           sg = viewport.getSelectionGroup();
 638           toggleSeqs = true;
 639
 640         }
 641         viewport.expandColSelection(sg, true);
 642         // finally invert the column selection and get the new sequence
 643         // selection and indicate it should be hidden.
 644         invertColSel_actionPerformed();
 645         toggleCols = true;
 646       }
 647     }
 648
 649     if (toggleSeqs)
 650     {
 651       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 652       {
 653         hide = true;
 654         viewport.hideAllSelectedSeqs();
 655       }
 656       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 657               .size() > 0))
 658       {
 659         viewport.showAllHiddenSeqs();
 660       }
 661     }
 662
 663     if (toggleCols)
 664     {
 665       if (viewport.getColumnSelection().getSelected().size() > 0)
 666       {
 667         viewport.hideSelectedColumns();
 668         if (!toggleSeqs)
 669         {
 670           viewport.setSelectionGroup(sg);
 671         }
 672       }
 673       else if (!hide)
 674       {
 675         viewport.showAllHiddenColumns();
 676       }
 677     }
 678   }
 679
 680   @Override
 681   public void keyReleased(KeyEvent evt)
 682   {
 683   }
 684
 685   @Override
 686   public void keyTyped(KeyEvent evt)
 687   {
 688   }
 689
 690   @Override
 691   public void itemStateChanged(ItemEvent evt)
 692   {
 693     if (evt.getSource() == displayNonconservedMenuItem)
 694     {
 695       displayNonconservedMenuItem_actionPerformed();
 696     }
 697     else if (evt.getSource() == colourTextMenuItem)
 698     {
 699       colourTextMenuItem_actionPerformed();
 700     }
 701     else if (evt.getSource() == wrapMenuItem)
 702     {
 703       wrapMenuItem_actionPerformed();
 704     }
 705     else if (evt.getSource() == scaleAbove)
 706     {
 707       viewport.setScaleAboveWrapped(scaleAbove.getState());
 708     }
 709     else if (evt.getSource() == scaleLeft)
 710     {
 711       viewport.setScaleLeftWrapped(scaleLeft.getState());
 712     }
 713     else if (evt.getSource() == scaleRight)
 714     {
 715       viewport.setScaleRightWrapped(scaleRight.getState());
 716     }
 717     else if (evt.getSource() == seqLimits)
 718     {
 719       seqLimits_itemStateChanged();
 720     }
 721     else if (evt.getSource() == viewBoxesMenuItem)
 722     {
 723       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 724     }
 725     else if (evt.getSource() == viewTextMenuItem)
 726     {
 727       viewport.setShowText(viewTextMenuItem.getState());
 728     }
 729     else if (evt.getSource() == renderGapsMenuItem)
 730     {
 731       viewport.setRenderGaps(renderGapsMenuItem.getState());
 732     }
 733     else if (evt.getSource() == annotationPanelMenuItem)
 734     {
 735       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 736       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 737     }
 738     else if (evt.getSource() == sequenceFeatures)
 739     {
 740       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 741       alignPanel.seqPanel.seqCanvas.repaint();
 742     }
 743     else if (evt.getSource() == conservationMenuItem)
 744     {
 745       conservationMenuItem_actionPerformed();
 746     }
 747     else if (evt.getSource() == abovePIDThreshold)
 748     {
 749       abovePIDThreshold_actionPerformed();
 750     }
 751     else if (evt.getSource() == applyToAllGroups)
 752     {
 753       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 754     }
 755     else if (evt.getSource() == autoCalculate)
 756     {
 757       viewport.autoCalculateConsensus = autoCalculate.getState();
 758     }
 759     else if (evt.getSource() == sortByTree)
 760     {
 761       viewport.sortByTree = sortByTree.getState();
 762     }
 763     else if (evt.getSource() == this.centreColumnLabelFlag)
 764     {
 765       centreColumnLabelFlag_stateChanged();
 766     }
 767     else if (evt.getSource() == this.followMouseOverFlag)
 768     {
 769       mouseOverFlag_stateChanged();
 770     }
 771     else if (evt.getSource() == showGroupConsensus)
 772     {
 773       showGroupConsensus_actionPerformed();
 774     }
 775     else if (evt.getSource() == showGroupConservation)
 776     {
 777       showGroupConservation_actionPerformed();
 778     }
 779     else if (evt.getSource() == showSequenceLogo)
 780     {
 781       showSequenceLogo_actionPerformed();
 782     }
 783     else if (evt.getSource() == normSequenceLogo)
 784     {
 785       normSequenceLogo_actionPerformed();
 786     }
 787     else if (evt.getSource() == showConsensusHistogram)
 788     {
 789       showConsensusHistogram_actionPerformed();
 790     }
 791     else if (evt.getSource() == applyAutoAnnotationSettings)
 792     {
 793       applyAutoAnnotationSettings_actionPerformed();
 794     }
 795     alignPanel.paintAlignment(true);
 796   }
 797
 798   private void mouseOverFlag_stateChanged()
 799   {
 800     viewport.followHighlight = followMouseOverFlag.getState();
 801     // TODO: could kick the scrollTo mechanism to reset view for current
 802     // searchresults.
 803   }
 804
 805   private void centreColumnLabelFlag_stateChanged()
 806   {
 807     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 808     this.alignPanel.annotationPanel.repaint();
 809   }
 810
 811   @Override
 812   public void actionPerformed(ActionEvent evt)
 813   {
 814     Object source = evt.getSource();
 815
 816     if (source == inputText)
 817     {
 818       inputText_actionPerformed();
 819     }
 820     else if (source == loadTree)
 821     {
 822       loadTree_actionPerformed();
 823     }
 824     else if (source == loadApplication)
 825     {
 826       launchFullApplication();
 827     }
 828     else if (source == loadAnnotations)
 829     {
 830       loadAnnotations();
 831     }
 832     else if (source == outputAnnotations)
 833     {
 834       outputAnnotations(true);
 835     }
 836     else if (source == outputFeatures)
 837     {
 838       outputFeatures(true, "Jalview");
 839     }
 840     else if (source == closeMenuItem)
 841     {
 842       closeMenuItem_actionPerformed();
 843     }
 844     else if (source == copy)
 845     {
 846       copy_actionPerformed();
 847     }
 848     else if (source == undoMenuItem)
 849     {
 850       undoMenuItem_actionPerformed();
 851     }
 852     else if (source == redoMenuItem)
 853     {
 854       redoMenuItem_actionPerformed();
 855     }
 856     else if (source == inputText)
 857     {
 858       inputText_actionPerformed();
 859     }
 860     else if (source == closeMenuItem)
 861     {
 862       closeMenuItem_actionPerformed();
 863     }
 864     else if (source == undoMenuItem)
 865     {
 866       undoMenuItem_actionPerformed();
 867     }
 868     else if (source == redoMenuItem)
 869     {
 870       redoMenuItem_actionPerformed();
 871     }
 872     else if (source == copy)
 873     {
 874       copy_actionPerformed();
 875     }
 876     else if (source == pasteNew)
 877     {
 878       pasteNew_actionPerformed();
 879     }
 880     else if (source == pasteThis)
 881     {
 882       pasteThis_actionPerformed();
 883     }
 884     else if (source == cut)
 885     {
 886       cut_actionPerformed();
 887     }
 888     else if (source == delete)
 889     {
 890       delete_actionPerformed();
 891     }
 892     else if (source == grpsFromSelection)
 893     {
 894       makeGrpsFromSelection_actionPerformed();
 895     }
 896     else if (source == deleteGroups)
 897     {
 898       deleteGroups_actionPerformed();
 899     }
 900     else if (source == selectAllSequenceMenuItem)
 901     {
 902       selectAllSequenceMenuItem_actionPerformed();
 903     }
 904     else if (source == deselectAllSequenceMenuItem)
 905     {
 906       deselectAllSequenceMenuItem_actionPerformed();
 907     }
 908     else if (source == invertSequenceMenuItem)
 909     {
 910       invertSequenceMenuItem_actionPerformed();
 911     }
 912     else if (source == invertColSel)
 913     {
 914       viewport.invertColumnSelection();
 915       alignPanel.paintAlignment(true);
 916     }
 917     else if (source == remove2LeftMenuItem)
 918     {
 919       trimAlignment(true);
 920     }
 921     else if (source == remove2RightMenuItem)
 922     {
 923       trimAlignment(false);
 924     }
 925     else if (source == removeGappedColumnMenuItem)
 926     {
 927       removeGappedColumnMenuItem_actionPerformed();
 928     }
 929     else if (source == removeAllGapsMenuItem)
 930     {
 931       removeAllGapsMenuItem_actionPerformed();
 932     }
 933     else if (source == findMenuItem)
 934     {
 935       findMenuItem_actionPerformed();
 936     }
 937     else if (source == font)
 938     {
 939       new FontChooser(alignPanel);
 940     }
 941     else if (source == newView)
 942     {
 943       newView(null);
 944     }
 945     else if (source == showColumns)
 946     {
 947       viewport.showAllHiddenColumns();
 948       alignPanel.paintAlignment(true);
 949     }
 950     else if (source == showSeqs)
 951     {
 952       viewport.showAllHiddenSeqs();
 953       alignPanel.paintAlignment(true);
 954     }
 955     else if (source == hideColumns)
 956     {
 957       viewport.hideSelectedColumns();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == hideSequences
 961             && viewport.getSelectionGroup() != null)
 962     {
 963       viewport.hideAllSelectedSeqs();
 964       alignPanel.paintAlignment(true);
 965     }
 966     else if (source == hideAllButSelection)
 967     {
 968       toggleHiddenRegions(false, false);
 969       alignPanel.paintAlignment(true);
 970     }
 971     else if (source == hideAllSelection)
 972     {
 973       SequenceGroup sg = viewport.getSelectionGroup();
 974       viewport.expandColSelection(sg, false);
 975       viewport.hideAllSelectedSeqs();
 976       viewport.hideSelectedColumns();
 977       alignPanel.paintAlignment(true);
 978     }
 979     else if (source == showAllHidden)
 980     {
 981       viewport.showAllHiddenColumns();
 982       viewport.showAllHiddenSeqs();
 983       alignPanel.paintAlignment(true);
 984     }
 985     else if (source == showGroupConsensus)
 986     {
 987       showGroupConsensus_actionPerformed();
 988     }
 989     else if (source == showGroupConservation)
 990     {
 991       showGroupConservation_actionPerformed();
 992     }
 993     else if (source == showSequenceLogo)
 994     {
 995       showSequenceLogo_actionPerformed();
 996     }
 997     else if (source == normSequenceLogo)
 998     {
 999       normSequenceLogo_actionPerformed();
1000     }
1001     else if (source == showConsensusHistogram)
1002     {
1003       showConsensusHistogram_actionPerformed();
1004     }
1005     else if (source == applyAutoAnnotationSettings)
1006     {
1007       applyAutoAnnotationSettings_actionPerformed();
1008     }
1009     else if (source == featureSettings)
1010     {
1011       new FeatureSettings(alignPanel);
1012     }
1013     else if (source == alProperties)
1014     {
1015       StringBuffer contents = new jalview.io.AlignmentProperties(
1016               viewport.getAlignment()).formatAsString();
1017       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1018       cap.setText(contents.toString());
1019       Frame frame = new Frame();
1020       frame.add(cap);
1021       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1022               "label.alignment_properties", new String[]
1023               { getTitle() }), 400, 250);
1024     }
1025     else if (source == overviewMenuItem)
1026     {
1027       overviewMenuItem_actionPerformed();
1028     }
1029     else if (source == noColourmenuItem)
1030     {
1031       changeColour(null);
1032     }
1033     else if (source == clustalColour)
1034     {
1035       abovePIDThreshold.setState(false);
1036       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1037     }
1038     else if (source == zappoColour)
1039     {
1040       changeColour(new ZappoColourScheme());
1041     }
1042     else if (source == taylorColour)
1043     {
1044       changeColour(new TaylorColourScheme());
1045     }
1046     else if (source == hydrophobicityColour)
1047     {
1048       changeColour(new HydrophobicColourScheme());
1049     }
1050     else if (source == helixColour)
1051     {
1052       changeColour(new HelixColourScheme());
1053     }
1054     else if (source == strandColour)
1055     {
1056       changeColour(new StrandColourScheme());
1057     }
1058     else if (source == turnColour)
1059     {
1060       changeColour(new TurnColourScheme());
1061     }
1062     else if (source == buriedColour)
1063     {
1064       changeColour(new BuriedColourScheme());
1065     }
