src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.FeatureRenderer;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.EditCommand.Action;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.ColumnSelection;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.io.AnnotationFile;
  46 import jalview.io.AppletFormatAdapter;
  47 import jalview.io.FeaturesFile;
  48 import jalview.io.TCoffeeScoreFile;
  49 import jalview.schemes.Blosum62ColourScheme;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.ClustalxColourScheme;
  52 import jalview.schemes.ColourSchemeI;
  53 import jalview.schemes.HelixColourScheme;
  54 import jalview.schemes.HydrophobicColourScheme;
  55 import jalview.schemes.NucleotideColourScheme;
  56 import jalview.schemes.PIDColourScheme;
  57 import jalview.schemes.PurinePyrimidineColourScheme;
  58 import jalview.schemes.RNAHelicesColourChooser;
  59 import jalview.schemes.RNAInteractionColourScheme;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.structures.models.AAStructureBindingModel;
  67 import jalview.util.MessageManager;
  68
  69 import java.awt.BorderLayout;
  70 import java.awt.Canvas;
  71 import java.awt.CheckboxMenuItem;
  72 import java.awt.Color;
  73 import java.awt.Font;
  74 import java.awt.FontMetrics;
  75 import java.awt.Frame;
  76 import java.awt.Graphics;
  77 import java.awt.Label;
  78 import java.awt.Menu;
  79 import java.awt.MenuBar;
  80 import java.awt.MenuItem;
  81 import java.awt.event.ActionEvent;
  82 import java.awt.event.ActionListener;
  83 import java.awt.event.FocusEvent;
  84 import java.awt.event.FocusListener;
  85 import java.awt.event.ItemEvent;
  86 import java.awt.event.ItemListener;
  87 import java.awt.event.KeyEvent;
  88 import java.awt.event.KeyListener;
  89 import java.awt.event.WindowAdapter;
  90 import java.awt.event.WindowEvent;
  91 import java.io.IOException;
  92 import java.net.URL;
  93 import java.net.URLEncoder;
  94 import java.util.Arrays;
  95 import java.util.Hashtable;
  96 import java.util.List;
  97 import java.util.Map;
  98 import java.util.StringTokenizer;
  99 import java.util.Vector;
 100
 101 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 102         ItemListener, KeyListener, AlignViewControllerGuiI
 103 {
 104   public AlignViewControllerI avc;
 105
 106   public AlignmentPanel alignPanel;
 107
 108   public AlignViewport viewport;
 109
 110   int DEFAULT_WIDTH = 700;
 111
 112   int DEFAULT_HEIGHT = 500;
 113
 114   String jalviewServletURL;
 115
 116   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 117           String title, boolean embedded)
 118   {
 119     if (applet != null)
 120     {
 121       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 122     }
 123
 124     try
 125     {
 126       jbInit();
 127     } catch (Exception ex)
 128     {
 129       ex.printStackTrace();
 130     }
 131     // need to get window geometry before we calculate alignment layout
 132     if (applet != null)
 133     {
 134       String param;
 135       try
 136       {
 137         param = applet.getParameter("windowWidth");
 138         if (param != null)
 139         {
 140           int width = Integer.parseInt(param);
 141           DEFAULT_WIDTH = width;
 142         }
 143         param = applet.getParameter("windowHeight");
 144         if (param != null)
 145         {
 146           int height = Integer.parseInt(param);
 147           DEFAULT_HEIGHT = height;
 148         }
 149       } catch (Exception ex)
 150       {
 151       }
 152     }
 153     viewport = new AlignViewport(al, applet);
 154     alignPanel = new AlignmentPanel(this, viewport);
 155     avc = new jalview.controller.AlignViewController(this, viewport,
 156             alignPanel);
 157     viewport.updateConservation(alignPanel);
 158     viewport.updateConsensus(alignPanel);
 159
 160     annotationPanelMenuItem.setState(viewport.showAnnotation);
 161     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 162     followMouseOverFlag.setState(viewport.getFollowHighlight());
 163     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 164     showGroupConservation.setState(viewport.isShowGroupConservation());
 165     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 166     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 167     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 168     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 169
 170     seqLimits.setState(viewport.showJVSuffix);
 171
 172     if (applet != null)
 173     {
 174       String param = applet.getParameter("sortBy");
 175       if (param != null)
 176       {
 177         if (param.equalsIgnoreCase("Id"))
 178         {
 179           sortIDMenuItem_actionPerformed();
 180         }
 181         else if (param.equalsIgnoreCase("Pairwise Identity"))
 182         {
 183           sortPairwiseMenuItem_actionPerformed();
 184         }
 185         else if (param.equalsIgnoreCase("Length"))
 186         {
 187           sortLengthMenuItem_actionPerformed();
 188         }
 189       }
 190
 191       param = applet.getParameter("wrap");
 192       if (param != null)
 193       {
 194         if (param.equalsIgnoreCase("true"))
 195         {
 196           wrapMenuItem.setState(true);
 197           wrapMenuItem_actionPerformed();
 198         }
 199       }
 200       param = applet.getParameter("centrecolumnlabels");
 201       if (param != null)
 202       {
 203         centreColumnLabelFlag.setState(true);
 204         centreColumnLabelFlag_stateChanged();
 205       }
 206
 207     }
 208     if (viewport.getAlignment().isNucleotide())
 209     {
 210       viewport.updateStrucConsensus(alignPanel);
 211       if (viewport.getAlignment().hasRNAStructure())
 212       {
 213         RNAHelixColour.setEnabled(true);
 214       }
 215       else
 216       {
 217         RNAHelixColour.setEnabled(false);
 218       }
 219     }
 220     else
 221     {
 222       RNAHelixColour.setEnabled(false);
 223       purinePyrimidineColour.setEnabled(false);
 224     }
 225     // Some JVMS send keyevents to Top frame or lowest panel,
 226     // Havent worked out why yet. So add to both this frame and seqCanvas for
 227     // now
 228     this.addKeyListener(this);
 229     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 230     alignPanel.idPanel.idCanvas.addKeyListener(this);
 231     alignPanel.scalePanel.addKeyListener(this);
 232     alignPanel.annotationPanel.addKeyListener(this);
 233     alignPanel.annotationPanelHolder.addKeyListener(this);
 234     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 235     alignPanel.alabels.addKeyListener(this);
 236     createAlignFrameWindow(embedded, title);
 237
 238     validate();
 239     alignPanel.adjustAnnotationHeight();
 240     alignPanel.paintAlignment(true);
 241   }
 242
 243   public AlignViewport getAlignViewport()
 244   {
 245     return viewport;
 246   }
 247
 248   public SeqCanvas getSeqcanvas()
 249   {
 250     return alignPanel.seqPanel.seqCanvas;
 251   }
 252
 253   /**
 254    * Load a features file onto the alignment
 255    *
 256    * @param file
 257    *          file URL, content, or other resolvable path
 258    * @param type
 259    *          is protocol for accessing data referred to by file
 260    */
 261
 262   public boolean parseFeaturesFile(String file, String type)
 263   {
 264     return parseFeaturesFile(file, type, true);
 265   }
 266
 267   /**
 268    * Load a features file onto the alignment
 269    *
 270    * @param file
 271    *          file URL, content, or other resolvable path
 272    * @param type
 273    *          is protocol for accessing data referred to by file
 274    * @param autoenabledisplay
 275    *          when true, display features flag will be automatically enabled if
 276    *          features are loaded
 277    * @return true if data parsed as a features file
 278    */
 279   public boolean parseFeaturesFile(String file, String type,
 280           boolean autoenabledisplay)
 281   {
 282     // TODO: test if importing a features file onto an alignment which already
 283     // has features with links overwrites the original links.
 284
 285     Hashtable featureLinks = new Hashtable();
 286     boolean featuresFile = false;
 287     try
 288     {
 289       featuresFile = new jalview.io.FeaturesFile(file, type)
 290               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 291                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 292                       true, viewport.applet.getDefaultParameter(
 293                               "relaxedidmatch", false));
 294     } catch (Exception ex)
 295     {
 296       ex.printStackTrace();
 297     }
 298
 299     if (featuresFile)
 300     {
 301       if (featureLinks.size() > 0)
 302       {
 303         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 304       }
 305       if (autoenabledisplay)
 306       {
 307         viewport.setShowSequenceFeatures(true);
 308         sequenceFeatures.setState(true);
 309       }
 310       if (alignPanel.seqPanel.seqCanvas.fr != null)
 311       {
 312         // update the min/max ranges where necessary
 313         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 314       }
 315       if (viewport.featureSettings != null)
 316       {
 317         viewport.featureSettings.refreshTable();
 318       }
 319       alignPanel.paintAlignment(true);
 320       statusBar.setText(MessageManager
 321               .getString("label.successfully_added_features_alignment"));
 322     }
 323     return featuresFile;
 324   }
 325
 326   @Override
 327   public void keyPressed(KeyEvent evt)
 328   {
 329     if (viewport.cursorMode
 330             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 331                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 332                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 333             && Character.isDigit(evt.getKeyChar()))
 334     {
 335       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 336     }
 337
 338     switch (evt.getKeyCode())
 339     {
 340     case 27: // escape key
 341       deselectAllSequenceMenuItem_actionPerformed();
 342
 343       alignPanel.alabels.cancelDrag();
 344       break;
 345     case KeyEvent.VK_X:
 346       if (evt.isControlDown() || evt.isMetaDown())
 347       {
 348         cut_actionPerformed();
 349       }
 350       break;
 351     case KeyEvent.VK_C:
 352       if (viewport.cursorMode && !evt.isControlDown())
 353       {
 354         alignPanel.seqPanel.setCursorColumn();
 355       }
 356       if (evt.isControlDown() || evt.isMetaDown())
 357       {
 358         copy_actionPerformed();
 359       }
 360       break;
 361     case KeyEvent.VK_V:
 362       if (evt.isControlDown())
 363       {
 364         paste(evt.isShiftDown());
 365       }
 366       break;
 367     case KeyEvent.VK_A:
 368       if (evt.isControlDown() || evt.isMetaDown())
 369       {
 370         selectAllSequenceMenuItem_actionPerformed();
 371       }
 372       break;
 373     case KeyEvent.VK_DOWN:
 374       if (viewport.cursorMode)
 375       {
 376         alignPanel.seqPanel.moveCursor(0, 1);
 377       }
 378       else
 379       {
 380         moveSelectedSequences(false);
 381       }
 382       break;
 383
 384     case KeyEvent.VK_UP:
 385       if (viewport.cursorMode)
 386       {
 387         alignPanel.seqPanel.moveCursor(0, -1);
 388       }
 389       else
 390       {
 391         moveSelectedSequences(true);
 392       }
 393       break;
 394
 395     case KeyEvent.VK_LEFT:
 396       if (evt.isAltDown() || !viewport.cursorMode)
 397       {
 398         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 399       }
 400       else
 401       {
 402         alignPanel.seqPanel.moveCursor(-1, 0);
 403       }
 404       break;
 405
 406     case KeyEvent.VK_RIGHT:
 407       if (evt.isAltDown() || !viewport.cursorMode)
 408       {
 409         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 410       }
 411       else
 412       {
 413         alignPanel.seqPanel.moveCursor(1, 0);
 414       }
 415       break;
 416
 417     case KeyEvent.VK_SPACE:
 418       if (viewport.cursorMode)
 419       {
 420         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 421                 || evt.isShiftDown() || evt.isAltDown());
 422       }
 423       break;
 424
 425     case KeyEvent.VK_DELETE:
 426     case KeyEvent.VK_BACK_SPACE:
 427       if (viewport.cursorMode)
 428       {
 429         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 430                 || evt.isShiftDown() || evt.isAltDown());
 431       }
 432       else
 433       {
 434         cut_actionPerformed();
 435         alignPanel.seqPanel.seqCanvas.repaint();
 436       }
 437       break;
 438
 439     case KeyEvent.VK_S:
 440       if (viewport.cursorMode)
 441       {
 442         alignPanel.seqPanel.setCursorRow();
 443       }
 444       break;
 445     case KeyEvent.VK_P:
 446       if (viewport.cursorMode)
 447       {
 448         alignPanel.seqPanel.setCursorPosition();
 449       }
 450       break;
 451
 452     case KeyEvent.VK_ENTER:
 453     case KeyEvent.VK_COMMA:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.setCursorRowAndColumn();
 457       }
 458       break;
 459
 460     case KeyEvent.VK_Q:
 461       if (viewport.cursorMode)
 462       {
 463         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 464       }
 465       break;
 466     case KeyEvent.VK_M:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_F2:
 474       viewport.cursorMode = !viewport.cursorMode;
 475       statusBar.setText(MessageManager.formatMessage(
 476               "label.keyboard_editing_mode", new String[]
 477               { (viewport.cursorMode ? "on" : "off") }));
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 481         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 482       }
 483       break;
 484
 485     case KeyEvent.VK_F:
 486       if (evt.isControlDown())
 487       {
 488         findMenuItem_actionPerformed();
 489       }
 490       break;
 491
 492     case KeyEvent.VK_H:
 493     {
 494       boolean toggleSeqs = !evt.isControlDown();
 495       boolean toggleCols = !evt.isShiftDown();
 496       toggleHiddenRegions(toggleSeqs, toggleCols);
 497       break;
 498     }
 499
 500     case KeyEvent.VK_PAGE_UP:
 501       if (viewport.wrapAlignment)
 502       {
 503         alignPanel.scrollUp(true);
 504       }
 505       else
 506       {
 507         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 508                 - viewport.endSeq + viewport.startSeq);
 509       }
 510       break;
 511
 512     case KeyEvent.VK_PAGE_DOWN:
 513       if (viewport.wrapAlignment)
 514       {
 515         alignPanel.scrollUp(false);
 516       }
 517       else
 518       {
 519         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 520                 + viewport.endSeq - viewport.startSeq);
 521       }
 522       break;
 523
 524     case KeyEvent.VK_Z:
 525       if (evt.isControlDown())
 526       {
 527         undoMenuItem_actionPerformed();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_Y:
 532       if (evt.isControlDown())
 533       {
 534         redoMenuItem_actionPerformed();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_L:
 539       if (evt.isControlDown())
 540       {
 541         trimAlignment(true);
 542       }
 543       break;
 544
 545     case KeyEvent.VK_R:
 546       if (evt.isControlDown())
 547       {
 548         trimAlignment(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_E:
 553       if (evt.isControlDown())
 554       {
 555         if (evt.isShiftDown())
 556         {
 557           this.removeAllGapsMenuItem_actionPerformed();
 558         }
 559         else
 560         {
 561           removeGappedColumnMenuItem_actionPerformed();
 562         }
 563       }
 564       break;
 565     case KeyEvent.VK_I:
 566       if (evt.isControlDown())
 567       {
 568         if (evt.isAltDown())
 569         {
 570           invertColSel_actionPerformed();
 571         }
 572         else
 573         {
 574           invertSequenceMenuItem_actionPerformed();
 575         }
 576       }
 577       break;
 578
 579     case KeyEvent.VK_G:
 580       if (evt.isControlDown())
 581       {
 582         if (evt.isShiftDown())
 583         {
 584           this.unGroup_actionPerformed();
 585         }
 586         else
 587         {
 588           this.createGroup_actionPerformed();
 589         }
 590       }
 591       break;
 592
 593     case KeyEvent.VK_U:
 594       if (evt.isControlDown())
 595       {
 596         this.deleteGroups_actionPerformed();
 597       }
 598       break;
 599
 600     case KeyEvent.VK_T:
 601       if (evt.isControlDown())
 602       {
 603         newView(null);
 604       }
 605       break;
 606
 607     }
 608     alignPanel.paintAlignment(true);
 609   }
 610
 611   /**
 612    * called by key handler and the hide all/show all menu items
 613    *
 614    * @param toggleSeqs
 615    * @param toggleCols
 616    */
 617   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 618   {
 619     boolean hide = false;
 620     SequenceGroup sg = viewport.getSelectionGroup();
 621     if (!toggleSeqs && !toggleCols)
 622     {
 623       // Hide everything by the current selection - this is a hack - we do the
 624       // invert and then hide
 625       // first check that there will be visible columns after the invert.
