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