1066     else if (source == nucleotideColour)
1067     {
1068       changeColour(new NucleotideColourScheme());
1069     }
1070     else if (source == purinePyrimidineColour)
1071     {
1072       changeColour(new PurinePyrimidineColourScheme());
1073     }
1074     else if (source == RNAInteractionColour)
1075     {
1076       changeColour(new RNAInteractionColourScheme());
1077     }
1078     else if (source == RNAHelixColour)
1079     {
1080       new RNAHelicesColourChooser(viewport, alignPanel);
1081     }
1082     else if (source == modifyPID)
1083     {
1084       modifyPID_actionPerformed();
1085     }
1086     else if (source == modifyConservation)
1087     {
1088       modifyConservation_actionPerformed();
1089     }
1090     else if (source == userDefinedColour)
1091     {
1092       new UserDefinedColours(alignPanel, null);
1093     }
1094     else if (source == PIDColour)
1095     {
1096       changeColour(new PIDColourScheme());
1097     }
1098     else if (source == BLOSUM62Colour)
1099     {
1100       changeColour(new Blosum62ColourScheme());
1101     }
1102     else if (source == tcoffeeColour)
1103     {
1104       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1105     }
1106     else if (source == annotationColour)
1107     {
1108       new AnnotationColourChooser(viewport, alignPanel);
1109     }
1110     else if (source == annotationColumnSelection)
1111     {
1112       new AnnotationColumnChooser(viewport, alignPanel);
1113     }
1114     else if (source == sortPairwiseMenuItem)
1115     {
1116       sortPairwiseMenuItem_actionPerformed();
1117     }
1118     else if (source == sortIDMenuItem)
1119     {
1120       sortIDMenuItem_actionPerformed();
1121     }
1122     else if (source == sortLengthMenuItem)
1123     {
1124       sortLengthMenuItem_actionPerformed();
1125     }
1126     else if (source == sortGroupMenuItem)
1127     {
1128       sortGroupMenuItem_actionPerformed();
1129     }
1130     else if (source == removeRedundancyMenuItem)
1131     {
1132       removeRedundancyMenuItem_actionPerformed();
1133     }
1134     else if (source == pairwiseAlignmentMenuItem)
1135     {
1136       pairwiseAlignmentMenuItem_actionPerformed();
1137     }
1138     else if (source == PCAMenuItem)
1139     {
1140       PCAMenuItem_actionPerformed();
1141     }
1142     else if (source == averageDistanceTreeMenuItem)
1143     {
1144       averageDistanceTreeMenuItem_actionPerformed();
1145     }
1146     else if (source == neighbourTreeMenuItem)
1147     {
1148       neighbourTreeMenuItem_actionPerformed();
1149     }
1150     else if (source == njTreeBlosumMenuItem)
1151     {
1152       njTreeBlosumMenuItem_actionPerformed();
1153     }
1154     else if (source == avDistanceTreeBlosumMenuItem)
1155     {
1156       avTreeBlosumMenuItem_actionPerformed();
1157     }
1158     else if (source == documentation)
1159     {
1160       documentation_actionPerformed();
1161     }
1162     else if (source == about)
1163     {
1164       about_actionPerformed();
1165     }
1166
1167   }
1168
1169   public void inputText_actionPerformed()
1170   {
1171     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1172     Frame frame = new Frame();
1173     frame.add(cap);
1174     jalview.bin.JalviewLite.addFrame(frame,
1175             MessageManager.getString("label.input_cut_paste"), 500, 500);
1176   }
1177
1178   protected void outputText_actionPerformed(ActionEvent e)
1179   {
1180     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1181     Frame frame = new Frame();
1182     frame.add(cap);
1183     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184             "label.alignment_output_command", new String[]
1185             { e.getActionCommand() }), 600, 500);
1186     cap.setText(new AppletFormatAdapter().formatSequences(
1187             e.getActionCommand(), viewport.getAlignment(),
1188             viewport.getShowJVSuffix()));
1189   }
1190
1191   public void loadAnnotations()
1192   {
1193     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1194     cap.setText(MessageManager
1195             .getString("label.paste_features_annotations_Tcoffee_here"));
1196     cap.setAnnotationImport();
1197     Frame frame = new Frame();
1198     frame.add(cap);
1199     jalview.bin.JalviewLite.addFrame(frame,
1200             MessageManager.getString("action.paste_annotations"), 400, 300);
1201
1202   }
1203
1204   public String outputAnnotations(boolean displayTextbox)
1205   {
1206     String annotation = new AnnotationFile()
1207             .printAnnotationsForView(viewport);
1208
1209     if (displayTextbox)
1210     {
1211       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212       Frame frame = new Frame();
1213       frame.add(cap);
1214       jalview.bin.JalviewLite.addFrame(frame,
1215               MessageManager.getString("label.annotations"), 600, 500);
1216       cap.setText(annotation);
1217     }
1218
1219     return annotation;
1220   }
1221
1222   private Map<String,Object> getDisplayedFeatureCols()
1223   {
1224     if (alignPanel.getFeatureRenderer() != null
1225             && viewport.getFeaturesDisplayed()!= null)
1226     {
1227       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1228
1229     }
1230     return null;
1231   }
1232
1233   public String outputFeatures(boolean displayTextbox, String format)
1234   {
1235     String features;
1236     if (format.equalsIgnoreCase("Jalview"))
1237     {
1238       features = new FeaturesFile().printJalviewFormat(viewport
1239               .getAlignment().getSequencesArray(),
1240               getDisplayedFeatureCols());
1241     }
1242     else
1243     {
1244       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1245               .getSequencesArray(), getDisplayedFeatureCols());
1246     }
1247
1248     if (displayTextbox)
1249     {
1250       boolean frimport = false;
1251       if (features == null || features.equals("No Features Visible"))
1252       {
1253         features = "# No features visible - paste some and import them here.";
1254         frimport = true;
1255       }
1256
1257       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1258       if (frimport)
1259       {
1260         cap.setAnnotationImport();
1261       }
1262       Frame frame = new Frame();
1263       frame.add(cap);
1264       jalview.bin.JalviewLite.addFrame(frame,
1265               MessageManager.getString("label.features"), 600, 500);
1266       cap.setText(features);
1267     }
1268     else
1269     {
1270       if (features == null)
1271       {
1272         features = "";
1273       }
1274     }
1275
1276     return features;
1277   }
1278
1279   void launchFullApplication()
1280   {
1281     StringBuffer url = new StringBuffer(jalviewServletURL);
1282
1283     url.append("?open="
1284             + appendProtocol(viewport.applet.getParameter("file")));
1285
1286     if (viewport.applet.getParameter("features") != null)
1287     {
1288       url.append("&features=");
1289       url.append(appendProtocol(viewport.applet.getParameter("features")));
1290     }
1291
1292     if (viewport.applet.getParameter("annotations") != null)
1293     {
1294       url.append("&annotations=");
1295       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1296     }
1297
1298     if (viewport.applet.getParameter("jnetfile") != null)
1299     {
1300       url.append("&annotations=");
1301       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1302     }
1303
1304     if (viewport.applet.getParameter("defaultColour") != null)
1305     {
1306       url.append("&colour="
1307               + removeWhiteSpace(viewport.applet
1308                       .getParameter("defaultColour")));
1309     }
1310
1311     if (viewport.applet.getParameter("userDefinedColour") != null)
1312     {
1313       url.append("&colour="
1314               + removeWhiteSpace(viewport.applet
1315                       .getParameter("userDefinedColour")));
1316     }
1317     if (viewport.applet.getParameter("tree") != null)
1318     {
1319       url.append("&tree="
1320               + appendProtocol(viewport.applet.getParameter("tree")));
1321     }
1322     if (viewport.applet.getParameter("treeFile") != null)
1323     {
1324       url.append("&tree="
1325               + appendProtocol(viewport.applet.getParameter("treeFile")));
1326     }
1327
1328     showURL(url.toString(), "FULL_APP");
1329   }
1330
1331   String removeWhiteSpace(String colour)
1332   {
1333     StringBuffer sb = new StringBuffer();
1334     for (int i = 0; i < colour.length(); i++)
1335     {
1336       if (Character.isWhitespace(colour.charAt(i)))
1337       {
1338         sb.append("%20");
1339       }
1340       else
1341       {
1342         sb.append(colour.charAt(i));
1343       }
1344     }
1345
1346     return sb.toString();
1347   }
1348
1349   String appendProtocol(String url)
1350   {
1351     try
1352     {
1353       new URL(url);
1354       url = URLEncoder.encode(url);
1355     }
1356     /*
1357      * When we finally deprecate 1.1 compatibility, we can start to use
1358      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1359      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1360      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1361      * ex.printStackTrace(); }
1362      */
1363     catch (java.net.MalformedURLException ex)
1364     {
1365       url = viewport.applet.getCodeBase() + url;
1366     }
1367     return url;
1368   }
1369
1370   public void closeMenuItem_actionPerformed()
1371   {
1372     PaintRefresher.RemoveComponent(alignPanel);
1373     if (alignPanel.seqPanel != null
1374             && alignPanel.seqPanel.seqCanvas != null)
1375     {
1376       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1377     }
1378     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1379     {
1380       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1381     }
1382
1383     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1384     {
1385       System.exit(0);
1386     }
1387     else
1388     {
1389     }
1390     viewport = null;
1391     alignPanel = null;
1392     this.dispose();
1393   }
1394
1395   /**
1396    * TODO: JAL-1104
1397    */
1398   void updateEditMenuBar()
1399   {
1400
1401     if (viewport.historyList.size() > 0)
1402     {
1403       undoMenuItem.setEnabled(true);
1404       CommandI command = (CommandI) viewport.historyList.peek();
1405       undoMenuItem.setLabel(MessageManager.formatMessage(
1406               "label.undo_command", new String[]
1407               { command.getDescription() }));
1408     }
1409     else
1410     {
1411       undoMenuItem.setEnabled(false);
1412       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1413     }
1414
1415     if (viewport.redoList.size() > 0)
1416     {
1417       redoMenuItem.setEnabled(true);
1418
1419       CommandI command = (CommandI) viewport.redoList.peek();
1420       redoMenuItem.setLabel(MessageManager.formatMessage(
1421               "label.redo_command", new String[]
1422               { command.getDescription() }));
1423     }
1424     else
1425     {
1426       redoMenuItem.setEnabled(false);
1427       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1428     }
1429   }
1430
1431   /**
1432    * TODO: JAL-1104
1433    */
1434   @Override
1435   public void addHistoryItem(CommandI command)
1436   {
1437     if (command.getSize() > 0)
1438     {
1439       viewport.historyList.push(command);
1440       viewport.redoList.removeAllElements();
1441       updateEditMenuBar();
1442       viewport.updateHiddenColumns();
1443     }
1444   }
1445
1446   /**
1447    * TODO: JAL-1104 DOCUMENT ME!
1448    *
1449    * @param e
1450    *          DOCUMENT ME!
1451    */
1452   protected void undoMenuItem_actionPerformed()
1453   {
1454     if (viewport.historyList.size() < 1)
1455     {
1456       return;
1457     }
1458
1459     CommandI command = (CommandI) viewport.historyList.pop();
1460     viewport.redoList.push(command);
1461     command.undoCommand(null);
1462
1463     AlignViewport originalSource = getOriginatingSource(command);
1464     // JBPNote Test
1465     if (originalSource != viewport)
1466     {
1467       System.err
1468               .println("Warning: Viewport object mismatch whilst undoing");
1469     }
1470     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1471                                           // viewport.getColumnSelection().getHiddenColumns()
1472                                           // != null;
1473     updateEditMenuBar();
1474     originalSource.firePropertyChange("alignment", null, originalSource
1475             .getAlignment().getSequences());
1476   }
1477
1478   /**
1479    * TODO: JAL-1104 DOCUMENT ME!
1480    *
1481    * @param e
1482    *          DOCUMENT ME!
