src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.appletgui;
  20
  21 import jalview.analysis.AlignmentSorter;
  22 import jalview.analysis.Conservation;
  23 import jalview.api.AlignViewControllerGuiI;
  24 import jalview.api.AlignViewControllerI;
  25 import jalview.api.SequenceStructureBinding;
  26 import jalview.bin.JalviewLite;
  27 import jalview.commands.CommandI;
  28 import jalview.commands.EditCommand;
  29 import jalview.commands.OrderCommand;
  30 import jalview.commands.RemoveGapColCommand;
  31 import jalview.commands.RemoveGapsCommand;
  32 import jalview.commands.SlideSequencesCommand;
  33 import jalview.commands.TrimRegionCommand;
  34 import jalview.datamodel.Alignment;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.AlignmentOrder;
  37 import jalview.datamodel.ColumnSelection;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.Sequence;
  40 import jalview.datamodel.SequenceGroup;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.io.AnnotationFile;
  43 import jalview.io.AppletFormatAdapter;
  44 import jalview.io.FeaturesFile;
  45 import jalview.io.TCoffeeScoreFile;
  46 import jalview.schemes.Blosum62ColourScheme;
  47 import jalview.schemes.BuriedColourScheme;
  48 import jalview.schemes.ClustalxColourScheme;
  49 import jalview.schemes.ColourSchemeI;
  50 import jalview.schemes.HelixColourScheme;
  51 import jalview.schemes.HydrophobicColourScheme;
  52 import jalview.schemes.NucleotideColourScheme;
  53 import jalview.schemes.PIDColourScheme;
  54 import jalview.schemes.PurinePyrimidineColourScheme;
  55 import jalview.schemes.RNAHelicesColourChooser;
  56 import jalview.schemes.RNAInteractionColourScheme;\r
  57 import jalview.schemes.ResidueProperties;
  58 import jalview.schemes.StrandColourScheme;
  59 import jalview.schemes.TCoffeeColourScheme;
  60 import jalview.schemes.TaylorColourScheme;
  61 import jalview.schemes.TurnColourScheme;
  62 import jalview.schemes.ZappoColourScheme;
  63 import jalview.structure.StructureSelectionManager;
  64 import jalview.util.MessageManager;
  65
  66 import java.awt.BorderLayout;
  67 import java.awt.Canvas;
  68 import java.awt.CheckboxMenuItem;
  69 import java.awt.Color;
  70 import java.awt.Font;
  71 import java.awt.FontMetrics;
  72 import java.awt.Frame;
  73 import java.awt.Graphics;
  74 import java.awt.Label;
  75 import java.awt.Menu;
  76 import java.awt.MenuBar;
  77 import java.awt.MenuItem;
  78 import java.awt.event.ActionEvent;
  79 import java.awt.event.ActionListener;
  80 import java.awt.event.FocusEvent;
  81 import java.awt.event.FocusListener;
  82 import java.awt.event.ItemEvent;
  83 import java.awt.event.ItemListener;
  84 import java.awt.event.KeyEvent;
  85 import java.awt.event.KeyListener;
  86 import java.awt.event.WindowAdapter;
  87 import java.awt.event.WindowEvent;
  88 import java.io.IOException;
  89 import java.net.URL;
  90 import java.net.URLEncoder;
  91 import java.util.Enumeration;
  92 import java.util.Hashtable;
  93 import java.util.List;
  94 import java.util.StringTokenizer;
  95 import java.util.Vector;
  96
  97 public class AlignFrame extends EmbmenuFrame implements ActionListener,
  98         ItemListener, KeyListener, AlignViewControllerGuiI
  99 {
 100   public AlignViewControllerI avc;
 101   public AlignmentPanel alignPanel;
 102
 103   public AlignViewport viewport;
 104
 105   int DEFAULT_WIDTH = 700;
 106
 107   int DEFAULT_HEIGHT = 500;
 108
 109   String jalviewServletURL;
 110
 111   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 112           String title, boolean embedded)
 113   {
 114     if (applet != null)
 115     {
 116       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 117     }
 118
 119     try
 120     {
 121       jbInit();
 122     } catch (Exception ex)
 123     {
 124       ex.printStackTrace();
 125     }
 126     // need to get window geometry before we calculate alignment layout
 127     if (applet != null)
 128     {
 129       String param;
 130       try
 131       {
 132         param = applet.getParameter("windowWidth");
 133         if (param != null)
 134         {
 135           int width = Integer.parseInt(param);
 136           DEFAULT_WIDTH = width;
 137         }
 138         param = applet.getParameter("windowHeight");
 139         if (param != null)
 140         {
 141           int height = Integer.parseInt(param);
 142           DEFAULT_HEIGHT = height;
 143         }
 144       } catch (Exception ex)
 145       {
 146       }
 147     }
 148     viewport = new AlignViewport(al, applet);
 149     alignPanel = new AlignmentPanel(this, viewport);
 150     avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
 151     viewport.updateConservation(alignPanel);
 152     viewport.updateConsensus(alignPanel);
 153
 154     annotationPanelMenuItem.setState(viewport.showAnnotation);
 155     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 156     followMouseOverFlag.setState(viewport.getFollowHighlight());
 157     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 158     showGroupConservation.setState(viewport.isShowGroupConservation());
 159     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 160     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 161     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 162
 163     seqLimits.setState(viewport.showJVSuffix);
 164
 165     if (applet != null)
 166     {
 167       String param = applet.getParameter("sortBy");
 168       if (param != null)
 169       {
 170         if (param.equalsIgnoreCase("Id"))
 171         {
 172           sortIDMenuItem_actionPerformed();
 173         }
 174         else if (param.equalsIgnoreCase("Pairwise Identity"))
 175         {
 176           sortPairwiseMenuItem_actionPerformed();
 177         }
 178         else if (param.equalsIgnoreCase("Length"))
 179         {
 180           sortLengthMenuItem_actionPerformed();
 181         }
 182       }
 183
 184       param = applet.getParameter("wrap");
 185       if (param != null)
 186       {
 187         if (param.equalsIgnoreCase("true"))
 188         {
 189           wrapMenuItem.setState(true);
 190           wrapMenuItem_actionPerformed();
 191         }
 192       }
 193       param = applet.getParameter("centrecolumnlabels");
 194       if (param != null)
 195       {
 196         centreColumnLabelFlag.setState(true);
 197         centreColumnLabelFlag_stateChanged();
 198       }
 199
 200     }
 201     if (viewport.getAlignment().isNucleotide())
 202     {
 203       viewport.updateStrucConsensus(alignPanel);
 204       if (viewport.getAlignment().hasRNAStructure())
 205       {
 206         RNAHelixColour.setEnabled(true);
 207       }
 208       else
 209       {
 210         RNAHelixColour.setEnabled(false);
 211       }
 212     }
 213     else
 214     {
 215       RNAHelixColour.setEnabled(false);
 216       purinePyrimidineColour.setEnabled(false);
 217     }
 218     // Some JVMS send keyevents to Top frame or lowest panel,
 219     // Havent worked out why yet. So add to both this frame and seqCanvas for
 220     // now
 221     this.addKeyListener(this);
 222     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 223     alignPanel.idPanel.idCanvas.addKeyListener(this);
 224     alignPanel.scalePanel.addKeyListener(this);
 225     alignPanel.annotationPanel.addKeyListener(this);
 226     alignPanel.annotationPanelHolder.addKeyListener(this);
 227     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 228     alignPanel.alabels.addKeyListener(this);
 229     createAlignFrameWindow(embedded, title);
 230
 231     validate();
 232     alignPanel.adjustAnnotationHeight();
 233     alignPanel.paintAlignment(true);
 234   }
 235
 236   public AlignViewport getAlignViewport()
 237   {
 238     return viewport;
 239   }
 240
 241   public SeqCanvas getSeqcanvas()
 242   {
 243     return alignPanel.seqPanel.seqCanvas;
 244   }
 245
 246   /**
 247    * Load a features file onto the alignment
 248    *
 249    * @param file
 250    *          file URL, content, or other resolvable path
 251    * @param type
 252    *          is protocol for accessing data referred to by file
 253    */
 254
 255   public boolean parseFeaturesFile(String file, String type)
 256   {
 257     return parseFeaturesFile(file, type, true);
 258   }
 259
 260   /**
 261    * Load a features file onto the alignment
 262    *
 263    * @param file
 264    *          file URL, content, or other resolvable path
 265    * @param type
 266    *          is protocol for accessing data referred to by file
 267    * @param autoenabledisplay
 268    *          when true, display features flag will be automatically enabled if
 269    *          features are loaded
 270    * @return true if data parsed as a features file
 271    */
 272   public boolean parseFeaturesFile(String file, String type,
 273           boolean autoenabledisplay)
 274   {
 275     // TODO: test if importing a features file onto an alignment which already
 276     // has features with links overwrites the original links.
 277
 278     Hashtable featureLinks = new Hashtable();
 279     boolean featuresFile = false;
 280     try
 281     {
 282       featuresFile = new jalview.io.FeaturesFile(file, type)
 283               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 284                       .getFeatureRenderer().featureColours, featureLinks,
 285                       true, viewport.applet.getDefaultParameter(
 286                               "relaxedidmatch", false));
 287     } catch (Exception ex)
 288     {
 289       ex.printStackTrace();
 290     }
 291
 292     if (featuresFile)
 293     {
 294       if (featureLinks.size() > 0)
 295       {
 296         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 297       }
 298       if (autoenabledisplay)
 299       {
 300         viewport.showSequenceFeatures = true;
 301         sequenceFeatures.setState(true);
 302       }
 303       if (viewport.featureSettings != null)
 304       {
 305         viewport.featureSettings.refreshTable();
 306       }
 307       alignPanel.paintAlignment(true);
 308       statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
 309     }
 310     return featuresFile;
 311   }
 312
 313   @Override
 314   public void keyPressed(KeyEvent evt)
 315   {
 316     if (viewport.cursorMode
 317             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 318                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 319                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 320             && Character.isDigit(evt.getKeyChar()))
 321       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 322
 323     switch (evt.getKeyCode())
 324     {
 325     case 27: // escape key
 326       deselectAllSequenceMenuItem_actionPerformed();
 327
 328       alignPanel.alabels.cancelDrag();
 329       break;
 330     case KeyEvent.VK_X:
 331       if (evt.isControlDown() || evt.isMetaDown())
 332       {
 333         cut_actionPerformed();
 334       }
 335       break;
 336     case KeyEvent.VK_C:
 337       if (viewport.cursorMode && !evt.isControlDown())
 338       {
 339         alignPanel.seqPanel.setCursorColumn();
 340       }
 341       if (evt.isControlDown() || evt.isMetaDown())
 342       {
 343         copy_actionPerformed();
 344       }
 345       break;
 346     case KeyEvent.VK_V:
 347       if (evt.isControlDown())
 348       {
 349         paste(evt.isShiftDown());
 350       }
 351       break;
 352     case KeyEvent.VK_A:
 353       if (evt.isControlDown() || evt.isMetaDown())
 354       {
 355         selectAllSequenceMenuItem_actionPerformed();
 356       }
 357       break;
 358     case KeyEvent.VK_DOWN:
 359       if (viewport.cursorMode)
 360       {
 361         alignPanel.seqPanel.moveCursor(0, 1);
 362       }
 363       else
 364       {
 365         moveSelectedSequences(false);
 366       }
 367       break;
 368
 369     case KeyEvent.VK_UP:
 370       if (viewport.cursorMode)
 371       {
 372         alignPanel.seqPanel.moveCursor(0, -1);
 373       }
 374       else
 375       {
 376         moveSelectedSequences(true);
 377       }
 378       break;
 379
 380     case KeyEvent.VK_LEFT:
 381       if (evt.isAltDown() || !viewport.cursorMode)
 382         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 383       else
 384         alignPanel.seqPanel.moveCursor(-1, 0);
 385       break;
 386
 387     case KeyEvent.VK_RIGHT:
 388       if (evt.isAltDown() || !viewport.cursorMode)
 389         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 390       else
 391         alignPanel.seqPanel.moveCursor(1, 0);
 392       break;
 393
 394     case KeyEvent.VK_SPACE:
 395       if (viewport.cursorMode)
 396       {
 397         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 398                 || evt.isShiftDown() || evt.isAltDown());
 399       }
 400       break;
 401
 402     case KeyEvent.VK_DELETE:
 403     case KeyEvent.VK_BACK_SPACE:
 404       if (viewport.cursorMode)
 405       {
 406         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 407                 || evt.isShiftDown() || evt.isAltDown());
 408       }
 409       else
 410       {
 411         cut_actionPerformed();
 412         alignPanel.seqPanel.seqCanvas.repaint();
 413       }
 414       break;
 415
 416     case KeyEvent.VK_S:
 417       if (viewport.cursorMode)
 418       {
 419         alignPanel.seqPanel.setCursorRow();
 420       }
 421       break;
 422     case KeyEvent.VK_P:
 423       if (viewport.cursorMode)
 424       {
 425         alignPanel.seqPanel.setCursorPosition();
 426       }
 427       break;
 428
 429     case KeyEvent.VK_ENTER:
 430     case KeyEvent.VK_COMMA:
 431       if (viewport.cursorMode)
 432       {
 433         alignPanel.seqPanel.setCursorRowAndColumn();
 434       }
 435       break;
 436
 437     case KeyEvent.VK_Q:
 438       if (viewport.cursorMode)
 439       {
 440         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 441       }
 442       break;
 443     case KeyEvent.VK_M:
 444       if (viewport.cursorMode)
 445       {
 446         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 447       }
 448       break;
 449
 450     case KeyEvent.VK_F2:
 451       viewport.cursorMode = !viewport.cursorMode;
 452       statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 456         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 457       }
 458       break;
 459
 460     case KeyEvent.VK_F:
 461       if (evt.isControlDown())
 462       {
 463         findMenuItem_actionPerformed();
 464       }
 465       break;
 466
 467     case KeyEvent.VK_H:
 468     {
 469       boolean toggleSeqs = !evt.isControlDown();
 470       boolean toggleCols = !evt.isShiftDown();
 471       toggleHiddenRegions(toggleSeqs, toggleCols);
 472       break;
 473     }
 474
 475     case KeyEvent.VK_PAGE_UP:
 476       if (viewport.wrapAlignment)
 477       {
 478         alignPanel.scrollUp(true);
 479       }
 480       else
 481       {
 482         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 483                 - viewport.endSeq + viewport.startSeq);
 484       }
 485       break;
 486
 487     case KeyEvent.VK_PAGE_DOWN:
 488       if (viewport.wrapAlignment)
 489       {
 490         alignPanel.scrollUp(false);
 491       }
 492       else
 493       {
 494         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 495                 + viewport.endSeq - viewport.startSeq);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_Z:
 500       if (evt.isControlDown())
 501       {
 502         undoMenuItem_actionPerformed();
 503       }
 504       break;
 505
 506     case KeyEvent.VK_Y:
 507       if (evt.isControlDown())
 508       {
 509         redoMenuItem_actionPerformed();
 510       }
 511       break;
 512
 513     case KeyEvent.VK_L:
 514       if (evt.isControlDown())
 515       {
 516         trimAlignment(true);
 517       }
 518       break;
 519
 520     case KeyEvent.VK_R:
 521       if (evt.isControlDown())
 522       {
 523         trimAlignment(false);
 524       }
 525       break;
 526
 527     case KeyEvent.VK_E:
 528       if (evt.isControlDown())
 529       {
 530         if (evt.isShiftDown())
 531         {
 532           this.removeAllGapsMenuItem_actionPerformed();
 533         }
 534         else
 535         {
 536           removeGappedColumnMenuItem_actionPerformed();
 537         }
 538       }
 539       break;
 540     case KeyEvent.VK_I:
 541       if (evt.isControlDown())
 542       {
 543         if (evt.isAltDown())
 544         {
 545           invertColSel_actionPerformed();
 546         }
 547         else
 548         {
 549           invertSequenceMenuItem_actionPerformed();
 550         }
 551       }
 552       break;
 553
 554     case KeyEvent.VK_G:
 555       if (evt.isControlDown())
 556       {
 557         if (evt.isShiftDown())
 558         {
 559           this.unGroup_actionPerformed();
 560         }
 561         else
 562         {
 563           this.createGroup_actionPerformed();
 564         }
 565       }
 566       break;
 567
 568     case KeyEvent.VK_U:
 569       if (evt.isControlDown())
 570       {
 571         this.deleteGroups_actionPerformed();
 572       }
 573       break;
 574
 575     case KeyEvent.VK_T:
 576       if (evt.isControlDown())
 577       {
 578         newView(null);
 579       }
 580       break;
 581
 582     }
 583     alignPanel.paintAlignment(true);
 584   }
 585
 586   /**
 587    * called by key handler and the hide all/show all menu items
 588    *
 589    * @param toggleSeqs
 590    * @param toggleCols
 591    */
 592   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 593   {
 594     boolean hide = false;
 595     SequenceGroup sg = viewport.getSelectionGroup();
 596     if (!toggleSeqs && !toggleCols)
 597     {
 598       // Hide everything by the current selection - this is a hack - we do the
 599       // invert and then hide
 600       // first check that there will be visible columns after the invert.