 626       if ((viewport.getColumnSelection() != null
 627               && viewport.getColumnSelection().getSelected() != null && viewport
 628               .getColumnSelection().getSelected().size() > 0)
 629               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 630                       .getEndRes()))
 631       {
 632         // now invert the sequence set, if required - empty selection implies
 633         // that no hiding is required.
 634         if (sg != null)
 635         {
 636           invertSequenceMenuItem_actionPerformed();
 637           sg = viewport.getSelectionGroup();
 638           toggleSeqs = true;
 639
 640         }
 641         viewport.expandColSelection(sg, true);
 642         // finally invert the column selection and get the new sequence
 643         // selection and indicate it should be hidden.
 644         invertColSel_actionPerformed();
 645         toggleCols = true;
 646       }
 647     }
 648
 649     if (toggleSeqs)
 650     {
 651       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 652       {
 653         hide = true;
 654         viewport.hideAllSelectedSeqs();
 655       }
 656       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 657               .size() > 0))
 658       {
 659         viewport.showAllHiddenSeqs();
 660       }
 661     }
 662
 663     if (toggleCols)
 664     {
 665       if (viewport.getColumnSelection().getSelected().size() > 0)
 666       {
 667         viewport.hideSelectedColumns();
 668         if (!toggleSeqs)
 669         {
 670           viewport.setSelectionGroup(sg);
 671         }
 672       }
 673       else if (!hide)
 674       {
 675         viewport.showAllHiddenColumns();
 676       }
 677     }
 678   }
 679
 680   @Override
 681   public void keyReleased(KeyEvent evt)
 682   {
 683   }
 684
 685   @Override
 686   public void keyTyped(KeyEvent evt)
 687   {
 688   }
 689
 690   @Override
 691   public void itemStateChanged(ItemEvent evt)
 692   {
 693     if (evt.getSource() == displayNonconservedMenuItem)
 694     {
 695       displayNonconservedMenuItem_actionPerformed();
 696     }
 697     else if (evt.getSource() == colourTextMenuItem)
 698     {
 699       colourTextMenuItem_actionPerformed();
 700     }
 701     else if (evt.getSource() == wrapMenuItem)
 702     {
 703       wrapMenuItem_actionPerformed();
 704     }
 705     else if (evt.getSource() == scaleAbove)
 706     {
 707       viewport.setScaleAboveWrapped(scaleAbove.getState());
 708     }
 709     else if (evt.getSource() == scaleLeft)
 710     {
 711       viewport.setScaleLeftWrapped(scaleLeft.getState());
 712     }
 713     else if (evt.getSource() == scaleRight)
 714     {
 715       viewport.setScaleRightWrapped(scaleRight.getState());
 716     }
 717     else if (evt.getSource() == seqLimits)
 718     {
 719       seqLimits_itemStateChanged();
 720     }
 721     else if (evt.getSource() == viewBoxesMenuItem)
 722     {
 723       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 724     }
 725     else if (evt.getSource() == viewTextMenuItem)
 726     {
 727       viewport.setShowText(viewTextMenuItem.getState());
 728     }
 729     else if (evt.getSource() == renderGapsMenuItem)
 730     {
 731       viewport.setRenderGaps(renderGapsMenuItem.getState());
 732     }
 733     else if (evt.getSource() == annotationPanelMenuItem)
 734     {
 735       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 736       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 737     }
 738     else if (evt.getSource() == sequenceFeatures)
 739     {
 740       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 741       alignPanel.seqPanel.seqCanvas.repaint();
 742     }
 743     else if (evt.getSource() == conservationMenuItem)
 744     {
 745       conservationMenuItem_actionPerformed();
 746     }
 747     else if (evt.getSource() == abovePIDThreshold)
 748     {
 749       abovePIDThreshold_actionPerformed();
 750     }
 751     else if (evt.getSource() == applyToAllGroups)
 752     {
 753       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 754     }
 755     else if (evt.getSource() == autoCalculate)
 756     {
 757       viewport.autoCalculateConsensus = autoCalculate.getState();
 758     }
 759     else if (evt.getSource() == sortByTree)
 760     {
 761       viewport.sortByTree = sortByTree.getState();
 762     }
 763     else if (evt.getSource() == this.centreColumnLabelFlag)
 764     {
 765       centreColumnLabelFlag_stateChanged();
 766     }
 767     else if (evt.getSource() == this.followMouseOverFlag)
 768     {
 769       mouseOverFlag_stateChanged();
 770     }
 771     else if (evt.getSource() == showGroupConsensus)
 772     {
 773       showGroupConsensus_actionPerformed();
 774     }
 775     else if (evt.getSource() == showGroupConservation)
 776     {
 777       showGroupConservation_actionPerformed();
 778     }
 779     else if (evt.getSource() == showSequenceLogo)
 780     {
 781       showSequenceLogo_actionPerformed();
 782     }
 783     else if (evt.getSource() == normSequenceLogo)
 784     {
 785       normSequenceLogo_actionPerformed();
 786     }
 787     else if (evt.getSource() == showConsensusHistogram)
 788     {
 789       showConsensusHistogram_actionPerformed();
 790     }
 791     else if (evt.getSource() == applyAutoAnnotationSettings)
 792     {
 793       applyAutoAnnotationSettings_actionPerformed();
 794     }
 795     alignPanel.paintAlignment(true);
 796   }
 797
 798   private void mouseOverFlag_stateChanged()
 799   {
 800     viewport.followHighlight = followMouseOverFlag.getState();
 801     // TODO: could kick the scrollTo mechanism to reset view for current
 802     // searchresults.
 803   }
 804
 805   private void centreColumnLabelFlag_stateChanged()
 806   {
 807     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 808     this.alignPanel.annotationPanel.repaint();
 809   }
 810
 811   @Override
 812   public void actionPerformed(ActionEvent evt)
 813   {
 814     Object source = evt.getSource();
 815
 816     if (source == inputText)
 817     {
 818       inputText_actionPerformed();
 819     }
 820     else if (source == loadTree)
 821     {
 822       loadTree_actionPerformed();
 823     }
 824     else if (source == loadApplication)
 825     {
 826       launchFullApplication();
 827     }
 828     else if (source == loadAnnotations)
 829     {
 830       loadAnnotations();
 831     }
 832     else if (source == outputAnnotations)
 833     {
 834       outputAnnotations(true);
 835     }
 836     else if (source == outputFeatures)
 837     {
 838       outputFeatures(true, "Jalview");
 839     }
 840     else if (source == closeMenuItem)
 841     {
 842       closeMenuItem_actionPerformed();
 843     }
 844     else if (source == copy)
 845     {
 846       copy_actionPerformed();
 847     }
 848     else if (source == undoMenuItem)
 849     {
 850       undoMenuItem_actionPerformed();
 851     }
 852     else if (source == redoMenuItem)
 853     {
 854       redoMenuItem_actionPerformed();
 855     }
 856     else if (source == inputText)
 857     {
 858       inputText_actionPerformed();
 859     }
 860     else if (source == closeMenuItem)
 861     {
 862       closeMenuItem_actionPerformed();
 863     }
 864     else if (source == undoMenuItem)
 865     {
 866       undoMenuItem_actionPerformed();
 867     }
 868     else if (source == redoMenuItem)
 869     {
 870       redoMenuItem_actionPerformed();
 871     }
 872     else if (source == copy)
 873     {
 874       copy_actionPerformed();
 875     }
 876     else if (source == pasteNew)
 877     {
 878       pasteNew_actionPerformed();
 879     }
 880     else if (source == pasteThis)
 881     {
 882       pasteThis_actionPerformed();
 883     }
 884     else if (source == cut)
 885     {
 886       cut_actionPerformed();
 887     }
 888     else if (source == delete)
 889     {
 890       delete_actionPerformed();
 891     }
 892     else if (source == grpsFromSelection)
 893     {
 894       makeGrpsFromSelection_actionPerformed();
 895     }
 896     else if (source == deleteGroups)
 897     {
 898       deleteGroups_actionPerformed();
 899     }
 900     else if (source == selectAllSequenceMenuItem)
 901     {
 902       selectAllSequenceMenuItem_actionPerformed();
 903     }
 904     else if (source == deselectAllSequenceMenuItem)
 905     {
 906       deselectAllSequenceMenuItem_actionPerformed();
 907     }
 908     else if (source == invertSequenceMenuItem)
 909     {
 910       invertSequenceMenuItem_actionPerformed();
 911     }
 912     else if (source == invertColSel)
 913     {
 914       viewport.invertColumnSelection();
 915       alignPanel.paintAlignment(true);
 916     }
 917     else if (source == remove2LeftMenuItem)
 918     {
 919       trimAlignment(true);
 920     }
 921     else if (source == remove2RightMenuItem)
 922     {
 923       trimAlignment(false);
 924     }
 925     else if (source == removeGappedColumnMenuItem)
 926     {
 927       removeGappedColumnMenuItem_actionPerformed();
 928     }
 929     else if (source == removeAllGapsMenuItem)
 930     {
 931       removeAllGapsMenuItem_actionPerformed();
 932     }
 933     else if (source == findMenuItem)
 934     {
 935       findMenuItem_actionPerformed();
 936     }
 937     else if (source == font)
 938     {
 939       new FontChooser(alignPanel);
 940     }
 941     else if (source == newView)
 942     {
 943       newView(null);
 944     }
 945     else if (source == showColumns)
 946     {
 947       viewport.showAllHiddenColumns();
 948       alignPanel.paintAlignment(true);
 949     }
 950     else if (source == showSeqs)
 951     {
 952       viewport.showAllHiddenSeqs();
 953       alignPanel.paintAlignment(true);
 954     }
 955     else if (source == hideColumns)
 956     {
 957       viewport.hideSelectedColumns();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == hideSequences
 961             && viewport.getSelectionGroup() != null)
 962     {
 963       viewport.hideAllSelectedSeqs();
 964       alignPanel.paintAlignment(true);
 965     }
 966     else if (source == hideAllButSelection)
 967     {
 968       toggleHiddenRegions(false, false);
 969       alignPanel.paintAlignment(true);
 970     }
 971     else if (source == hideAllSelection)
 972     {
 973       SequenceGroup sg = viewport.getSelectionGroup();
 974       viewport.expandColSelection(sg, false);
 975       viewport.hideAllSelectedSeqs();
 976       viewport.hideSelectedColumns();
 977       alignPanel.paintAlignment(true);
 978     }
 979     else if (source == showAllHidden)
 980     {
 981       viewport.showAllHiddenColumns();
 982       viewport.showAllHiddenSeqs();
 983       alignPanel.paintAlignment(true);
 984     }
 985     else if (source == showGroupConsensus)
 986     {
 987       showGroupConsensus_actionPerformed();
 988     }
 989     else if (source == showGroupConservation)
 990     {
 991       showGroupConservation_actionPerformed();
 992     }
 993     else if (source == showSequenceLogo)
 994     {
 995       showSequenceLogo_actionPerformed();
 996     }
 997     else if (source == normSequenceLogo)
 998     {
 999       normSequenceLogo_actionPerformed();
1000     }
1001     else if (source == showConsensusHistogram)
1002     {
1003       showConsensusHistogram_actionPerformed();
1004     }
1005     else if (source == applyAutoAnnotationSettings)
1006     {
1007       applyAutoAnnotationSettings_actionPerformed();
1008     }
1009     else if (source == featureSettings)
1010     {
1011       new FeatureSettings(alignPanel);
1012     }
1013     else if (source == alProperties)
1014     {
1015       StringBuffer contents = new jalview.io.AlignmentProperties(
1016               viewport.getAlignment()).formatAsString();
1017       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1018       cap.setText(contents.toString());
1019       Frame frame = new Frame();
1020       frame.add(cap);
1021       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1022               "label.alignment_properties", new String[]
1023               { getTitle() }), 400, 250);
1024     }
1025     else if (source == overviewMenuItem)
1026     {
1027       overviewMenuItem_actionPerformed();
1028     }
1029     else if (source == noColourmenuItem)
1030     {
1031       changeColour(null);
1032     }
1033     else if (source == clustalColour)
1034     {
1035       abovePIDThreshold.setState(false);
1036       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1037     }
1038     else if (source == zappoColour)
1039     {
1040       changeColour(new ZappoColourScheme());
1041     }
1042     else if (source == taylorColour)
1043     {
1044       changeColour(new TaylorColourScheme());
1045     }
1046     else if (source == hydrophobicityColour)
1047     {
1048       changeColour(new HydrophobicColourScheme());
1049     }
1050     else if (source == helixColour)
1051     {
1052       changeColour(new HelixColourScheme());
1053     }
1054     else if (source == strandColour)
1055     {
1056       changeColour(new StrandColourScheme());
1057     }
1058     else if (source == turnColour)