1483    */
1484   protected void redoMenuItem_actionPerformed()
1485   {
1486     if (viewport.redoList.size() < 1)
1487     {
1488       return;
1489     }
1490
1491     CommandI command = (CommandI) viewport.redoList.pop();
1492     viewport.historyList.push(command);
1493     command.doCommand(null);
1494
1495     AlignViewport originalSource = getOriginatingSource(command);
1496     // JBPNote Test
1497     if (originalSource != viewport)
1498     {
1499       System.err
1500               .println("Warning: Viewport object mismatch whilst re-doing");
1501     }
1502     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1503                                           // viewport.getColumnSelection().getHiddenColumns()
1504                                           // != null;
1505
1506     updateEditMenuBar();
1507     originalSource.firePropertyChange("alignment", null, originalSource
1508             .getAlignment().getSequences());
1509   }
1510
1511   AlignViewport getOriginatingSource(CommandI command)
1512   {
1513     AlignViewport originalSource = null;
1514     // For sequence removal and addition, we need to fire
1515     // the property change event FROM the viewport where the
1516     // original alignment was altered
1517     AlignmentI al = null;
1518     if (command instanceof EditCommand)
1519     {
1520       EditCommand editCommand = (EditCommand) command;
1521       al = editCommand.getAlignment();
1522       Vector comps = (Vector) PaintRefresher.components.get(viewport
1523               .getSequenceSetId());
1524       for (int i = 0; i < comps.size(); i++)
1525       {
1526         if (comps.elementAt(i) instanceof AlignmentPanel)
1527         {
1528           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1529           {
1530             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1531             break;
1532           }
1533         }
1534       }
1535     }
1536
1537     if (originalSource == null)
1538     {
1539       // The original view is closed, we must validate
1540       // the current view against the closed view first
1541       if (al != null)
1542       {
1543         PaintRefresher.validateSequences(al, viewport.getAlignment());
1544       }
1545
1546       originalSource = viewport;
1547     }
1548
1549     return originalSource;
1550   }
1551
1552   public void moveSelectedSequences(boolean up)
1553   {
1554     SequenceGroup sg = viewport.getSelectionGroup();
1555     if (sg == null)
1556     {
1557       return;
1558     }
1559     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1560             up ? null : viewport.getHiddenRepSequences(), up);
1561     alignPanel.paintAlignment(true);
1562   }
1563
1564   synchronized void slideSequences(boolean right, int size)
1565   {
1566     List<SequenceI> sg = new Vector<SequenceI>();
1567     if (viewport.cursorMode)
1568     {
1569       sg.add(viewport.getAlignment().getSequenceAt(
1570               alignPanel.seqPanel.seqCanvas.cursorY));
1571     }
1572     else if (viewport.getSelectionGroup() != null
1573             && viewport.getSelectionGroup().getSize() != viewport
1574                     .getAlignment().getHeight())
1575     {
1576       sg = viewport.getSelectionGroup().getSequences(
1577               viewport.getHiddenRepSequences());
1578     }
1579
1580     if (sg.size() < 1)
1581     {
1582       return;
1583     }
1584
1585     Vector<SequenceI> invertGroup = new Vector();
1586
1587     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1588     {
1589       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1590       {
1591         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1592       }
1593     }
1594
1595     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1596
1597     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1598             .size()]);
1599     for (int i = 0; i < invertGroup.size(); i++)
1600     {
1601       seqs2[i] = invertGroup.elementAt(i);
1602     }
1603
1604     SlideSequencesCommand ssc;
1605     if (right)
1606     {
1607       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1608               size, viewport.getGapCharacter());
1609     }
1610     else
1611     {
1612       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1613               size, viewport.getGapCharacter());
1614     }
1615
1616     int groupAdjustment = 0;
1617     if (ssc.getGapsInsertedBegin() && right)
1618     {
1619       if (viewport.cursorMode)
1620       {
1621         alignPanel.seqPanel.moveCursor(size, 0);
1622       }
1623       else
1624       {
1625         groupAdjustment = size;
1626       }
1627     }
1628     else if (!ssc.getGapsInsertedBegin() && !right)
1629     {
1630       if (viewport.cursorMode)
1631       {
1632         alignPanel.seqPanel.moveCursor(-size, 0);
1633       }
1634       else
1635       {
1636         groupAdjustment = -size;
1637       }
1638     }
1639
1640     if (groupAdjustment != 0)
1641     {
1642       viewport.getSelectionGroup().setStartRes(
1643               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1644       viewport.getSelectionGroup().setEndRes(
1645               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1646     }
1647
1648     boolean appendHistoryItem = false;
1649     if (viewport.historyList != null && viewport.historyList.size() > 0
1650             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1651     {
1652       appendHistoryItem = ssc
1653               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1654                       .peek());
1655     }
1656
1657     if (!appendHistoryItem)
1658     {
1659       addHistoryItem(ssc);
1660     }
1661
1662     repaint();
1663   }
1664
1665   static StringBuffer copiedSequences;
1666
1667   static Vector copiedHiddenColumns;
1668
1669   protected void copy_actionPerformed()
1670   {
1671     if (viewport.getSelectionGroup() == null)
1672     {
1673       return;
1674     }
1675
1676     SequenceGroup sg = viewport.getSelectionGroup();
1677     copiedSequences = new StringBuffer();
1678     Hashtable orderedSeqs = new Hashtable();
1679     for (int i = 0; i < sg.getSize(); i++)
1680     {
1681       SequenceI seq = sg.getSequenceAt(i);
1682       int index = viewport.getAlignment().findIndex(seq);
1683       orderedSeqs.put(index + "", seq);
1684     }
1685
1686     int index = 0, startRes, endRes;
1687     char ch;
1688
1689     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1690     {
1691       copiedHiddenColumns = new Vector();
1692       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1693       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1694       {
1695         copiedHiddenColumns.addElement(new int[]
1696         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1697       }
1698     }
1699     else
1700     {
1701       copiedHiddenColumns = null;
1702     }
1703
1704     for (int i = 0; i < sg.getSize(); i++)
1705     {
1706       SequenceI seq = null;
1707
1708       while (seq == null)
1709       {
1710         if (orderedSeqs.containsKey(index + ""))
1711         {
1712           seq = (SequenceI) orderedSeqs.get(index + "");
1713           index++;
1714
1715           break;
1716         }
1717         else
1718         {
1719           index++;
1720         }
1721       }
1722
1723       // FIND START RES
1724       // Returns residue following index if gap
1725       startRes = seq.findPosition(sg.getStartRes());
1726
1727       // FIND END RES
1728       // Need to find the residue preceeding index if gap
1729       endRes = 0;
1730
1731       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1732       {
1733         ch = seq.getCharAt(j);
1734         if (!jalview.util.Comparison.isGap((ch)))
1735         {
1736           endRes++;
1737         }
1738       }
1739
1740       if (endRes > 0)
1741       {
1742         endRes += seq.getStart() - 1;
1743       }
1744
1745       copiedSequences.append(seq.getName()
1746               + "\t"
1747               + startRes
1748               + "\t"
1749               + endRes
1750               + "\t"
1751               + seq.getSequenceAsString(sg.getStartRes(),
1752                       sg.getEndRes() + 1) + "\n");
1753     }
1754
1755   }
1756
1757   protected void pasteNew_actionPerformed()
1758   {
1759     paste(true);
1760   }
1761
1762   protected void pasteThis_actionPerformed()
1763   {
1764     paste(false);
1765   }
1766
1767   void paste(boolean newAlignment)
1768   {
1769     try
1770     {
1771
1772       if (copiedSequences == null)
1773       {
1774         return;
1775       }
1776
1777       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1778       Vector seqs = new Vector();
1779       while (st.hasMoreElements())
1780       {
1781         String name = st.nextToken();
1782         int start = Integer.parseInt(st.nextToken());
1783         int end = Integer.parseInt(st.nextToken());
1784         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1785       }
1786       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1787       for (int i = 0; i < seqs.size(); i++)
1788       {
1789         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1790       }
1791
1792       if (newAlignment)
1793       {
1794         String newtitle = MessageManager.getString("label.copied_sequences");
1795         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1796         {
1797           newtitle = getTitle();
1798         }
1799         else
1800         {
1801           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1802         }
1803         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1804                 viewport.applet, newtitle, false);
1805         if (copiedHiddenColumns != null)
1806         {
1807           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1808           {
1809             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1810             af.viewport.hideColumns(region[0], region[1]);
1811           }
1812         }
1813
1814         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1815                 DEFAULT_HEIGHT);
1816       }
1817       else
1818       {
1819         addSequences(newSeqs);
1820       }
1821
1822     } catch (Exception ex)
1823     {
1824     } // could be anything being pasted in here
1825
1826   }
1827
1828   void addSequences(SequenceI[] seqs)
1829   {
1830     for (int i = 0; i < seqs.length; i++)
1831     {
1832       viewport.getAlignment().addSequence(seqs[i]);
1833     }
1834
1835     // !newAlignment
1836     addHistoryItem(new EditCommand(
1837             MessageManager.getString("label.add_sequences"), Action.PASTE,
1838             seqs, 0, viewport.getAlignment().getWidth(),
1839             viewport.getAlignment()));
1840
1841     viewport.setEndSeq(viewport.getAlignment().getHeight());
1842     viewport.getAlignment().getWidth();
1843     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1844             .getSequences());
1845
1846   }
1847
1848   protected void cut_actionPerformed()
1849   {
1850     copy_actionPerformed();
1851     delete_actionPerformed();
1852   }
1853
1854   protected void delete_actionPerformed()
1855   {
1856
1857     SequenceGroup sg = viewport.getSelectionGroup();
1858     if (sg == null)
1859     {
1860       return;
1861     }
1862
1863     Vector seqs = new Vector();
1864     SequenceI seq;
1865     for (int i = 0; i < sg.getSize(); i++)
1866     {
1867       seq = sg.getSequenceAt(i);
1868       seqs.addElement(seq);
1869     }
1870
1871     // If the cut affects all sequences, remove highlighted columns
1872     if (sg.getSize() == viewport.getAlignment().getHeight())
1873     {
1874       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1875               sg.getEndRes() + 1);
1876     }
1877
1878     SequenceI[] cut = new SequenceI[seqs.size()];
1879     for (int i = 0; i < seqs.size(); i++)
1880     {
1881       cut[i] = (SequenceI) seqs.elementAt(i);
1882     }
1883
1884     /*
1885      * //ADD HISTORY ITEM
1886      */
1887     addHistoryItem(new EditCommand(
1888             MessageManager.getString("label.cut_sequences"), Action.CUT,
1889             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1890             viewport.getAlignment()));
1891
1892     viewport.setSelectionGroup(null);
1893     viewport.getAlignment().deleteGroup(sg);
1894
1895     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1896             .getSequences());
1897
1898     if (viewport.getAlignment().getHeight() < 1)
1899     {
1900       this.setVisible(false);
1901     }
1902     viewport.sendSelection();
1903   }
1904
1905   /**
1906    * group consensus toggled
1907    *
1908    */
1909   protected void showGroupConsensus_actionPerformed()
1910   {
1911     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1912     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1913
1914   }
1915
1916   /**
1917    * group conservation toggled.