 601       if ((viewport.getColumnSelection() != null
 602               && viewport.getColumnSelection().getSelected() != null && viewport
 603               .getColumnSelection().getSelected().size() > 0)
 604               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 605                       .getEndRes()))
 606       {
 607         // now invert the sequence set, if required - empty selection implies
 608         // that no hiding is required.
 609         if (sg != null)
 610         {
 611           invertSequenceMenuItem_actionPerformed();
 612           sg = viewport.getSelectionGroup();
 613           toggleSeqs = true;
 614
 615         }
 616         viewport.expandColSelection(sg, true);
 617         // finally invert the column selection and get the new sequence
 618         // selection and indicate it should be hidden.
 619         invertColSel_actionPerformed();
 620         toggleCols = true;
 621       }
 622     }
 623
 624     if (toggleSeqs)
 625     {
 626       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 627       {
 628         hide = true;
 629         viewport.hideAllSelectedSeqs();
 630       }
 631       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 632               .size() > 0))
 633       {
 634         viewport.showAllHiddenSeqs();
 635       }
 636     }
 637
 638     if (toggleCols)
 639     {
 640       if (viewport.getColumnSelection().getSelected().size() > 0)
 641       {
 642         viewport.hideSelectedColumns();
 643         if (!toggleSeqs)
 644         {
 645           viewport.setSelectionGroup(sg);
 646         }
 647       }
 648       else if (!hide)
 649       {
 650         viewport.showAllHiddenColumns();
 651       }
 652     }
 653   }
 654
 655   @Override
 656   public void keyReleased(KeyEvent evt)
 657   {
 658   }
 659
 660   @Override
 661   public void keyTyped(KeyEvent evt)
 662   {
 663   }
 664
 665   @Override
 666   public void itemStateChanged(ItemEvent evt)
 667   {
 668     if (evt.getSource() == displayNonconservedMenuItem)
 669     {
 670       displayNonconservedMenuItem_actionPerformed();
 671     }
 672     else if (evt.getSource() == colourTextMenuItem)
 673     {
 674       colourTextMenuItem_actionPerformed();
 675     }
 676     else if (evt.getSource() == wrapMenuItem)
 677     {
 678       wrapMenuItem_actionPerformed();
 679     }
 680     else if (evt.getSource() == scaleAbove)
 681     {
 682       viewport.setScaleAboveWrapped(scaleAbove.getState());
 683     }
 684     else if (evt.getSource() == scaleLeft)
 685     {
 686       viewport.setScaleLeftWrapped(scaleLeft.getState());
 687     }
 688     else if (evt.getSource() == scaleRight)
 689     {
 690       viewport.setScaleRightWrapped(scaleRight.getState());
 691     }
 692     else if (evt.getSource() == seqLimits)
 693     {
 694       seqLimits_itemStateChanged();
 695     }
 696     else if (evt.getSource() == viewBoxesMenuItem)
 697     {
 698       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 699     }
 700     else if (evt.getSource() == viewTextMenuItem)
 701     {
 702       viewport.setShowText(viewTextMenuItem.getState());
 703     }
 704     else if (evt.getSource() == renderGapsMenuItem)
 705     {
 706       viewport.setRenderGaps(renderGapsMenuItem.getState());
 707     }
 708     else if (evt.getSource() == annotationPanelMenuItem)
 709     {
 710       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 711       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 712     }
 713     else if (evt.getSource() == sequenceFeatures)
 714     {
 715       viewport.showSequenceFeatures(sequenceFeatures.getState());
 716       alignPanel.seqPanel.seqCanvas.repaint();
 717     }
 718     else if (evt.getSource() == conservationMenuItem)
 719     {
 720       conservationMenuItem_actionPerformed();
 721     }
 722     else if (evt.getSource() == abovePIDThreshold)
 723     {
 724       abovePIDThreshold_actionPerformed();
 725     }
 726     else if (evt.getSource() == applyToAllGroups)
 727     {
 728       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 729     }
 730     else if (evt.getSource() == autoCalculate)
 731     {
 732       viewport.autoCalculateConsensus = autoCalculate.getState();
 733     }
 734     else if (evt.getSource() == sortByTree)
 735     {
 736       viewport.sortByTree = sortByTree.getState();
 737     }
 738     else if (evt.getSource() == this.centreColumnLabelFlag)
 739     {
 740       centreColumnLabelFlag_stateChanged();
 741     }
 742     else if (evt.getSource() == this.followMouseOverFlag)
 743     {
 744       mouseOverFlag_stateChanged();
 745     }
 746     else if (evt.getSource() == showGroupConsensus)
 747     {
 748       showGroupConsensus_actionPerformed();
 749     }
 750     else if (evt.getSource() == showGroupConservation)
 751     {
 752       showGroupConservation_actionPerformed();
 753     }
 754     else if (evt.getSource() == showSequenceLogo)
 755     {
 756       showSequenceLogo_actionPerformed();
 757     }
 758     else if (evt.getSource() == normSequenceLogo)
 759     {
 760       normSequenceLogo_actionPerformed();
 761     }
 762     else if (evt.getSource() == showConsensusHistogram)
 763     {
 764       showConsensusHistogram_actionPerformed();
 765     }
 766     else if (evt.getSource() == applyAutoAnnotationSettings)
 767     {
 768       applyAutoAnnotationSettings_actionPerformed();
 769     }
 770     alignPanel.paintAlignment(true);
 771   }
 772
 773   private void mouseOverFlag_stateChanged()
 774   {
 775     viewport.followHighlight = followMouseOverFlag.getState();
 776     // TODO: could kick the scrollTo mechanism to reset view for current
 777     // searchresults.
 778   }
 779
 780   private void centreColumnLabelFlag_stateChanged()
 781   {
 782     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 783     this.alignPanel.annotationPanel.repaint();
 784   }
 785
 786   @Override
 787   public void actionPerformed(ActionEvent evt)
 788   {
 789     Object source = evt.getSource();
 790
 791     if (source == inputText)
 792     {
 793       inputText_actionPerformed();
 794     }
 795     else if (source == loadTree)
 796     {
 797       loadTree_actionPerformed();
 798     }
 799     else if (source == loadApplication)
 800     {
 801       launchFullApplication();
 802     }
 803     else if (source == loadAnnotations)
 804     {
 805       loadAnnotations();
 806     }
 807     else if (source == outputAnnotations)
 808     {
 809       outputAnnotations(true);
 810     }
 811     else if (source == outputFeatures)
 812     {
 813       outputFeatures(true, "Jalview");
 814     }
 815     else if (source == closeMenuItem)
 816     {
 817       closeMenuItem_actionPerformed();
 818     }
 819     else if (source == copy)
 820     {
 821       copy_actionPerformed();
 822     }
 823     else if (source == undoMenuItem)
 824     {
 825       undoMenuItem_actionPerformed();
 826     }
 827     else if (source == redoMenuItem)
 828     {
 829       redoMenuItem_actionPerformed();
 830     }
 831     else if (source == inputText)
 832     {
 833       inputText_actionPerformed();
 834     }
 835     else if (source == closeMenuItem)
 836     {
 837       closeMenuItem_actionPerformed();
 838     }
 839     else if (source == undoMenuItem)
 840     {
 841       undoMenuItem_actionPerformed();
 842     }
 843     else if (source == redoMenuItem)
 844     {
 845       redoMenuItem_actionPerformed();
 846     }
 847     else if (source == copy)
 848     {
 849       copy_actionPerformed();
 850     }
 851     else if (source == pasteNew)
 852     {
 853       pasteNew_actionPerformed();
 854     }
 855     else if (source == pasteThis)
 856     {
 857       pasteThis_actionPerformed();
 858     }
 859     else if (source == cut)
 860     {
 861       cut_actionPerformed();
 862     }
 863     else if (source == delete)
 864     {
 865       delete_actionPerformed();
 866     }
 867     else if (source == grpsFromSelection)
 868     {
 869       makeGrpsFromSelection_actionPerformed();
 870     }
 871     else if (source == deleteGroups)
 872     {
 873       deleteGroups_actionPerformed();
 874     }
 875     else if (source == selectAllSequenceMenuItem)
 876     {
 877       selectAllSequenceMenuItem_actionPerformed();
 878     }
 879     else if (source == deselectAllSequenceMenuItem)
 880     {
 881       deselectAllSequenceMenuItem_actionPerformed();
 882     }
 883     else if (source == invertSequenceMenuItem)
 884     {
 885       invertSequenceMenuItem_actionPerformed();
 886     }
 887     else if (source == invertColSel)
 888     {
 889       viewport.invertColumnSelection();
 890       alignPanel.paintAlignment(true);
 891     }
 892     else if (source == remove2LeftMenuItem)
 893     {
 894       trimAlignment(true);
 895     }
 896     else if (source == remove2RightMenuItem)
 897     {
 898       trimAlignment(false);
 899     }
 900     else if (source == removeGappedColumnMenuItem)
 901     {
 902       removeGappedColumnMenuItem_actionPerformed();
 903     }
 904     else if (source == removeAllGapsMenuItem)
 905     {
 906       removeAllGapsMenuItem_actionPerformed();
 907     }
 908     else if (source == findMenuItem)
 909     {
 910       findMenuItem_actionPerformed();
 911     }
 912     else if (source == font)
 913     {
 914       new FontChooser(alignPanel);
 915     }
 916     else if (source == newView)
 917     {
 918       newView(null);
 919     }
 920     else if (source == showColumns)
 921     {
 922       viewport.showAllHiddenColumns();
 923       alignPanel.paintAlignment(true);
 924     }
 925     else if (source == showSeqs)
 926     {
 927       viewport.showAllHiddenSeqs();
 928       alignPanel.paintAlignment(true);
 929     }
 930     else if (source == hideColumns)
 931     {
 932       viewport.hideSelectedColumns();
 933       alignPanel.paintAlignment(true);
 934     }
 935     else if (source == hideSequences
 936             && viewport.getSelectionGroup() != null)
 937     {
 938       viewport.hideAllSelectedSeqs();
 939       alignPanel.paintAlignment(true);
 940     }
 941     else if (source == hideAllButSelection)
 942     {
 943       toggleHiddenRegions(false, false);
 944       alignPanel.paintAlignment(true);
 945     }
 946     else if (source == hideAllSelection)
 947     {
 948       SequenceGroup sg = viewport.getSelectionGroup();
 949       viewport.expandColSelection(sg, false);
 950       viewport.hideAllSelectedSeqs();
 951       viewport.hideSelectedColumns();
 952       alignPanel.paintAlignment(true);
 953     }
 954     else if (source == showAllHidden)
 955     {
 956       viewport.showAllHiddenColumns();
 957       viewport.showAllHiddenSeqs();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == showGroupConsensus)
 961     {
 962       showGroupConsensus_actionPerformed();
 963     }
 964     else if (source == showGroupConservation)
 965     {
 966       showGroupConservation_actionPerformed();
 967     }
 968     else if (source == showSequenceLogo)
 969     {
 970       showSequenceLogo_actionPerformed();
 971     }
 972     else if (source == normSequenceLogo)
 973     {
 974       normSequenceLogo_actionPerformed();
 975     }
 976     else if (source == showConsensusHistogram)
 977     {
 978       showConsensusHistogram_actionPerformed();
 979     }
 980     else if (source == applyAutoAnnotationSettings)
 981     {
 982       applyAutoAnnotationSettings_actionPerformed();
 983     }
 984     else if (source == featureSettings)
 985     {
 986       new FeatureSettings(alignPanel);
 987     }
 988     else if (source == alProperties)
 989     {
 990       StringBuffer contents = new jalview.io.AlignmentProperties(
 991               viewport.getAlignment()).formatAsString();
 992       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 993       cap.setText(contents.toString());
 994       Frame frame = new Frame();
 995       frame.add(cap);
 996       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
 997                   400, 250);
 998     }
 999     else if (source == overviewMenuItem)
1000     {
1001       overviewMenuItem_actionPerformed();
1002     }
1003     else if (source == noColourmenuItem)
1004     {
1005       changeColour(null);
1006     }
1007     else if (source == clustalColour)
1008     {
1009       abovePIDThreshold.setState(false);