1059     {
1060       changeColour(new TurnColourScheme());
1061     }
1062     else if (source == buriedColour)
1063     {
1064       changeColour(new BuriedColourScheme());
1065     }
1066     else if (source == nucleotideColour)
1067     {
1068       changeColour(new NucleotideColourScheme());
1069     }
1070     else if (source == purinePyrimidineColour)
1071     {
1072       changeColour(new PurinePyrimidineColourScheme());
1073     }
1074     else if (source == RNAInteractionColour)
1075     {
1076       changeColour(new RNAInteractionColourScheme());
1077     }
1078     else if (source == RNAHelixColour)
1079     {
1080       new RNAHelicesColourChooser(viewport, alignPanel);
1081     }
1082     else if (source == modifyPID)
1083     {
1084       modifyPID_actionPerformed();
1085     }
1086     else if (source == modifyConservation)
1087     {
1088       modifyConservation_actionPerformed();
1089     }
1090     else if (source == userDefinedColour)
1091     {
1092       new UserDefinedColours(alignPanel, null);
1093     }
1094     else if (source == PIDColour)
1095     {
1096       changeColour(new PIDColourScheme());
1097     }
1098     else if (source == BLOSUM62Colour)
1099     {
1100       changeColour(new Blosum62ColourScheme());
1101     }
1102     else if (source == tcoffeeColour)
1103     {
1104       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1105     }
1106     else if (source == annotationColour)
1107     {
1108       new AnnotationColourChooser(viewport, alignPanel);
1109     }
1110     else if (source == annotationColumnSelection)
1111     {
1112       new AnnotationColumnChooser(viewport, alignPanel);
1113     }
1114     else if (source == sortPairwiseMenuItem)
1115     {
1116       sortPairwiseMenuItem_actionPerformed();
1117     }
1118     else if (source == sortIDMenuItem)
1119     {
1120       sortIDMenuItem_actionPerformed();
1121     }
1122     else if (source == sortLengthMenuItem)
1123     {
1124       sortLengthMenuItem_actionPerformed();
1125     }
1126     else if (source == sortGroupMenuItem)
1127     {
1128       sortGroupMenuItem_actionPerformed();
1129     }
1130     else if (source == removeRedundancyMenuItem)
1131     {
1132       removeRedundancyMenuItem_actionPerformed();
1133     }
1134     else if (source == pairwiseAlignmentMenuItem)
1135     {
1136       pairwiseAlignmentMenuItem_actionPerformed();
1137     }
1138     else if (source == PCAMenuItem)
1139     {
1140       PCAMenuItem_actionPerformed();
1141     }
1142     else if (source == averageDistanceTreeMenuItem)
1143     {
1144       averageDistanceTreeMenuItem_actionPerformed();
1145     }
1146     else if (source == neighbourTreeMenuItem)
1147     {
1148       neighbourTreeMenuItem_actionPerformed();
1149     }
1150     else if (source == njTreeBlosumMenuItem)
1151     {
1152       njTreeBlosumMenuItem_actionPerformed();
1153     }
1154     else if (source == avDistanceTreeBlosumMenuItem)
1155     {
1156       avTreeBlosumMenuItem_actionPerformed();
1157     }
1158     else if (source == documentation)
1159     {
1160       documentation_actionPerformed();
1161     }
1162     else if (source == about)
1163     {
1164       about_actionPerformed();
1165     }
1166
1167   }
1168
1169   public void inputText_actionPerformed()
1170   {
1171     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1172     Frame frame = new Frame();
1173     frame.add(cap);
1174     jalview.bin.JalviewLite.addFrame(frame,
1175             MessageManager.getString("label.input_cut_paste"), 500, 500);
1176   }
1177
1178   protected void outputText_actionPerformed(ActionEvent e)
1179   {
1180     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1181     Frame frame = new Frame();
1182     frame.add(cap);
1183     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184             "label.alignment_output_command", new String[]
1185             { e.getActionCommand() }), 600, 500);
1186     cap.setText(new AppletFormatAdapter().formatSequences(
1187             e.getActionCommand(), viewport.getAlignment(),
1188             viewport.showJVSuffix));
1189   }
1190
1191   public void loadAnnotations()
1192   {
1193     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1194     cap.setText(MessageManager
1195             .getString("label.paste_features_annotations_Tcoffee_here"));
1196     cap.setAnnotationImport();
1197     Frame frame = new Frame();
1198     frame.add(cap);
1199     jalview.bin.JalviewLite.addFrame(frame,
1200             MessageManager.getString("action.paste_annotations"), 400, 300);
1201
1202   }
1203
1204   public String outputAnnotations(boolean displayTextbox)
1205   {
1206     String annotation = new AnnotationFile()
1207             .printAnnotationsForView(viewport);
1208
1209     if (displayTextbox)
1210     {
1211       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212       Frame frame = new Frame();
1213       frame.add(cap);
1214       jalview.bin.JalviewLite.addFrame(frame,
1215               MessageManager.getString("label.annotations"), 600, 500);
1216       cap.setText(annotation);
1217     }
1218
1219     return annotation;
1220   }
1221
1222   private Map<String,Object> getDisplayedFeatureCols()
1223   {
1224     if (alignPanel.getFeatureRenderer() != null
1225             && viewport.getFeaturesDisplayed()!= null)
1226     {
1227       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1228
1229     }
1230     return null;
1231   }
1232
1233   public String outputFeatures(boolean displayTextbox, String format)
1234   {
1235     String features;
1236     if (format.equalsIgnoreCase("Jalview"))
1237     {
1238       features = new FeaturesFile().printJalviewFormat(viewport
1239               .getAlignment().getSequencesArray(),
1240               getDisplayedFeatureCols());
1241     }
1242     else
1243     {
1244       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1245               .getSequencesArray(), getDisplayedFeatureCols());
1246     }
1247
1248     if (displayTextbox)
1249     {
1250       boolean frimport = false;
1251       if (features == null || features.equals("No Features Visible"))
1252       {
1253         features = "# No features visible - paste some and import them here.";
1254         frimport = true;
1255       }
1256
1257       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1258       if (frimport)
1259       {
1260         cap.setAnnotationImport();
1261       }
1262       Frame frame = new Frame();
1263       frame.add(cap);
1264       jalview.bin.JalviewLite.addFrame(frame,
1265               MessageManager.getString("label.features"), 600, 500);
1266       cap.setText(features);
1267     }
1268     else
1269     {
1270       if (features == null)
1271       {
1272         features = "";
1273       }
1274     }
1275
1276     return features;
1277   }
1278
1279   void launchFullApplication()
1280   {
1281     StringBuffer url = new StringBuffer(jalviewServletURL);
1282
1283     // allow servlet parameters to be passed in applet parameter
1284     String firstSep = url.indexOf("?") > url.indexOf("/") ? "&" : "?";
1285     url.append(firstSep);
1286
1287     url.append("open="
1288             + appendProtocol(viewport.applet.getParameter("file")));
1289
1290     if (viewport.applet.getParameter("features") != null)
1291     {
1292       url.append("&features=");
1293       url.append(appendProtocol(viewport.applet.getParameter("features")));
1294     }
1295
1296     if (viewport.applet.getParameter("annotations") != null)
1297     {
1298       url.append("&annotations=");
1299       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1300     }
1301
1302     if (viewport.applet.getParameter("jnetfile") != null)
1303     {
1304       url.append("&annotations=");
1305       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1306     }
1307
1308     if (viewport.applet.getParameter("defaultColour") != null)
1309     {
1310       url.append("&colour="
1311               + removeWhiteSpace(viewport.applet
1312                       .getParameter("defaultColour")));
1313     }
1314
1315     if (viewport.applet.getParameter("userDefinedColour") != null)
1316     {
1317       url.append("&colour="
1318               + removeWhiteSpace(viewport.applet
1319                       .getParameter("userDefinedColour")));
1320     }
1321     if (viewport.applet.getParameter("tree") != null)
1322     {
1323       url.append("&tree="
1324               + appendProtocol(viewport.applet.getParameter("tree")));
1325     }
1326     if (viewport.applet.getParameter("treeFile") != null)
1327     {
1328       url.append("&tree="
1329               + appendProtocol(viewport.applet.getParameter("treeFile")));
1330     }
1331
1332     showURL(url.toString(), "FULL_APP");
1333   }
1334
1335   String removeWhiteSpace(String colour)
1336   {
1337     StringBuffer sb = new StringBuffer();
1338     for (int i = 0; i < colour.length(); i++)
1339     {
1340       if (Character.isWhitespace(colour.charAt(i)))
1341       {
1342         sb.append("%20");
1343       }
1344       else
1345       {
1346         sb.append(colour.charAt(i));
1347       }
1348     }
1349
1350     return sb.toString();
1351   }
1352
1353   String appendProtocol(String url)
1354   {
1355     try
1356     {
1357       new URL(url);
1358       url = URLEncoder.encode(url);
1359     }
1360     /*
1361      * When we finally deprecate 1.1 compatibility, we can start to use
1362      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1363      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1364      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1365      * ex.printStackTrace(); }
1366      */
1367     catch (java.net.MalformedURLException ex)
1368     {
1369       url = viewport.applet.getCodeBase() + url;
1370     }
1371     return url;
1372   }
1373
1374   public void closeMenuItem_actionPerformed()
1375   {
1376     PaintRefresher.RemoveComponent(alignPanel);
1377     if (alignPanel.seqPanel != null
1378             && alignPanel.seqPanel.seqCanvas != null)
1379     {
1380       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1381     }
1382     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1383     {
1384       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1385     }
1386
1387     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1388     {
1389       System.exit(0);
1390     }
1391     else
1392     {
1393     }
1394     viewport = null;
1395     alignPanel = null;
1396     this.dispose();
1397   }
1398
1399   /**
1400    * TODO: JAL-1104
1401    */
1402   void updateEditMenuBar()
1403   {
1404
1405     if (viewport.historyList.size() > 0)
1406     {
1407       undoMenuItem.setEnabled(true);
1408       CommandI command = (CommandI) viewport.historyList.peek();
1409       undoMenuItem.setLabel(MessageManager.formatMessage(
1410               "label.undo_command", new String[]
1411               { command.getDescription() }));
1412     }
1413     else
1414     {
1415       undoMenuItem.setEnabled(false);
1416       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1417     }
1418
1419     if (viewport.redoList.size() > 0)
1420     {
1421       redoMenuItem.setEnabled(true);
1422
1423       CommandI command = (CommandI) viewport.redoList.peek();
1424       redoMenuItem.setLabel(MessageManager.formatMessage(
1425               "label.redo_command", new String[]
1426               { command.getDescription() }));
1427     }
1428     else
1429     {
1430       redoMenuItem.setEnabled(false);
1431       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1432     }
1433   }
1434
1435   /**
1436    * TODO: JAL-1104
1437    */
1438   @Override
1439   public void addHistoryItem(CommandI command)
1440   {
1441     if (command.getSize() > 0)
1442     {
1443       viewport.historyList.push(command);
1444       viewport.redoList.removeAllElements();
1445       updateEditMenuBar();
1446       viewport.updateHiddenColumns();
1447     }
1448   }
1449
1450   /**
1451    * TODO: JAL-1104 DOCUMENT ME!
1452    *
1453    * @param e
1454    *          DOCUMENT ME!
1455    */
1456   protected void undoMenuItem_actionPerformed()
1457   {
1458     if (viewport.historyList.size() < 1)
1459     {
1460       return;
1461     }
1462
1463     CommandI command = (CommandI) viewport.historyList.pop();
1464     viewport.redoList.push(command);
1465     command.undoCommand(null);
1466
1467     AlignViewport originalSource = getOriginatingSource(command);
1468     // JBPNote Test
1469     if (originalSource != viewport)
1470     {
1471       System.err
1472               .println("Warning: Viewport object mismatch whilst undoing");
1473     }
1474     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1475                                           // viewport.getColumnSelection().getHiddenColumns()
1476                                           // != null;
1477     updateEditMenuBar();
1478     originalSource.firePropertyChange("alignment", null, originalSource
1479             .getAlignment().getSequences());
1480   }
1481
1482   /**
1483    * TODO: JAL-1104 DOCUMENT ME!
1484    *
1485    * @param e
1486    *          DOCUMENT ME!