1918    */
1919   protected void showGroupConservation_actionPerformed()
1920   {
1921     viewport.setShowGroupConservation(showGroupConservation.getState());
1922     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1923   }
1924
1925   /*
1926    * (non-Javadoc)
1927    *
1928    * @see
1929    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1930    * .event.ActionEvent)
1931    */
1932   protected void showConsensusHistogram_actionPerformed()
1933   {
1934     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1935     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1936   }
1937
1938   /*
1939    * (non-Javadoc)
1940    *
1941    * @see
1942    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1943    * .event.ActionEvent)
1944    */
1945   protected void showSequenceLogo_actionPerformed()
1946   {
1947     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1948     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1949   }
1950
1951   protected void normSequenceLogo_actionPerformed()
1952   {
1953     showSequenceLogo.setState(true);
1954     viewport.setShowSequenceLogo(true);
1955     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1956     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1957   }
1958
1959   protected void applyAutoAnnotationSettings_actionPerformed()
1960   {
1961     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1962   }
1963
1964   protected void makeGrpsFromSelection_actionPerformed()
1965   {
1966     if (avc.makeGroupsFromSelection())
1967     {
1968       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1969       alignPanel.updateAnnotation();
1970       alignPanel.paintAlignment(true);
1971     }
1972   }
1973
1974   protected void createGroup_actionPerformed()
1975   {
1976     avc.createGroup();
1977   }
1978
1979   protected void unGroup_actionPerformed()
1980   {
1981     if (avc.unGroup())
1982     {
1983       alignPanel.alignmentChanged();
1984     }
1985   }
1986
1987   protected void deleteGroups_actionPerformed()
1988   {
1989     if (avc.deleteGroups())
1990     {
1991       alignPanel.alignmentChanged();
1992     }
1993   }
1994
1995   public void selectAllSequenceMenuItem_actionPerformed()
1996   {
1997     SequenceGroup sg = new SequenceGroup();
1998     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1999     {
2000       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2001     }
2002     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2003     viewport.setSelectionGroup(sg);
2004     alignPanel.paintAlignment(true);
2005     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2006     viewport.sendSelection();
2007   }
2008
2009   public void deselectAllSequenceMenuItem_actionPerformed()
2010   {
2011     if (viewport.cursorMode)
2012     {
2013       alignPanel.seqPanel.keyboardNo1 = null;
2014       alignPanel.seqPanel.keyboardNo2 = null;
2015     }
2016     viewport.setSelectionGroup(null);
2017     viewport.getColumnSelection().clear();
2018     viewport.setSelectionGroup(null);
2019     alignPanel.idPanel.idCanvas.searchResults = null;
2020     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2021     alignPanel.paintAlignment(true);
2022     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2023     viewport.sendSelection();
2024   }
2025
2026   public void invertSequenceMenuItem_actionPerformed()
2027   {
2028     SequenceGroup sg = viewport.getSelectionGroup();
2029     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2030     {
2031       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2032     }
2033
2034     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2035     viewport.sendSelection();
2036   }
2037
2038   public void invertColSel_actionPerformed()
2039   {
2040     viewport.invertColumnSelection();
2041     alignPanel.paintAlignment(true);
2042     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2043     viewport.sendSelection();
2044   }
2045
2046   void trimAlignment(boolean trimLeft)
2047   {
2048     ColumnSelection colSel = viewport.getColumnSelection();
2049     int column;
2050
2051     if (colSel.size() > 0)
2052     {
2053       if (trimLeft)
2054       {
2055         column = colSel.getMin();
2056       }
2057       else
2058       {
2059         column = colSel.getMax();
2060       }
2061
2062       SequenceI[] seqs;
2063       if (viewport.getSelectionGroup() != null)
2064       {
2065         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2066                 viewport.getHiddenRepSequences());
2067       }
2068       else
2069       {
2070         seqs = viewport.getAlignment().getSequencesArray();
2071       }
2072
2073       TrimRegionCommand trimRegion;
2074       if (trimLeft)
2075       {
2076         trimRegion = new TrimRegionCommand("Remove Left",
2077                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2078                 viewport.getAlignment(), viewport.getColumnSelection(),
2079                 viewport.getSelectionGroup());
2080         viewport.setStartRes(0);
2081       }
2082       else
2083       {
2084         trimRegion = new TrimRegionCommand("Remove Right",
2085                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2086                 viewport.getAlignment(), viewport.getColumnSelection(),
2087                 viewport.getSelectionGroup());
2088       }
2089
2090       statusBar.setText(MessageManager.formatMessage(
2091               "label.removed_columns", new String[]
2092               { Integer.valueOf(trimRegion.getSize()).toString() }));
2093       addHistoryItem(trimRegion);
2094
2095       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2096       {
2097         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2098                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2099         {
2100           viewport.getAlignment().deleteGroup(sg);
2101         }
2102       }
2103
2104       viewport.firePropertyChange("alignment", null, viewport
2105               .getAlignment().getSequences());
2106     }
2107   }
2108
2109   public void removeGappedColumnMenuItem_actionPerformed()
2110   {
2111     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2112
2113     SequenceI[] seqs;
2114     if (viewport.getSelectionGroup() != null)
2115     {
2116       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2117               viewport.getHiddenRepSequences());
2118       start = viewport.getSelectionGroup().getStartRes();
2119       end = viewport.getSelectionGroup().getEndRes();
2120     }
2121     else
2122     {
2123       seqs = viewport.getAlignment().getSequencesArray();
2124     }
2125
2126     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2127             "Remove Gapped Columns", seqs, start, end,
2128             viewport.getAlignment());
2129
2130     addHistoryItem(removeGapCols);
2131
2132     statusBar.setText(MessageManager.formatMessage(
2133             "label.removed_empty_columns", new String[]
2134             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2135
2136     // This is to maintain viewport position on first residue
2137     // of first sequence
2138     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2139     int startRes = seq.findPosition(viewport.startRes);
2140     // ShiftList shifts;
2141     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2142     // edit.alColumnChanges=shifts.getInverse();
2143     // if (viewport.hasHiddenColumns)
2144     // viewport.getColumnSelection().compensateForEdits(shifts);
2145     viewport.setStartRes(seq.findIndex(startRes) - 1);
2146     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2147             .getSequences());
2148
2149   }
2150
2151   public void removeAllGapsMenuItem_actionPerformed()
2152   {
2153     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2154
2155     SequenceI[] seqs;
2156     if (viewport.getSelectionGroup() != null)
2157     {
2158       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2159               viewport.getHiddenRepSequences());
2160       start = viewport.getSelectionGroup().getStartRes();
2161       end = viewport.getSelectionGroup().getEndRes();
2162     }
2163     else
2164     {
2165       seqs = viewport.getAlignment().getSequencesArray();
2166     }
2167
2168     // This is to maintain viewport position on first residue
2169     // of first sequence
2170     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2171     int startRes = seq.findPosition(viewport.startRes);
2172
2173     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2174             viewport.getAlignment()));
2175
2176     viewport.setStartRes(seq.findIndex(startRes) - 1);
2177
2178     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2179             .getSequences());
2180
2181   }
2182
2183   public void findMenuItem_actionPerformed()
2184   {
2185     new Finder(alignPanel);
2186   }
2187
2188   /**
2189    * create a new view derived from the current view
2190    *
2191    * @param viewtitle
2192    * @return frame for the new view
2193    */
2194   public AlignFrame newView(String viewtitle)
2195   {
2196     AlignmentI newal;
2197     if (viewport.hasHiddenRows())
2198     {
2199       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2200               .getFullAlignment().getSequencesArray());
2201     }
2202     else
2203     {
2204       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2205     }
2206
2207     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2208     {
2209       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2210       {
2211         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2212         {
2213           newal.addAnnotation(viewport.getAlignment()
2214                   .getAlignmentAnnotation()[i]);
2215         }
2216       }
2217     }
2218
2219     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2220
2221     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2222     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2223     PaintRefresher.Register(newaf.alignPanel,
2224             newaf.alignPanel.av.getSequenceSetId());
2225
2226     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2227             newaf.alignPanel.av.getSequenceSetId());
2228     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2229             newaf.alignPanel.av.getSequenceSetId());
2230
2231     Vector comps = (Vector) PaintRefresher.components.get(viewport
2232             .getSequenceSetId());
2233     int viewSize = -1;
2234     for (int i = 0; i < comps.size(); i++)
2235     {
2236       if (comps.elementAt(i) instanceof AlignmentPanel)
2237       {
2238         viewSize++;
2239       }
2240     }
2241
2242     String title = new String(this.getTitle());
2243     if (viewtitle != null)
2244     {
2245       title = viewtitle + " ( " + title + ")";
2246     }
2247     else
2248     {
2249       if (title.indexOf("(View") > -1)
2250       {
2251         title = title.substring(0, title.indexOf("(View"));
2252       }
2253       title += "(View " + viewSize + ")";
2254     }
2255
2256     newaf.setTitle(title.toString());
2257
2258     newaf.viewport.historyList = viewport.historyList;
2259     newaf.viewport.redoList = viewport.redoList;
2260     return newaf;
2261   }
2262
2263   /**
2264    *
2265    * @return list of feature groups on the view
2266    */
2267   public String[] getFeatureGroups()
2268   {
2269     FeatureRenderer fr = null;
2270     if (alignPanel != null
2271             && (fr = alignPanel.getFeatureRenderer()) != null)
2272     {
2273       List gps = fr.getFeatureGroups();
2274       int p=0;
2275       String[] _gps = new String[gps.size()];
2276       for (Object gp:gps)
2277       {
2278         _gps[p++] = gp.toString();
2279       }
2280       return _gps;
2281     }
2282     return null;
2283   }
2284
2285   /**
2286    * get sequence feature groups that are hidden or shown
2287    *
2288    * @param visible
2289    *          true is visible
2290    * @return list
2291    */
2292   public String[] getFeatureGroupsOfState(boolean visible)
2293   {
2294     FeatureRenderer fr = null;
2295     if (alignPanel != null
2296             && (fr = alignPanel.getFeatureRenderer()) != null)
2297     {
2298       List gps = fr.getGroups(visible);
2299       int p=0;
2300       String[] _gps = new String[gps.size()];
2301       for (Object gp:gps)
2302       {
2303         _gps[p++] = gp.toString();
2304       }
2305       return _gps;
2306     }
2307     return null;
2308   }
2309
2310   /**
2311    * Change the display state for the given feature groups
2312    *
2313    * @param groups
2314    *          list of group strings
2315    * @param state
2316    *          visible or invisible
2317    */
2318   public void setFeatureGroupState(String[] groups, boolean state)
2319   {
2320     FeatureRenderer fr = null;
2321     this.sequenceFeatures.setState(true);
2322     viewport.setShowSequenceFeatures(true);
2323     if (alignPanel != null
2324             && (fr = alignPanel.getFeatureRenderer()) != null)
2325     {
2326
2327       fr.setGroupVisibility(Arrays.asList(groups), state);
2328       alignPanel.seqPanel.seqCanvas.repaint();
2329       if (alignPanel.overviewPanel != null)
2330       {
2331         alignPanel.overviewPanel.updateOverviewImage();
2332       }
2333     }
2334   }
2335
2336   public void seqLimits_itemStateChanged()
2337   {
2338     viewport.setShowJVSuffix(seqLimits.getState());
2339     alignPanel.fontChanged();
2340     alignPanel.paintAlignment(true);
2341   }
2342
2343   protected void colourTextMenuItem_actionPerformed()
2344   {
2345     viewport.setColourText(colourTextMenuItem.getState());
2346     alignPanel.paintAlignment(true);
2347   }
2348
2349   protected void displayNonconservedMenuItem_actionPerformed()
2350   {
2351     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2352     alignPanel.paintAlignment(true);
2353   }
2354
2355   protected void wrapMenuItem_actionPerformed()
2356   {
2357     viewport.setWrapAlignment(wrapMenuItem.getState());
2358     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2359     scaleAbove.setEnabled(wrapMenuItem.getState());
2360     scaleLeft.setEnabled(wrapMenuItem.getState());
2361     scaleRight.setEnabled(wrapMenuItem.getState());
2362     alignPanel.paintAlignment(true);
2363   }
2364
2365   public void overviewMenuItem_actionPerformed()
2366   {
2367     if (alignPanel.overviewPanel != null)
2368     {
2369       return;
2370     }
2371
2372     Frame frame = new Frame();
2373     OverviewPanel overview = new OverviewPanel(alignPanel);
2374     frame.add(overview);
2375     // +50 must allow for applet frame window
2376     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2377             "label.overview_params", new String[]
2378             { this.getTitle() }), overview.getPreferredSize().width,
2379             overview.getPreferredSize().height + 50);
2380
2381     frame.pack();
2382     final AlignmentPanel ap = alignPanel;
2383     frame.addWindowListener(new WindowAdapter()
2384     {
2385       @Override
2386       public void windowClosing(WindowEvent e)
2387       {
2388         if (ap != null)
2389         {
2390           ap.setOverviewPanel(null);
2391         }
2392       };
2393     });
2394
2395     alignPanel.setOverviewPanel(overview);
2396
2397   }
2398
2399   void changeColour(ColourSchemeI cs)
2400   {
2401     int threshold = 0;
2402
2403     if (cs != null)
2404     {
2405       if (viewport.getAbovePIDThreshold())
2406       {
2407         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2408                 cs, "Background"));
2409       }
2410
2411       if (viewport.getConservationSelected())
2412       {
2413         cs.setConservationApplied(true);
2414         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2415                 cs, "Background"));
2416       }
2417       else
2418       {
2419         cs.setConservationApplied(false);
2420       }
2421     }
2422     viewport.setGlobalColourScheme(cs);
2423
2424     if (alignPanel.getOverviewPanel() != null)
2425     {
2426       alignPanel.getOverviewPanel().updateOverviewImage();
2427     }
2428
2429     jalview.structure.StructureSelectionManager
2430             .getStructureSelectionManager(viewport.applet)
2431             .sequenceColoursChanged(alignPanel);
2432
2433     alignPanel.paintAlignment(true);
2434   }
2435
2436   protected void modifyPID_actionPerformed()
2437   {
2438     if (viewport.getAbovePIDThreshold()
2439             && viewport.getGlobalColourScheme() != null)
2440     {
2441       SliderPanel.setPIDSliderSource(alignPanel,
2442               viewport.getGlobalColourScheme(), "Background");
2443       SliderPanel.showPIDSlider();
2444     }
2445   }
2446
2447   protected void modifyConservation_actionPerformed()
2448   {
2449     if (viewport.getConservationSelected()
2450             && viewport.getGlobalColourScheme() != null)
2451     {
2452       SliderPanel.setConservationSlider(alignPanel,
2453               viewport.getGlobalColourScheme(), "Background");
2454       SliderPanel.showConservationSlider();
2455     }
2456   }
2457
2458   protected void conservationMenuItem_actionPerformed()
2459   {
2460     viewport.setConservationSelected(conservationMenuItem.getState());
2461
2462     viewport.setAbovePIDThreshold(false);
2463     abovePIDThreshold.setState(false);
2464
2465     changeColour(viewport.getGlobalColourScheme());
2466
2467     modifyConservation_actionPerformed();
2468   }
2469
2470   public void abovePIDThreshold_actionPerformed()
2471   {
2472     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2473
2474     conservationMenuItem.setState(false);
2475     viewport.setConservationSelected(false);
2476
2477     changeColour(viewport.getGlobalColourScheme());
2478
2479     modifyPID_actionPerformed();
2480   }
2481
2482   public void sortPairwiseMenuItem_actionPerformed()
2483   {
2484     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2485     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2486             .getAlignment().getSequenceAt(0), null);
2487
2488     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2489             viewport.getAlignment()));
2490     alignPanel.paintAlignment(true);
2491   }
2492
2493   public void sortIDMenuItem_actionPerformed()
2494   {
2495     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2496     AlignmentSorter.sortByID(viewport.getAlignment());
2497     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2498             viewport.getAlignment()));
2499     alignPanel.paintAlignment(true);
2500   }
2501
2502   public void sortLengthMenuItem_actionPerformed()
2503   {
2504     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2505     AlignmentSorter.sortByLength(viewport.getAlignment());
2506     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2507             viewport.getAlignment()));
2508     alignPanel.paintAlignment(true);
2509   }
2510
2511   public void sortGroupMenuItem_actionPerformed()
2512   {
2513     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2514     AlignmentSorter.sortByGroup(viewport.getAlignment());
2515     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2516             viewport.getAlignment()));
2517     alignPanel.paintAlignment(true);
2518
2519   }
2520
2521   public void removeRedundancyMenuItem_actionPerformed()
2522   {
2523     new RedundancyPanel(alignPanel);
2524   }
2525
2526   public void pairwiseAlignmentMenuItem_actionPerformed()
2527   {
2528     if (viewport.getSelectionGroup() != null
2529             && viewport.getSelectionGroup().getSize() > 1)
2530     {
2531       Frame frame = new Frame();
2532       frame.add(new PairwiseAlignPanel(alignPanel));
2533       jalview.bin.JalviewLite.addFrame(frame,
2534               MessageManager.getString("action.pairwise_alignment"), 600,
2535               500);
2536     }
2537   }
2538
2539   public void PCAMenuItem_actionPerformed()
2540   {
2541     // are the sequences aligned?