1010       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1011     }
1012     else if (source == zappoColour)
1013     {
1014       changeColour(new ZappoColourScheme());
1015     }
1016     else if (source == taylorColour)
1017     {
1018       changeColour(new TaylorColourScheme());
1019     }
1020     else if (source == hydrophobicityColour)
1021     {
1022       changeColour(new HydrophobicColourScheme());
1023     }
1024     else if (source == helixColour)
1025     {
1026       changeColour(new HelixColourScheme());
1027     }
1028     else if (source == strandColour)
1029     {
1030       changeColour(new StrandColourScheme());
1031     }
1032     else if (source == turnColour)
1033     {
1034       changeColour(new TurnColourScheme());
1035     }
1036     else if (source == buriedColour)
1037     {
1038       changeColour(new BuriedColourScheme());
1039     }
1040     else if (source == nucleotideColour)
1041     {
1042       changeColour(new NucleotideColourScheme());
1043     }
1044     else if (source == purinePyrimidineColour)
1045     {
1046       changeColour(new PurinePyrimidineColourScheme());
1047     }
1048     else if (source == RNAInteractionColour)\r
1049     {\r
1050       changeColour(new RNAInteractionColourScheme());\r
1051     }\r
1052     else if (source == RNAHelixColour)
1053     {
1054       new RNAHelicesColourChooser(viewport, alignPanel);
1055     }
1056     else if (source == modifyPID)
1057     {
1058       modifyPID_actionPerformed();
1059     }
1060     else if (source == modifyConservation)
1061     {
1062       modifyConservation_actionPerformed();
1063     }
1064     else if (source == userDefinedColour)
1065     {
1066       new UserDefinedColours(alignPanel, null);
1067     }
1068     else if (source == PIDColour)
1069     {
1070       changeColour(new PIDColourScheme());
1071     }
1072     else if (source == BLOSUM62Colour)
1073     {
1074       changeColour(new Blosum62ColourScheme());
1075     }
1076     else if (source == tcoffeeColour)
1077     {
1078       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1079     }
1080     else if (source == annotationColour)
1081     {
1082       new AnnotationColourChooser(viewport, alignPanel);
1083     }
1084     else if (source == sortPairwiseMenuItem)
1085     {
1086       sortPairwiseMenuItem_actionPerformed();
1087     }
1088     else if (source == sortIDMenuItem)
1089     {
1090       sortIDMenuItem_actionPerformed();
1091     }
1092     else if (source == sortLengthMenuItem)
1093     {
1094       sortLengthMenuItem_actionPerformed();
1095     }
1096     else if (source == sortGroupMenuItem)
1097     {
1098       sortGroupMenuItem_actionPerformed();
1099     }
1100     else if (source == removeRedundancyMenuItem)
1101     {
1102       removeRedundancyMenuItem_actionPerformed();
1103     }
1104     else if (source == pairwiseAlignmentMenuItem)
1105     {
1106       pairwiseAlignmentMenuItem_actionPerformed();
1107     }
1108     else if (source == PCAMenuItem)
1109     {
1110       PCAMenuItem_actionPerformed();
1111     }
1112     else if (source == averageDistanceTreeMenuItem)
1113     {
1114       averageDistanceTreeMenuItem_actionPerformed();
1115     }
1116     else if (source == neighbourTreeMenuItem)
1117     {
1118       neighbourTreeMenuItem_actionPerformed();
1119     }
1120     else if (source == njTreeBlosumMenuItem)
1121     {
1122       njTreeBlosumMenuItem_actionPerformed();
1123     }
1124     else if (source == avDistanceTreeBlosumMenuItem)
1125     {
1126       avTreeBlosumMenuItem_actionPerformed();
1127     }
1128     else if (source == documentation)
1129     {
1130       documentation_actionPerformed();
1131     }
1132     else if (source == about)
1133     {
1134       about_actionPerformed();
1135     }
1136
1137   }
1138
1139   public void inputText_actionPerformed()
1140   {
1141     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1142     Frame frame = new Frame();
1143     frame.add(cap);
1144     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
1145   }
1146
1147   protected void outputText_actionPerformed(ActionEvent e)
1148   {
1149     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1150     Frame frame = new Frame();
1151     frame.add(cap);
1152     jalview.bin.JalviewLite.addFrame(frame,
1153                 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
1154     cap.setText(new AppletFormatAdapter().formatSequences(
1155             e.getActionCommand(), viewport.getAlignment(),
1156             viewport.showJVSuffix));
1157   }
1158
1159   public void loadAnnotations()
1160   {
1161     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1162     cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
1163     cap.setAnnotationImport();
1164     Frame frame = new Frame();
1165     frame.add(cap);
1166     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
1167
1168   }
1169
1170   public String outputAnnotations(boolean displayTextbox)
1171   {
1172     String annotation = new AnnotationFile().printAnnotations(
1173             viewport.showAnnotation ? viewport.getAlignment()
1174                     .getAlignmentAnnotation() : null, viewport
1175                     .getAlignment().getGroups(), ((Alignment) viewport
1176                     .getAlignment()).alignmentProperties);
1177
1178     if (displayTextbox)
1179     {
1180       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1181       Frame frame = new Frame();
1182       frame.add(cap);
1183       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
1184       cap.setText(annotation);
1185     }
1186
1187     return annotation;
1188   }
1189
1190   private Hashtable getDisplayedFeatureCols()
1191   {
1192     if (alignPanel.getFeatureRenderer() != null
1193             && viewport.featuresDisplayed != null)
1194     {
1195       FeatureRenderer fr = alignPanel.getFeatureRenderer();
1196       Hashtable fcols = new Hashtable();
1197       Enumeration en = viewport.featuresDisplayed.keys();
1198       while (en.hasMoreElements())
1199       {
1200         Object col = en.nextElement();
1201         fcols.put(col, fr.featureColours.get(col));
1202       }
1203       return fcols;
1204     }
1205     return null;
1206   }
1207
1208   public String outputFeatures(boolean displayTextbox, String format)
1209   {
1210     String features;
1211     if (format.equalsIgnoreCase("Jalview"))
1212     {
1213       features = new FeaturesFile().printJalviewFormat(viewport
1214               .getAlignment().getSequencesArray(),
1215               getDisplayedFeatureCols());
1216     }
1217     else
1218     {
1219       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1220               .getSequencesArray(), getDisplayedFeatureCols());
1221     }
1222
1223     if (displayTextbox)
1224     {
1225       boolean frimport = false;
1226       if (features == null || features.equals("No Features Visible"))
1227       {
1228         features = "# No features visible - paste some and import them here.";
1229         frimport = true;
1230       }
1231
1232       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1233       if (frimport)
1234       {
1235         cap.setAnnotationImport();
1236       }
1237       Frame frame = new Frame();
1238       frame.add(cap);
1239       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
1240       cap.setText(features);
1241     }
1242     else
1243     {
1244       if (features == null)
1245         features = "";
1246     }
1247
1248     return features;
1249   }
1250
1251   void launchFullApplication()
1252   {
1253     StringBuffer url = new StringBuffer(jalviewServletURL);
1254
1255     url.append("?open="
1256             + appendProtocol(viewport.applet.getParameter("file")));
1257
1258     if (viewport.applet.getParameter("features") != null)
1259     {
1260       url.append("&features=");
1261       url.append(appendProtocol(viewport.applet.getParameter("features")));
1262     }
1263
1264     if (viewport.applet.getParameter("annotations") != null)
1265     {
1266       url.append("&annotations=");
1267       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1268     }
1269
1270     if (viewport.applet.getParameter("jnetfile") != null)
1271     {
1272       url.append("&annotations=");
1273       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1274     }
1275
1276     if (viewport.applet.getParameter("defaultColour") != null)
1277     {
1278       url.append("&colour="
1279               + removeWhiteSpace(viewport.applet
1280                       .getParameter("defaultColour")));
1281     }
1282
1283     if (viewport.applet.getParameter("userDefinedColour") != null)
1284     {
1285       url.append("&colour="
1286               + removeWhiteSpace(viewport.applet
1287                       .getParameter("userDefinedColour")));
1288     }
1289     if (viewport.applet.getParameter("tree") != null)
1290     {
1291       url.append("&tree="
1292               + appendProtocol(viewport.applet.getParameter("tree")));
1293     }
1294     if (viewport.applet.getParameter("treeFile") != null)
1295     {
1296       url.append("&tree="
1297               + appendProtocol(viewport.applet.getParameter("treeFile")));
1298     }
1299
1300     showURL(url.toString(), "FULL_APP");
1301   }
1302
1303   String removeWhiteSpace(String colour)
1304   {
1305     StringBuffer sb = new StringBuffer();
1306     for (int i = 0; i < colour.length(); i++)
1307     {
1308       if (Character.isWhitespace(colour.charAt(i)))
1309       {
1310         sb.append("%20");
1311       }
1312       else
1313       {
1314         sb.append(colour.charAt(i));
1315       }
1316     }
1317
1318     return sb.toString();
1319   }
1320
1321   String appendProtocol(String url)
1322   {
1323     try
1324     {
1325       new URL(url);
1326       url = URLEncoder.encode(url);
1327     }
1328     /*
1329      * When we finally deprecate 1.1 compatibility, we can start to use
1330      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1331      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1332      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1333      * ex.printStackTrace(); }
1334      */
1335     catch (java.net.MalformedURLException ex)
1336     {
1337       url = viewport.applet.getCodeBase() + url;
1338     }
1339     return url;
1340   }
1341
1342   public void closeMenuItem_actionPerformed()
1343   {
1344     PaintRefresher.RemoveComponent(alignPanel);
1345     if (alignPanel.seqPanel != null
1346             && alignPanel.seqPanel.seqCanvas != null)
1347     {
1348       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1349     }
1350     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1351     {
1352       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1353     }
1354
1355     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1356     {
1357       System.exit(0);
1358     }
1359     else
1360     {
1361     }
1362     viewport = null;
1363     alignPanel = null;
1364     this.dispose();
1365   }
1366
1367   /**
1368    * TODO: JAL-1104
1369    */
1370   void updateEditMenuBar()
1371   {
1372
1373     if (viewport.historyList.size() > 0)
1374     {
1375       undoMenuItem.setEnabled(true);
1376       CommandI command = (CommandI) viewport.historyList.peek();
1377       undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1378     }
1379     else
1380     {
1381       undoMenuItem.setEnabled(false);
1382       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1383     }
1384
1385     if (viewport.redoList.size() > 0)
1386     {
1387       redoMenuItem.setEnabled(true);
1388
1389       CommandI command = (CommandI) viewport.redoList.peek();
1390       redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1391     }
1392     else
1393     {
1394       redoMenuItem.setEnabled(false);
1395       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1396     }
1397   }
1398
1399   /**
1400    * TODO: JAL-1104
1401    */
1402   public void addHistoryItem(CommandI command)
1403   {
1404     if (command.getSize() > 0)
1405     {
1406       viewport.historyList.push(command);
1407       viewport.redoList.removeAllElements();
1408       updateEditMenuBar();
1409       viewport.updateHiddenColumns();
1410     }
1411   }
1412
1413   /**
1414    * TODO: JAL-1104 DOCUMENT ME!
1415    *
1416    * @param e
1417    *          DOCUMENT ME!