1487    */
1488   protected void redoMenuItem_actionPerformed()
1489   {
1490     if (viewport.redoList.size() < 1)
1491     {
1492       return;
1493     }
1494
1495     CommandI command = (CommandI) viewport.redoList.pop();
1496     viewport.historyList.push(command);
1497     command.doCommand(null);
1498
1499     AlignViewport originalSource = getOriginatingSource(command);
1500     // JBPNote Test
1501     if (originalSource != viewport)
1502     {
1503       System.err
1504               .println("Warning: Viewport object mismatch whilst re-doing");
1505     }
1506     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1507                                           // viewport.getColumnSelection().getHiddenColumns()
1508                                           // != null;
1509
1510     updateEditMenuBar();
1511     originalSource.firePropertyChange("alignment", null, originalSource
1512             .getAlignment().getSequences());
1513   }
1514
1515   AlignViewport getOriginatingSource(CommandI command)
1516   {
1517     AlignViewport originalSource = null;
1518     // For sequence removal and addition, we need to fire
1519     // the property change event FROM the viewport where the
1520     // original alignment was altered
1521     AlignmentI al = null;
1522     if (command instanceof EditCommand)
1523     {
1524       EditCommand editCommand = (EditCommand) command;
1525       al = editCommand.getAlignment();
1526       Vector comps = (Vector) PaintRefresher.components.get(viewport
1527               .getSequenceSetId());
1528       for (int i = 0; i < comps.size(); i++)
1529       {
1530         if (comps.elementAt(i) instanceof AlignmentPanel)
1531         {
1532           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1533           {
1534             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1535             break;
1536           }
1537         }
1538       }
1539     }
1540
1541     if (originalSource == null)
1542     {
1543       // The original view is closed, we must validate
1544       // the current view against the closed view first
1545       if (al != null)
1546       {
1547         PaintRefresher.validateSequences(al, viewport.getAlignment());
1548       }
1549
1550       originalSource = viewport;
1551     }
1552
1553     return originalSource;
1554   }
1555
1556   public void moveSelectedSequences(boolean up)
1557   {
1558     SequenceGroup sg = viewport.getSelectionGroup();
1559     if (sg == null)
1560     {
1561       return;
1562     }
1563     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1564             up ? null : viewport.getHiddenRepSequences(), up);
1565     alignPanel.paintAlignment(true);
1566   }
1567
1568   synchronized void slideSequences(boolean right, int size)
1569   {
1570     List<SequenceI> sg = new Vector<SequenceI>();
1571     if (viewport.cursorMode)
1572     {
1573       sg.add(viewport.getAlignment().getSequenceAt(
1574               alignPanel.seqPanel.seqCanvas.cursorY));
1575     }
1576     else if (viewport.getSelectionGroup() != null
1577             && viewport.getSelectionGroup().getSize() != viewport
1578                     .getAlignment().getHeight())
1579     {
1580       sg = viewport.getSelectionGroup().getSequences(
1581               viewport.getHiddenRepSequences());
1582     }
1583
1584     if (sg.size() < 1)
1585     {
1586       return;
1587     }
1588
1589     Vector<SequenceI> invertGroup = new Vector();
1590
1591     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1592     {
1593       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1594       {
1595         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1596       }
1597     }
1598
1599     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1600
1601     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1602             .size()]);
1603     for (int i = 0; i < invertGroup.size(); i++)
1604     {
1605       seqs2[i] = invertGroup.elementAt(i);
1606     }
1607
1608     SlideSequencesCommand ssc;
1609     if (right)
1610     {
1611       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1612               size, viewport.getGapCharacter());
1613     }
1614     else
1615     {
1616       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1617               size, viewport.getGapCharacter());
1618     }
1619
1620     int groupAdjustment = 0;
1621     if (ssc.getGapsInsertedBegin() && right)
1622     {
1623       if (viewport.cursorMode)
1624       {
1625         alignPanel.seqPanel.moveCursor(size, 0);
1626       }
1627       else
1628       {
1629         groupAdjustment = size;
1630       }
1631     }
1632     else if (!ssc.getGapsInsertedBegin() && !right)
1633     {
1634       if (viewport.cursorMode)
1635       {
1636         alignPanel.seqPanel.moveCursor(-size, 0);
1637       }
1638       else
1639       {
1640         groupAdjustment = -size;
1641       }
1642     }
1643
1644     if (groupAdjustment != 0)
1645     {
1646       viewport.getSelectionGroup().setStartRes(
1647               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1648       viewport.getSelectionGroup().setEndRes(
1649               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1650     }
1651
1652     boolean appendHistoryItem = false;
1653     if (viewport.historyList != null && viewport.historyList.size() > 0
1654             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1655     {
1656       appendHistoryItem = ssc
1657               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1658                       .peek());
1659     }
1660
1661     if (!appendHistoryItem)
1662     {
1663       addHistoryItem(ssc);
1664     }
1665
1666     repaint();
1667   }
1668
1669   static StringBuffer copiedSequences;
1670
1671   static Vector copiedHiddenColumns;
1672
1673   protected void copy_actionPerformed()
1674   {
1675     if (viewport.getSelectionGroup() == null)
1676     {
1677       return;
1678     }
1679
1680     SequenceGroup sg = viewport.getSelectionGroup();
1681     copiedSequences = new StringBuffer();
1682     Hashtable orderedSeqs = new Hashtable();
1683     for (int i = 0; i < sg.getSize(); i++)
1684     {
1685       SequenceI seq = sg.getSequenceAt(i);
1686       int index = viewport.getAlignment().findIndex(seq);
1687       orderedSeqs.put(index + "", seq);
1688     }
1689
1690     int index = 0, startRes, endRes;
1691     char ch;
1692
1693     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1694     {
1695       copiedHiddenColumns = new Vector();
1696       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1697       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1698       {
1699
1700         copiedHiddenColumns.addElement(new int[]
1701         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1702       }
1703     }
1704     else
1705     {
1706       copiedHiddenColumns = null;
1707     }
1708
1709     for (int i = 0; i < sg.getSize(); i++)
1710     {
1711       SequenceI seq = null;
1712
1713       while (seq == null)
1714       {
1715         if (orderedSeqs.containsKey(index + ""))
1716         {
1717           seq = (SequenceI) orderedSeqs.get(index + "");
1718           index++;
1719
1720           break;
1721         }
1722         else
1723         {
1724           index++;
1725         }
1726       }
1727
1728       // FIND START RES
1729       // Returns residue following index if gap
1730       startRes = seq.findPosition(sg.getStartRes());
1731
1732       // FIND END RES
1733       // Need to find the residue preceeding index if gap
1734       endRes = 0;
1735
1736       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1737       {
1738         ch = seq.getCharAt(j);
1739         if (!jalview.util.Comparison.isGap((ch)))
1740         {
1741           endRes++;
1742         }
1743       }
1744
1745       if (endRes > 0)
1746       {
1747         endRes += seq.getStart() - 1;
1748       }
1749
1750       copiedSequences.append(seq.getName()
1751               + "\t"
1752               + startRes
1753               + "\t"
1754               + endRes
1755               + "\t"
1756               + seq.getSequenceAsString(sg.getStartRes(),
1757                       sg.getEndRes() + 1) + "\n");
1758     }
1759
1760   }
1761
1762   protected void pasteNew_actionPerformed()
1763   {
1764     paste(true);
1765   }
1766
1767   protected void pasteThis_actionPerformed()
1768   {
1769     paste(false);
1770   }
1771
1772   void paste(boolean newAlignment)
1773   {
1774     try
1775     {
1776
1777       if (copiedSequences == null)
1778       {
1779         return;
1780       }
1781
1782       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1783       Vector seqs = new Vector();
1784       while (st.hasMoreElements())
1785       {
1786         String name = st.nextToken();
1787         int start = Integer.parseInt(st.nextToken());
1788         int end = Integer.parseInt(st.nextToken());
1789         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1790       }
1791       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1792       for (int i = 0; i < seqs.size(); i++)
1793       {
1794         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1795       }
1796
1797       if (newAlignment)
1798       {
1799         String newtitle = MessageManager.getString("label.copied_sequences");
1800         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1801         {
1802           newtitle = getTitle();
1803         }
1804         else
1805         {
1806           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1807         }
1808         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1809                 viewport.applet, newtitle, false);
1810         if (copiedHiddenColumns != null)
1811         {
1812           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1813           {
1814             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1815             af.viewport.hideColumns(region[0], region[1]);
1816           }
1817         }
1818
1819         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1820                 DEFAULT_HEIGHT);
1821       }
1822       else
1823       {
1824         addSequences(newSeqs);
1825       }
1826
1827     } catch (Exception ex)
1828     {
1829     } // could be anything being pasted in here
1830
1831   }
1832
1833   void addSequences(SequenceI[] seqs)
1834   {
1835     for (int i = 0; i < seqs.length; i++)
1836     {
1837       viewport.getAlignment().addSequence(seqs[i]);
1838     }
1839
1840     // !newAlignment
1841     addHistoryItem(new EditCommand(
1842             MessageManager.getString("label.add_sequences"), Action.PASTE,
1843             seqs, 0, viewport.getAlignment().getWidth(),
1844             viewport.getAlignment()));
1845
1846     viewport.setEndSeq(viewport.getAlignment().getHeight());
1847     viewport.getAlignment().getWidth();
1848     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1849             .getSequences());
1850
1851   }
1852
1853   protected void cut_actionPerformed()
1854   {
1855     copy_actionPerformed();
1856     delete_actionPerformed();
1857   }
1858
1859   protected void delete_actionPerformed()
1860   {
1861
1862     SequenceGroup sg = viewport.getSelectionGroup();
1863     if (sg == null)
1864     {
1865       return;
1866     }
1867
1868     Vector seqs = new Vector();
1869     SequenceI seq;
1870     for (int i = 0; i < sg.getSize(); i++)
1871     {
1872       seq = sg.getSequenceAt(i);
1873       seqs.addElement(seq);
1874     }
1875
1876     // If the cut affects all sequences, remove highlighted columns
1877     if (sg.getSize() == viewport.getAlignment().getHeight())
1878     {
1879       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1880               sg.getEndRes() + 1);
1881     }
1882
1883     SequenceI[] cut = new SequenceI[seqs.size()];
1884     for (int i = 0; i < seqs.size(); i++)
1885     {
1886       cut[i] = (SequenceI) seqs.elementAt(i);
1887     }
1888
1889     /*
1890      * //ADD HISTORY ITEM
1891      */
1892     addHistoryItem(new EditCommand(
1893             MessageManager.getString("label.cut_sequences"), Action.CUT,
1894             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1895             viewport.getAlignment()));
1896
1897     viewport.setSelectionGroup(null);
1898     viewport.getAlignment().deleteGroup(sg);
1899
1900     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1901             .getSequences());
1902
1903     if (viewport.getAlignment().getHeight() < 1)
1904     {
1905       this.setVisible(false);
1906     }
1907     viewport.sendSelection();
1908   }
1909
1910   /**
1911    * group consensus toggled
1912    *
1913    */
1914   protected void showGroupConsensus_actionPerformed()
1915   {
1916     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1917     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1918
1919   }
1920
1921   /**
1922    * group conservation toggled.
1923    */
1924   protected void showGroupConservation_actionPerformed()
1925   {
1926     viewport.setShowGroupConservation(showGroupConservation.getState());
1927     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1928   }
1929
1930   /*
1931    * (non-Javadoc)
1932    *
1933    * @see
1934    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1935    * .event.ActionEvent)
1936    */
1937   protected void showConsensusHistogram_actionPerformed()
1938   {
1939     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1940     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1941   }
1942
1943   /*
1944    * (non-Javadoc)
1945    *
1946    * @see
1947    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1948    * .event.ActionEvent)
1949    */
1950   protected void showSequenceLogo_actionPerformed()
1951   {
1952     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1953     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1954   }
1955
1956   protected void normSequenceLogo_actionPerformed()
1957   {
1958     showSequenceLogo.setState(true);
1959     viewport.setShowSequenceLogo(true);
1960     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1961     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1962   }
1963
1964   protected void applyAutoAnnotationSettings_actionPerformed()
1965   {
1966     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1967   }
1968
1969   protected void makeGrpsFromSelection_actionPerformed()
1970   {
1971     if (avc.makeGroupsFromSelection())
1972     {
1973       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1974       alignPanel.updateAnnotation();
1975       alignPanel.paintAlignment(true);
1976     }
1977   }
1978
1979   protected void createGroup_actionPerformed()
1980   {
1981     avc.createGroup();
1982   }
1983
1984   protected void unGroup_actionPerformed()
1985   {
1986     if (avc.unGroup())
1987     {
1988       alignPanel.alignmentChanged();
1989     }
1990   }
1991
1992   protected void deleteGroups_actionPerformed()
1993   {
1994     if (avc.deleteGroups())
1995     {
1996       alignPanel.alignmentChanged();
1997     }
1998   }
1999
2000   public void selectAllSequenceMenuItem_actionPerformed()
2001   {
2002     SequenceGroup sg = new SequenceGroup();
2003     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2004     {
2005       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2006     }
2007     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2008     viewport.setSelectionGroup(sg);
2009     alignPanel.paintAlignment(true);
2010     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2011     viewport.sendSelection();
2012   }
2013
2014   public void deselectAllSequenceMenuItem_actionPerformed()
2015   {
2016     if (viewport.cursorMode)
2017     {
2018       alignPanel.seqPanel.keyboardNo1 = null;
2019       alignPanel.seqPanel.keyboardNo2 = null;
2020     }
2021     viewport.setSelectionGroup(null);
2022     viewport.getColumnSelection().clear();
2023     viewport.setSelectionGroup(null);
2024     alignPanel.idPanel.idCanvas.searchResults = null;
2025     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2026     alignPanel.paintAlignment(true);
2027     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2028     viewport.sendSelection();
2029   }
2030
2031   public void invertSequenceMenuItem_actionPerformed()
2032   {
2033     SequenceGroup sg = viewport.getSelectionGroup();
2034     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2035     {
2036       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2037     }
2038
2039     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2040     viewport.sendSelection();
2041   }
2042
2043   public void invertColSel_actionPerformed()
2044   {
2045     viewport.invertColumnSelection();
2046     alignPanel.paintAlignment(true);
2047     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2048     viewport.sendSelection();
2049   }
2050
2051   void trimAlignment(boolean trimLeft)
2052   {
2053     ColumnSelection colSel = viewport.getColumnSelection();
2054     int column;
2055
2056     if (colSel.size() > 0)
2057     {
2058       if (trimLeft)
2059       {
2060         column = colSel.getMin();
2061       }
2062       else
2063       {