2542     if (!viewport.getAlignment().isAligned(false))
2543     {
2544       SequenceI current;
2545       int Width = viewport.getAlignment().getWidth();
2546
2547       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2548       {
2549         current = viewport.getAlignment().getSequenceAt(i);
2550
2551         if (current.getLength() < Width)
2552         {
2553           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2554         }
2555       }
2556       alignPanel.paintAlignment(true);
2557     }
2558
2559     if ((viewport.getSelectionGroup() != null
2560             && viewport.getSelectionGroup().getSize() < 4 && viewport
2561             .getSelectionGroup().getSize() > 0)
2562             || viewport.getAlignment().getHeight() < 4)
2563     {
2564       return;
2565     }
2566
2567     try
2568     {
2569       new PCAPanel(viewport);
2570     } catch (java.lang.OutOfMemoryError ex)
2571     {
2572     }
2573
2574   }
2575
2576   public void averageDistanceTreeMenuItem_actionPerformed()
2577   {
2578     NewTreePanel("AV", "PID", "Average distance tree using PID");
2579   }
2580
2581   public void neighbourTreeMenuItem_actionPerformed()
2582   {
2583     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2584   }
2585
2586   protected void njTreeBlosumMenuItem_actionPerformed()
2587   {
2588     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2589   }
2590
2591   protected void avTreeBlosumMenuItem_actionPerformed()
2592   {
2593     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2594   }
2595
2596   void NewTreePanel(String type, String pwType, String title)
2597   {
2598     // are the sequences aligned?
2599     if (!viewport.getAlignment().isAligned(false))
2600     {
2601       SequenceI current;
2602       int Width = viewport.getAlignment().getWidth();
2603
2604       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2605       {
2606         current = viewport.getAlignment().getSequenceAt(i);
2607
2608         if (current.getLength() < Width)
2609         {
2610           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2611         }
2612       }
2613       alignPanel.paintAlignment(true);
2614
2615     }
2616
2617     if ((viewport.getSelectionGroup() != null && viewport
2618             .getSelectionGroup().getSize() > 1)
2619             || (viewport.getAlignment().getHeight() > 1))
2620     {
2621       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2622
2623       addTreeMenuItem(tp, title);
2624
2625       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2626     }
2627   }
2628
2629   void loadTree_actionPerformed()
2630   {
2631     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2632     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2633     cap.setTreeImport();
2634     Frame frame = new Frame();
2635     frame.add(cap);
2636     jalview.bin.JalviewLite.addFrame(frame,
2637             MessageManager.getString("label.paste_newick_file"), 400, 300);
2638   }
2639
2640   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2641   {
2642     TreePanel tp = new TreePanel(alignPanel, treeFile,
2643             MessageManager.getString("label.load_tree_from_file"), tree);
2644     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2645     addTreeMenuItem(tp, treeFile);
2646   }
2647
2648   /**
2649    * sort the alignment using the given treePanel
2650    *
2651    * @param treePanel
2652    *          tree used to sort view
2653    * @param title
2654    *          string used for undo event name
2655    */
2656   public void sortByTree(TreePanel treePanel, String title)
2657   {
2658     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2659     AlignmentSorter
2660             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2661     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2662     // HistoryItem.SORT));
2663     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2664             "label.order_by_params", new String[]
2665             { title }), oldOrder, viewport.getAlignment()));
2666     alignPanel.paintAlignment(true);
2667   }
2668
2669   /**
2670    * Do any automatic reordering of the alignment and add the necessary bits to
2671    * the menu structure for the new tree
2672    *
2673    * @param treePanel
2674    * @param title
2675    */
2676   protected void addTreeMenuItem(final TreePanel treePanel,
2677           final String title)
2678   {
2679     final MenuItem item = new MenuItem(title);
2680     sortByTreeMenu.add(item);
2681     item.addActionListener(new java.awt.event.ActionListener()
2682     {
2683       @Override
2684       public void actionPerformed(ActionEvent evt)
2685       {
2686         sortByTree(treePanel, title); // treePanel.getTitle());
2687       }
2688     });
2689
2690     treePanel.addWindowListener(new WindowAdapter()
2691     {
2692       @Override
2693       public void windowOpened(WindowEvent e)
2694       {
2695         if (viewport.sortByTree)
2696         {
2697           sortByTree(treePanel, title);
2698         }
2699         super.windowOpened(e);
2700       }
2701
2702       @Override
2703       public void windowClosing(WindowEvent e)
2704       {
2705         sortByTreeMenu.remove(item);
2706       };
2707     });
2708   }
2709
2710   public boolean sortBy(AlignmentOrder alorder, String undoname)
2711   {
2712     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2713     if (viewport.applet.debug)
2714     {
2715       System.err.println("Sorting " + alorder.getOrder().size()
2716               + " in alignment '" + getTitle() + "'");
2717     }
2718     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2719     if (undoname != null)
2720     {
2721       addHistoryItem(new OrderCommand(undoname, oldOrder,
2722               viewport.getAlignment()));
2723     }
2724     alignPanel.paintAlignment(true);
2725     return true;
2726   }
2727
2728   protected void documentation_actionPerformed()
2729   {
2730     alignPanel.av.applet.openJalviewHelpUrl();
2731   }
2732
2733   protected void about_actionPerformed()
2734   {
2735
2736     class AboutPanel extends Canvas
2737     {
2738       String version;
2739
2740       String builddate;
2741
2742       public AboutPanel(String version, String builddate)
2743       {
2744         this.version = version;
2745         this.builddate = builddate;
2746       }
2747
2748       @Override
2749       public void paint(Graphics g)
2750       {
2751         g.setColor(Color.white);
2752         g.fillRect(0, 0, getSize().width, getSize().height);
2753         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2754         FontMetrics fm = g.getFontMetrics();
2755         int fh = fm.getHeight();
2756         int y = 5, x = 7;
2757         g.setColor(Color.black);
2758         // TODO: update this text for each release or centrally store it for
2759         // lite and application
2760         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2761         g.drawString(MessageManager.formatMessage(
2762                 "label.jalviewLite_release", new String[]
2763                 { version }), x, y += fh);
2764         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2765         g.drawString(MessageManager.formatMessage(
2766                 "label.jaview_build_date", new String[]
2767                 { builddate }), x, y += fh);
2768         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2769         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2770                 x, y += fh * 1.5);
2771         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2772                 x + 50, y += fh + 8);
2773         g.drawString(
2774                 MessageManager.getString("label.jalview_dev_managers"), x,
2775                 y += fh);
2776         g.drawString(MessageManager
2777                 .getString("label.jalview_distribution_lists"), x, y += fh);
2778         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2779                 x, y += fh + 8);
2780         g.drawString(
2781                 MessageManager.getString("label.jalview_cite_1_authors"),
2782                 x, y += fh);
2783         g.drawString(
2784                 MessageManager.getString("label.jalview_cite_1_title"), x,
2785                 y += fh);
2786         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2787                 x, y += fh);
2788       }
2789     }
2790
2791     Frame frame = new Frame();
2792     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2793             .getBuildDate()));
2794     jalview.bin.JalviewLite.addFrame(frame,
2795             MessageManager.getString("label.jalview"), 580, 220);
2796
2797   }
2798
2799   public void showURL(String url, String target)
2800   {
2801     if (viewport.applet == null)
2802     {
2803       System.out.println("Not running as applet - no browser available.");
2804     }
2805     else
2806     {
2807       viewport.applet.showURL(url, target);
2808     }
2809   }
2810
2811   // ////////////////////////////////////////////////////////////////////////////////
2812   // JBuilder Graphics here
2813
2814   MenuBar alignFrameMenuBar = new MenuBar();
2815
2816   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2817
2818   MenuItem loadApplication = new MenuItem(
2819           MessageManager.getString("label.view_full_application"));
2820
2821   MenuItem loadTree = new MenuItem(
2822           MessageManager.getString("label.load_associated_tree"));
2823
2824   MenuItem loadAnnotations = new MenuItem(
2825           MessageManager.getString("label.load_features_annotations"));
2826
2827   MenuItem outputFeatures = new MenuItem(
2828           MessageManager.getString("label.export_features").concat("..."));
2829
2830   MenuItem outputAnnotations = new MenuItem(
2831           MessageManager.getString("label.export_annotations").concat("..."));
2832
2833   MenuItem closeMenuItem = new MenuItem(
2834           MessageManager.getString("action.close"));
2835
2836   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2837
2838   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2839
2840   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2841
2842   Menu calculateMenu = new Menu(
2843           MessageManager.getString("action.calculate"));
2844
2845   MenuItem selectAllSequenceMenuItem = new MenuItem(
2846           MessageManager.getString("action.select_all"));
2847
2848   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2849           MessageManager.getString("action.deselect_all"));
2850
2851   MenuItem invertSequenceMenuItem = new MenuItem(
2852           MessageManager.getString("action.invert_selection"));
2853
2854   MenuItem remove2LeftMenuItem = new MenuItem();
2855
2856   MenuItem remove2RightMenuItem = new MenuItem();
2857
2858   MenuItem removeGappedColumnMenuItem = new MenuItem();
2859
2860   MenuItem removeAllGapsMenuItem = new MenuItem();
2861
2862   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2863
2864   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2865
2866   MenuItem sortPairwiseMenuItem = new MenuItem();
2867
2868   MenuItem sortIDMenuItem = new MenuItem();
2869
2870   MenuItem sortLengthMenuItem = new MenuItem();
2871
2872   MenuItem sortGroupMenuItem = new MenuItem();
2873
2874   MenuItem removeRedundancyMenuItem = new MenuItem();
2875
2876   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2877
2878   MenuItem PCAMenuItem = new MenuItem();
2879
2880   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2881
2882   MenuItem neighbourTreeMenuItem = new MenuItem();
2883
2884   BorderLayout borderLayout1 = new BorderLayout();
2885
2886   public Label statusBar = new Label();
2887
2888   Menu outputTextboxMenu = new Menu();
2889
2890   MenuItem clustalColour = new MenuItem();
2891
2892   MenuItem zappoColour = new MenuItem();
2893
2894   MenuItem taylorColour = new MenuItem();
2895
2896   MenuItem hydrophobicityColour = new MenuItem();
2897
2898   MenuItem helixColour = new MenuItem();
2899
2900   MenuItem strandColour = new MenuItem();
2901
2902   MenuItem turnColour = new MenuItem();
2903
2904   MenuItem buriedColour = new MenuItem();
2905
2906   MenuItem purinePyrimidineColour = new MenuItem();
2907
2908   MenuItem RNAInteractionColour = new MenuItem();
2909
2910   MenuItem RNAHelixColour = new MenuItem();
2911
2912   MenuItem userDefinedColour = new MenuItem();
2913
2914   MenuItem PIDColour = new MenuItem();
2915
2916   MenuItem BLOSUM62Colour = new MenuItem();
2917
2918   MenuItem tcoffeeColour = new MenuItem();
2919
2920   MenuItem njTreeBlosumMenuItem = new MenuItem();
2921
2922   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2923
2924   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2925
