src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.appletgui;
  20
  21 import jalview.analysis.AlignmentSorter;
  22 import jalview.analysis.Conservation;
  23 import jalview.api.AlignViewControllerGuiI;
  24 import jalview.api.AlignViewControllerI;
  25 import jalview.api.SequenceStructureBinding;
  26 import jalview.bin.JalviewLite;
  27 import jalview.commands.CommandI;
  28 import jalview.commands.EditCommand;
  29 import jalview.commands.OrderCommand;
  30 import jalview.commands.RemoveGapColCommand;
  31 import jalview.commands.RemoveGapsCommand;
  32 import jalview.commands.SlideSequencesCommand;
  33 import jalview.commands.TrimRegionCommand;
  34 import jalview.datamodel.Alignment;
  35 import jalview.datamodel.AlignmentI;
  36 import jalview.datamodel.AlignmentOrder;
  37 import jalview.datamodel.ColumnSelection;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.Sequence;
  40 import jalview.datamodel.SequenceGroup;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.io.AnnotationFile;
  43 import jalview.io.AppletFormatAdapter;
  44 import jalview.io.FeaturesFile;
  45 import jalview.io.TCoffeeScoreFile;
  46 import jalview.schemes.Blosum62ColourScheme;
  47 import jalview.schemes.BuriedColourScheme;
  48 import jalview.schemes.ClustalxColourScheme;
  49 import jalview.schemes.ColourSchemeI;
  50 import jalview.schemes.HelixColourScheme;
  51 import jalview.schemes.HydrophobicColourScheme;
  52 import jalview.schemes.NucleotideColourScheme;
  53 import jalview.schemes.PIDColourScheme;
  54 import jalview.schemes.PurinePyrimidineColourScheme;
  55 import jalview.schemes.RNAHelicesColourChooser;
  56 import jalview.schemes.ResidueProperties;
  57 import jalview.schemes.StrandColourScheme;
  58 import jalview.schemes.TCoffeeColourScheme;
  59 import jalview.schemes.TaylorColourScheme;
  60 import jalview.schemes.TurnColourScheme;
  61 import jalview.schemes.ZappoColourScheme;
  62 import jalview.structure.StructureSelectionManager;
  63 import jalview.util.MessageManager;
  64
  65 import java.awt.BorderLayout;
  66 import java.awt.Canvas;
  67 import java.awt.CheckboxMenuItem;
  68 import java.awt.Color;
  69 import java.awt.Font;
  70 import java.awt.FontMetrics;
  71 import java.awt.Frame;
  72 import java.awt.Graphics;
  73 import java.awt.Label;
  74 import java.awt.Menu;
  75 import java.awt.MenuBar;
  76 import java.awt.MenuItem;
  77 import java.awt.event.ActionEvent;
  78 import java.awt.event.ActionListener;
  79 import java.awt.event.FocusEvent;
  80 import java.awt.event.FocusListener;
  81 import java.awt.event.ItemEvent;
  82 import java.awt.event.ItemListener;
  83 import java.awt.event.KeyEvent;
  84 import java.awt.event.KeyListener;
  85 import java.awt.event.WindowAdapter;
  86 import java.awt.event.WindowEvent;
  87 import java.io.IOException;
  88 import java.net.URL;
  89 import java.net.URLEncoder;
  90 import java.util.Enumeration;
  91 import java.util.Hashtable;
  92 import java.util.List;
  93 import java.util.StringTokenizer;
  94 import java.util.Vector;
  95
  96 public class AlignFrame extends EmbmenuFrame implements ActionListener,
  97         ItemListener, KeyListener, AlignViewControllerGuiI
  98 {
  99   public AlignViewControllerI avc;
 100   public AlignmentPanel alignPanel;
 101
 102   public AlignViewport viewport;
 103
 104   int DEFAULT_WIDTH = 700;
 105
 106   int DEFAULT_HEIGHT = 500;
 107
 108   String jalviewServletURL;
 109
 110   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 111           String title, boolean embedded)
 112   {
 113     if (applet != null)
 114     {
 115       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 116     }
 117
 118     try
 119     {
 120       jbInit();
 121     } catch (Exception ex)
 122     {
 123       ex.printStackTrace();
 124     }
 125     // need to get window geometry before we calculate alignment layout
 126     if (applet != null)
 127     {
 128       String param;
 129       try
 130       {
 131         param = applet.getParameter("windowWidth");
 132         if (param != null)
 133         {
 134           int width = Integer.parseInt(param);
 135           DEFAULT_WIDTH = width;
 136         }
 137         param = applet.getParameter("windowHeight");
 138         if (param != null)
 139         {
 140           int height = Integer.parseInt(param);
 141           DEFAULT_HEIGHT = height;
 142         }
 143       } catch (Exception ex)
 144       {
 145       }
 146     }
 147     viewport = new AlignViewport(al, applet);