2064         column = colSel.getMax();
2065       }
2066
2067       SequenceI[] seqs;
2068       if (viewport.getSelectionGroup() != null)
2069       {
2070         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2071                 viewport.getHiddenRepSequences());
2072       }
2073       else
2074       {
2075         seqs = viewport.getAlignment().getSequencesArray();
2076       }
2077
2078       TrimRegionCommand trimRegion;
2079       if (trimLeft)
2080       {
2081         trimRegion = new TrimRegionCommand("Remove Left",
2082                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2083                 viewport.getAlignment(), viewport.getColumnSelection(),
2084                 viewport.getSelectionGroup());
2085         viewport.setStartRes(0);
2086       }
2087       else
2088       {
2089         trimRegion = new TrimRegionCommand("Remove Right",
2090                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2091                 viewport.getAlignment(), viewport.getColumnSelection(),
2092                 viewport.getSelectionGroup());
2093       }
2094
2095       statusBar.setText(MessageManager.formatMessage(
2096               "label.removed_columns", new String[]
2097               { Integer.valueOf(trimRegion.getSize()).toString() }));
2098       addHistoryItem(trimRegion);
2099
2100       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2101       {
2102         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2103                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2104         {
2105           viewport.getAlignment().deleteGroup(sg);
2106         }
2107       }
2108
2109       viewport.firePropertyChange("alignment", null, viewport
2110               .getAlignment().getSequences());
2111     }
2112   }
2113
2114   public void removeGappedColumnMenuItem_actionPerformed()
2115   {
2116     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2117
2118     SequenceI[] seqs;
2119     if (viewport.getSelectionGroup() != null)
2120     {
2121       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2122               viewport.getHiddenRepSequences());
2123       start = viewport.getSelectionGroup().getStartRes();
2124       end = viewport.getSelectionGroup().getEndRes();
2125     }
2126     else
2127     {
2128       seqs = viewport.getAlignment().getSequencesArray();
2129     }
2130
2131     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2132             "Remove Gapped Columns", seqs, start, end,
2133             viewport.getAlignment());
2134
2135     addHistoryItem(removeGapCols);
2136
2137     statusBar.setText(MessageManager.formatMessage(
2138             "label.removed_empty_columns", new String[]
2139             { Integer.valueOf(removeGapCols.getSize()).toString() }));
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     // ShiftList shifts;
2146     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2147     // edit.alColumnChanges=shifts.getInverse();
2148     // if (viewport.hasHiddenColumns)
2149     // viewport.getColumnSelection().compensateForEdits(shifts);
2150     viewport.setStartRes(seq.findIndex(startRes) - 1);
2151     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2152             .getSequences());
2153
2154   }
2155
2156   public void removeAllGapsMenuItem_actionPerformed()
2157   {
2158     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2159
2160     SequenceI[] seqs;
2161     if (viewport.getSelectionGroup() != null)
2162     {
2163       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2164               viewport.getHiddenRepSequences());
2165       start = viewport.getSelectionGroup().getStartRes();
2166       end = viewport.getSelectionGroup().getEndRes();
2167     }
2168     else
2169     {
2170       seqs = viewport.getAlignment().getSequencesArray();
2171     }
2172
2173     // This is to maintain viewport position on first residue
2174     // of first sequence
2175     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2176     int startRes = seq.findPosition(viewport.startRes);
2177
2178     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2179             viewport.getAlignment()));
2180
2181     viewport.setStartRes(seq.findIndex(startRes) - 1);
2182
2183     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2184             .getSequences());
2185
2186   }
2187
2188   public void findMenuItem_actionPerformed()
2189   {
2190     new Finder(alignPanel);
2191   }
2192
2193   /**
2194    * create a new view derived from the current view
2195    *
2196    * @param viewtitle
2197    * @return frame for the new view
2198    */
2199   public AlignFrame newView(String viewtitle)
2200   {
2201     AlignmentI newal;
2202     if (viewport.hasHiddenRows())
2203     {
2204       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2205               .getFullAlignment().getSequencesArray());
2206     }
2207     else
2208     {
2209       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2210     }
2211
2212     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2213     {
2214       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2215       {
2216         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2217         {
2218           newal.addAnnotation(viewport.getAlignment()
2219                   .getAlignmentAnnotation()[i]);
2220         }
2221       }
2222     }
2223
2224     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2225
2226     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2227     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2228     PaintRefresher.Register(newaf.alignPanel,
2229             newaf.alignPanel.av.getSequenceSetId());
2230
2231     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2232             newaf.alignPanel.av.getSequenceSetId());
2233     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2234             newaf.alignPanel.av.getSequenceSetId());
2235
2236     Vector comps = (Vector) PaintRefresher.components.get(viewport
2237             .getSequenceSetId());
2238     int viewSize = -1;
2239     for (int i = 0; i < comps.size(); i++)
2240     {
2241       if (comps.elementAt(i) instanceof AlignmentPanel)
2242       {
2243         viewSize++;
2244       }
2245     }
2246
2247     String title = new String(this.getTitle());
2248     if (viewtitle != null)
2249     {
2250       title = viewtitle + " ( " + title + ")";
2251     }
2252     else
2253     {
2254       if (title.indexOf("(View") > -1)
2255       {
2256         title = title.substring(0, title.indexOf("(View"));
2257       }
2258       title += "(View " + viewSize + ")";
2259     }
2260
2261     newaf.setTitle(title.toString());
2262
2263     newaf.viewport.historyList = viewport.historyList;
2264     newaf.viewport.redoList = viewport.redoList;
2265     return newaf;
2266   }
2267
2268   /**
2269    *
2270    * @return list of feature groups on the view
2271    */
2272   public String[] getFeatureGroups()
2273   {
2274     FeatureRenderer fr = null;
2275     if (alignPanel != null
2276             && (fr = alignPanel.getFeatureRenderer()) != null)
2277     {
2278       List gps = fr.getFeatureGroups();
2279       int p=0;
2280       String[] _gps = new String[gps.size()];
2281       for (Object gp:gps)
2282       {
2283         _gps[p++] = gp.toString();
2284       }
2285       return _gps;
2286     }
2287     return null;
2288   }
2289
2290   /**
2291    * get sequence feature groups that are hidden or shown
2292    *
2293    * @param visible
2294    *          true is visible
2295    * @return list
2296    */
2297   public String[] getFeatureGroupsOfState(boolean visible)
2298   {
2299     FeatureRenderer fr = null;
2300     if (alignPanel != null
2301             && (fr = alignPanel.getFeatureRenderer()) != null)
2302     {
2303       List gps = fr.getGroups(visible);
2304       int p=0;
2305       String[] _gps = new String[gps.size()];
2306       for (Object gp:gps)
2307       {
2308         _gps[p++] = gp.toString();
2309       }
2310       return _gps;
2311     }
2312     return null;
2313   }
2314
2315   /**
2316    * Change the display state for the given feature groups
2317    *
2318    * @param groups
2319    *          list of group strings
2320    * @param state
2321    *          visible or invisible
2322    */
2323   public void setFeatureGroupState(String[] groups, boolean state)
2324   {
2325     FeatureRenderer fr = null;
2326     this.sequenceFeatures.setState(true);
2327     viewport.setShowSequenceFeatures(true);
2328     if (alignPanel != null
2329             && (fr = alignPanel.getFeatureRenderer()) != null)
2330     {
2331
2332       fr.setGroupVisibility(Arrays.asList(groups), state);
2333       alignPanel.seqPanel.seqCanvas.repaint();
2334       if (alignPanel.overviewPanel != null)
2335       {
2336         alignPanel.overviewPanel.updateOverviewImage();
2337       }
2338     }
2339   }
2340
2341   public void seqLimits_itemStateChanged()
2342   {
2343     viewport.setShowJVSuffix(seqLimits.getState());
2344     alignPanel.fontChanged();
2345     alignPanel.paintAlignment(true);
2346   }
2347
2348   protected void colourTextMenuItem_actionPerformed()
2349   {
2350     viewport.setColourText(colourTextMenuItem.getState());
2351     alignPanel.paintAlignment(true);
2352   }
2353
2354   protected void displayNonconservedMenuItem_actionPerformed()
2355   {
2356     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2357     alignPanel.paintAlignment(true);
2358   }
2359
2360   protected void wrapMenuItem_actionPerformed()
2361   {
2362     viewport.setWrapAlignment(wrapMenuItem.getState());
2363     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2364     scaleAbove.setEnabled(wrapMenuItem.getState());
2365     scaleLeft.setEnabled(wrapMenuItem.getState());
2366     scaleRight.setEnabled(wrapMenuItem.getState());
2367     alignPanel.paintAlignment(true);
2368   }
2369
2370   public void overviewMenuItem_actionPerformed()
2371   {
2372     if (alignPanel.overviewPanel != null)
2373     {
2374       return;
2375     }
2376
2377     Frame frame = new Frame();
2378     OverviewPanel overview = new OverviewPanel(alignPanel);
2379     frame.add(overview);
2380     // +50 must allow for applet frame window
2381     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2382             "label.overview_params", new String[]
2383             { this.getTitle() }), overview.getPreferredSize().width,
2384             overview.getPreferredSize().height + 50);
2385
2386     frame.pack();
2387     final AlignmentPanel ap = alignPanel;
2388     frame.addWindowListener(new WindowAdapter()
2389     {
2390       @Override
2391       public void windowClosing(WindowEvent e)
2392       {
2393         if (ap != null)
2394         {
2395           ap.setOverviewPanel(null);
2396         }
2397       };
2398     });
2399
2400     alignPanel.setOverviewPanel(overview);
2401
2402   }
2403
2404   void changeColour(ColourSchemeI cs)
2405   {
2406     int threshold = 0;
2407
2408     if (cs != null)
2409     {
2410       if (viewport.getAbovePIDThreshold())
2411       {
2412         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2413                 cs, "Background"));
2414       }
2415
2416       if (viewport.getConservationSelected())
2417       {
2418         cs.setConservationApplied(true);
2419         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2420                 cs, "Background"));
2421       }
2422       else
2423       {
2424         cs.setConservationApplied(false);
2425       }
2426     }
2427     viewport.setGlobalColourScheme(cs);
2428
2429     if (alignPanel.getOverviewPanel() != null)
2430     {
2431       alignPanel.getOverviewPanel().updateOverviewImage();
2432     }
2433
2434     jalview.structure.StructureSelectionManager
2435             .getStructureSelectionManager(viewport.applet)
2436             .sequenceColoursChanged(alignPanel);
2437
2438     alignPanel.paintAlignment(true);
2439   }
2440
2441   protected void modifyPID_actionPerformed()
2442   {
2443     if (viewport.getAbovePIDThreshold()
2444             && viewport.getGlobalColourScheme() != null)
2445     {
2446       SliderPanel.setPIDSliderSource(alignPanel,
2447               viewport.getGlobalColourScheme(), "Background");
2448       SliderPanel.showPIDSlider();
2449     }
2450   }
2451
2452   protected void modifyConservation_actionPerformed()
2453   {
2454     if (viewport.getConservationSelected()
2455             && viewport.getGlobalColourScheme() != null)
2456     {
2457       SliderPanel.setConservationSlider(alignPanel,
2458               viewport.getGlobalColourScheme(), "Background");
2459       SliderPanel.showConservationSlider();
2460     }
2461   }
2462
2463   protected void conservationMenuItem_actionPerformed()
2464   {
2465     viewport.setConservationSelected(conservationMenuItem.getState());
2466
2467     viewport.setAbovePIDThreshold(false);
2468     abovePIDThreshold.setState(false);
2469
2470     changeColour(viewport.getGlobalColourScheme());
2471
2472     modifyConservation_actionPerformed();
2473   }
2474
2475   public void abovePIDThreshold_actionPerformed()
2476   {
2477     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2478
2479     conservationMenuItem.setState(false);
2480     viewport.setConservationSelected(false);
2481
2482     changeColour(viewport.getGlobalColourScheme());
2483
2484     modifyPID_actionPerformed();
2485   }
2486
2487   public void sortPairwiseMenuItem_actionPerformed()
2488   {
2489     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2490     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2491             .getAlignment().getSequenceAt(0), null);
2492
2493     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2494             viewport.getAlignment()));
2495     alignPanel.paintAlignment(true);
2496   }
2497
2498   public void sortIDMenuItem_actionPerformed()
2499   {
2500     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2501     AlignmentSorter.sortByID(viewport.getAlignment());
2502     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2503             viewport.getAlignment()));
2504     alignPanel.paintAlignment(true);
2505   }
2506
2507   public void sortLengthMenuItem_actionPerformed()
2508   {
2509     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2510     AlignmentSorter.sortByLength(viewport.getAlignment());
2511     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2512             viewport.getAlignment()));
2513     alignPanel.paintAlignment(true);
2514   }
2515
2516   public void sortGroupMenuItem_actionPerformed()
2517   {
2518     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2519     AlignmentSorter.sortByGroup(viewport.getAlignment());
2520     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2521             viewport.getAlignment()));
2522     alignPanel.paintAlignment(true);
2523
2524   }
2525
2526   public void removeRedundancyMenuItem_actionPerformed()
2527   {
2528     new RedundancyPanel(alignPanel);
2529   }
2530
2531   public void pairwiseAlignmentMenuItem_actionPerformed()
2532   {
2533     if (viewport.getSelectionGroup() != null
2534             && viewport.getSelectionGroup().getSize() > 1)
2535     {
2536       Frame frame = new Frame();
2537       frame.add(new PairwiseAlignPanel(alignPanel));
2538       jalview.bin.JalviewLite.addFrame(frame,
2539               MessageManager.getString("action.pairwise_alignment"), 600,
2540               500);
2541     }
2542   }
2543
2544   public void PCAMenuItem_actionPerformed()
2545   {
2546     // are the sequences aligned?
2547     if (!viewport.getAlignment().isAligned(false))
2548     {
2549       SequenceI current;
2550       int Width = viewport.getAlignment().getWidth();
2551
2552       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2553       {
2554         current = viewport.getAlignment().getSequenceAt(i);
2555
2556         if (current.getLength() < Width)
2557         {
2558           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2559         }
2560       }
2561       alignPanel.paintAlignment(true);
2562     }
2563
2564     if ((viewport.getSelectionGroup() != null
2565             && viewport.getSelectionGroup().getSize() < 4 && viewport
2566             .getSelectionGroup().getSize() > 0)
2567             || viewport.getAlignment().getHeight() < 4)
2568     {
2569       return;
2570     }
2571
2572     try
2573     {
2574       new PCAPanel(viewport);
2575     } catch (java.lang.OutOfMemoryError ex)
2576     {
2577     }
2578
2579   }
2580
2581   public void averageDistanceTreeMenuItem_actionPerformed()
2582   {
2583     NewTreePanel("AV", "PID", "Average distance tree using PID");
2584   }
2585
2586   public void neighbourTreeMenuItem_actionPerformed()
2587   {
2588     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2589   }
2590
2591   protected void njTreeBlosumMenuItem_actionPerformed()
2592   {
2593     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2594   }
2595
2596   protected void avTreeBlosumMenuItem_actionPerformed()
2597   {
2598     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2599   }
2600
2601   void NewTreePanel(String type, String pwType, String title)
2602   {
2603     // are the sequences aligned?