2926   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2927
2928   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2929
2930   MenuItem alProperties = new MenuItem(
2931           MessageManager.getString("label.alignment_props"));
2932
2933   MenuItem overviewMenuItem = new MenuItem();
2934
2935   MenuItem undoMenuItem = new MenuItem();
2936
2937   MenuItem redoMenuItem = new MenuItem();
2938
2939   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2940
2941   MenuItem noColourmenuItem = new MenuItem();
2942
2943   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2944
2945   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2946
2947   MenuItem findMenuItem = new MenuItem();
2948
2949   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2950
2951   MenuItem nucleotideColour = new MenuItem();
2952
2953   MenuItem deleteGroups = new MenuItem();
2954
2955   MenuItem grpsFromSelection = new MenuItem();
2956
2957   MenuItem createGroup = new MenuItem();
2958
2959   MenuItem unGroup = new MenuItem();
2960
2961   MenuItem delete = new MenuItem();
2962
2963   MenuItem copy = new MenuItem();
2964
2965   MenuItem cut = new MenuItem();
2966
2967   Menu pasteMenu = new Menu();
2968
2969   MenuItem pasteNew = new MenuItem();
2970
2971   MenuItem pasteThis = new MenuItem();
2972
2973   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2974
2975   MenuItem font = new MenuItem();
2976
2977   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2978
2979   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2980
2981   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2982
2983   MenuItem modifyPID = new MenuItem();
2984
2985   MenuItem modifyConservation = new MenuItem();
2986
2987   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2988           "Autocalculate Consensus", true);
2989
2990   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2991           "Sort Alignment With New Tree", true);
2992
2993   Menu sortByTreeMenu = new Menu();
2994
2995   Menu sort = new Menu();
2996
2997   Menu calculate = new Menu();
2998
2999   MenuItem inputText = new MenuItem();
3000
3001   Menu helpMenu = new Menu();
3002
3003   MenuItem documentation = new MenuItem();
3004
3005   MenuItem about = new MenuItem();
3006
3007   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3008
3009   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3010
3011   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3012
3013   Menu autoAnnMenu = new Menu();
3014
3015   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3016
3017   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3018
3019   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3020
3021   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3022
3023   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3024
3025   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3026
3027   private void jbInit() throws Exception
3028   {
3029
3030     setMenuBar(alignFrameMenuBar);
3031
3032     MenuItem item;
3033
3034     // dynamically fill save as menu with available formats
3035     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3036     {
3037
3038       item = new MenuItem(
3039               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3040
3041       item.addActionListener(new java.awt.event.ActionListener()
3042       {
3043         @Override
3044         public void actionPerformed(ActionEvent e)
3045         {
3046           outputText_actionPerformed(e);
3047         }
3048       });
3049
3050       outputTextboxMenu.add(item);
3051     }
3052     closeMenuItem.addActionListener(this);
3053     loadApplication.addActionListener(this);
3054
3055     loadTree.addActionListener(this);
3056     loadAnnotations.addActionListener(this);
3057     outputFeatures.addActionListener(this);
3058     outputAnnotations.addActionListener(this);
3059     selectAllSequenceMenuItem.addActionListener(this);
3060     deselectAllSequenceMenuItem.addActionListener(this);
3061     invertSequenceMenuItem.addActionListener(this);
3062     remove2LeftMenuItem.setLabel(MessageManager
3063             .getString("action.remove_left"));
3064     remove2LeftMenuItem.addActionListener(this);
3065     remove2RightMenuItem.setLabel(MessageManager
3066             .getString("action.remove_right"));
3067     remove2RightMenuItem.addActionListener(this);
3068     removeGappedColumnMenuItem.setLabel(MessageManager
3069             .getString("action.remove_empty_columns"));
3070     removeGappedColumnMenuItem.addActionListener(this);
3071     removeAllGapsMenuItem.setLabel(MessageManager
3072             .getString("action.remove_all_gaps"));
3073     removeAllGapsMenuItem.addActionListener(this);
3074     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3075     viewBoxesMenuItem.setState(true);
3076     viewBoxesMenuItem.addItemListener(this);
3077     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3078     viewTextMenuItem.setState(true);
3079     viewTextMenuItem.addItemListener(this);
3080     sortPairwiseMenuItem.setLabel(MessageManager
3081             .getString("action.by_pairwise_id"));
3082     sortPairwiseMenuItem.addActionListener(this);
3083     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3084     sortIDMenuItem.addActionListener(this);
3085     sortLengthMenuItem.setLabel(MessageManager
3086             .getString("action.by_length"));
3087     sortLengthMenuItem.addActionListener(this);
3088     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3089     sortGroupMenuItem.addActionListener(this);
3090     removeRedundancyMenuItem.setLabel(MessageManager
3091             .getString("action.remove_redundancy").concat("..."));
3092     removeRedundancyMenuItem.addActionListener(this);
3093     pairwiseAlignmentMenuItem.setLabel(MessageManager
3094             .getString("action.pairwise_alignment"));
3095     pairwiseAlignmentMenuItem.addActionListener(this);
3096     PCAMenuItem.setLabel(MessageManager
3097             .getString("label.principal_component_analysis"));
3098     PCAMenuItem.addActionListener(this);
3099     averageDistanceTreeMenuItem.setLabel(MessageManager
3100             .getString("label.average_distance_identity"));
3101     averageDistanceTreeMenuItem.addActionListener(this);
3102     neighbourTreeMenuItem.setLabel(MessageManager
3103             .getString("label.neighbour_joining_identity"));
3104     neighbourTreeMenuItem.addActionListener(this);
3105     statusBar.setBackground(Color.white);
3106     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3107     statusBar.setText(MessageManager.getString("label.status_bar"));
3108     outputTextboxMenu.setLabel(MessageManager
3109             .getString("label.out_to_textbox"));
3110     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3111
3112     clustalColour.addActionListener(this);
3113     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3114     zappoColour.addActionListener(this);
3115     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3116     taylorColour.addActionListener(this);
3117     hydrophobicityColour.setLabel(MessageManager
3118             .getString("label.hydrophobicity"));
3119     hydrophobicityColour.addActionListener(this);
3120     helixColour
3121             .setLabel(MessageManager.getString("label.helix_propensity"));
3122     helixColour.addActionListener(this);
3123     strandColour.setLabel(MessageManager
3124             .getString("label.strand_propensity"));
3125     strandColour.addActionListener(this);
3126     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3127     turnColour.addActionListener(this);
3128     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3129     buriedColour.addActionListener(this);
3130     purinePyrimidineColour.setLabel(MessageManager
3131             .getString("label.purine_pyrimidine"));
3132     purinePyrimidineColour.addActionListener(this);
3133     RNAInteractionColour.setLabel(MessageManager
3134             .getString("label.rna_interaction"));
3135     RNAInteractionColour.addActionListener(this);
3136     RNAHelixColour.setLabel(MessageManager
3137             .getString("action.by_rna_helixes"));
3138     RNAHelixColour.addActionListener(this);
3139     userDefinedColour.setLabel(MessageManager
3140             .getString("action.user_defined"));
3141     userDefinedColour.addActionListener(this);
3142     PIDColour.setLabel(MessageManager
3143             .getString("label.percentage_identity"));
3144     PIDColour.addActionListener(this);
3145     BLOSUM62Colour.setLabel(MessageManager
3146             .getString("label.blosum62_score"));
3147     BLOSUM62Colour.addActionListener(this);
3148     tcoffeeColour
3149             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3150     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3151                                      // provided
3152     tcoffeeColour.addActionListener(this);
3153     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3154             .getString("label.average_distance_bloslum62"));
3155     avDistanceTreeBlosumMenuItem.addActionListener(this);
3156     njTreeBlosumMenuItem.setLabel(MessageManager
3157             .getString("label.neighbour_blosum62"));
3158     njTreeBlosumMenuItem.addActionListener(this);
3159     annotationPanelMenuItem.setLabel(MessageManager
3160             .getString("label.show_annotations"));
3161     annotationPanelMenuItem.addItemListener(this);
3162     colourTextMenuItem.setLabel(MessageManager
3163             .getString("label.colour_text"));
3164     colourTextMenuItem.addItemListener(this);
3165     displayNonconservedMenuItem.setLabel(MessageManager
3166             .getString("label.show_non_conversed"));
3167     displayNonconservedMenuItem.addItemListener(this);
3168     alProperties.addActionListener(this);
3169     overviewMenuItem.setLabel(MessageManager
3170             .getString("label.overview_window"));
3171     overviewMenuItem.addActionListener(this);
3172     undoMenuItem.setEnabled(false);
3173     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3174     undoMenuItem.addActionListener(this);
3175     redoMenuItem.setEnabled(false);
3176     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3177     redoMenuItem.addActionListener(this);
3178     conservationMenuItem.setLabel(MessageManager
3179             .getString("action.by_conservation"));
3180     conservationMenuItem.addItemListener(this);
3181     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3182     noColourmenuItem.addActionListener(this);
3183     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3184     wrapMenuItem.addItemListener(this);
3185     renderGapsMenuItem.setLabel(MessageManager
3186             .getString("action.show_gaps"));
3187     renderGapsMenuItem.setState(true);
3188     renderGapsMenuItem.addItemListener(this);
3189     findMenuItem.setLabel(MessageManager.getString("action.find"));
3190     findMenuItem.addActionListener(this);
3191     abovePIDThreshold.setLabel(MessageManager
3192             .getString("label.above_identity_threshold"));
3193     abovePIDThreshold.addItemListener(this);
3194     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3195     nucleotideColour.addActionListener(this);
3196     deleteGroups.setLabel(MessageManager
3197             .getString("action.undefine_groups"));
3198     deleteGroups.addActionListener(this);
3199     grpsFromSelection.setLabel(MessageManager
3200             .getString("action.make_groups_selection"));
3201     grpsFromSelection.addActionListener(this);
3202     createGroup.setLabel(MessageManager.getString("action.create_group"));
3203     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3204     copy.setLabel(MessageManager.getString("action.copy"));
3205     copy.addActionListener(this);
3206     cut.setLabel(MessageManager.getString("action.cut"));
3207     cut.addActionListener(this);
3208     delete.setLabel(MessageManager.getString("action.delete"));
3209     delete.addActionListener(this);
3210     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3211     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3212     pasteNew.addActionListener(this);
3213     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3214     pasteThis.addActionListener(this);
3215     applyToAllGroups.setLabel(MessageManager
3216             .getString("label.apply_colour_to_all_groups"));
3217     applyToAllGroups.setState(true);
3218     applyToAllGroups.addItemListener(this);
3219     font.setLabel(MessageManager.getString("action.font"));
3220     font.addActionListener(this);
3221     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3222     scaleAbove.setState(true);