1418    */
1419   protected void undoMenuItem_actionPerformed()
1420   {
1421     if (viewport.historyList.size() < 1)
1422     {
1423       return;
1424     }
1425
1426     CommandI command = (CommandI) viewport.historyList.pop();
1427     viewport.redoList.push(command);
1428     command.undoCommand(null);
1429
1430     AlignViewport originalSource = getOriginatingSource(command);
1431     // JBPNote Test
1432     if (originalSource != viewport)
1433     {
1434       System.err
1435               .println("Warning: Viewport object mismatch whilst undoing");
1436     }
1437     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1438                                           // viewport.getColumnSelection().getHiddenColumns()
1439                                           // != null;
1440     updateEditMenuBar();
1441     originalSource.firePropertyChange("alignment", null, originalSource
1442             .getAlignment().getSequences());
1443   }
1444
1445   /**
1446    * TODO: JAL-1104 DOCUMENT ME!
1447    *
1448    * @param e
1449    *          DOCUMENT ME!
1450    */
1451   protected void redoMenuItem_actionPerformed()
1452   {
1453     if (viewport.redoList.size() < 1)
1454     {
1455       return;
1456     }
1457
1458     CommandI command = (CommandI) viewport.redoList.pop();
1459     viewport.historyList.push(command);
1460     command.doCommand(null);
1461
1462     AlignViewport originalSource = getOriginatingSource(command);
1463     // JBPNote Test
1464     if (originalSource != viewport)
1465     {
1466       System.err
1467               .println("Warning: Viewport object mismatch whilst re-doing");
1468     }
1469     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1470                                           // viewport.getColumnSelection().getHiddenColumns()
1471                                           // != null;
1472
1473     updateEditMenuBar();
1474     originalSource.firePropertyChange("alignment", null, originalSource
1475             .getAlignment().getSequences());
1476   }
1477
1478   AlignViewport getOriginatingSource(CommandI command)
1479   {
1480     AlignViewport originalSource = null;
1481     // For sequence removal and addition, we need to fire
1482     // the property change event FROM the viewport where the
1483     // original alignment was altered
1484     AlignmentI al = null;
1485     if (command instanceof EditCommand)
1486     {
1487       EditCommand editCommand = (EditCommand) command;
1488       al = editCommand.getAlignment();
1489       Vector comps = (Vector) PaintRefresher.components.get(viewport
1490               .getSequenceSetId());
1491       for (int i = 0; i < comps.size(); i++)
1492       {
1493         if (comps.elementAt(i) instanceof AlignmentPanel)
1494         {
1495           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1496           {
1497             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1498             break;
1499           }
1500         }
1501       }
1502     }
1503
1504     if (originalSource == null)
1505     {
1506       // The original view is closed, we must validate
1507       // the current view against the closed view first
1508       if (al != null)
1509       {
1510         PaintRefresher.validateSequences(al, viewport.getAlignment());
1511       }
1512
1513       originalSource = viewport;
1514     }
1515
1516     return originalSource;
1517   }
1518
1519   public void moveSelectedSequences(boolean up)
1520   {
1521     SequenceGroup sg = viewport.getSelectionGroup();
1522     if (sg == null)
1523     {
1524       return;
1525     }
1526     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1527             up ? null : viewport.getHiddenRepSequences(), up);
1528     alignPanel.paintAlignment(true);
1529   }
1530
1531   synchronized void slideSequences(boolean right, int size)
1532   {
1533     List<SequenceI> sg = new Vector<SequenceI>();
1534     if (viewport.cursorMode)
1535     {
1536       sg.add(viewport.getAlignment().getSequenceAt(
1537               alignPanel.seqPanel.seqCanvas.cursorY));
1538     }
1539     else if (viewport.getSelectionGroup() != null
1540             && viewport.getSelectionGroup().getSize() != viewport
1541                     .getAlignment().getHeight())
1542     {
1543       sg = viewport.getSelectionGroup().getSequences(
1544               viewport.getHiddenRepSequences());
1545     }
1546
1547     if (sg.size() < 1)
1548     {
1549       return;
1550     }
1551
1552     Vector<SequenceI> invertGroup = new Vector();
1553
1554     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1555     {
1556       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1557         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1558     }
1559
1560     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1561
1562     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1563             .size()]);
1564     for (int i = 0; i < invertGroup.size(); i++)
1565       seqs2[i] = invertGroup.elementAt(i);
1566
1567     SlideSequencesCommand ssc;
1568     if (right)
1569       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1570               size, viewport.getGapCharacter());
1571     else
1572       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1573               size, viewport.getGapCharacter());
1574
1575     int groupAdjustment = 0;
1576     if (ssc.getGapsInsertedBegin() && right)
1577     {
1578       if (viewport.cursorMode)
1579         alignPanel.seqPanel.moveCursor(size, 0);
1580       else
1581         groupAdjustment = size;
1582     }
1583     else if (!ssc.getGapsInsertedBegin() && !right)
1584     {
1585       if (viewport.cursorMode)
1586         alignPanel.seqPanel.moveCursor(-size, 0);
1587       else
1588         groupAdjustment = -size;
1589     }
1590
1591     if (groupAdjustment != 0)
1592     {
1593       viewport.getSelectionGroup().setStartRes(
1594               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1595       viewport.getSelectionGroup().setEndRes(
1596               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1597     }
1598
1599     boolean appendHistoryItem = false;
1600     if (viewport.historyList != null && viewport.historyList.size() > 0
1601             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1602     {
1603       appendHistoryItem = ssc
1604               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1605                       .peek());
1606     }
1607
1608     if (!appendHistoryItem)
1609       addHistoryItem(ssc);
1610
1611     repaint();
1612   }
1613
1614   static StringBuffer copiedSequences;
1615
1616   static Vector copiedHiddenColumns;
1617
1618   protected void copy_actionPerformed()
1619   {
1620     if (viewport.getSelectionGroup() == null)
1621     {
1622       return;
1623     }
1624
1625     SequenceGroup sg = viewport.getSelectionGroup();
1626     copiedSequences = new StringBuffer();
1627     Hashtable orderedSeqs = new Hashtable();
1628     for (int i = 0; i < sg.getSize(); i++)
1629     {
1630       SequenceI seq = sg.getSequenceAt(i);
1631       int index = viewport.getAlignment().findIndex(seq);
1632       orderedSeqs.put(index + "", seq);
1633     }
1634
1635     int index = 0, startRes, endRes;
1636     char ch;
1637
1638     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1639     {
1640       copiedHiddenColumns = new Vector();
1641       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1642       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1643               .size(); i++)
1644       {
1645         int[] region = (int[]) viewport.getColumnSelection()
1646                 .getHiddenColumns().elementAt(i);
1647
1648         copiedHiddenColumns.addElement(new int[]
1649         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1650       }
1651     }
1652     else
1653     {
1654       copiedHiddenColumns = null;
1655     }
1656
1657     for (int i = 0; i < sg.getSize(); i++)
1658     {
1659       SequenceI seq = null;
1660
1661       while (seq == null)
1662       {
1663         if (orderedSeqs.containsKey(index + ""))
1664         {
1665           seq = (SequenceI) orderedSeqs.get(index + "");
1666           index++;
1667
1668           break;
1669         }
1670         else
1671         {
1672           index++;
1673         }
1674       }
1675
1676       // FIND START RES
1677       // Returns residue following index if gap
1678       startRes = seq.findPosition(sg.getStartRes());
1679
1680       // FIND END RES
1681       // Need to find the residue preceeding index if gap
1682       endRes = 0;
1683
1684       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1685       {
1686         ch = seq.getCharAt(j);
1687         if (!jalview.util.Comparison.isGap((ch)))
1688         {
1689           endRes++;
1690         }
1691       }
1692
1693       if (endRes > 0)
1694       {
1695         endRes += seq.getStart() - 1;
1696       }
1697
1698       copiedSequences.append(seq.getName()
1699               + "\t"
1700               + startRes
1701               + "\t"
1702               + endRes
1703               + "\t"
1704               + seq.getSequenceAsString(sg.getStartRes(),
1705                       sg.getEndRes() + 1) + "\n");
1706     }
1707
1708   }
1709
1710   protected void pasteNew_actionPerformed()
1711   {
1712     paste(true);
1713   }
1714
1715   protected void pasteThis_actionPerformed()
1716   {
1717     paste(false);
1718   }
1719
1720   void paste(boolean newAlignment)
1721   {
1722     try
1723     {
1724
1725       if (copiedSequences == null)
1726       {
1727         return;
1728       }
1729
1730       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1731       Vector seqs = new Vector();
1732       while (st.hasMoreElements())
1733       {
1734         String name = st.nextToken();
1735         int start = Integer.parseInt(st.nextToken());
1736         int end = Integer.parseInt(st.nextToken());
1737         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1738       }
1739       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1740       for (int i = 0; i < seqs.size(); i++)
1741       {
1742         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1743       }
1744
1745       if (newAlignment)
1746       {
1747         String newtitle = new String("Copied sequences");
1748         if (getTitle().startsWith("Copied sequences"))
1749         {
1750           newtitle = getTitle();
1751         }
1752         else
1753         {
1754           newtitle = newtitle.concat("- from " + getTitle());
1755         }
1756         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1757                 viewport.applet, newtitle, false);
1758         if (copiedHiddenColumns != null)
1759         {
1760           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1761           {
1762             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1763             af.viewport.hideColumns(region[0], region[1]);
1764           }
1765         }
1766
1767         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1768                 DEFAULT_HEIGHT);
1769       }
1770       else
1771       {
1772         addSequences(newSeqs);
1773       }
1774
1775     } catch (Exception ex)
1776     {
1777     } // could be anything being pasted in here
1778
1779   }
1780
1781   void addSequences(SequenceI[] seqs)
1782   {
1783     for (int i = 0; i < seqs.length; i++)
1784     {
1785       viewport.getAlignment().addSequence(seqs[i]);
1786     }
1787
1788     // !newAlignment
1789     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1790             seqs, 0, viewport.getAlignment().getWidth(),
1791             viewport.getAlignment()));
1792
1793     viewport.setEndSeq(viewport.getAlignment().getHeight());
1794     viewport.getAlignment().getWidth();
1795     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1796             .getSequences());
1797
1798   }
1799
1800   protected void cut_actionPerformed()
1801   {
1802     copy_actionPerformed();
1803     delete_actionPerformed();
1804   }
1805
1806   protected void delete_actionPerformed()
1807   {
1808
1809     SequenceGroup sg = viewport.getSelectionGroup();
1810     if (sg == null)
1811     {
1812       return;
1813     }
1814
1815     Vector seqs = new Vector();
1816     SequenceI seq;
1817     for (int i = 0; i < sg.getSize(); i++)
1818     {
1819       seq = sg.getSequenceAt(i);
1820       seqs.addElement(seq);
1821     }
1822
1823     // If the cut affects all sequences, remove highlighted columns
1824     if (sg.getSize() == viewport.getAlignment().getHeight())
1825     {
1826       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1827               sg.getEndRes() + 1);
1828     }
1829
1830     SequenceI[] cut = new SequenceI[seqs.size()];
1831     for (int i = 0; i < seqs.size(); i++)
1832     {
1833       cut[i] = (SequenceI) seqs.elementAt(i);
1834     }
1835
1836     /*
1837      * //ADD HISTORY ITEM
1838      */
1839     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1840             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1841             viewport.getAlignment()));
1842
1843     viewport.setSelectionGroup(null);
1844     viewport.getAlignment().deleteGroup(sg);
1845
1846     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1847             .getSequences());
1848
1849     if (viewport.getAlignment().getHeight() < 1)
1850     {
1851       this.setVisible(false);
1852     }
1853     viewport.sendSelection();
1854   }
1855
1856   /**
1857    * group consensus toggled
1858    *
1859    */
1860   protected void showGroupConsensus_actionPerformed()
1861   {
1862     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1863     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1864
1865   }
1866
1867   /**
1868    * group conservation toggled.