 148     alignPanel = new AlignmentPanel(this, viewport);
 149     avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
 150     viewport.updateConservation(alignPanel);
 151     viewport.updateConsensus(alignPanel);
 152
 153     annotationPanelMenuItem.setState(viewport.showAnnotation);
 154     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 155     followMouseOverFlag.setState(viewport.getFollowHighlight());
 156     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 157     showGroupConservation.setState(viewport.isShowGroupConservation());
 158     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 159     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 160     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 161     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 162
 163     seqLimits.setState(viewport.showJVSuffix);
 164
 165     if (applet != null)
 166     {
 167       String param = applet.getParameter("sortBy");
 168       if (param != null)
 169       {
 170         if (param.equalsIgnoreCase("Id"))
 171         {
 172           sortIDMenuItem_actionPerformed();
 173         }
 174         else if (param.equalsIgnoreCase("Pairwise Identity"))
 175         {
 176           sortPairwiseMenuItem_actionPerformed();
 177         }
 178         else if (param.equalsIgnoreCase("Length"))
 179         {
 180           sortLengthMenuItem_actionPerformed();
 181         }
 182       }
 183
 184       param = applet.getParameter("wrap");
 185       if (param != null)
 186       {
 187         if (param.equalsIgnoreCase("true"))
 188         {
 189           wrapMenuItem.setState(true);
 190           wrapMenuItem_actionPerformed();
 191         }
 192       }
 193       param = applet.getParameter("centrecolumnlabels");
 194       if (param != null)
 195       {
 196         centreColumnLabelFlag.setState(true);
 197         centreColumnLabelFlag_stateChanged();
 198       }
 199
 200     }
 201     if (viewport.getAlignment().isNucleotide())
 202     {
 203       viewport.updateStrucConsensus(alignPanel);
 204       if (viewport.getAlignment().hasRNAStructure())
 205       {
 206         RNAHelixColour.setEnabled(true);
 207       }
 208       else
 209       {
 210         RNAHelixColour.setEnabled(false);
 211       }
 212     }
 213     else
 214     {
 215       RNAHelixColour.setEnabled(false);
 216       purinePyrimidineColour.setEnabled(false);
 217     }
 218     // Some JVMS send keyevents to Top frame or lowest panel,
 219     // Havent worked out why yet. So add to both this frame and seqCanvas for
 220     // now
 221     this.addKeyListener(this);
 222     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 223     alignPanel.idPanel.idCanvas.addKeyListener(this);
 224     alignPanel.scalePanel.addKeyListener(this);
 225     alignPanel.annotationPanel.addKeyListener(this);
 226     alignPanel.annotationPanelHolder.addKeyListener(this);
 227     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 228     alignPanel.alabels.addKeyListener(this);
 229     createAlignFrameWindow(embedded, title);
 230
 231     validate();
 232     alignPanel.adjustAnnotationHeight();
 233     alignPanel.paintAlignment(true);
 234   }
 235
 236   public AlignViewport getAlignViewport()
 237   {
 238     return viewport;
 239   }
 240
 241   public SeqCanvas getSeqcanvas()
 242   {
 243     return alignPanel.seqPanel.seqCanvas;
 244   }
 245
 246   /**
 247    * Load a features file onto the alignment
 248    *
 249    * @param file
 250    *          file URL, content, or other resolvable path
 251    * @param type
 252    *          is protocol for accessing data referred to by file
 253    */
 254
 255   public boolean parseFeaturesFile(String file, String type)
 256   {
 257     return parseFeaturesFile(file, type, true);
 258   }
 259
 260   /**
 261    * Load a features file onto the alignment
 262    *
 263    * @param file
 264    *          file URL, content, or other resolvable path
 265    * @param type
 266    *          is protocol for accessing data referred to by file
 267    * @param autoenabledisplay
 268    *          when true, display features flag will be automatically enabled if
 269    *          features are loaded
 270    * @return true if data parsed as a features file
 271    */
 272   public boolean parseFeaturesFile(String file, String type,
 273           boolean autoenabledisplay)
 274   {
 275     // TODO: test if importing a features file onto an alignment which already
 276     // has features with links overwrites the original links.
