src/jalview/appletgui/AlignFrame.java

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