1869    */
1870   protected void showGroupConservation_actionPerformed()
1871   {
1872     viewport.setShowGroupConservation(showGroupConservation.getState());
1873     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1874   }
1875
1876   /*
1877    * (non-Javadoc)
1878    *
1879    * @see
1880    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1881    * .event.ActionEvent)
1882    */
1883   protected void showConsensusHistogram_actionPerformed()
1884   {
1885     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1886     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1887   }
1888
1889   /*
1890    * (non-Javadoc)
1891    *
1892    * @see
1893    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1894    * .event.ActionEvent)
1895    */
1896   protected void showSequenceLogo_actionPerformed()
1897   {
1898     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1899     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1900   }
1901
1902   protected void normSequenceLogo_actionPerformed()
1903   {
1904     showSequenceLogo.setState(true);
1905     viewport.setShowSequenceLogo(true);
1906     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1907     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1908   }
1909
1910   protected void applyAutoAnnotationSettings_actionPerformed()
1911   {
1912     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1913   }
1914
1915   protected void makeGrpsFromSelection_actionPerformed()
1916   {
1917     if (avc.makeGroupsFromSelection()) {
1918       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1919       alignPanel.updateAnnotation();
1920       alignPanel.paintAlignment(true);
1921     }
1922   }
1923
1924   protected void createGroup_actionPerformed()
1925   {
1926     avc.createGroup();
1927   }
1928   protected void unGroup_actionPerformed()
1929   {
1930     if (avc.unGroup())
1931     {
1932       alignPanel.alignmentChanged();
1933     }
1934   }
1935   protected void deleteGroups_actionPerformed()
1936   {
1937     if (avc.deleteGroups())
1938     {
1939       alignPanel.alignmentChanged();
1940     }
1941   }
1942
1943   public void selectAllSequenceMenuItem_actionPerformed()
1944   {
1945     SequenceGroup sg = new SequenceGroup();
1946     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1947     {
1948       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1949     }
1950     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1951     viewport.setSelectionGroup(sg);
1952     alignPanel.paintAlignment(true);
1953     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1954     viewport.sendSelection();
1955   }
1956
1957   public void deselectAllSequenceMenuItem_actionPerformed()
1958   {
1959     if (viewport.cursorMode)
1960     {
1961       alignPanel.seqPanel.keyboardNo1 = null;
1962       alignPanel.seqPanel.keyboardNo2 = null;
1963     }
1964     viewport.setSelectionGroup(null);
1965     viewport.getColumnSelection().clear();
1966     viewport.setSelectionGroup(null);
1967     alignPanel.idPanel.idCanvas.searchResults = null;
1968     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1969     alignPanel.paintAlignment(true);
1970     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1971     viewport.sendSelection();
1972   }
1973
1974   public void invertSequenceMenuItem_actionPerformed()
1975   {
1976     SequenceGroup sg = viewport.getSelectionGroup();
1977     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1978     {
1979       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1980     }
1981
1982     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1983     viewport.sendSelection();
1984   }
1985
1986   public void invertColSel_actionPerformed()
1987   {
1988     viewport.invertColumnSelection();
1989     alignPanel.paintAlignment(true);
1990     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1991     viewport.sendSelection();
1992   }
1993
1994   void trimAlignment(boolean trimLeft)
1995   {
1996     ColumnSelection colSel = viewport.getColumnSelection();
1997     int column;
1998
1999     if (colSel.size() > 0)
2000     {
2001       if (trimLeft)
2002       {
2003         column = colSel.getMin();
2004       }
2005       else
2006       {
2007         column = colSel.getMax();
2008       }
2009
2010       SequenceI[] seqs;
2011       if (viewport.getSelectionGroup() != null)
2012       {
2013         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2014                 viewport.getHiddenRepSequences());
2015       }
2016       else
2017       {
2018         seqs = viewport.getAlignment().getSequencesArray();
2019       }
2020
2021       TrimRegionCommand trimRegion;
2022       if (trimLeft)
2023       {
2024         trimRegion = new TrimRegionCommand("Remove Left",
2025                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2026                 viewport.getAlignment(), viewport.getColumnSelection(),
2027                 viewport.getSelectionGroup());
2028         viewport.setStartRes(0);
2029       }
2030       else
2031       {
2032         trimRegion = new TrimRegionCommand("Remove Right",
2033                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2034                 viewport.getAlignment(), viewport.getColumnSelection(),
2035                 viewport.getSelectionGroup());
2036       }
2037
2038       statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2039       addHistoryItem(trimRegion);
2040
2041       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2042       {
2043         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2044                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2045         {
2046           viewport.getAlignment().deleteGroup(sg);
2047         }
2048       }
2049
2050       viewport.firePropertyChange("alignment", null, viewport
2051               .getAlignment().getSequences());
2052     }
2053   }
2054
2055   public void removeGappedColumnMenuItem_actionPerformed()
2056   {
2057     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2058
2059     SequenceI[] seqs;
2060     if (viewport.getSelectionGroup() != null)
2061     {
2062       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2063               viewport.getHiddenRepSequences());
2064       start = viewport.getSelectionGroup().getStartRes();
2065       end = viewport.getSelectionGroup().getEndRes();
2066     }
2067     else
2068     {
2069       seqs = viewport.getAlignment().getSequencesArray();
2070     }
2071
2072     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2073             "Remove Gapped Columns", seqs, start, end,
2074             viewport.getAlignment());
2075
2076     addHistoryItem(removeGapCols);
2077
2078     statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2079
2080     // This is to maintain viewport position on first residue
2081     // of first sequence
2082     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2083     int startRes = seq.findPosition(viewport.startRes);
2084     // ShiftList shifts;
2085     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2086     // edit.alColumnChanges=shifts.getInverse();
2087     // if (viewport.hasHiddenColumns)
2088     // viewport.getColumnSelection().compensateForEdits(shifts);
2089     viewport.setStartRes(seq.findIndex(startRes) - 1);
2090     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2091             .getSequences());
2092
2093   }
2094
2095   public void removeAllGapsMenuItem_actionPerformed()
2096   {
2097     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2098
2099     SequenceI[] seqs;
2100     if (viewport.getSelectionGroup() != null)
2101     {
2102       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2103               viewport.getHiddenRepSequences());
2104       start = viewport.getSelectionGroup().getStartRes();
2105       end = viewport.getSelectionGroup().getEndRes();
2106     }
2107     else
2108     {
2109       seqs = viewport.getAlignment().getSequencesArray();
2110     }
2111
2112     // This is to maintain viewport position on first residue
2113     // of first sequence
2114     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2115     int startRes = seq.findPosition(viewport.startRes);
2116
2117     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2118             viewport.getAlignment()));
2119
2120     viewport.setStartRes(seq.findIndex(startRes) - 1);
2121
2122     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2123             .getSequences());
2124
2125   }
2126
2127   public void findMenuItem_actionPerformed()
2128   {
2129     new Finder(alignPanel);
2130   }
2131
2132   /**
2133    * create a new view derived from the current view
2134    *
2135    * @param viewtitle
2136    * @return frame for the new view
2137    */
2138   public AlignFrame newView(String viewtitle)
2139   {
2140     AlignmentI newal;
2141     if (viewport.hasHiddenRows())
2142     {
2143       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2144               .getFullAlignment().getSequencesArray());
2145     }
2146     else
2147     {
2148       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2149     }
2150
2151     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2152     {
2153       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2154       {
2155         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2156         {
2157           newal.addAnnotation(viewport.getAlignment()
2158                   .getAlignmentAnnotation()[i]);
2159         }
2160       }
2161     }
2162
2163     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2164
2165     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2166     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2167     PaintRefresher.Register(newaf.alignPanel,
2168             newaf.alignPanel.av.getSequenceSetId());
2169
2170     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2171             newaf.alignPanel.av.getSequenceSetId());
2172     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2173             newaf.alignPanel.av.getSequenceSetId());
2174
2175     Vector comps = (Vector) PaintRefresher.components.get(viewport
2176             .getSequenceSetId());
2177     int viewSize = -1;
2178     for (int i = 0; i < comps.size(); i++)
2179     {
2180       if (comps.elementAt(i) instanceof AlignmentPanel)
2181       {
2182         viewSize++;
2183       }
2184     }
2185
2186     String title = new String(this.getTitle());
2187     if (viewtitle != null)
2188     {
2189       title = viewtitle + " ( " + title + ")";
2190     }
2191     else
2192     {
2193       if (title.indexOf("(View") > -1)
2194       {
2195         title = title.substring(0, title.indexOf("(View"));
2196       }
2197       title += "(View " + viewSize + ")";
2198     }
2199
2200     newaf.setTitle(title.toString());
2201
2202     newaf.viewport.historyList = viewport.historyList;
2203     newaf.viewport.redoList = viewport.redoList;
2204     return newaf;
2205   }
2206
2207   /**
2208    *
2209    * @return list of feature groups on the view
2210    */
2211   public String[] getFeatureGroups()
2212   {
2213     FeatureRenderer fr = null;
2214     if (alignPanel != null
2215             && (fr = alignPanel.getFeatureRenderer()) != null)
2216     {
2217       return fr.getGroups();
2218     }
2219     return null;
2220   }
2221
2222   /**
2223    * get sequence feature groups that are hidden or shown
2224    *
2225    * @param visible
2226    *          true is visible
2227    * @return list
2228    */
2229   public String[] getFeatureGroupsOfState(boolean visible)
2230   {
2231     FeatureRenderer fr = null;
2232     if (alignPanel != null
2233             && (fr = alignPanel.getFeatureRenderer()) != null)
2234     {
2235       return fr.getGroups(visible);
2236     }
2237     return null;
2238   }
2239
2240   /**
2241    * Change the display state for the given feature groups
2242    *
2243    * @param groups
2244    *          list of group strings
2245    * @param state
2246    *          visible or invisible
2247    */
2248   public void setFeatureGroupState(String[] groups, boolean state)
2249   {
2250     FeatureRenderer fr = null;
2251     this.sequenceFeatures.setState(true);
2252     viewport.showSequenceFeatures(true);
2253     if (alignPanel != null
2254             && (fr = alignPanel.getFeatureRenderer()) != null)
2255     {
2256       fr.setGroupState(groups, state);
2257       alignPanel.seqPanel.seqCanvas.repaint();
2258       if (alignPanel.overviewPanel != null)
2259       {
2260         alignPanel.overviewPanel.updateOverviewImage();
2261       }
2262     }
2263   }
2264
2265   public void seqLimits_itemStateChanged()
2266   {
2267     viewport.setShowJVSuffix(seqLimits.getState());
2268     alignPanel.fontChanged();
2269     alignPanel.paintAlignment(true);
2270   }
2271
2272   protected void colourTextMenuItem_actionPerformed()
2273   {
2274     viewport.setColourText(colourTextMenuItem.getState());
2275     alignPanel.paintAlignment(true);
2276   }
2277
2278   protected void displayNonconservedMenuItem_actionPerformed()
2279   {
2280     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2281     alignPanel.paintAlignment(true);
2282   }
2283
2284   protected void wrapMenuItem_actionPerformed()
2285   {
2286     viewport.setWrapAlignment(wrapMenuItem.getState());
2287     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2288     scaleAbove.setEnabled(wrapMenuItem.getState());
2289     scaleLeft.setEnabled(wrapMenuItem.getState());
2290     scaleRight.setEnabled(wrapMenuItem.getState());
2291     alignPanel.paintAlignment(true);
2292   }
2293
2294   public void overviewMenuItem_actionPerformed()
2295   {
2296     if (alignPanel.overviewPanel != null)
2297     {
2298       return;
2299     }
2300
2301     Frame frame = new Frame();
2302     OverviewPanel overview = new OverviewPanel(alignPanel);
2303     frame.add(overview);
2304     // +50 must allow for applet frame window
2305     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
2306             overview.getPreferredSize().width,
2307             overview.getPreferredSize().height + 50);
2308
2309     frame.pack();
2310     final AlignmentPanel ap = alignPanel;
2311     frame.addWindowListener(new WindowAdapter()
2312     {
2313       @Override
2314       public void windowClosing(WindowEvent e)
2315       {
2316         if (ap != null)
2317         {
2318           ap.setOverviewPanel(null);
2319         }
2320       };
2321     });
2322
2323     alignPanel.setOverviewPanel(overview);
2324
2325   }
2326
2327   void changeColour(ColourSchemeI cs)
2328   {
2329     int threshold = 0;
2330
2331     if (cs != null)
2332     {
2333       if (viewport.getAbovePIDThreshold())
2334       {
2335         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2336                 "Background");
2337
2338         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2339
2340         viewport.setGlobalColourScheme(cs);
2341       }
2342       else
2343       {
2344         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2345       }
2346
2347       if (viewport.getConservationSelected())
2348       {
2349
2350         Alignment al = (Alignment) viewport.getAlignment();
2351         Conservation c = new Conservation("All",
2352                 ResidueProperties.propHash, 3, al.getSequences(), 0,
2353                 al.getWidth() - 1);
2354
2355         c.calculate();
2356         c.verdict(false, viewport.getConsPercGaps());
2357
2358         cs.setConservation(c);
2359
2360         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2361                 cs, "Background"));
2362
2363       }
2364       else
2365       {
2366         cs.setConservation(null);
2367       }
2368
2369       cs.setConsensus(viewport.getSequenceConsensusHash());
2370
2371     }
2372     viewport.setGlobalColourScheme(cs);
2373
2374     if (alignPanel.getOverviewPanel() != null)
2375     {
2376       alignPanel.getOverviewPanel().updateOverviewImage();
2377     }
2378
2379     jalview.structure.StructureSelectionManager
2380             .getStructureSelectionManager(viewport.applet)
2381             .sequenceColoursChanged(alignPanel);
2382
2383     alignPanel.paintAlignment(true);
2384   }
2385
2386   protected void modifyPID_actionPerformed()
2387   {
2388     if (viewport.getAbovePIDThreshold()
2389             && viewport.getGlobalColourScheme() != null)
2390     {
2391       SliderPanel.setPIDSliderSource(alignPanel,
2392               viewport.getGlobalColourScheme(), "Background");
2393       SliderPanel.showPIDSlider();
2394     }
2395   }
2396
2397   protected void modifyConservation_actionPerformed()
2398   {
2399     if (viewport.getConservationSelected()
2400             && viewport.getGlobalColourScheme() != null)
2401     {
2402       SliderPanel.setConservationSlider(alignPanel,
2403               viewport.getGlobalColourScheme(), "Background");
2404       SliderPanel.showConservationSlider();
2405     }
2406   }
2407
2408   protected void conservationMenuItem_actionPerformed()
2409   {
2410     viewport.setConservationSelected(conservationMenuItem.getState());
2411
2412     viewport.setAbovePIDThreshold(false);
2413     abovePIDThreshold.setState(false);
2414
2415     changeColour(viewport.getGlobalColourScheme());
2416
2417     modifyConservation_actionPerformed();
2418   }
2419
2420   public void abovePIDThreshold_actionPerformed()
2421   {
2422     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2423
2424     conservationMenuItem.setState(false);
2425     viewport.setConservationSelected(false);
2426
2427     changeColour(viewport.getGlobalColourScheme());
2428
2429     modifyPID_actionPerformed();
2430   }
2431
2432   public void sortPairwiseMenuItem_actionPerformed()
2433   {
2434     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2435     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2436             .getAlignment().getSequenceAt(0), null);
2437
2438     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2439             viewport.getAlignment()));
2440     alignPanel.paintAlignment(true);
2441   }
2442
2443   public void sortIDMenuItem_actionPerformed()
2444   {
2445     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2446     AlignmentSorter.sortByID(viewport.getAlignment());
2447     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2448             viewport.getAlignment()));
2449     alignPanel.paintAlignment(true);
2450   }
2451
2452   public void sortLengthMenuItem_actionPerformed()
2453   {
2454     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2455     AlignmentSorter.sortByLength(viewport.getAlignment());
2456     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2457             viewport.getAlignment()));
2458     alignPanel.paintAlignment(true);
2459   }
2460
2461   public void sortGroupMenuItem_actionPerformed()
2462   {
2463     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2464     AlignmentSorter.sortByGroup(viewport.getAlignment());
2465     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2466             viewport.getAlignment()));
2467     alignPanel.paintAlignment(true);
2468
2469   }
2470
2471   public void removeRedundancyMenuItem_actionPerformed()
2472   {
2473     new RedundancyPanel(alignPanel);
2474   }
2475
2476   public void pairwiseAlignmentMenuItem_actionPerformed()
2477   {
2478     if (viewport.getSelectionGroup() != null
2479             && viewport.getSelectionGroup().getSize() > 1)
2480     {
2481       Frame frame = new Frame();
2482       frame.add(new PairwiseAlignPanel(alignPanel));
2483       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
2484               500);
2485     }
2486   }
2487
2488   public void PCAMenuItem_actionPerformed()
2489   {
2490     // are the sequences aligned?