 277
 278     Hashtable featureLinks = new Hashtable();
 279     boolean featuresFile = false;
 280     try
 281     {
 282       featuresFile = new jalview.io.FeaturesFile(file, type)
 283               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 284                       .getFeatureRenderer().featureColours, featureLinks,
 285                       true, viewport.applet.getDefaultParameter(
 286                               "relaxedidmatch", false));
 287     } catch (Exception ex)
 288     {
 289       ex.printStackTrace();
 290     }
 291
 292     if (featuresFile)
 293     {
 294       if (featureLinks.size() > 0)
 295       {
 296         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 297       }
 298       if (autoenabledisplay)
 299       {
 300         viewport.showSequenceFeatures = true;
 301         sequenceFeatures.setState(true);
 302       }
 303       if (viewport.featureSettings != null)
 304       {
 305         viewport.featureSettings.refreshTable();
 306       }
 307       alignPanel.paintAlignment(true);
 308       statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
 309     }
 310     return featuresFile;
 311   }
 312
 313   @Override
 314   public void keyPressed(KeyEvent evt)
 315   {
 316     if (viewport.cursorMode
 317             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 318                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 319                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 320             && Character.isDigit(evt.getKeyChar()))
 321       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 322
 323     switch (evt.getKeyCode())
 324     {
 325     case 27: // escape key
 326       deselectAllSequenceMenuItem_actionPerformed();
 327
 328       alignPanel.alabels.cancelDrag();
 329       break;
 330     case KeyEvent.VK_X:
 331       if (evt.isControlDown() || evt.isMetaDown())
 332       {
 333         cut_actionPerformed();
 334       }
 335       break;
 336     case KeyEvent.VK_C:
 337       if (viewport.cursorMode && !evt.isControlDown())
 338       {
 339         alignPanel.seqPanel.setCursorColumn();
 340       }
 341       if (evt.isControlDown() || evt.isMetaDown())
 342       {
 343         copy_actionPerformed();
 344       }
 345       break;
 346     case KeyEvent.VK_V:
 347       if (evt.isControlDown())
 348       {
 349         paste(evt.isShiftDown());
 350       }
 351       break;
 352     case KeyEvent.VK_A:
 353       if (evt.isControlDown() || evt.isMetaDown())
 354       {
 355         selectAllSequenceMenuItem_actionPerformed();
 356       }
 357       break;
 358     case KeyEvent.VK_DOWN:
 359       if (viewport.cursorMode)
 360       {
 361         alignPanel.seqPanel.moveCursor(0, 1);
 362       }
 363       else
 364       {
 365         moveSelectedSequences(false);
 366       }
 367       break;
 368
 369     case KeyEvent.VK_UP:
 370       if (viewport.cursorMode)
 371       {
 372         alignPanel.seqPanel.moveCursor(0, -1);
 373       }
 374       else
 375       {
 376         moveSelectedSequences(true);
 377       }
 378       break;
 379
 380     case KeyEvent.VK_LEFT:
 381       if (evt.isAltDown() || !viewport.cursorMode)
 382         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 383       else
 384         alignPanel.seqPanel.moveCursor(-1, 0);
 385       break;
 386
 387     case KeyEvent.VK_RIGHT:
 388       if (evt.isAltDown() || !viewport.cursorMode)
 389         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 390       else
 391         alignPanel.seqPanel.moveCursor(1, 0);
 392       break;
 393
 394     case KeyEvent.VK_SPACE:
 395       if (viewport.cursorMode)
 396       {
 397         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 398                 || evt.isShiftDown() || evt.isAltDown());
 399       }
 400       break;
 401
 402     case KeyEvent.VK_DELETE:
 403     case KeyEvent.VK_BACK_SPACE:
 404       if (viewport.cursorMode)
 405       {
 406         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 407                 || evt.isShiftDown() || evt.isAltDown());
 408       }
 409       else
 410       {
 411         cut_actionPerformed();
 412         alignPanel.seqPanel.seqCanvas.repaint();
 413       }
 414       break;
 415
 416     case KeyEvent.VK_S:
 417       if (viewport.cursorMode)
 418       {
 419         alignPanel.seqPanel.setCursorRow();
 420       }
 421       break;
 422     case KeyEvent.VK_P:
 423       if (viewport.cursorMode)