2604     if (!viewport.getAlignment().isAligned(false))
2605     {
2606       SequenceI current;
2607       int Width = viewport.getAlignment().getWidth();
2608
2609       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2610       {
2611         current = viewport.getAlignment().getSequenceAt(i);
2612
2613         if (current.getLength() < Width)
2614         {
2615           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2616         }
2617       }
2618       alignPanel.paintAlignment(true);
2619
2620     }
2621
2622     if ((viewport.getSelectionGroup() != null && viewport
2623             .getSelectionGroup().getSize() > 1)
2624             || (viewport.getAlignment().getHeight() > 1))
2625     {
2626       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2627
2628       addTreeMenuItem(tp, title);
2629
2630       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2631     }
2632   }
2633
2634   void loadTree_actionPerformed()
2635   {
2636     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2637     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2638     cap.setTreeImport();
2639     Frame frame = new Frame();
2640     frame.add(cap);
2641     jalview.bin.JalviewLite.addFrame(frame,
2642             MessageManager.getString("label.paste_newick_file"), 400, 300);
2643   }
2644
2645   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2646   {
2647     TreePanel tp = new TreePanel(alignPanel, treeFile,
2648             MessageManager.getString("label.load_tree_from_file"), tree);
2649     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2650     addTreeMenuItem(tp, treeFile);
2651   }
2652
2653   /**
2654    * sort the alignment using the given treePanel
2655    *
2656    * @param treePanel
2657    *          tree used to sort view
2658    * @param title
2659    *          string used for undo event name
2660    */
2661   public void sortByTree(TreePanel treePanel, String title)
2662   {
2663     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2664     AlignmentSorter
2665             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2666     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2667     // HistoryItem.SORT));
2668     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2669             "label.order_by_params", new String[]
2670             { title }), oldOrder, viewport.getAlignment()));
2671     alignPanel.paintAlignment(true);
2672   }
2673
2674   /**
2675    * Do any automatic reordering of the alignment and add the necessary bits to
2676    * the menu structure for the new tree
2677    *
2678    * @param treePanel
2679    * @param title
2680    */
2681   protected void addTreeMenuItem(final TreePanel treePanel,
2682           final String title)
2683   {
2684     final MenuItem item = new MenuItem(title);
2685     sortByTreeMenu.add(item);
2686     item.addActionListener(new java.awt.event.ActionListener()
2687     {
2688       @Override
2689       public void actionPerformed(ActionEvent evt)
2690       {
2691         sortByTree(treePanel, title); // treePanel.getTitle());
2692       }
2693     });
2694
2695     treePanel.addWindowListener(new WindowAdapter()
2696     {
2697       @Override
2698       public void windowOpened(WindowEvent e)
2699       {
2700         if (viewport.sortByTree)
2701         {
2702           sortByTree(treePanel, title);
2703         }
2704         super.windowOpened(e);
2705       }
2706
2707       @Override
2708       public void windowClosing(WindowEvent e)
2709       {
2710         sortByTreeMenu.remove(item);
2711       };
2712     });
2713   }
2714
2715   public boolean sortBy(AlignmentOrder alorder, String undoname)
2716   {
2717     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2718     if (viewport.applet.debug)
2719     {
2720       System.err.println("Sorting " + alorder.getOrder().size()
2721               + " in alignment '" + getTitle() + "'");
2722     }
2723     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2724     if (undoname != null)
2725     {
2726       addHistoryItem(new OrderCommand(undoname, oldOrder,
2727               viewport.getAlignment()));
2728     }
2729     alignPanel.paintAlignment(true);
2730     return true;
2731   }
2732
2733   protected void documentation_actionPerformed()
2734   {
2735     alignPanel.av.applet.openJalviewHelpUrl();
2736   }
2737
2738   protected void about_actionPerformed()
2739   {
2740
2741     class AboutPanel extends Canvas
2742     {
2743       String version;
2744
2745       String builddate;
2746
2747       public AboutPanel(String version, String builddate)
2748       {
2749         this.version = version;
2750         this.builddate = builddate;
2751       }
2752
2753       @Override
2754       public void paint(Graphics g)
2755       {
2756         g.setColor(Color.white);
2757         g.fillRect(0, 0, getSize().width, getSize().height);
2758         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2759         FontMetrics fm = g.getFontMetrics();
2760         int fh = fm.getHeight();
2761         int y = 5, x = 7;
2762         g.setColor(Color.black);
2763         // TODO: update this text for each release or centrally store it for
2764         // lite and application
2765         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2766         g.drawString(MessageManager.formatMessage(
2767                 "label.jalviewLite_release", new String[]
2768                 { version }), x, y += fh);
2769         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2770         g.drawString(MessageManager.formatMessage(
2771                 "label.jaview_build_date", new String[]
2772                 { builddate }), x, y += fh);
2773         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2774         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2775                 x, y += fh * 1.5);
2776         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2777                 x + 50, y += fh + 8);
2778         g.drawString(
2779                 MessageManager.getString("label.jalview_dev_managers"), x,
2780                 y += fh);
2781         g.drawString(MessageManager
2782                 .getString("label.jalview_distribution_lists"), x, y += fh);
2783         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2784                 x, y += fh + 8);
2785         g.drawString(
2786                 MessageManager.getString("label.jalview_cite_1_authors"),
2787                 x, y += fh);
2788         g.drawString(
2789                 MessageManager.getString("label.jalview_cite_1_title"), x,
2790                 y += fh);
2791         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2792                 x, y += fh);
2793       }
2794     }
2795
2796     Frame frame = new Frame();
2797     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2798             .getBuildDate()));
2799     jalview.bin.JalviewLite.addFrame(frame,
2800             MessageManager.getString("label.jalview"), 580, 220);
2801
2802   }
2803
2804   public void showURL(String url, String target)
2805   {
2806     if (viewport.applet == null)
2807     {
2808       System.out.println("Not running as applet - no browser available.");
2809     }
2810     else
2811     {
2812       viewport.applet.showURL(url, target);
2813     }
2814   }
2815
2816   // ////////////////////////////////////////////////////////////////////////////////
2817   // JBuilder Graphics here
2818
2819   MenuBar alignFrameMenuBar = new MenuBar();
2820
2821   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2822
2823   MenuItem loadApplication = new MenuItem(
2824           MessageManager.getString("label.view_full_application"));
2825
2826   MenuItem loadTree = new MenuItem(
2827           MessageManager.getString("label.load_associated_tree"));
2828
2829   MenuItem loadAnnotations = new MenuItem(
2830           MessageManager.getString("label.load_features_annotations"));
2831
2832   MenuItem outputFeatures = new MenuItem(
2833           MessageManager.getString("label.export_features").concat("..."));
2834
2835   MenuItem outputAnnotations = new MenuItem(
2836           MessageManager.getString("label.export_annotations").concat("..."));
2837
2838   MenuItem closeMenuItem = new MenuItem(
2839           MessageManager.getString("action.close"));
2840
2841   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2842
2843   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2844
2845   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2846
2847   Menu calculateMenu = new Menu(
2848           MessageManager.getString("action.calculate"));
2849
2850   MenuItem selectAllSequenceMenuItem = new MenuItem(
2851           MessageManager.getString("action.select_all"));
2852
2853   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2854           MessageManager.getString("action.deselect_all"));
2855
2856   MenuItem invertSequenceMenuItem = new MenuItem(
2857           MessageManager.getString("action.invert_selection"));
2858
2859   MenuItem remove2LeftMenuItem = new MenuItem();
2860
2861   MenuItem remove2RightMenuItem = new MenuItem();
2862
2863   MenuItem removeGappedColumnMenuItem = new MenuItem();
2864
2865   MenuItem removeAllGapsMenuItem = new MenuItem();
2866
2867   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2868
2869   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2870
2871   MenuItem sortPairwiseMenuItem = new MenuItem();
2872
2873   MenuItem sortIDMenuItem = new MenuItem();
2874
2875   MenuItem sortLengthMenuItem = new MenuItem();
2876
2877   MenuItem sortGroupMenuItem = new MenuItem();
2878
2879   MenuItem removeRedundancyMenuItem = new MenuItem();
2880
2881   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2882
2883   MenuItem PCAMenuItem = new MenuItem();
2884
2885   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2886
2887   MenuItem neighbourTreeMenuItem = new MenuItem();
2888
2889   BorderLayout borderLayout1 = new BorderLayout();
2890
2891   public Label statusBar = new Label();
2892
2893   Menu outputTextboxMenu = new Menu();
2894
2895   MenuItem clustalColour = new MenuItem();
2896
2897   MenuItem zappoColour = new MenuItem();
2898
2899   MenuItem taylorColour = new MenuItem();
2900
2901   MenuItem hydrophobicityColour = new MenuItem();
2902
2903   MenuItem helixColour = new MenuItem();
2904
2905   MenuItem strandColour = new MenuItem();
2906
2907   MenuItem turnColour = new MenuItem();
2908
2909   MenuItem buriedColour = new MenuItem();
2910
2911   MenuItem purinePyrimidineColour = new MenuItem();
2912
2913   MenuItem RNAInteractionColour = new MenuItem();
2914
2915   MenuItem RNAHelixColour = new MenuItem();
2916
2917   MenuItem userDefinedColour = new MenuItem();
2918
2919   MenuItem PIDColour = new MenuItem();
2920
2921   MenuItem BLOSUM62Colour = new MenuItem();
2922
2923   MenuItem tcoffeeColour = new MenuItem();
2924
2925   MenuItem njTreeBlosumMenuItem = new MenuItem();
2926
2927   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2928
2929   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2930
2931   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2932
2933   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2934
2935   MenuItem alProperties = new MenuItem(
2936           MessageManager.getString("label.alignment_props"));
2937
2938   MenuItem overviewMenuItem = new MenuItem();
2939
2940   MenuItem undoMenuItem = new MenuItem();
2941
2942   MenuItem redoMenuItem = new MenuItem();
2943
2944   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2945
2946   MenuItem noColourmenuItem = new MenuItem();
2947
2948   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2949
2950   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2951
2952   MenuItem findMenuItem = new MenuItem();
2953
2954   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2955
2956   MenuItem nucleotideColour = new MenuItem();
2957
2958   MenuItem deleteGroups = new MenuItem();
2959
2960   MenuItem grpsFromSelection = new MenuItem();
2961
2962   MenuItem createGroup = new MenuItem();
2963
2964   MenuItem unGroup = new MenuItem();
2965
2966   MenuItem delete = new MenuItem();
2967
2968   MenuItem copy = new MenuItem();
2969
2970   MenuItem cut = new MenuItem();
2971
2972   Menu pasteMenu = new Menu();
2973
2974   MenuItem pasteNew = new MenuItem();
2975
2976   MenuItem pasteThis = new MenuItem();
2977
2978   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2979
2980   MenuItem font = new MenuItem();
2981
2982   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2983
2984   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2985
2986   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2987
2988   MenuItem modifyPID = new MenuItem();
2989
2990   MenuItem modifyConservation = new MenuItem();
2991
2992   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2993           "Autocalculate Consensus", true);
2994
2995   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2996           "Sort Alignment With New Tree", true);
2997
2998   Menu sortByTreeMenu = new Menu();
2999
3000   Menu sort = new Menu();
3001
3002   Menu calculate = new Menu();
3003
3004   MenuItem inputText = new MenuItem();
3005
3006   Menu helpMenu = new Menu();
3007
3008   MenuItem documentation = new MenuItem();
3009
3010   MenuItem about = new MenuItem();
3011
3012   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3013
3014   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3015
3016   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3017
3018   Menu autoAnnMenu = new Menu();
3019
3020   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3021
3022   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3023
3024   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3025
3026   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3027
3028   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3029
3030   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3031
3032   private void jbInit() throws Exception
3033   {
3034
3035     setMenuBar(alignFrameMenuBar);
3036
3037     MenuItem item;
3038
3039     // dynamically fill save as menu with available formats
3040     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3041     {
3042
3043       item = new MenuItem(
3044               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3045
3046       item.addActionListener(new java.awt.event.ActionListener()
3047       {
3048         @Override
3049         public void actionPerformed(ActionEvent e)
3050         {
3051           outputText_actionPerformed(e);
3052         }
3053       });
3054
3055       outputTextboxMenu.add(item);
3056     }
3057     closeMenuItem.addActionListener(this);
3058     loadApplication.addActionListener(this);
3059
3060     loadTree.addActionListener(this);
3061     loadAnnotations.addActionListener(this);
3062     outputFeatures.addActionListener(this);
3063     outputAnnotations.addActionListener(this);
3064     selectAllSequenceMenuItem.addActionListener(this);
3065     deselectAllSequenceMenuItem.addActionListener(this);
3066     invertSequenceMenuItem.addActionListener(this);
3067     remove2LeftMenuItem.setLabel(MessageManager
3068             .getString("action.remove_left"));
3069     remove2LeftMenuItem.addActionListener(this);
3070     remove2RightMenuItem.setLabel(MessageManager
3071             .getString("action.remove_right"));
3072     remove2RightMenuItem.addActionListener(this);
3073     removeGappedColumnMenuItem.setLabel(MessageManager
3074             .getString("action.remove_empty_columns"));
3075     removeGappedColumnMenuItem.addActionListener(this);
3076     removeAllGapsMenuItem.setLabel(MessageManager
3077             .getString("action.remove_all_gaps"));
3078     removeAllGapsMenuItem.addActionListener(this);
3079     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3080     viewBoxesMenuItem.setState(true);
3081     viewBoxesMenuItem.addItemListener(this);
3082     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3083     viewTextMenuItem.setState(true);
3084     viewTextMenuItem.addItemListener(this);
3085     sortPairwiseMenuItem.setLabel(MessageManager
3086             .getString("action.by_pairwise_id"));
3087     sortPairwiseMenuItem.addActionListener(this);
3088     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3089     sortIDMenuItem.addActionListener(this);
3090     sortLengthMenuItem.setLabel(MessageManager
3091             .getString("action.by_length"));
3092     sortLengthMenuItem.addActionListener(this);
3093     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3094     sortGroupMenuItem.addActionListener(this);
3095     removeRedundancyMenuItem.setLabel(MessageManager
3096             .getString("action.remove_redundancy").concat("..."));
3097     removeRedundancyMenuItem.addActionListener(this);
3098     pairwiseAlignmentMenuItem.setLabel(MessageManager
3099             .getString("action.pairwise_alignment"));
3100     pairwiseAlignmentMenuItem.addActionListener(this);
3101     PCAMenuItem.setLabel(MessageManager
3102             .getString("label.principal_component_analysis"));
3103     PCAMenuItem.addActionListener(this);
3104     averageDistanceTreeMenuItem.setLabel(MessageManager
3105             .getString("label.average_distance_identity"));
3106     averageDistanceTreeMenuItem.addActionListener(this);
3107     neighbourTreeMenuItem.setLabel(MessageManager
3108             .getString("label.neighbour_joining_identity"));
3109     neighbourTreeMenuItem.addActionListener(this);
3110     statusBar.setBackground(Color.white);
3111     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3112     statusBar.setText(MessageManager.getString("label.status_bar"));
3113     outputTextboxMenu.setLabel(MessageManager
3114             .getString("label.out_to_textbox"));
3115     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3116
3117     clustalColour.addActionListener(this);
3118     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3119     zappoColour.addActionListener(this);
3120     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3121     taylorColour.addActionListener(this);
3122     hydrophobicityColour.setLabel(MessageManager
3123             .getString("label.hydrophobicity"));