2491     if (!viewport.getAlignment().isAligned(false))
2492     {
2493       SequenceI current;
2494       int Width = viewport.getAlignment().getWidth();
2495
2496       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2497       {
2498         current = viewport.getAlignment().getSequenceAt(i);
2499
2500         if (current.getLength() < Width)
2501         {
2502           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2503         }
2504       }
2505       alignPanel.paintAlignment(true);
2506     }
2507
2508     if ((viewport.getSelectionGroup() != null
2509             && viewport.getSelectionGroup().getSize() < 4 && viewport
2510             .getSelectionGroup().getSize() > 0)
2511             || viewport.getAlignment().getHeight() < 4)
2512     {
2513       return;
2514     }
2515
2516     try
2517     {
2518       new PCAPanel(viewport);
2519     } catch (java.lang.OutOfMemoryError ex)
2520     {
2521     }
2522
2523   }
2524
2525   public void averageDistanceTreeMenuItem_actionPerformed()
2526   {
2527     NewTreePanel("AV", "PID", "Average distance tree using PID");
2528   }
2529
2530   public void neighbourTreeMenuItem_actionPerformed()
2531   {
2532     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2533   }
2534
2535   protected void njTreeBlosumMenuItem_actionPerformed()
2536   {
2537     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2538   }
2539
2540   protected void avTreeBlosumMenuItem_actionPerformed()
2541   {
2542     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2543   }
2544
2545   void NewTreePanel(String type, String pwType, String title)
2546   {
2547     // are the sequences aligned?
2548     if (!viewport.getAlignment().isAligned(false))
2549     {
2550       SequenceI current;
2551       int Width = viewport.getAlignment().getWidth();
2552
2553       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2554       {
2555         current = viewport.getAlignment().getSequenceAt(i);
2556
2557         if (current.getLength() < Width)
2558         {
2559           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2560         }
2561       }
2562       alignPanel.paintAlignment(true);
2563
2564     }
2565
2566     if ((viewport.getSelectionGroup() != null && viewport
2567             .getSelectionGroup().getSize() > 1)
2568             || (viewport.getAlignment().getHeight() > 1))
2569     {
2570       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2571
2572       addTreeMenuItem(tp, title);
2573
2574       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2575     }
2576   }
2577
2578   void loadTree_actionPerformed()
2579   {
2580     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2581     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2582     cap.setTreeImport();
2583     Frame frame = new Frame();
2584     frame.add(cap);
2585     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
2586   }
2587
2588   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2589   {
2590     TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
2591     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2592     addTreeMenuItem(tp, treeFile);
2593   }
2594
2595   /**
2596    * sort the alignment using the given treePanel
2597    *
2598    * @param treePanel
2599    *          tree used to sort view
2600    * @param title
2601    *          string used for undo event name
2602    */
2603   public void sortByTree(TreePanel treePanel, String title)
2604   {
2605     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2606     AlignmentSorter
2607             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2608     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2609     // HistoryItem.SORT));
2610     addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
2611             viewport.getAlignment()));
2612     alignPanel.paintAlignment(true);
2613   }
2614
2615   /**
2616    * Do any automatic reordering of the alignment and add the necessary bits to
2617    * the menu structure for the new tree
2618    *
2619    * @param treePanel
2620    * @param title
2621    */
2622   protected void addTreeMenuItem(final TreePanel treePanel,
2623           final String title)
2624   {
2625     final MenuItem item = new MenuItem(title);
2626     sortByTreeMenu.add(item);
2627     item.addActionListener(new java.awt.event.ActionListener()
2628     {
2629       @Override
2630       public void actionPerformed(ActionEvent evt)
2631       {
2632         sortByTree(treePanel, title); // treePanel.getTitle());
2633       }
2634     });
2635
2636     treePanel.addWindowListener(new WindowAdapter()
2637     {
2638       @Override
2639       public void windowOpened(WindowEvent e)
2640       {
2641         if (viewport.sortByTree)
2642         {
2643           sortByTree(treePanel, title);
2644         }
2645         super.windowOpened(e);
2646       }
2647
2648       @Override
2649       public void windowClosing(WindowEvent e)
2650       {
2651         sortByTreeMenu.remove(item);
2652       };
2653     });
2654   }
2655
2656   public boolean sortBy(AlignmentOrder alorder, String undoname)
2657   {
2658     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2659     if (viewport.applet.debug)
2660     {
2661       System.err.println("Sorting " + alorder.getOrder().size()
2662               + " in alignment '" + getTitle() + "'");
2663     }
2664     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2665     if (undoname != null)
2666     {
2667       addHistoryItem(new OrderCommand(undoname, oldOrder,
2668               viewport.getAlignment()));
2669     }
2670     alignPanel.paintAlignment(true);
2671     return true;
2672   }
2673
2674   protected void documentation_actionPerformed()
2675   {
2676     alignPanel.av.applet.openJalviewHelpUrl();
2677   }
2678
2679   protected void about_actionPerformed()
2680   {
2681
2682     class AboutPanel extends Canvas
2683     {
2684       String version;
2685
2686       String builddate;
2687
2688       public AboutPanel(String version, String builddate)
2689       {
2690         this.version = version;
2691         this.builddate = builddate;
2692       }
2693
2694       @Override
2695       public void paint(Graphics g)
2696       {
2697         g.setColor(Color.white);
2698         g.fillRect(0, 0, getSize().width, getSize().height);
2699         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2700         FontMetrics fm = g.getFontMetrics();
2701         int fh = fm.getHeight();
2702         int y = 5, x = 7;
2703         g.setColor(Color.black);
2704         // TODO: update this text for each release or centrally store it for
2705         // lite and application
2706         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2707         g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
2708         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2709         g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
2710         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2711         g.drawString(
2712                 MessageManager.getString("label.jalview_authors_1"),
2713                 x, y += fh * 1.5);
2714         g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
2715         g.drawString(
2716                 MessageManager.getString("label.jalview_dev_managers"),
2717                 x, y += fh);
2718         g.drawString(
2719                 MessageManager.getString("label.jalview_distribution_lists"),
2720                 x, y += fh);
2721         g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
2722         g.drawString(
2723                 MessageManager.getString("label.jalview_cite_1_authors"),
2724                 x, y += fh);
2725         g.drawString(
2726                 MessageManager.getString("label.jalview_cite_1_title"),
2727                 x, y += fh);
2728         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2729                 x, y += fh);
2730       }
2731     }
2732
2733     Frame frame = new Frame();
2734     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2735             .getBuildDate()));
2736     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
2737
2738   }
2739
2740   public void showURL(String url, String target)
2741   {
2742     if (viewport.applet == null)
2743     {
2744       System.out.println("Not running as applet - no browser available.");
2745     }
2746     else
2747     {
2748       viewport.applet.showURL(url, target);
2749     }
2750   }
2751
2752   // ////////////////////////////////////////////////////////////////////////////////
2753   // JBuilder Graphics here
2754
2755   MenuBar alignFrameMenuBar = new MenuBar();
2756
2757   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2758
2759   MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
2760
2761   MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
2762
2763   MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
2764
2765   MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
2766
2767   MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
2768
2769   MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
2770
2771   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2772
2773   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2774
2775   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2776
2777   Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
2778
2779   MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
2780
2781   MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
2782
2783   MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
2784
2785   MenuItem remove2LeftMenuItem = new MenuItem();
2786
2787   MenuItem remove2RightMenuItem = new MenuItem();
2788
2789   MenuItem removeGappedColumnMenuItem = new MenuItem();
2790
2791   MenuItem removeAllGapsMenuItem = new MenuItem();
2792
2793   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2794
2795   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2796
2797   MenuItem sortPairwiseMenuItem = new MenuItem();
2798
2799   MenuItem sortIDMenuItem = new MenuItem();
2800
2801   MenuItem sortLengthMenuItem = new MenuItem();
2802
2803   MenuItem sortGroupMenuItem = new MenuItem();
2804
2805   MenuItem removeRedundancyMenuItem = new MenuItem();
2806
2807   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2808
2809   MenuItem PCAMenuItem = new MenuItem();
2810
2811   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2812
2813   MenuItem neighbourTreeMenuItem = new MenuItem();
2814
2815   BorderLayout borderLayout1 = new BorderLayout();
2816
2817   public Label statusBar = new Label();
2818
2819   Menu outputTextboxMenu = new Menu();
2820
2821   MenuItem clustalColour = new MenuItem();
2822
2823   MenuItem zappoColour = new MenuItem();
2824
2825   MenuItem taylorColour = new MenuItem();
2826
2827   MenuItem hydrophobicityColour = new MenuItem();
2828
2829   MenuItem helixColour = new MenuItem();
2830
2831   MenuItem strandColour = new MenuItem();
2832
2833   MenuItem turnColour = new MenuItem();
2834
2835   MenuItem buriedColour = new MenuItem();
2836
2837   MenuItem purinePyrimidineColour = new MenuItem();
2838
2839   MenuItem RNAInteractionColour = new MenuItem();\r
2840 \r
2841   MenuItem RNAHelixColour = new MenuItem();
2842
2843   MenuItem userDefinedColour = new MenuItem();
2844
2845   MenuItem PIDColour = new MenuItem();
2846
2847   MenuItem BLOSUM62Colour = new MenuItem();
2848
2849   MenuItem tcoffeeColour = new MenuItem();
2850
2851   MenuItem njTreeBlosumMenuItem = new MenuItem();
2852
2853   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2854
2855   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2856
2857   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2858
2859   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2860
2861   MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
2862
2863   MenuItem overviewMenuItem = new MenuItem();
2864
2865   MenuItem undoMenuItem = new MenuItem();
2866
2867   MenuItem redoMenuItem = new MenuItem();
2868
2869   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2870
2871   MenuItem noColourmenuItem = new MenuItem();
2872
2873   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2874
2875   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2876
2877   MenuItem findMenuItem = new MenuItem();
2878
2879   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2880
2881   MenuItem nucleotideColour = new MenuItem();
2882
2883   MenuItem deleteGroups = new MenuItem();
2884
2885   MenuItem grpsFromSelection = new MenuItem();
2886
2887   MenuItem createGroup = new MenuItem();
2888
2889   MenuItem unGroup = new MenuItem();
2890
2891   MenuItem delete = new MenuItem();
2892
2893   MenuItem copy = new MenuItem();
2894
2895   MenuItem cut = new MenuItem();
2896
2897   Menu pasteMenu = new Menu();
2898
2899   MenuItem pasteNew = new MenuItem();
2900
2901   MenuItem pasteThis = new MenuItem();
2902
2903   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2904
2905   MenuItem font = new MenuItem();
2906
2907   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2908
2909   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2910
2911   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2912
2913   MenuItem modifyPID = new MenuItem();
2914
2915   MenuItem modifyConservation = new MenuItem();
2916
2917   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2918           "Autocalculate Consensus", true);
2919
2920   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2921           "Sort Alignment With New Tree", true);
2922
2923   Menu sortByTreeMenu = new Menu();
2924
2925   Menu sort = new Menu();
2926
2927   Menu calculate = new Menu();
2928
2929   MenuItem inputText = new MenuItem();
2930
2931   Menu helpMenu = new Menu();
2932
2933   MenuItem documentation = new MenuItem();
2934
2935   MenuItem about = new MenuItem();
2936
2937   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2938
2939   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2940
2941   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2942
2943   Menu autoAnnMenu = new Menu();
2944
2945   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2946
2947   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2948
2949   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2950
2951   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2952
2953   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2954
2955   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2956
2957   private void jbInit() throws Exception
2958   {
2959
2960     setMenuBar(alignFrameMenuBar);
2961
2962     MenuItem item;
2963
2964     // dynamically fill save as menu with available formats
2965     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2966     {
2967
2968       item = new MenuItem(
2969               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2970
2971       item.addActionListener(new java.awt.event.ActionListener()
2972       {
2973         @Override
2974         public void actionPerformed(ActionEvent e)
2975         {
2976           outputText_actionPerformed(e);
2977         }
2978       });
2979
2980       outputTextboxMenu.add(item);
2981     }
2982     closeMenuItem.addActionListener(this);
2983     loadApplication.addActionListener(this);
2984
2985     loadTree.addActionListener(this);
2986     loadAnnotations.addActionListener(this);
2987     outputFeatures.addActionListener(this);
2988     outputAnnotations.addActionListener(this);
2989     selectAllSequenceMenuItem.addActionListener(this);
2990     deselectAllSequenceMenuItem.addActionListener(this);
2991     invertSequenceMenuItem.addActionListener(this);
2992     remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
2993     remove2LeftMenuItem.addActionListener(this);
2994     remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
2995     remove2RightMenuItem.addActionListener(this);
2996     removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
2997     removeGappedColumnMenuItem.addActionListener(this);
2998     removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
2999     removeAllGapsMenuItem.addActionListener(this);
3000     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3001     viewBoxesMenuItem.setState(true);
3002     viewBoxesMenuItem.addItemListener(this);
3003     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3004     viewTextMenuItem.setState(true);
3005     viewTextMenuItem.addItemListener(this);
3006     sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
3007     sortPairwiseMenuItem.addActionListener(this);
3008     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3009     sortIDMenuItem.addActionListener(this);
3010     sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
3011     sortLengthMenuItem.addActionListener(this);
3012     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3013     sortGroupMenuItem.addActionListener(this);
3014     removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
3015     removeRedundancyMenuItem.addActionListener(this);
3016     pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
3017     pairwiseAlignmentMenuItem.addActionListener(this);