3223     scaleAbove.setEnabled(false);
3224     scaleAbove.addItemListener(this);
3225     scaleLeft.setEnabled(false);
3226     scaleLeft.setState(true);
3227     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3228     scaleLeft.addItemListener(this);
3229     scaleRight.setEnabled(false);
3230     scaleRight.setState(true);
3231     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3232     scaleRight.addItemListener(this);
3233     modifyPID.setLabel(MessageManager
3234             .getString("label.modify_identity_thereshold"));
3235     modifyPID.addActionListener(this);
3236     modifyConservation.setLabel(MessageManager
3237             .getString("label.modify_conservation_thereshold"));
3238     modifyConservation.addActionListener(this);
3239     sortByTreeMenu.setLabel(MessageManager
3240             .getString("action.by_tree_order"));
3241     sort.setLabel(MessageManager.getString("action.sort"));
3242     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3243     autoCalculate.addItemListener(this);
3244     sortByTree.addItemListener(this);
3245     inputText
3246             .setLabel(MessageManager.getString("label.input_from_textbox"));
3247     inputText.addActionListener(this);
3248     centreColumnLabelFlag.setLabel(MessageManager
3249             .getString("label.centre_column_labels"));
3250     centreColumnLabelFlag.addItemListener(this);
3251     followMouseOverFlag.setLabel(MessageManager
3252             .getString("label.automatic_scrolling"));
3253     followMouseOverFlag.addItemListener(this);
3254     helpMenu.setLabel(MessageManager.getString("action.help"));
3255     documentation.setLabel(MessageManager.getString("label.documentation"));
3256     documentation.addActionListener(this);
3257
3258     about.setLabel(MessageManager.getString("label.about"));
3259     about.addActionListener(this);
3260     seqLimits.setState(true);
3261     seqLimits.setLabel(MessageManager
3262             .getString("label.show_sequence_limits"));
3263     seqLimits.addItemListener(this);
3264     featureSettings.setLabel(MessageManager
3265             .getString("label.feature_settings"));
3266     featureSettings.addActionListener(this);
3267     sequenceFeatures.setLabel(MessageManager
3268             .getString("label.sequence_features"));
3269     sequenceFeatures.addItemListener(this);
3270     sequenceFeatures.setState(false);
3271     annotationColour.setLabel(MessageManager
3272             .getString("action.by_annotation"));
3273     annotationColour.addActionListener(this);
3274
3275     annotationColumnSelection.setLabel("Select by Annotation");
3276     annotationColumnSelection.addActionListener(this);
3277
3278     invertSequenceMenuItem.setLabel(MessageManager
3279             .getString("action.invert_sequence_selection"));
3280     invertColSel.setLabel(MessageManager
3281             .getString("action.invert_column_selection"));
3282     menu1.setLabel(MessageManager.getString("action.show"));
3283     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3284     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3285     menu2.setLabel(MessageManager.getString("action.hide"));
3286     hideColumns
3287             .setLabel(MessageManager.getString("label.selected_columns"));
3288     hideSequences.setLabel(MessageManager
3289             .getString("label.selected_sequences"));
3290     hideAllButSelection.setLabel(MessageManager
3291             .getString("label.all_but_selected_region"));
3292     hideAllSelection.setLabel(MessageManager
3293             .getString("label.selected_region"));
3294     showAllHidden.setLabel(MessageManager
3295             .getString("label.all_sequences_columns"));
3296     showGroupConsensus.setLabel(MessageManager
3297             .getString("label.group_consensus"));
3298     showGroupConservation.setLabel(MessageManager
3299             .getString("label.group_conservation"));
3300     showConsensusHistogram.setLabel(MessageManager
3301             .getString("label.show_consensus_histogram"));
3302     showSequenceLogo.setLabel(MessageManager
3303             .getString("label.show_consensus_logo"));
3304     normSequenceLogo.setLabel(MessageManager
3305             .getString("label.norm_consensus_logo"));
3306     applyAutoAnnotationSettings.setLabel(MessageManager
3307             .getString("label.apply_all_groups"));
3308     applyAutoAnnotationSettings.setState(true);
3309     autoAnnMenu.setLabel(MessageManager
3310             .getString("label.autocalculated_annotation"));
3311
3312     invertColSel.addActionListener(this);
3313     showColumns.addActionListener(this);
3314     showSeqs.addActionListener(this);
3315     hideColumns.addActionListener(this);
3316     hideSequences.addActionListener(this);
3317     hideAllButSelection.addActionListener(this);
3318     hideAllSelection.addActionListener(this);
3319     showAllHidden.addActionListener(this);
3320     showGroupConsensus.addItemListener(this);
3321     showGroupConservation.addItemListener(this);
3322     showConsensusHistogram.addItemListener(this);
3323     showSequenceLogo.addItemListener(this);
3324     normSequenceLogo.addItemListener(this);
3325
3326     applyAutoAnnotationSettings.addItemListener(this);
3327     formatMenu.setLabel(MessageManager.getString("action.format"));
3328     selectMenu.setLabel(MessageManager.getString("action.select"));
3329     newView.setLabel(MessageManager.getString("action.new_view"));
3330     newView.addActionListener(this);
3331     alignFrameMenuBar.add(fileMenu);
3332     alignFrameMenuBar.add(editMenu);
3333     alignFrameMenuBar.add(selectMenu);
3334     alignFrameMenuBar.add(viewMenu);
3335     alignFrameMenuBar.add(formatMenu);
3336     alignFrameMenuBar.add(colourMenu);
3337     alignFrameMenuBar.add(calculateMenu);
3338     alignFrameMenuBar.add(helpMenu);
3339
3340     fileMenu.add(inputText);
3341     fileMenu.add(loadTree);
3342     fileMenu.add(loadAnnotations);
3343
3344     fileMenu.addSeparator();
3345     fileMenu.add(outputTextboxMenu);
3346     fileMenu.add(outputFeatures);
3347     fileMenu.add(outputAnnotations);
3348
3349     if (jalviewServletURL != null)
3350     {
3351       fileMenu.add(loadApplication);
3352     }
3353
3354     fileMenu.addSeparator();
3355     fileMenu.add(closeMenuItem);
3356
3357     editMenu.add(undoMenuItem);
3358     editMenu.add(redoMenuItem);
3359     editMenu.add(cut);
3360     editMenu.add(copy);
3361     editMenu.add(pasteMenu);
3362     editMenu.add(delete);
3363     editMenu.addSeparator();
3364     editMenu.add(remove2LeftMenuItem);
3365     editMenu.add(remove2RightMenuItem);
3366     editMenu.add(removeGappedColumnMenuItem);
3367     editMenu.add(removeAllGapsMenuItem);
3368     editMenu.add(removeRedundancyMenuItem);
3369     viewMenu.add(newView);
3370     viewMenu.addSeparator();
3371     viewMenu.add(menu1);
3372     viewMenu.add(menu2);
3373     viewMenu.addSeparator();
3374     viewMenu.add(followMouseOverFlag);
3375     viewMenu.add(annotationPanelMenuItem);
3376     autoAnnMenu.add(applyAutoAnnotationSettings);
3377     autoAnnMenu.add(showConsensusHistogram);
3378     autoAnnMenu.add(showSequenceLogo);
3379     autoAnnMenu.add(normSequenceLogo);
3380     autoAnnMenu.addSeparator();
3381     autoAnnMenu.add(showGroupConservation);
3382     autoAnnMenu.add(showGroupConsensus);
3383     viewMenu.add(autoAnnMenu);
3384     viewMenu.addSeparator();
3385     viewMenu.add(sequenceFeatures);
3386     viewMenu.add(featureSettings);
3387     viewMenu.addSeparator();
3388     viewMenu.add(alProperties);
3389     viewMenu.addSeparator();
3390     viewMenu.add(overviewMenuItem);
3391     colourMenu.add(applyToAllGroups);
3392     colourMenu.addSeparator();
3393     colourMenu.add(noColourmenuItem);
3394     colourMenu.add(clustalColour);
3395     colourMenu.add(BLOSUM62Colour);
3396     colourMenu.add(PIDColour);
3397     colourMenu.add(zappoColour);
3398     colourMenu.add(taylorColour);
3399     colourMenu.add(hydrophobicityColour);
3400     colourMenu.add(helixColour);
3401     colourMenu.add(strandColour);
3402     colourMenu.add(turnColour);
3403     colourMenu.add(buriedColour);
3404     colourMenu.add(nucleotideColour);
3405     colourMenu.add(purinePyrimidineColour);
3406     // colourMenu.add(RNAInteractionColour);
3407     colourMenu.add(tcoffeeColour);
3408     colourMenu.add(userDefinedColour);
3409     colourMenu.addSeparator();
3410     colourMenu.add(conservationMenuItem);
3411     colourMenu.add(modifyConservation);
3412     colourMenu.add(abovePIDThreshold);
3413     colourMenu.add(modifyPID);
3414     colourMenu.add(annotationColour);
3415     colourMenu.add(RNAHelixColour);
3416     calculateMenu.add(sort);
3417     calculateMenu.add(calculate);
3418     calculateMenu.addSeparator();
3419     calculateMenu.add(pairwiseAlignmentMenuItem);
3420     calculateMenu.add(PCAMenuItem);
3421     calculateMenu.add(autoCalculate);
3422     calculateMenu.add(sortByTree);
3423     this.add(statusBar, BorderLayout.SOUTH);
3424     pasteMenu.add(pasteNew);
3425     pasteMenu.add(pasteThis);
3426     sort.add(sortIDMenuItem);
3427     sort.add(sortLengthMenuItem);
3428     sort.add(sortByTreeMenu);
3429     sort.add(sortGroupMenuItem);
3430     sort.add(sortPairwiseMenuItem);
3431     calculate.add(averageDistanceTreeMenuItem);
3432     calculate.add(neighbourTreeMenuItem);
3433     calculate.add(avDistanceTreeBlosumMenuItem);
3434     calculate.add(njTreeBlosumMenuItem);
3435     helpMenu.add(documentation);
3436     helpMenu.add(about);
3437     menu1.add(showColumns);
3438     menu1.add(showSeqs);
3439     menu1.add(showAllHidden);
3440     menu2.add(hideColumns);
3441     menu2.add(hideSequences);
3442     menu2.add(hideAllSelection);
3443     menu2.add(hideAllButSelection);
3444     formatMenu.add(font);
3445     formatMenu.add(seqLimits);
3446     formatMenu.add(wrapMenuItem);
3447     formatMenu.add(scaleAbove);
3448     formatMenu.add(scaleLeft);
3449     formatMenu.add(scaleRight);
3450     formatMenu.add(viewBoxesMenuItem);
3451     formatMenu.add(viewTextMenuItem);
3452     formatMenu.add(colourTextMenuItem);
3453     formatMenu.add(displayNonconservedMenuItem);
3454     formatMenu.add(renderGapsMenuItem);
3455     formatMenu.add(centreColumnLabelFlag);
3456     selectMenu.add(findMenuItem);
3457     selectMenu.addSeparator();
3458     selectMenu.add(selectAllSequenceMenuItem);
3459     selectMenu.add(deselectAllSequenceMenuItem);
3460     selectMenu.add(invertSequenceMenuItem);
3461     selectMenu.add(invertColSel);
3462     selectMenu.add(createGroup);
3463     selectMenu.add(unGroup);
3464     selectMenu.add(grpsFromSelection);
3465     selectMenu.add(deleteGroups);
3466     selectMenu.add(annotationColumnSelection);
3467
3468   }
3469
3470   public void setStatus(String string)
3471   {
3472     statusBar.setText(string);
3473   };
3474
3475   MenuItem featureSettings = new MenuItem();
3476
3477   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3478
3479   MenuItem annotationColour = new MenuItem();
3480
3481   MenuItem annotationColumnSelection = new MenuItem();
3482
3483   MenuItem invertColSel = new MenuItem();
3484
3485   Menu menu1 = new Menu();
3486
3487   MenuItem showColumns = new MenuItem();
3488
3489   MenuItem showSeqs = new MenuItem();
3490
3491   Menu menu2 = new Menu();
3492
3493   MenuItem hideColumns = new MenuItem();
3494
3495   MenuItem hideSequences = new MenuItem();
3496
3497   MenuItem hideAllButSelection = new MenuItem();
3498
3499   MenuItem hideAllSelection = new MenuItem();
3500
3501   MenuItem showAllHidden = new MenuItem();
3502
3503   Menu formatMenu = new Menu();
3504
3505   Menu selectMenu = new Menu();
3506
3507   MenuItem newView = new MenuItem();
3508
3509   /**
3510    * Attach the alignFrame panels after embedding menus, if necessary. This used
3511    * to be called setEmbedded, but is now creates the dropdown menus in a
3512    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3513    *
3514    * @param reallyEmbedded
3515    *          true to attach the view to the applet area on the page rather than
3516    *          in a new window
3517    */
3518   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3519   {
3520     if (reallyEmbedded)
3521     {
3522       // ////
3523       // Explicly build the embedded menu panel for the on-page applet
3524       //
3525       // view cannot be closed if its actually on the page
3526       fileMenu.remove(closeMenuItem);
3527       fileMenu.remove(3); // Remove Seperator
3528       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3529               Font.PLAIN, 11, false); // use our own fonts.