3124     hydrophobicityColour.addActionListener(this);
3125     helixColour
3126             .setLabel(MessageManager.getString("label.helix_propensity"));
3127     helixColour.addActionListener(this);
3128     strandColour.setLabel(MessageManager
3129             .getString("label.strand_propensity"));
3130     strandColour.addActionListener(this);
3131     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3132     turnColour.addActionListener(this);
3133     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3134     buriedColour.addActionListener(this);
3135     purinePyrimidineColour.setLabel(MessageManager
3136             .getString("label.purine_pyrimidine"));
3137     purinePyrimidineColour.addActionListener(this);
3138     RNAInteractionColour.setLabel(MessageManager
3139             .getString("label.rna_interaction"));
3140     RNAInteractionColour.addActionListener(this);
3141     RNAHelixColour.setLabel(MessageManager
3142             .getString("action.by_rna_helixes"));
3143     RNAHelixColour.addActionListener(this);
3144     userDefinedColour.setLabel(MessageManager
3145             .getString("action.user_defined"));
3146     userDefinedColour.addActionListener(this);
3147     PIDColour.setLabel(MessageManager
3148             .getString("label.percentage_identity"));
3149     PIDColour.addActionListener(this);
3150     BLOSUM62Colour.setLabel(MessageManager
3151             .getString("label.blosum62_score"));
3152     BLOSUM62Colour.addActionListener(this);
3153     tcoffeeColour
3154             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3155     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3156                                      // provided
3157     tcoffeeColour.addActionListener(this);
3158     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3159             .getString("label.average_distance_bloslum62"));
3160     avDistanceTreeBlosumMenuItem.addActionListener(this);
3161     njTreeBlosumMenuItem.setLabel(MessageManager
3162             .getString("label.neighbour_blosum62"));
3163     njTreeBlosumMenuItem.addActionListener(this);
3164     annotationPanelMenuItem.setLabel(MessageManager
3165             .getString("label.show_annotations"));
3166     annotationPanelMenuItem.addItemListener(this);
3167     colourTextMenuItem.setLabel(MessageManager
3168             .getString("label.colour_text"));
3169     colourTextMenuItem.addItemListener(this);
3170     displayNonconservedMenuItem.setLabel(MessageManager
3171             .getString("label.show_non_conversed"));
3172     displayNonconservedMenuItem.addItemListener(this);
3173     alProperties.addActionListener(this);
3174     overviewMenuItem.setLabel(MessageManager
3175             .getString("label.overview_window"));
3176     overviewMenuItem.addActionListener(this);
3177     undoMenuItem.setEnabled(false);
3178     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3179     undoMenuItem.addActionListener(this);
3180     redoMenuItem.setEnabled(false);
3181     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3182     redoMenuItem.addActionListener(this);
3183     conservationMenuItem.setLabel(MessageManager
3184             .getString("action.by_conservation"));
3185     conservationMenuItem.addItemListener(this);
3186     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3187     noColourmenuItem.addActionListener(this);
3188     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3189     wrapMenuItem.addItemListener(this);
3190     renderGapsMenuItem.setLabel(MessageManager
3191             .getString("action.show_gaps"));
3192     renderGapsMenuItem.setState(true);
3193     renderGapsMenuItem.addItemListener(this);
3194     findMenuItem.setLabel(MessageManager.getString("action.find"));
3195     findMenuItem.addActionListener(this);
3196     abovePIDThreshold.setLabel(MessageManager
3197             .getString("label.above_identity_threshold"));
3198     abovePIDThreshold.addItemListener(this);
3199     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3200     nucleotideColour.addActionListener(this);
3201     deleteGroups.setLabel(MessageManager
3202             .getString("action.undefine_groups"));
3203     deleteGroups.addActionListener(this);
3204     grpsFromSelection.setLabel(MessageManager
3205             .getString("action.make_groups_selection"));
3206     grpsFromSelection.addActionListener(this);
3207     createGroup.setLabel(MessageManager.getString("action.create_group"));
3208     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3209     copy.setLabel(MessageManager.getString("action.copy"));
3210     copy.addActionListener(this);
3211     cut.setLabel(MessageManager.getString("action.cut"));
3212     cut.addActionListener(this);
3213     delete.setLabel(MessageManager.getString("action.delete"));
3214     delete.addActionListener(this);
3215     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3216     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3217     pasteNew.addActionListener(this);
3218     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3219     pasteThis.addActionListener(this);
3220     applyToAllGroups.setLabel(MessageManager
3221             .getString("label.apply_colour_to_all_groups"));
3222     applyToAllGroups.setState(true);
3223     applyToAllGroups.addItemListener(this);
3224     font.setLabel(MessageManager.getString("action.font"));
3225     font.addActionListener(this);
3226     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3227     scaleAbove.setState(true);
3228     scaleAbove.setEnabled(false);
3229     scaleAbove.addItemListener(this);
3230     scaleLeft.setEnabled(false);
3231     scaleLeft.setState(true);
3232     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3233     scaleLeft.addItemListener(this);
3234     scaleRight.setEnabled(false);
3235     scaleRight.setState(true);
3236     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3237     scaleRight.addItemListener(this);
3238     modifyPID.setLabel(MessageManager
3239             .getString("label.modify_identity_thereshold"));
3240     modifyPID.addActionListener(this);
3241     modifyConservation.setLabel(MessageManager
3242             .getString("label.modify_conservation_thereshold"));
3243     modifyConservation.addActionListener(this);
3244     sortByTreeMenu.setLabel(MessageManager
3245             .getString("action.by_tree_order"));
3246     sort.setLabel(MessageManager.getString("action.sort"));
3247     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3248     autoCalculate.addItemListener(this);
3249     sortByTree.addItemListener(this);
3250     inputText
3251             .setLabel(MessageManager.getString("label.input_from_textbox"));
3252     inputText.addActionListener(this);
3253     centreColumnLabelFlag.setLabel(MessageManager
3254             .getString("label.centre_column_labels"));
3255     centreColumnLabelFlag.addItemListener(this);
3256     followMouseOverFlag.setLabel(MessageManager
3257             .getString("label.automatic_scrolling"));
3258     followMouseOverFlag.addItemListener(this);
3259     helpMenu.setLabel(MessageManager.getString("action.help"));
3260     documentation.setLabel(MessageManager.getString("label.documentation"));
3261     documentation.addActionListener(this);
3262
3263     about.setLabel(MessageManager.getString("label.about"));
3264     about.addActionListener(this);
3265     seqLimits.setState(true);
3266     seqLimits.setLabel(MessageManager
3267             .getString("label.show_sequence_limits"));
3268     seqLimits.addItemListener(this);
3269     featureSettings.setLabel(MessageManager
3270             .getString("label.feature_settings"));
3271     featureSettings.addActionListener(this);
3272     sequenceFeatures.setLabel(MessageManager
3273             .getString("label.sequence_features"));
3274     sequenceFeatures.addItemListener(this);
3275     sequenceFeatures.setState(false);
3276     annotationColour.setLabel(MessageManager
3277             .getString("action.by_annotation"));
3278     annotationColour.addActionListener(this);
3279
3280     annotationColumnSelection.setLabel("Select by Annotation");
3281     annotationColumnSelection.addActionListener(this);
3282
3283     invertSequenceMenuItem.setLabel(MessageManager
3284             .getString("action.invert_sequence_selection"));
3285     invertColSel.setLabel(MessageManager
3286             .getString("action.invert_column_selection"));
3287     menu1.setLabel(MessageManager.getString("action.show"));
3288     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3289     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3290     menu2.setLabel(MessageManager.getString("action.hide"));
3291     hideColumns
3292             .setLabel(MessageManager.getString("label.selected_columns"));
3293     hideSequences.setLabel(MessageManager
3294             .getString("label.selected_sequences"));
3295     hideAllButSelection.setLabel(MessageManager
3296             .getString("label.all_but_selected_region"));
3297     hideAllSelection.setLabel(MessageManager
3298             .getString("label.selected_region"));
3299     showAllHidden.setLabel(MessageManager
3300             .getString("label.all_sequences_columns"));
3301     showGroupConsensus.setLabel(MessageManager
3302             .getString("label.group_consensus"));
3303     showGroupConservation.setLabel(MessageManager
3304             .getString("label.group_conservation"));
3305     showConsensusHistogram.setLabel(MessageManager
3306             .getString("label.show_consensus_histogram"));
3307     showSequenceLogo.setLabel(MessageManager
3308             .getString("label.show_consensus_logo"));
3309     normSequenceLogo.setLabel(MessageManager
3310             .getString("label.norm_consensus_logo"));
3311     applyAutoAnnotationSettings.setLabel(MessageManager
3312             .getString("label.apply_all_groups"));
3313     applyAutoAnnotationSettings.setState(true);
3314     autoAnnMenu.setLabel(MessageManager
3315             .getString("label.autocalculated_annotation"));
3316
3317     invertColSel.addActionListener(this);
3318     showColumns.addActionListener(this);
3319     showSeqs.addActionListener(this);
3320     hideColumns.addActionListener(this);
3321     hideSequences.addActionListener(this);
3322     hideAllButSelection.addActionListener(this);
3323     hideAllSelection.addActionListener(this);
3324     showAllHidden.addActionListener(this);
3325     showGroupConsensus.addItemListener(this);
3326     showGroupConservation.addItemListener(this);
3327     showConsensusHistogram.addItemListener(this);
3328     showSequenceLogo.addItemListener(this);
3329     normSequenceLogo.addItemListener(this);
3330
3331     applyAutoAnnotationSettings.addItemListener(this);
3332     formatMenu.setLabel(MessageManager.getString("action.format"));
3333     selectMenu.setLabel(MessageManager.getString("action.select"));
3334     newView.setLabel(MessageManager.getString("action.new_view"));
3335     newView.addActionListener(this);
3336     alignFrameMenuBar.add(fileMenu);
3337     alignFrameMenuBar.add(editMenu);
3338     alignFrameMenuBar.add(selectMenu);
3339     alignFrameMenuBar.add(viewMenu);
3340     alignFrameMenuBar.add(formatMenu);
3341     alignFrameMenuBar.add(colourMenu);
3342     alignFrameMenuBar.add(calculateMenu);
3343     alignFrameMenuBar.add(helpMenu);
3344
3345     fileMenu.add(inputText);
3346     fileMenu.add(loadTree);
3347     fileMenu.add(loadAnnotations);
3348
3349     fileMenu.addSeparator();
3350     fileMenu.add(outputTextboxMenu);
3351     fileMenu.add(outputFeatures);
3352     fileMenu.add(outputAnnotations);
3353
3354     if (jalviewServletURL != null)
3355     {
3356       fileMenu.add(loadApplication);
3357     }
3358
3359     fileMenu.addSeparator();
3360     fileMenu.add(closeMenuItem);
3361
3362     editMenu.add(undoMenuItem);
3363     editMenu.add(redoMenuItem);
3364     editMenu.add(cut);
3365     editMenu.add(copy);
3366     editMenu.add(pasteMenu);
3367     editMenu.add(delete);
3368     editMenu.addSeparator();
3369     editMenu.add(remove2LeftMenuItem);
3370     editMenu.add(remove2RightMenuItem);
3371     editMenu.add(removeGappedColumnMenuItem);
3372     editMenu.add(removeAllGapsMenuItem);
3373     editMenu.add(removeRedundancyMenuItem);
3374     viewMenu.add(newView);
3375     viewMenu.addSeparator();
3376     viewMenu.add(menu1);
3377     viewMenu.add(menu2);
3378     viewMenu.addSeparator();
3379     viewMenu.add(followMouseOverFlag);
3380     viewMenu.add(annotationPanelMenuItem);
3381     autoAnnMenu.add(applyAutoAnnotationSettings);
3382     autoAnnMenu.add(showConsensusHistogram);
3383     autoAnnMenu.add(showSequenceLogo);
3384     autoAnnMenu.add(normSequenceLogo);
3385     autoAnnMenu.addSeparator();
3386     autoAnnMenu.add(showGroupConservation);
3387     autoAnnMenu.add(showGroupConsensus);
3388     viewMenu.add(autoAnnMenu);
3389     viewMenu.addSeparator();
3390     viewMenu.add(sequenceFeatures);
3391     viewMenu.add(featureSettings);
3392     viewMenu.addSeparator();
3393     viewMenu.add(alProperties);
3394     viewMenu.addSeparator();
3395     viewMenu.add(overviewMenuItem);
3396     colourMenu.add(applyToAllGroups);
3397     colourMenu.addSeparator();
3398     colourMenu.add(noColourmenuItem);
3399     colourMenu.add(clustalColour);
3400     colourMenu.add(BLOSUM62Colour);
3401     colourMenu.add(PIDColour);
3402     colourMenu.add(zappoColour);
3403     colourMenu.add(taylorColour);
3404     colourMenu.add(hydrophobicityColour);
3405     colourMenu.add(helixColour);
3406     colourMenu.add(strandColour);
3407     colourMenu.add(turnColour);
3408     colourMenu.add(buriedColour);
3409     colourMenu.add(nucleotideColour);
3410     colourMenu.add(purinePyrimidineColour);
3411     // colourMenu.add(RNAInteractionColour);
3412     colourMenu.add(tcoffeeColour);
3413     colourMenu.add(userDefinedColour);
3414     colourMenu.addSeparator();
3415     colourMenu.add(conservationMenuItem);
3416     colourMenu.add(modifyConservation);
3417     colourMenu.add(abovePIDThreshold);
3418     colourMenu.add(modifyPID);
3419     colourMenu.add(annotationColour);
3420     colourMenu.add(RNAHelixColour);
3421     calculateMenu.add(sort);
3422     calculateMenu.add(calculate);
3423     calculateMenu.addSeparator();
3424     calculateMenu.add(pairwiseAlignmentMenuItem);
3425     calculateMenu.add(PCAMenuItem);
3426     calculateMenu.add(autoCalculate);
3427     calculateMenu.add(sortByTree);
3428     this.add(statusBar, BorderLayout.SOUTH);
3429     pasteMenu.add(pasteNew);
3430     pasteMenu.add(pasteThis);
3431     sort.add(sortIDMenuItem);
3432     sort.add(sortLengthMenuItem);
3433     sort.add(sortByTreeMenu);
3434     sort.add(sortGroupMenuItem);
3435     sort.add(sortPairwiseMenuItem);
3436     calculate.add(averageDistanceTreeMenuItem);
3437     calculate.add(neighbourTreeMenuItem);
3438     calculate.add(avDistanceTreeBlosumMenuItem);
3439     calculate.add(njTreeBlosumMenuItem);
3440     helpMenu.add(documentation);
3441     helpMenu.add(about);
3442     menu1.add(showColumns);
3443     menu1.add(showSeqs);
3444     menu1.add(showAllHidden);
3445     menu2.add(hideColumns);
3446     menu2.add(hideSequences);
3447     menu2.add(hideAllSelection);
3448     menu2.add(hideAllButSelection);
3449     formatMenu.add(font);
3450     formatMenu.add(seqLimits);
3451     formatMenu.add(wrapMenuItem);
3452     formatMenu.add(scaleAbove);
3453     formatMenu.add(scaleLeft);
3454     formatMenu.add(scaleRight);
3455     formatMenu.add(viewBoxesMenuItem);
3456     formatMenu.add(viewTextMenuItem);
3457     formatMenu.add(colourTextMenuItem);
3458     formatMenu.add(displayNonconservedMenuItem);
3459     formatMenu.add(renderGapsMenuItem);
3460     formatMenu.add(centreColumnLabelFlag);
3461     selectMenu.add(findMenuItem);
3462     selectMenu.addSeparator();
3463     selectMenu.add(selectAllSequenceMenuItem);
3464     selectMenu.add(deselectAllSequenceMenuItem);
3465     selectMenu.add(invertSequenceMenuItem);
3466     selectMenu.add(invertColSel);
3467     selectMenu.add(createGroup);
3468     selectMenu.add(unGroup);
3469     selectMenu.add(grpsFromSelection);
3470     selectMenu.add(deleteGroups);
3471     selectMenu.add(annotationColumnSelection);
3472
3473   }
3474
3475   public void setStatus(String string)
3476   {
3477     statusBar.setText(string);
3478   };
3479
3480   MenuItem featureSettings = new MenuItem();
3481
3482   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3483
3484   MenuItem annotationColour = new MenuItem();
3485
3486   MenuItem annotationColumnSelection = new MenuItem();
3487
3488   MenuItem invertColSel = new MenuItem();
3489
3490   Menu menu1 = new Menu();
3491
3492   MenuItem showColumns = new MenuItem();
3493
3494   MenuItem showSeqs = new MenuItem();
3495
3496   Menu menu2 = new Menu();
3497
3498   MenuItem hideColumns = new MenuItem();
3499
3500   MenuItem hideSequences = new MenuItem();
3501
3502   MenuItem hideAllButSelection = new MenuItem();
3503
3504   MenuItem hideAllSelection = new MenuItem();
3505
3506   MenuItem showAllHidden = new MenuItem();
3507
3508   Menu formatMenu = new Menu();
3509
3510   Menu selectMenu = new Menu();
3511
3512   MenuItem newView = new MenuItem();
3513
3514   /**
3515    * Attach the alignFrame panels after embedding menus, if necessary. This used
3516    * to be called setEmbedded, but is now creates the dropdown menus in a
3517    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3518    *
3519    * @param reallyEmbedded
3520    *          true to attach the view to the applet area on the page rather than
3521    *          in a new window
3522    */
3523   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3524   {
3525     if (reallyEmbedded)
3526     {
3527       // ////
3528       // Explicly build the embedded menu panel for the on-page applet
3529       //
3530       // view cannot be closed if its actually on the page
3531       fileMenu.remove(closeMenuItem);
3532       fileMenu.remove(3); // Remove Seperator
3533       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3534               Font.PLAIN, 11, false); // use our own fonts.