 424       {
 425         alignPanel.seqPanel.setCursorPosition();
 426       }
 427       break;
 428
 429     case KeyEvent.VK_ENTER:
 430     case KeyEvent.VK_COMMA:
 431       if (viewport.cursorMode)
 432       {
 433         alignPanel.seqPanel.setCursorRowAndColumn();
 434       }
 435       break;
 436
 437     case KeyEvent.VK_Q:
 438       if (viewport.cursorMode)
 439       {
 440         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 441       }
 442       break;
 443     case KeyEvent.VK_M:
 444       if (viewport.cursorMode)
 445       {
 446         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 447       }
 448       break;
 449
 450     case KeyEvent.VK_F2:
 451       viewport.cursorMode = !viewport.cursorMode;
 452       statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 456         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 457       }
 458       break;
 459
 460     case KeyEvent.VK_F:
 461       if (evt.isControlDown())
 462       {
 463         findMenuItem_actionPerformed();
 464       }
 465       break;
 466
 467     case KeyEvent.VK_H:
 468     {
 469       boolean toggleSeqs = !evt.isControlDown();
 470       boolean toggleCols = !evt.isShiftDown();
 471       toggleHiddenRegions(toggleSeqs, toggleCols);
 472       break;
 473     }
 474
 475     case KeyEvent.VK_PAGE_UP:
 476       if (viewport.wrapAlignment)
 477       {
 478         alignPanel.scrollUp(true);
 479       }
 480       else
 481       {
 482         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 483                 - viewport.endSeq + viewport.startSeq);
 484       }
 485       break;
 486
 487     case KeyEvent.VK_PAGE_DOWN:
 488       if (viewport.wrapAlignment)
 489       {
 490         alignPanel.scrollUp(false);
 491       }
 492       else
 493       {
 494         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 495                 + viewport.endSeq - viewport.startSeq);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_Z:
 500       if (evt.isControlDown())
 501       {
 502         undoMenuItem_actionPerformed();
 503       }
 504       break;
 505
 506     case KeyEvent.VK_Y:
 507       if (evt.isControlDown())
 508       {
 509         redoMenuItem_actionPerformed();
 510       }
 511       break;
 512
 513     case KeyEvent.VK_L:
 514       if (evt.isControlDown())
 515       {
 516         trimAlignment(true);
 517       }
 518       break;
 519
 520     case KeyEvent.VK_R:
 521       if (evt.isControlDown())
 522       {
 523         trimAlignment(false);
 524       }
 525       break;
 526
 527     case KeyEvent.VK_E:
 528       if (evt.isControlDown())
 529       {
 530         if (evt.isShiftDown())
 531         {
 532           this.removeAllGapsMenuItem_actionPerformed();
 533         }
 534         else
 535         {
 536           removeGappedColumnMenuItem_actionPerformed();
 537         }
 538       }
 539       break;
 540     case KeyEvent.VK_I:
 541       if (evt.isControlDown())
 542       {
 543         if (evt.isAltDown())
 544         {
 545           invertColSel_actionPerformed();
 546         }
 547         else
 548         {
 549           invertSequenceMenuItem_actionPerformed();
 550         }
 551       }
 552       break;
 553
 554     case KeyEvent.VK_G:
 555       if (evt.isControlDown())
 556       {
 557         if (evt.isShiftDown())
 558         {
 559           this.unGroup_actionPerformed();
 560         }
 561         else
 562         {
 563           this.createGroup_actionPerformed();
 564         }
 565       }
 566       break;
 567
 568     case KeyEvent.VK_U:
 569       if (evt.isControlDown())
 570       {
 571         this.deleteGroups_actionPerformed();
 572       }
 573       break;
 574
 575     case KeyEvent.VK_T:
 576       if (evt.isControlDown())
 577       {
 578         newView(null);
 579       }
 580       break;
 581
 582     }
 583     alignPanel.paintAlignment(true);
 584   }
 585
 586   /**
 587    * called by key handler and the hide all/show all menu items
 588    *
 589    * @param toggleSeqs
 590    * @param toggleCols
 591    */
 592   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 593   {
 594     boolean hide = false;
 595     SequenceGroup sg = viewport.getSelectionGroup();
 596     if (!toggleSeqs && !toggleCols)
 597     {
 598       // Hide everything by the current selection - this is a hack - we do the
 599       // invert and then hide
 600       // first check that there will be visible columns after the invert.