3530       // and actually add the components to the applet area
3531       viewport.applet.setLayout(new BorderLayout());
3532       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3533       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3534       alignPanel.setSize(viewport.applet.getSize().width,
3535               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3536                       - statusBar.HEIGHT);
3537       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3538       final AlignFrame me = this;
3539       viewport.applet.addFocusListener(new FocusListener()
3540       {
3541
3542         @Override
3543         public void focusLost(FocusEvent e)
3544         {
3545           if (me.viewport.applet.currentAlignFrame == me)
3546           {
3547             me.viewport.applet.currentAlignFrame = null;
3548           }
3549         }
3550
3551         @Override
3552         public void focusGained(FocusEvent e)
3553         {
3554           me.viewport.applet.currentAlignFrame = me;
3555         }
3556       });
3557       viewport.applet.validate();
3558     }
3559     else
3560     {
3561       // //////
3562       // test and embed menu bar if necessary.
3563       //
3564       if (embedMenuIfNeeded(alignPanel))
3565       {
3566         // adjust for status bar height too
3567         alignPanel.setSize(getSize().width, getSize().height
3568                 - statusBar.HEIGHT);
3569       }
3570       add(statusBar, BorderLayout.SOUTH);
3571       add(alignPanel, BorderLayout.CENTER);
3572       // and register with the applet so it can pass external API calls to us
3573       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3574               DEFAULT_HEIGHT);
3575     }
3576   }
3577
3578   /**
3579    * create a new binding between structures in an existing jmol viewer instance
3580    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3581    * this does not open a new Jmol window, or modify the display of the
3582    * structures in the original jmol window. Note This method doesn't work
3583    * without an additional javascript library to exchange messages between the
3584    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3585    *
3586    * @param viewer
3587    *          JmolViewer instance
3588    * @param sequenceIds
3589    *          - sequence Ids to search for associations
3590    */
3591   public SequenceStructureBinding addStructureViewInstance(
3592           Object jmolviewer, String[] sequenceIds)
3593   {
3594     org.jmol.api.JmolViewer viewer = null;
3595     try
3596     {
3597       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3598     } catch (ClassCastException ex)
3599     {
3600       System.err.println("Unsupported viewer object :"
3601               + jmolviewer.getClass());
3602     }
3603     if (viewer == null)
3604     {
3605       System.err.println("Can't use this object as a structure viewer:"
3606               + jmolviewer.getClass());
3607       return null;
3608     }
3609     SequenceI[] seqs = null;
3610     if (sequenceIds == null || sequenceIds.length == 0)
3611     {
3612       seqs = viewport.getAlignment().getSequencesArray();
3613     }
3614     else
3615     {
3616       Vector sqi = new Vector();
3617       AlignmentI al = viewport.getAlignment();
3618       for (int sid = 0; sid < sequenceIds.length; sid++)
3619       {
3620         SequenceI sq = al.findName(sequenceIds[sid]);
3621         if (sq != null)
3622         {
3623           sqi.addElement(sq);
3624         }
3625       }
3626       if (sqi.size() > 0)
3627       {
3628         seqs = new SequenceI[sqi.size()];
3629         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3630         {
3631           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3632         }
3633       }
3634       else
3635       {
3636         return null;
3637       }
3638     }
3639     AAStructureBindingModel jmv = null;
3640     // TODO: search for a jmv that involves viewer
3641     if (jmv == null)
3642     { // create a new viewer/jalview binding.
3643       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3644       { seqs });
3645     }
3646     return jmv;
3647
3648   }
3649
3650   /**
3651    * bind a pdb file to a sequence in the current view
3652    *
3653    * @param sequenceId
3654    *          - sequenceId within the dataset.
3655    * @param pdbEntryString
3656    *          - the short name for the PDB file
3657    * @param pdbFile
3658    *          - pdb file - either a URL or a valid PDB file.
3659    * @return true if binding was as success TODO: consider making an exception
3660    *         structure for indicating when PDB parsing or sequenceId location
3661    *         fails.
3662    */
3663   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3664           String pdbFile)
3665   {
3666     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3667     boolean needtoadd = false;
3668     if (toaddpdb != null)
3669     {
3670       Vector pdbe = toaddpdb.getPDBId();
3671       PDBEntry pdbentry = null;
3672       if (pdbe != null && pdbe.size() > 0)
3673       {
3674         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3675         {
3676           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3677           if (!pdbentry.getId().equals(pdbEntryString)
3678                   && !pdbentry.getFile().equals(pdbFile))
3679           {
3680             pdbentry = null;
3681           }
3682           else
3683           {
3684             continue;
3685           }
3686         }
3687       }
3688       if (pdbentry == null)
3689       {
3690         pdbentry = new PDBEntry();
3691         pdbentry.setId(pdbEntryString);
3692         pdbentry.setFile(pdbFile);
3693         needtoadd = true; // add this new entry to sequence.
3694       }
3695       // resolve data source
3696       // TODO: this code should be a refactored to an io package
3697       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3698       if (protocol == null)
3699       {
3700         return false;
3701       }
3702       if (needtoadd)
3703       {
3704         // make a note of the access mode and add
3705         if (pdbentry.getProperty() == null)
3706         {
3707           pdbentry.setProperty(new Hashtable());
3708         }
3709         pdbentry.getProperty().put("protocol", protocol);
3710         toaddpdb.addPDBId(pdbentry);
3711         alignPanel.getStructureSelectionManager()
3712                 .registerPDBEntry(pdbentry);
3713       }
3714     }
3715     return true;
3716   }
3717
3718   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3719   {
3720     if (seqs != null)
3721     {
3722       Vector sequences = new Vector();
3723       for (int i = 0; i < seqs.length; i++)
3724       {
3725         if (seqs[i] != null)
3726         {
3727           sequences.addElement(new Object[]
3728           { seqs[i], (chains != null) ? chains[i] : null });
3729         }
3730       }
3731       seqs = new SequenceI[sequences.size()];
3732       chains = new String[sequences.size()];
3733       for (int i = 0, isize = sequences.size(); i < isize; i++)
3734       {
3735         Object[] oj = (Object[]) sequences.elementAt(i);
3736
3737         seqs[i] = (SequenceI) oj[0];
3738         chains[i] = (String) oj[1];
3739       }
3740     }
3741     return new Object[]
3742     { seqs, chains };
3743
3744   }
3745
3746   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3747           SequenceI[] seqs, String[] chains, String protocol)
3748   {
3749     // Scrub any null sequences from the array
3750     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3751     seqs = (SequenceI[]) sqch[0];
3752     chains = (String[]) sqch[1];
3753     if (seqs == null || seqs.length == 0)
3754     {
3755       System.err
3756               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3757     }
3758     if (protocol == null || protocol.trim().length() == 0
3759             || protocol.equals("null"))
3760     {
3761       protocol = (String) pdb.getProperty().get("protocol");
3762       if (protocol == null)
3763       {
3764         System.err.println("Couldn't work out protocol to open structure: "
3765                 + pdb.getId());
3766         return;
3767       }
3768     }
3769     if (applet.useXtrnalSviewer)
3770     {
3771       // register the association(s) and quit, don't create any windows.
3772       if (StructureSelectionManager.getStructureSelectionManager(applet)
3773               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3774       {
3775         System.err.println("Failed to map " + pdb.getFile() + " ("
3776                 + protocol + ") to any sequences");
3777       }
3778       return;
3779     }
3780     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3781     {
3782       // can only do alignments with Jmol
3783       // find the last jmol window assigned to this alignment
3784       jalview.appletgui.AppletJmol ajm = null, tajm;
3785       Vector jmols = applet
3786               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3787       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3788       {
3789         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3790         if (tajm.ap.alignFrame == this)
3791         {
3792           ajm = tajm;
3793           break;
3794         }
3795       }
3796       if (ajm != null)
3797       {
3798         System.err
3799                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3800         // try and add the pdb structure
3801         // ajm.addS
3802         ajm = null;
3803       }
3804     }
3805     // otherwise, create a new window
3806     if (applet.jmolAvailable)
3807     {
3808       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3809               protocol);
3810       applet.lastFrameX += 40;
3811       applet.lastFrameY += 40;
3812     }
3813     else
3814     {
3815       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3816     }
3817
3818   }
3819
3820   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3821           SequenceI[][] seqs, String[][] chains, String[] protocols)
3822   {
3823     // TODO Auto-generated method stub
3824     System.err.println("Aligned Structure View: Not yet implemented.");
3825   }
3826
3827   /**
3828    * modify the current selection, providing the user has not made a selection
3829    * already.
3830    *
3831    * @param sel
3832    *          - sequences from this alignment
3833    * @param csel
3834    *          - columns to be selected on the alignment
3835    */
3836   public void select(SequenceGroup sel, ColumnSelection csel)
3837   {
3838     alignPanel.seqPanel.selection(sel, csel, null);
3839   }
3840
3841   public void scrollTo(int row, int column)
3842   {
3843     alignPanel.seqPanel.scrollTo(row, column);
3844   }
3845
3846   public void scrollToRow(int row)
3847   {
3848     alignPanel.seqPanel.scrollToRow(row);
3849   }
3850
3851   public void scrollToColumn(int column)
3852   {
3853     alignPanel.seqPanel.scrollToColumn(column);
3854   }
3855
3856   /**
3857    * @return the alignments unique ID.
3858    */
3859   public String getSequenceSetId()
3860   {
3861     return viewport.getSequenceSetId();
3862   }
3863
3864   /**
3865    * Load the (T-Coffee) score file from the specified url
3866    *
3867    * @param source
3868    *          File/URL/T-COFFEE score file contents
3869    * @throws IOException
3870    * @return true if alignment was annotated with data from source
3871    */
3872   public boolean loadScoreFile(String source) throws IOException
3873   {
3874
3875     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3876             AppletFormatAdapter.checkProtocol(source));
3877     if (!file.isValid())
3878     {
3879       // TODO: raise dialog for gui
3880       System.err.println("Problems parsing T-Coffee scores: "
3881               + file.getWarningMessage());
3882       System.err.println("Origin was:\n" + source);
3883       return false;
3884     }
3885
3886     /*
3887      * check that the score matrix matches the alignment dimensions
3888      */
3889     AlignmentI aln;
3890     if ((aln = viewport.getAlignment()) != null
3891             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3892                     .getWidth()))
3893     {
3894       // TODO: raise a dialog box here rather than bomb out.
3895       System.err
3896               .println("The scores matrix does not match the alignment dimensions");
3897
3898     }
3899
3900     // TODO add parameter to indicate if matching should be done
3901     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3902     {
3903       alignPanel.fontChanged();
3904       tcoffeeColour.setEnabled(true);
3905       // switch to this color
3906       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3907       return true;
3908     }
3909     else
3910     {
3911       System.err.println("Problems resolving T-Coffee scores:");
3912       if (file.getWarningMessage() != null)
3913       {
3914         System.err.println(file.getWarningMessage());
3915       }
3916     }
3917     return false;
3918   }
3919
3920 }