3535       // and actually add the components to the applet area
3536       viewport.applet.setLayout(new BorderLayout());
3537       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3538       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3539       alignPanel.setSize(viewport.applet.getSize().width,
3540               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3541                       - statusBar.HEIGHT);
3542       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3543       final AlignFrame me = this;
3544       viewport.applet.addFocusListener(new FocusListener()
3545       {
3546
3547         @Override
3548         public void focusLost(FocusEvent e)
3549         {
3550           if (me.viewport.applet.currentAlignFrame == me)
3551           {
3552             me.viewport.applet.currentAlignFrame = null;
3553           }
3554         }
3555
3556         @Override
3557         public void focusGained(FocusEvent e)
3558         {
3559           me.viewport.applet.currentAlignFrame = me;
3560         }
3561       });
3562       viewport.applet.validate();
3563     }
3564     else
3565     {
3566       // //////
3567       // test and embed menu bar if necessary.
3568       //
3569       if (embedMenuIfNeeded(alignPanel))
3570       {
3571         // adjust for status bar height too
3572         alignPanel.setSize(getSize().width, getSize().height
3573                 - statusBar.HEIGHT);
3574       }
3575       add(statusBar, BorderLayout.SOUTH);
3576       add(alignPanel, BorderLayout.CENTER);
3577       // and register with the applet so it can pass external API calls to us
3578       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3579               DEFAULT_HEIGHT);
3580     }
3581   }
3582
3583   /**
3584    * create a new binding between structures in an existing jmol viewer instance
3585    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3586    * this does not open a new Jmol window, or modify the display of the
3587    * structures in the original jmol window. Note This method doesn't work
3588    * without an additional javascript library to exchange messages between the
3589    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3590    *
3591    * @param viewer
3592    *          JmolViewer instance
3593    * @param sequenceIds
3594    *          - sequence Ids to search for associations
3595    */
3596   public SequenceStructureBinding addStructureViewInstance(
3597           Object jmolviewer, String[] sequenceIds)
3598   {
3599     org.jmol.api.JmolViewer viewer = null;
3600     try
3601     {
3602       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3603     } catch (ClassCastException ex)
3604     {
3605       System.err.println("Unsupported viewer object :"
3606               + jmolviewer.getClass());
3607     }
3608     if (viewer == null)
3609     {
3610       System.err.println("Can't use this object as a structure viewer:"
3611               + jmolviewer.getClass());
3612       return null;
3613     }
3614     SequenceI[] seqs = null;
3615     if (sequenceIds == null || sequenceIds.length == 0)
3616     {
3617       seqs = viewport.getAlignment().getSequencesArray();
3618     }
3619     else
3620     {
3621       Vector sqi = new Vector();
3622       AlignmentI al = viewport.getAlignment();
3623       for (int sid = 0; sid < sequenceIds.length; sid++)
3624       {
3625         SequenceI sq = al.findName(sequenceIds[sid]);
3626         if (sq != null)
3627         {
3628           sqi.addElement(sq);
3629         }
3630       }
3631       if (sqi.size() > 0)
3632       {
3633         seqs = new SequenceI[sqi.size()];
3634         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3635         {
3636           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3637         }
3638       }
3639       else
3640       {
3641         return null;
3642       }
3643     }
3644     AAStructureBindingModel jmv = null;
3645     // TODO: search for a jmv that involves viewer
3646     if (jmv == null)
3647     { // create a new viewer/jalview binding.
3648       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3649       { seqs });
3650     }
3651     return jmv;
3652
3653   }
3654
3655   /**
3656    * bind a pdb file to a sequence in the current view
3657    *
3658    * @param sequenceId
3659    *          - sequenceId within the dataset.
3660    * @param pdbEntryString
3661    *          - the short name for the PDB file
3662    * @param pdbFile
3663    *          - pdb file - either a URL or a valid PDB file.
3664    * @return true if binding was as success TODO: consider making an exception
3665    *         structure for indicating when PDB parsing or sequenceId location
3666    *         fails.
3667    */
3668   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3669           String pdbFile)
3670   {
3671     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3672     boolean needtoadd = false;
3673     if (toaddpdb != null)
3674     {
3675       Vector pdbe = toaddpdb.getPDBId();
3676       PDBEntry pdbentry = null;
3677       if (pdbe != null && pdbe.size() > 0)
3678       {
3679         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3680         {
3681           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3682           if (!pdbentry.getId().equals(pdbEntryString)
3683                   && !pdbentry.getFile().equals(pdbFile))
3684           {
3685             pdbentry = null;
3686           }
3687           else
3688           {
3689             continue;
3690           }
3691         }
3692       }
3693       if (pdbentry == null)
3694       {
3695         pdbentry = new PDBEntry();
3696         pdbentry.setId(pdbEntryString);
3697         pdbentry.setFile(pdbFile);
3698         needtoadd = true; // add this new entry to sequence.
3699       }
3700       // resolve data source
3701       // TODO: this code should be a refactored to an io package
3702       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3703       if (protocol == null)
3704       {
3705         return false;
3706       }
3707       if (needtoadd)
3708       {
3709         // make a note of the access mode and add
3710         if (pdbentry.getProperty() == null)
3711         {
3712           pdbentry.setProperty(new Hashtable());
3713         }
3714         pdbentry.getProperty().put("protocol", protocol);
3715         toaddpdb.addPDBId(pdbentry);
3716         alignPanel.getStructureSelectionManager()
3717                 .registerPDBEntry(pdbentry);
3718       }
3719     }
3720     return true;
3721   }
3722
3723   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3724   {
3725     if (seqs != null)
3726     {
3727       Vector sequences = new Vector();
3728       for (int i = 0; i < seqs.length; i++)
3729       {
3730         if (seqs[i] != null)
3731         {
3732           sequences.addElement(new Object[]
3733           { seqs[i], (chains != null) ? chains[i] : null });
3734         }
3735       }
3736       seqs = new SequenceI[sequences.size()];
3737       chains = new String[sequences.size()];
3738       for (int i = 0, isize = sequences.size(); i < isize; i++)
3739       {
3740         Object[] oj = (Object[]) sequences.elementAt(i);
3741
3742         seqs[i] = (SequenceI) oj[0];
3743         chains[i] = (String) oj[1];
3744       }
3745     }
3746     return new Object[]
3747     { seqs, chains };
3748
3749   }
3750
3751   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3752           SequenceI[] seqs, String[] chains, String protocol)
3753   {
3754     // Scrub any null sequences from the array
3755     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3756     seqs = (SequenceI[]) sqch[0];
3757     chains = (String[]) sqch[1];
3758     if (seqs == null || seqs.length == 0)
3759     {
3760       System.err
3761               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3762     }
3763     if (protocol == null || protocol.trim().length() == 0
3764             || protocol.equals("null"))
3765     {
3766       protocol = (String) pdb.getProperty().get("protocol");
3767       if (protocol == null)
3768       {
3769         System.err.println("Couldn't work out protocol to open structure: "
3770                 + pdb.getId());
3771         return;
3772       }
3773     }
3774     if (applet.useXtrnalSviewer)
3775     {
3776       // register the association(s) and quit, don't create any windows.
3777       if (StructureSelectionManager.getStructureSelectionManager(applet)
3778               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3779       {
3780         System.err.println("Failed to map " + pdb.getFile() + " ("
3781                 + protocol + ") to any sequences");
3782       }
3783       return;
3784     }
3785     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3786     {
3787       // can only do alignments with Jmol
3788       // find the last jmol window assigned to this alignment
3789       jalview.appletgui.AppletJmol ajm = null, tajm;
3790       Vector jmols = applet
3791               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3792       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3793       {
3794         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3795         if (tajm.ap.alignFrame == this)
3796         {
3797           ajm = tajm;
3798           break;
3799         }
3800       }
3801       if (ajm != null)
3802       {
3803         System.err
3804                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3805         // try and add the pdb structure
3806         // ajm.addS
3807         ajm = null;
3808       }
3809     }
3810     // otherwise, create a new window
3811     if (applet.jmolAvailable)
3812     {
3813       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3814               protocol);
3815       applet.lastFrameX += 40;
3816       applet.lastFrameY += 40;
3817     }
3818     else
3819     {
3820       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3821     }
3822
3823   }
3824
3825   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3826           SequenceI[][] seqs, String[][] chains, String[] protocols)
3827   {
3828     // TODO Auto-generated method stub
3829     System.err.println("Aligned Structure View: Not yet implemented.");
3830   }
3831
3832   /**
3833    * modify the current selection, providing the user has not made a selection
3834    * already.
3835    *
3836    * @param sel
3837    *          - sequences from this alignment
3838    * @param csel
3839    *          - columns to be selected on the alignment
3840    */
3841   public void select(SequenceGroup sel, ColumnSelection csel)
3842   {
3843     alignPanel.seqPanel.selection(sel, csel, null);
3844   }
3845
3846   public void scrollTo(int row, int column)
3847   {
3848     alignPanel.seqPanel.scrollTo(row, column);
3849   }
3850
3851   public void scrollToRow(int row)
3852   {
3853     alignPanel.seqPanel.scrollToRow(row);
3854   }
3855
3856   public void scrollToColumn(int column)
3857   {
3858     alignPanel.seqPanel.scrollToColumn(column);
3859   }
3860
3861   /**
3862    * @return the alignments unique ID.
3863    */
3864   public String getSequenceSetId()
3865   {
3866     return viewport.getSequenceSetId();
3867   }
3868
3869   /**
3870    * Load the (T-Coffee) score file from the specified url
3871    *
3872    * @param source
3873    *          File/URL/T-COFFEE score file contents
3874    * @throws IOException
3875    * @return true if alignment was annotated with data from source
3876    */
3877   public boolean loadScoreFile(String source) throws IOException
3878   {
3879
3880     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3881             AppletFormatAdapter.checkProtocol(source));
3882     if (!file.isValid())
3883     {
3884       // TODO: raise dialog for gui
3885       System.err.println("Problems parsing T-Coffee scores: "
3886               + file.getWarningMessage());
3887       System.err.println("Origin was:\n" + source);
3888       return false;
3889     }
3890
3891     /*
3892      * check that the score matrix matches the alignment dimensions
3893      */
3894     AlignmentI aln;
3895     if ((aln = viewport.getAlignment()) != null
3896             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3897                     .getWidth()))
3898     {
3899       // TODO: raise a dialog box here rather than bomb out.
3900       System.err
3901               .println("The scores matrix does not match the alignment dimensions");
3902
3903     }
3904
3905     // TODO add parameter to indicate if matching should be done
3906     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3907     {
3908       alignPanel.fontChanged();
3909       tcoffeeColour.setEnabled(true);
3910       // switch to this color
3911       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3912       return true;
3913     }
3914     else
3915     {
3916       System.err.println("Problems resolving T-Coffee scores:");
3917       if (file.getWarningMessage() != null)
3918       {
3919         System.err.println(file.getWarningMessage());
3920       }
3921     }
3922     return false;
3923   }
3924
3925 }