3018     PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
3019     PCAMenuItem.addActionListener(this);
3020     averageDistanceTreeMenuItem
3021             .setLabel(MessageManager.getString("label.average_distance_identity"));
3022     averageDistanceTreeMenuItem.addActionListener(this);
3023     neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
3024     neighbourTreeMenuItem.addActionListener(this);
3025     statusBar.setBackground(Color.white);
3026     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3027     statusBar.setText(MessageManager.getString("label.status_bar"));
3028     outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
3029     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3030
3031     clustalColour.addActionListener(this);
3032     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3033     zappoColour.addActionListener(this);
3034     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3035     taylorColour.addActionListener(this);
3036     hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
3037     hydrophobicityColour.addActionListener(this);
3038     helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
3039     helixColour.addActionListener(this);
3040     strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
3041     strandColour.addActionListener(this);
3042     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3043     turnColour.addActionListener(this);
3044     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3045     buriedColour.addActionListener(this);
3046     purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
3047     purinePyrimidineColour.addActionListener(this);
3048     RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));\r
3049     RNAInteractionColour.addActionListener(this);\r
3050     RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
3051     RNAHelixColour.addActionListener(this);
3052     userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
3053     userDefinedColour.addActionListener(this);
3054     PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
3055     PIDColour.addActionListener(this);
3056     BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
3057     BLOSUM62Colour.addActionListener(this);
3058     tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
3059     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3060                                      // provided
3061     tcoffeeColour.addActionListener(this);
3062     avDistanceTreeBlosumMenuItem
3063             .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
3064     avDistanceTreeBlosumMenuItem.addActionListener(this);
3065     njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
3066     njTreeBlosumMenuItem.addActionListener(this);
3067     annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
3068     annotationPanelMenuItem.addItemListener(this);
3069     colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
3070     colourTextMenuItem.addItemListener(this);
3071     displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
3072     displayNonconservedMenuItem.addItemListener(this);
3073     alProperties.addActionListener(this);
3074     overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
3075     overviewMenuItem.addActionListener(this);
3076     undoMenuItem.setEnabled(false);
3077     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3078     undoMenuItem.addActionListener(this);
3079     redoMenuItem.setEnabled(false);
3080     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3081     redoMenuItem.addActionListener(this);
3082     conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
3083     conservationMenuItem.addItemListener(this);
3084     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3085     noColourmenuItem.addActionListener(this);
3086     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3087     wrapMenuItem.addItemListener(this);
3088     renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
3089     renderGapsMenuItem.setState(true);
3090     renderGapsMenuItem.addItemListener(this);
3091     findMenuItem.setLabel(MessageManager.getString("action.find"));
3092     findMenuItem.addActionListener(this);
3093     abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
3094     abovePIDThreshold.addItemListener(this);
3095     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3096     nucleotideColour.addActionListener(this);
3097     deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
3098     deleteGroups.addActionListener(this);
3099     grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
3100     grpsFromSelection.addActionListener(this);
3101     createGroup.setLabel(MessageManager.getString("action.create_group"));
3102     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3103     copy.setLabel(MessageManager.getString("action.copy"));
3104     copy.addActionListener(this);
3105     cut.setLabel(MessageManager.getString("action.cut"));
3106     cut.addActionListener(this);
3107     delete.setLabel(MessageManager.getString("action.delete"));
3108     delete.addActionListener(this);
3109     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3110     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3111     pasteNew.addActionListener(this);
3112     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3113     pasteThis.addActionListener(this);
3114     applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
3115     applyToAllGroups.setState(true);
3116     applyToAllGroups.addItemListener(this);
3117     font.setLabel(MessageManager.getString("action.font"));
3118     font.addActionListener(this);
3119     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3120     scaleAbove.setState(true);
3121     scaleAbove.setEnabled(false);
3122     scaleAbove.addItemListener(this);
3123     scaleLeft.setEnabled(false);
3124     scaleLeft.setState(true);
3125     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3126     scaleLeft.addItemListener(this);
3127     scaleRight.setEnabled(false);
3128     scaleRight.setState(true);
3129     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3130     scaleRight.addItemListener(this);
3131     modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
3132     modifyPID.addActionListener(this);
3133     modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
3134     modifyConservation.addActionListener(this);
3135     sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
3136     sort.setLabel(MessageManager.getString("action.sort"));
3137     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3138     autoCalculate.addItemListener(this);
3139     sortByTree.addItemListener(this);
3140     inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
3141     inputText.addActionListener(this);
3142     centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
3143     centreColumnLabelFlag.addItemListener(this);
3144     followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
3145     followMouseOverFlag.addItemListener(this);
3146     helpMenu.setLabel(MessageManager.getString("action.help"));
3147     documentation.setLabel(MessageManager.getString("label.documentation"));
3148     documentation.addActionListener(this);
3149
3150     about.setLabel(MessageManager.getString("label.about"));
3151     about.addActionListener(this);
3152     seqLimits.setState(true);
3153     seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
3154     seqLimits.addItemListener(this);
3155     featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
3156     featureSettings.addActionListener(this);
3157     sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
3158     sequenceFeatures.addItemListener(this);
3159     sequenceFeatures.setState(false);
3160     annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
3161     annotationColour.addActionListener(this);
3162     invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
3163     invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
3164     menu1.setLabel(MessageManager.getString("action.show"));
3165     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3166     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3167     menu2.setLabel(MessageManager.getString("action.hide"));
3168     hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
3169     hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
3170     hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
3171     hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
3172     showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
3173     showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
3174     showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
3175     showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
3176     showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
3177     normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
3178     applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
3179     applyAutoAnnotationSettings.setState(true);
3180     autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
3181
3182     invertColSel.addActionListener(this);
3183     showColumns.addActionListener(this);
3184     showSeqs.addActionListener(this);
3185     hideColumns.addActionListener(this);
3186     hideSequences.addActionListener(this);
3187     hideAllButSelection.addActionListener(this);
3188     hideAllSelection.addActionListener(this);
3189     showAllHidden.addActionListener(this);
3190     showGroupConsensus.addItemListener(this);
3191     showGroupConservation.addItemListener(this);
3192     showConsensusHistogram.addItemListener(this);
3193     showSequenceLogo.addItemListener(this);
3194     normSequenceLogo.addItemListener(this);
3195
3196     applyAutoAnnotationSettings.addItemListener(this);
3197     formatMenu.setLabel(MessageManager.getString("action.format"));
3198     selectMenu.setLabel(MessageManager.getString("action.select"));
3199     newView.setLabel(MessageManager.getString("action.new_view"));
3200     newView.addActionListener(this);
3201     alignFrameMenuBar.add(fileMenu);
3202     alignFrameMenuBar.add(editMenu);
3203     alignFrameMenuBar.add(selectMenu);
3204     alignFrameMenuBar.add(viewMenu);
3205     alignFrameMenuBar.add(formatMenu);
3206     alignFrameMenuBar.add(colourMenu);
3207     alignFrameMenuBar.add(calculateMenu);
3208     alignFrameMenuBar.add(helpMenu);
3209
3210     fileMenu.add(inputText);
3211     fileMenu.add(loadTree);
3212     fileMenu.add(loadAnnotations);
3213
3214     fileMenu.addSeparator();
3215     fileMenu.add(outputTextboxMenu);
3216     fileMenu.add(outputFeatures);
3217     fileMenu.add(outputAnnotations);
3218
3219     if (jalviewServletURL != null)
3220     {
3221       fileMenu.add(loadApplication);
3222     }
3223
3224     fileMenu.addSeparator();
3225     fileMenu.add(closeMenuItem);
3226
3227     editMenu.add(undoMenuItem);
3228     editMenu.add(redoMenuItem);
3229     editMenu.add(cut);
3230     editMenu.add(copy);
3231     editMenu.add(pasteMenu);
3232     editMenu.add(delete);
3233     editMenu.addSeparator();
3234     editMenu.add(remove2LeftMenuItem);
3235     editMenu.add(remove2RightMenuItem);
3236     editMenu.add(removeGappedColumnMenuItem);
3237     editMenu.add(removeAllGapsMenuItem);
3238     editMenu.add(removeRedundancyMenuItem);
3239     viewMenu.add(newView);
3240     viewMenu.addSeparator();
3241     viewMenu.add(menu1);
3242     viewMenu.add(menu2);
3243     viewMenu.addSeparator();
3244     viewMenu.add(followMouseOverFlag);
3245     viewMenu.add(annotationPanelMenuItem);
3246     autoAnnMenu.add(applyAutoAnnotationSettings);
3247     autoAnnMenu.add(showConsensusHistogram);
3248     autoAnnMenu.add(showSequenceLogo);
3249     autoAnnMenu.add(normSequenceLogo);
3250     autoAnnMenu.addSeparator();
3251     autoAnnMenu.add(showGroupConservation);
3252     autoAnnMenu.add(showGroupConsensus);
3253     viewMenu.add(autoAnnMenu);
3254     viewMenu.addSeparator();
3255     viewMenu.add(sequenceFeatures);
3256     viewMenu.add(featureSettings);
3257     viewMenu.addSeparator();
3258     viewMenu.add(alProperties);
3259     viewMenu.addSeparator();
3260     viewMenu.add(overviewMenuItem);
3261     colourMenu.add(applyToAllGroups);
3262     colourMenu.addSeparator();
3263     colourMenu.add(noColourmenuItem);
3264     colourMenu.add(clustalColour);
3265     colourMenu.add(BLOSUM62Colour);
3266     colourMenu.add(PIDColour);
3267     colourMenu.add(zappoColour);
3268     colourMenu.add(taylorColour);
3269     colourMenu.add(hydrophobicityColour);
3270     colourMenu.add(helixColour);
3271     colourMenu.add(strandColour);
3272     colourMenu.add(turnColour);
3273     colourMenu.add(buriedColour);
3274     colourMenu.add(nucleotideColour);
3275     colourMenu.add(purinePyrimidineColour);
3276     //    colourMenu.add(RNAInteractionColour);\r
3277     colourMenu.add(tcoffeeColour);
3278     colourMenu.add(userDefinedColour);
3279     colourMenu.addSeparator();
3280     colourMenu.add(conservationMenuItem);
3281     colourMenu.add(modifyConservation);
3282     colourMenu.add(abovePIDThreshold);
3283     colourMenu.add(modifyPID);
3284     colourMenu.add(annotationColour);
3285     colourMenu.add(RNAHelixColour);
3286     calculateMenu.add(sort);
3287     calculateMenu.add(calculate);
3288     calculateMenu.addSeparator();
3289     calculateMenu.add(pairwiseAlignmentMenuItem);
3290     calculateMenu.add(PCAMenuItem);
3291     calculateMenu.add(autoCalculate);
3292     calculateMenu.add(sortByTree);
3293     this.add(statusBar, BorderLayout.SOUTH);
3294     pasteMenu.add(pasteNew);
3295     pasteMenu.add(pasteThis);
3296     sort.add(sortIDMenuItem);
3297     sort.add(sortLengthMenuItem);
3298     sort.add(sortByTreeMenu);
3299     sort.add(sortGroupMenuItem);
3300     sort.add(sortPairwiseMenuItem);
3301     calculate.add(averageDistanceTreeMenuItem);
3302     calculate.add(neighbourTreeMenuItem);
3303     calculate.add(avDistanceTreeBlosumMenuItem);
3304     calculate.add(njTreeBlosumMenuItem);
3305     helpMenu.add(documentation);
3306     helpMenu.add(about);
3307     menu1.add(showColumns);
3308     menu1.add(showSeqs);
3309     menu1.add(showAllHidden);
3310     menu2.add(hideColumns);
3311     menu2.add(hideSequences);
3312     menu2.add(hideAllSelection);
3313     menu2.add(hideAllButSelection);
3314     formatMenu.add(font);
3315     formatMenu.add(seqLimits);
3316     formatMenu.add(wrapMenuItem);
3317     formatMenu.add(scaleAbove);
3318     formatMenu.add(scaleLeft);
3319     formatMenu.add(scaleRight);
3320     formatMenu.add(viewBoxesMenuItem);
3321     formatMenu.add(viewTextMenuItem);
3322     formatMenu.add(colourTextMenuItem);
3323     formatMenu.add(displayNonconservedMenuItem);
3324     formatMenu.add(renderGapsMenuItem);
3325     formatMenu.add(centreColumnLabelFlag);
3326     selectMenu.add(findMenuItem);
3327     selectMenu.addSeparator();
3328     selectMenu.add(selectAllSequenceMenuItem);
3329     selectMenu.add(deselectAllSequenceMenuItem);
3330     selectMenu.add(invertSequenceMenuItem);
3331     selectMenu.add(invertColSel);
3332     selectMenu.add(createGroup);
3333     selectMenu.add(unGroup);
3334     selectMenu.add(grpsFromSelection);
3335     selectMenu.add(deleteGroups);
3336
3337   }
3338
3339
3340   public void setStatus(String string) {
3341     statusBar.setText(string);
3342   };
3343
3344   MenuItem featureSettings = new MenuItem();
3345
3346   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3347
3348   MenuItem annotationColour = new MenuItem();
3349
3350   MenuItem invertColSel = new MenuItem();
3351
3352   Menu menu1 = new Menu();
3353
3354   MenuItem showColumns = new MenuItem();
3355
3356   MenuItem showSeqs = new MenuItem();
3357
3358   Menu menu2 = new Menu();
3359
3360   MenuItem hideColumns = new MenuItem();
3361
3362   MenuItem hideSequences = new MenuItem();
3363
3364   MenuItem hideAllButSelection = new MenuItem();
3365
3366   MenuItem hideAllSelection = new MenuItem();
3367
3368   MenuItem showAllHidden = new MenuItem();
3369
3370   Menu formatMenu = new Menu();
3371
3372   Menu selectMenu = new Menu();
3373
3374   MenuItem newView = new MenuItem();
3375
3376   /**
3377    * Attach the alignFrame panels after embedding menus, if necessary. This used
3378    * to be called setEmbedded, but is now creates the dropdown menus in a
3379    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3380    *
3381    * @param reallyEmbedded
3382    *          true to attach the view to the applet area on the page rather than
3383    *          in a new window
3384    */
3385   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3386   {
3387     if (reallyEmbedded)
3388     {
3389       // ////
3390       // Explicly build the embedded menu panel for the on-page applet
3391       //
3392       // view cannot be closed if its actually on the page
3393       fileMenu.remove(closeMenuItem);
3394       fileMenu.remove(3); // Remove Seperator
3395       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3396               Font.PLAIN, 10, false); // use our own fonts.