 601       if ((viewport.getColumnSelection() != null
 602               && viewport.getColumnSelection().getSelected() != null && viewport
 603               .getColumnSelection().getSelected().size() > 0)
 604               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 605                       .getEndRes()))
 606       {
 607         // now invert the sequence set, if required - empty selection implies
 608         // that no hiding is required.
 609         if (sg != null)
 610         {
 611           invertSequenceMenuItem_actionPerformed();
 612           sg = viewport.getSelectionGroup();
 613           toggleSeqs = true;
 614
 615         }
 616         viewport.expandColSelection(sg, true);
 617         // finally invert the column selection and get the new sequence
 618         // selection and indicate it should be hidden.
 619         invertColSel_actionPerformed();
 620         toggleCols = true;
 621       }
 622     }
 623
 624     if (toggleSeqs)
 625     {
 626       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 627       {
 628         hide = true;
 629         viewport.hideAllSelectedSeqs();
 630       }
 631       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 632               .size() > 0))
 633       {
 634         viewport.showAllHiddenSeqs();
 635       }
 636     }
 637
 638     if (toggleCols)
 639     {
 640       if (viewport.getColumnSelection().getSelected().size() > 0)
 641       {
 642         viewport.hideSelectedColumns();
 643         if (!toggleSeqs)
 644         {
 645           viewport.setSelectionGroup(sg);
 646         }
 647       }
 648       else if (!hide)
 649       {
 650         viewport.showAllHiddenColumns();
 651       }
 652     }
 653   }
 654
 655   @Override
 656   public void keyReleased(KeyEvent evt)
 657   {
 658   }
 659
 660   @Override
 661   public void keyTyped(KeyEvent evt)
 662   {
 663   }
 664
 665   @Override
 666   public void itemStateChanged(ItemEvent evt)
 667   {
 668     if (evt.getSource() == displayNonconservedMenuItem)
 669     {
 670       displayNonconservedMenuItem_actionPerformed();
 671     }
 672     else if (evt.getSource() == colourTextMenuItem)
 673     {
 674       colourTextMenuItem_actionPerformed();
 675     }
 676     else if (evt.getSource() == wrapMenuItem)
 677     {
 678       wrapMenuItem_actionPerformed();
 679     }
 680     else if (evt.getSource() == scaleAbove)
 681     {
 682       viewport.setScaleAboveWrapped(scaleAbove.getState());
 683     }
 684     else if (evt.getSource() == scaleLeft)
 685     {
 686       viewport.setScaleLeftWrapped(scaleLeft.getState());
 687     }
 688     else if (evt.getSource() == scaleRight)
 689     {
 690       viewport.setScaleRightWrapped(scaleRight.getState());
 691     }
 692     else if (evt.getSource() == seqLimits)
 693     {
 694       seqLimits_itemStateChanged();
 695     }
 696     else if (evt.getSource() == viewBoxesMenuItem)
 697     {
 698       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 699     }
 700     else if (evt.getSource() == viewTextMenuItem)
 701     {
 702       viewport.setShowText(viewTextMenuItem.getState());
 703     }
 704     else if (evt.getSource() == renderGapsMenuItem)
 705     {
 706       viewport.setRenderGaps(renderGapsMenuItem.getState());
 707     }
 708     else if (evt.getSource() == annotationPanelMenuItem)
 709     {
 710       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 711       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 712     }
 713     else if (evt.getSource() == sequenceFeatures)
 714     {
 715       viewport.showSequenceFeatures(sequenceFeatures.getState());
 716       alignPanel.seqPanel.seqCanvas.repaint();
 717     }
 718     else if (evt.getSource() == conservationMenuItem)
 719     {
 720       conservationMenuItem_actionPerformed();
 721     }
 722     else if (evt.getSource() == abovePIDThreshold)
 723     {
 724       abovePIDThreshold_actionPerformed();
 725     }
 726     else if (evt.getSource() == applyToAllGroups)
 727     {
 728       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 729     }
 730     else if (evt.getSource() == autoCalculate)
 731     {
 732       viewport.autoCalculateConsensus = autoCalculate.getState();
 733     }
 734     else if (evt.getSource() == sortByTree)
 735     {
 736       viewport.sortByTree = sortByTree.getState();
 737     }
 738     else if (evt.getSource() == this.centreColumnLabelFlag)
 739     {
 740       centreColumnLabelFlag_stateChanged();
 741     }
 742     else if (evt.getSource() == this.followMouseOverFlag)
 743     {
 744       mouseOverFlag_stateChanged();
 745     }
 746     else if (evt.getSource() == showGroupConsensus)
 747     {
 748       showGroupConsensus_actionPerformed();
 749     }
 750     else if (evt.getSource() == showGroupConservation)
 751     {
 752       showGroupConservation_actionPerformed();
 753     }
 754     else if (evt.getSource() == showSequenceLogo)
 755     {
 756       showSequenceLogo_actionPerformed();
 757     }
 758     else if (evt.getSource() == normSequenceLogo)
 759     {
 760       normSequenceLogo_actionPerformed();
 761     }
 762     else if (evt.getSource() == showConsensusHistogram)
 763     {
 764       showConsensusHistogram_actionPerformed();
 765     }
 766     else if (evt.getSource() == applyAutoAnnotationSettings)
 767     {
 768       applyAutoAnnotationSettings_actionPerformed();
 769     }
 770     alignPanel.paintAlignment(true);
 771   }
 772
 773   private void mouseOverFlag_stateChanged()
 774   {
 775     viewport.followHighlight = followMouseOverFlag.getState();
 776     // TODO: could kick the scrollTo mechanism to reset view for current
 777     // searchresults.
 778   }
 779
 780   private void centreColumnLabelFlag_stateChanged()
 781   {
 782     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 783     this.alignPanel.annotationPanel.repaint();
 784   }
 785
 786   @Override
 787   public void actionPerformed(ActionEvent evt)
 788   {
 789     Object source = evt.getSource();
 790
 791     if (source == inputText)
 792     {
 793       inputText_actionPerformed();
 794     }
 795     else if (source == loadTree)
 796     {
 797       loadTree_actionPerformed();
 798     }
 799     else if (source == loadApplication)
 800     {
 801       launchFullApplication();
 802     }
 803     else if (source == loadAnnotations)
 804     {
 805       loadAnnotations();
 806     }
 807     else if (source == outputAnnotations)
 808     {
 809       outputAnnotations(true);
 810     }
 811     else if (source == outputFeatures)
 812     {
 813       outputFeatures(true, "Jalview");
 814     }
 815     else if (source == closeMenuItem)
 816     {
 817       closeMenuItem_actionPerformed();
 818     }
 819     else if (source == copy)
 820     {
 821       copy_actionPerformed();
 822     }
 823     else if (source == undoMenuItem)
 824     {
 825       undoMenuItem_actionPerformed();
 826     }
 827     else if (source == redoMenuItem)
 828     {
 829       redoMenuItem_actionPerformed();
 830     }
 831     else if (source == inputText)
 832     {
 833       inputText_actionPerformed();
 834     }
 835     else if (source == closeMenuItem)
 836     {
 837       closeMenuItem_actionPerformed();
 838     }
 839     else if (source == undoMenuItem)
 840     {
 841       undoMenuItem_actionPerformed();
 842     }
 843     else if (source == redoMenuItem)
 844     {
 845       redoMenuItem_actionPerformed();
 846     }
 847     else if (source == copy)
 848     {
 849       copy_actionPerformed();
 850     }
 851     else if (source == pasteNew)
 852     {
 853       pasteNew_actionPerformed();
 854     }
 855     else if (source == pasteThis)
 856     {
 857       pasteThis_actionPerformed();
 858     }
 859     else if (source == cut)
 860     {
 861       cut_actionPerformed();
 862     }
 863     else if (source == delete)
 864     {
 865       delete_actionPerformed();
 866     }
 867     else if (source == grpsFromSelection)
 868     {
 869       makeGrpsFromSelection_actionPerformed();
 870     }
 871     else if (source == deleteGroups)
 872     {
 873       deleteGroups_actionPerformed();
 874     }
 875     else if (source == selectAllSequenceMenuItem)
 876     {
 877       selectAllSequenceMenuItem_actionPerformed();
 878     }