3397       // and actually add the components to the applet area
3398       viewport.applet.setLayout(new BorderLayout());
3399       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3400       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3401       alignPanel.setSize(viewport.applet.getSize().width,
3402               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3403                       - statusBar.HEIGHT);
3404       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3405       final AlignFrame me = this;
3406       viewport.applet.addFocusListener(new FocusListener()
3407       {
3408
3409         @Override
3410         public void focusLost(FocusEvent e)
3411         {
3412           if (me.viewport.applet.currentAlignFrame == me)
3413           {
3414             me.viewport.applet.currentAlignFrame = null;
3415           }
3416         }
3417
3418         @Override
3419         public void focusGained(FocusEvent e)
3420         {
3421           me.viewport.applet.currentAlignFrame = me;
3422         }
3423       });
3424       viewport.applet.validate();
3425     }
3426     else
3427     {
3428       // //////
3429       // test and embed menu bar if necessary.
3430       //
3431       if (embedMenuIfNeeded(alignPanel))
3432       {
3433         // adjust for status bar height too
3434         alignPanel.setSize(getSize().width, getSize().height
3435                 - statusBar.HEIGHT);
3436       }
3437       add(statusBar, BorderLayout.SOUTH);
3438       add(alignPanel, BorderLayout.CENTER);
3439       // and register with the applet so it can pass external API calls to us
3440       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3441               DEFAULT_HEIGHT);
3442     }
3443   }
3444
3445   /**
3446    * create a new binding between structures in an existing jmol viewer instance
3447    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3448    * this does not open a new Jmol window, or modify the display of the
3449    * structures in the original jmol window. Note This method doesn't work
3450    * without an additional javascript library to exchange messages between the
3451    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3452    *
3453    * @param viewer
3454    *          JmolViewer instance
3455    * @param sequenceIds
3456    *          - sequence Ids to search for associations
3457    */
3458   public SequenceStructureBinding addStructureViewInstance(
3459           Object jmolviewer, String[] sequenceIds)
3460   {
3461     org.jmol.api.JmolViewer viewer = null;
3462     try
3463     {
3464       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3465     } catch (ClassCastException ex)
3466     {
3467       System.err.println("Unsupported viewer object :"
3468               + jmolviewer.getClass());
3469     }
3470     if (viewer == null)
3471     {
3472       System.err.println("Can't use this object as a structure viewer:"
3473               + jmolviewer.getClass());
3474       return null;
3475     }
3476     SequenceI[] seqs = null;
3477     if (sequenceIds == null || sequenceIds.length == 0)
3478     {
3479       seqs = viewport.getAlignment().getSequencesArray();
3480     }
3481     else
3482     {
3483       Vector sqi = new Vector();
3484       AlignmentI al = viewport.getAlignment();
3485       for (int sid = 0; sid < sequenceIds.length; sid++)
3486       {
3487         SequenceI sq = al.findName(sequenceIds[sid]);
3488         if (sq != null)
3489         {
3490           sqi.addElement(sq);
3491         }
3492       }
3493       if (sqi.size() > 0)
3494       {
3495         seqs = new SequenceI[sqi.size()];
3496         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3497         {
3498           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3499         }
3500       }
3501       else
3502       {
3503         return null;
3504       }
3505     }
3506     ExtJmol jmv = null;
3507     // TODO: search for a jmv that involves viewer
3508     if (jmv == null)
3509     { // create a new viewer/jalview binding.
3510       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3511       { seqs });
3512     }
3513     return jmv;
3514
3515   }
3516
3517   /**
3518    * bind a pdb file to a sequence in the current view
3519    *
3520    * @param sequenceId
3521    *          - sequenceId within the dataset.
3522    * @param pdbEntryString
3523    *          - the short name for the PDB file
3524    * @param pdbFile
3525    *          - pdb file - either a URL or a valid PDB file.
3526    * @return true if binding was as success TODO: consider making an exception
3527    *         structure for indicating when PDB parsing or sequenceId location
3528    *         fails.
3529    */
3530   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3531           String pdbFile)
3532   {
3533     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3534     boolean needtoadd = false;
3535     if (toaddpdb != null)
3536     {
3537       Vector pdbe = toaddpdb.getPDBId();
3538       PDBEntry pdbentry = null;
3539       if (pdbe != null && pdbe.size() > 0)
3540       {
3541         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3542         {
3543           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3544           if (!pdbentry.getId().equals(pdbEntryString)
3545                   && !pdbentry.getFile().equals(pdbFile))
3546           {
3547             pdbentry = null;
3548           }
3549           else
3550           {
3551             continue;
3552           }
3553         }
3554       }
3555       if (pdbentry == null)
3556       {
3557         pdbentry = new PDBEntry();
3558         pdbentry.setId(pdbEntryString);
3559         pdbentry.setFile(pdbFile);
3560         needtoadd = true; // add this new entry to sequence.
3561       }
3562       // resolve data source
3563       // TODO: this code should be a refactored to an io package
3564       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3565       if (protocol == null)
3566       {
3567         return false;
3568       }
3569       if (needtoadd)
3570       {
3571         // make a note of the access mode and add
3572         if (pdbentry.getProperty() == null)
3573         {
3574           pdbentry.setProperty(new Hashtable());
3575         }
3576         pdbentry.getProperty().put("protocol", protocol);
3577         toaddpdb.addPDBId(pdbentry);
3578       }
3579     }
3580     return true;
3581   }
3582
3583   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3584   {
3585     if (seqs != null)
3586     {
3587       Vector sequences = new Vector();
3588       for (int i = 0; i < seqs.length; i++)
3589       {
3590         if (seqs[i] != null)
3591         {
3592           sequences.addElement(new Object[]
3593           { seqs[i], (chains != null) ? chains[i] : null });
3594         }
3595       }
3596       seqs = new SequenceI[sequences.size()];
3597       chains = new String[sequences.size()];
3598       for (int i = 0, isize = sequences.size(); i < isize; i++)
3599       {
3600         Object[] oj = (Object[]) sequences.elementAt(i);
3601
3602         seqs[i] = (SequenceI) oj[0];
3603         chains[i] = (String) oj[1];
3604       }
3605     }
3606     return new Object[]
3607     { seqs, chains };
3608
3609   }
3610
3611   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3612           SequenceI[] seqs, String[] chains, String protocol)
3613   {
3614     // Scrub any null sequences from the array
3615     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3616     seqs = (SequenceI[]) sqch[0];
3617     chains = (String[]) sqch[1];
3618     if (seqs == null || seqs.length == 0)
3619     {
3620       System.err
3621               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3622     }
3623     if (protocol == null || protocol.trim().length() == 0
3624             || protocol.equals("null"))
3625     {
3626       protocol = (String) pdb.getProperty().get("protocol");
3627       if (protocol == null)
3628       {
3629         System.err.println("Couldn't work out protocol to open structure: "
3630                 + pdb.getId());
3631         return;
3632       }
3633     }
3634     if (applet.useXtrnalSviewer)
3635     {
3636       // register the association(s) and quit, don't create any windows.
3637       if (StructureSelectionManager.getStructureSelectionManager(applet)
3638               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3639       {
3640         System.err.println("Failed to map " + pdb.getFile() + " ("
3641                 + protocol + ") to any sequences");
3642       }
3643       return;
3644     }
3645     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3646     {
3647       // can only do alignments with Jmol
3648       // find the last jmol window assigned to this alignment
3649       jalview.appletgui.AppletJmol ajm = null, tajm;
3650       Vector jmols = applet
3651               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3652       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3653       {
3654         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3655         if (tajm.ap.alignFrame == this)
3656         {
3657           ajm = tajm;
3658           break;
3659         }
3660       }
3661       if (ajm != null)
3662       {
3663         System.err
3664                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3665         // try and add the pdb structure
3666         // ajm.addS
3667         ajm = null;
3668       }
3669     }
3670     // otherwise, create a new window
3671     if (applet.jmolAvailable)
3672     {
3673       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3674               protocol);
3675       applet.lastFrameX += 40;
3676       applet.lastFrameY += 40;
3677     }
3678     else
3679     {
3680       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3681     }
3682
3683   }
3684
3685   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3686           SequenceI[][] seqs, String[][] chains, String[] protocols)
3687   {
3688     // TODO Auto-generated method stub
3689     System.err.println("Aligned Structure View: Not yet implemented.");
3690   }
3691
3692   /**
3693    * modify the current selection, providing the user has not made a selection
3694    * already.
3695    *
3696    * @param sel
3697    *          - sequences from this alignment
3698    * @param csel
3699    *          - columns to be selected on the alignment
3700    */
3701   public void select(SequenceGroup sel, ColumnSelection csel)
3702   {
3703     alignPanel.seqPanel.selection(sel, csel, null);
3704   }
3705
3706   public void scrollTo(int row, int column)
3707   {
3708     alignPanel.seqPanel.scrollTo(row, column);
3709   }
3710
3711   public void scrollToRow(int row)
3712   {
3713     alignPanel.seqPanel.scrollToRow(row);
3714   }
3715
3716   public void scrollToColumn(int column)
3717   {
3718     alignPanel.seqPanel.scrollToColumn(column);
3719   }
3720
3721   /**
3722    * @return the alignments unique ID.
3723    */
3724   public String getSequenceSetId()
3725   {
3726     return viewport.getSequenceSetId();
3727   }
3728
3729   /**
3730    * Load the (T-Coffee) score file from the specified url
3731    *
3732    * @param source
3733    *          File/URL/T-COFFEE score file contents
3734    * @throws IOException
3735    * @return true if alignment was annotated with data from source
3736    */
3737   public boolean loadScoreFile(String source) throws IOException
3738   {
3739
3740     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3741             AppletFormatAdapter.checkProtocol(source));
3742     if (!file.isValid())
3743     {
3744       // TODO: raise dialog for gui
3745       System.err.println("Problems parsing T-Coffee scores: "
3746               + file.getWarningMessage());
3747       System.err.println("Origin was:\n" + source);
3748       return false;
3749     }
3750
3751     /*
3752      * check that the score matrix matches the alignment dimensions
3753      */
3754     AlignmentI aln;
3755     if ((aln = viewport.getAlignment()) != null
3756             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3757                     .getWidth()))
3758     {
3759       // TODO: raise a dialog box here rather than bomb out.
3760       System.err
3761               .println("The scores matrix does not match the alignment dimensions");
3762
3763     }
3764
3765     // TODO add parameter to indicate if matching should be done
3766     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3767     {
3768       alignPanel.fontChanged();
3769       tcoffeeColour.setEnabled(true);
3770       // switch to this color
3771       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3772       return true;
3773     }
3774     else
3775     {
3776       System.err.println("Problems resolving T-Coffee scores:");
3777       if (file.getWarningMessage() != null)
3778       {
3779         System.err.println(file.getWarningMessage());
3780       }
3781     }
3782     return false;
3783   }
3784
3785 }