 879     else if (source == deselectAllSequenceMenuItem)
 880     {
 881       deselectAllSequenceMenuItem_actionPerformed();
 882     }
 883     else if (source == invertSequenceMenuItem)
 884     {
 885       invertSequenceMenuItem_actionPerformed();
 886     }
 887     else if (source == invertColSel)
 888     {
 889       viewport.invertColumnSelection();
 890       alignPanel.paintAlignment(true);
 891     }
 892     else if (source == remove2LeftMenuItem)
 893     {
 894       trimAlignment(true);
 895     }
 896     else if (source == remove2RightMenuItem)
 897     {
 898       trimAlignment(false);
 899     }
 900     else if (source == removeGappedColumnMenuItem)
 901     {
 902       removeGappedColumnMenuItem_actionPerformed();
 903     }
 904     else if (source == removeAllGapsMenuItem)
 905     {
 906       removeAllGapsMenuItem_actionPerformed();
 907     }
 908     else if (source == findMenuItem)
 909     {
 910       findMenuItem_actionPerformed();
 911     }
 912     else if (source == font)
 913     {
 914       new FontChooser(alignPanel);
 915     }
 916     else if (source == newView)
 917     {
 918       newView(null);
 919     }
 920     else if (source == showColumns)
 921     {
 922       viewport.showAllHiddenColumns();
 923       alignPanel.paintAlignment(true);
 924     }
 925     else if (source == showSeqs)
 926     {
 927       viewport.showAllHiddenSeqs();
 928       alignPanel.paintAlignment(true);
 929     }
 930     else if (source == hideColumns)
 931     {
 932       viewport.hideSelectedColumns();
 933       alignPanel.paintAlignment(true);
 934     }
 935     else if (source == hideSequences
 936             && viewport.getSelectionGroup() != null)
 937     {
 938       viewport.hideAllSelectedSeqs();
 939       alignPanel.paintAlignment(true);
 940     }
 941     else if (source == hideAllButSelection)
 942     {
 943       toggleHiddenRegions(false, false);
 944       alignPanel.paintAlignment(true);
 945     }
 946     else if (source == hideAllSelection)
 947     {
 948       SequenceGroup sg = viewport.getSelectionGroup();
 949       viewport.expandColSelection(sg, false);
 950       viewport.hideAllSelectedSeqs();
 951       viewport.hideSelectedColumns();
 952       alignPanel.paintAlignment(true);
 953     }
 954     else if (source == showAllHidden)
 955     {
 956       viewport.showAllHiddenColumns();
 957       viewport.showAllHiddenSeqs();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == showGroupConsensus)
 961     {
 962       showGroupConsensus_actionPerformed();
 963     }
 964     else if (source == showGroupConservation)
 965     {
 966       showGroupConservation_actionPerformed();
 967     }
 968     else if (source == showSequenceLogo)
 969     {
 970       showSequenceLogo_actionPerformed();
 971     }
 972     else if (source == normSequenceLogo)
 973     {
 974       normSequenceLogo_actionPerformed();
 975     }
 976     else if (source == showConsensusHistogram)
 977     {
 978       showConsensusHistogram_actionPerformed();
 979     }
 980     else if (source == applyAutoAnnotationSettings)
 981     {
 982       applyAutoAnnotationSettings_actionPerformed();
 983     }
 984     else if (source == featureSettings)
 985     {
 986       new FeatureSettings(alignPanel);
 987     }
 988     else if (source == alProperties)
 989     {
 990       StringBuffer contents = new jalview.io.AlignmentProperties(
 991               viewport.getAlignment()).formatAsString();
 992       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
 993       cap.setText(contents.toString());
 994       Frame frame = new Frame();
 995       frame.add(cap);
 996       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
 997                   400, 250);
 998     }
 999     else if (source == overviewMenuItem)
1000     {
1001       overviewMenuItem_actionPerformed();
1002     }
1003     else if (source == noColourmenuItem)
1004     {
1005       changeColour(null);
1006     }
1007     else if (source == clustalColour)
1008     {
1009       abovePIDThreshold.setState(false);
1010       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1011     }
1012     else if (source == zappoColour)
1013     {
1014       changeColour(new ZappoColourScheme());
1015     }
1016     else if (source == taylorColour)
1017     {
1018       changeColour(new TaylorColourScheme());
1019     }
1020     else if (source == hydrophobicityColour)
1021     {
1022       changeColour(new HydrophobicColourScheme());
1023     }
1024     else if (source == helixColour)
1025     {
1026       changeColour(new HelixColourScheme());
1027     }
1028     else if (source == strandColour)
1029     {
1030       changeColour(new StrandColourScheme());
1031     }
1032     else if (source == turnColour)
1033     {
1034       changeColour(new TurnColourScheme());
1035     }
1036     else if (source == buriedColour)
1037     {
1038       changeColour(new BuriedColourScheme());
1039     }
1040     else if (source == nucleotideColour)
1041     {
1042       changeColour(new NucleotideColourScheme());
1043     }
1044     else if (source == purinePyrimidineColour)
1045     {
1046       changeColour(new PurinePyrimidineColourScheme());
1047     }
1048     else if (source == RNAHelixColour)
1049     {
1050       new RNAHelicesColourChooser(viewport, alignPanel);
1051     }
1052     else if (source == modifyPID)
1053     {
1054       modifyPID_actionPerformed();
1055     }
1056     else if (source == modifyConservation)
1057     {
1058       modifyConservation_actionPerformed();
1059     }
1060     else if (source == userDefinedColour)
1061     {
1062       new UserDefinedColours(alignPanel, null);
1063     }
1064     else if (source == PIDColour)
1065     {
1066       changeColour(new PIDColourScheme());
1067     }
1068     else if (source == BLOSUM62Colour)
1069     {
1070       changeColour(new Blosum62ColourScheme());
1071     }
1072     else if (source == tcoffeeColour)
1073     {
1074       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1075     }
1076     else if (source == annotationColour)
1077     {
1078       new AnnotationColourChooser(viewport, alignPanel);
1079     }
1080     else if (source == sortPairwiseMenuItem)
1081     {
1082       sortPairwiseMenuItem_actionPerformed();
1083     }
1084     else if (source == sortIDMenuItem)
1085     {
1086       sortIDMenuItem_actionPerformed();
1087     }
1088     else if (source == sortLengthMenuItem)
1089     {
1090       sortLengthMenuItem_actionPerformed();
1091     }
1092     else if (source == sortGroupMenuItem)
1093     {
1094       sortGroupMenuItem_actionPerformed();
1095     }
1096     else if (source == removeRedundancyMenuItem)
1097     {
1098       removeRedundancyMenuItem_actionPerformed();
1099     }
1100     else if (source == pairwiseAlignmentMenuItem)
1101     {
1102       pairwiseAlignmentMenuItem_actionPerformed();
1103     }
1104     else if (source == PCAMenuItem)
1105     {
1106       PCAMenuItem_actionPerformed();
1107     }
1108     else if (source == averageDistanceTreeMenuItem)
1109     {
1110       averageDistanceTreeMenuItem_actionPerformed();
1111     }
1112     else if (source == neighbourTreeMenuItem)
1113     {
1114       neighbourTreeMenuItem_actionPerformed();
1115     }
1116     else if (source == njTreeBlosumMenuItem)
1117     {
1118       njTreeBlosumMenuItem_actionPerformed();
1119     }
1120     else if (source == avDistanceTreeBlosumMenuItem)
1121     {
1122       avTreeBlosumMenuItem_actionPerformed();
1123     }
1124     else if (source == documentation)
1125     {
1126       documentation_actionPerformed();
1127     }
1128     else if (source == about)
1129     {
1130       about_actionPerformed();
1131     }
1132
1133   }
1134
1135   public void inputText_actionPerformed()
1136   {
1137     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1138     Frame frame = new Frame();
1139     frame.add(cap);
1140     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
1141   }
1142
1143   protected void outputText_actionPerformed(ActionEvent e)
1144   {
1145     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1146     Frame frame = new Frame();
1147     frame.add(cap);
1148     jalview.bin.JalviewLite.addFrame(frame,
1149                 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
1150     cap.setText(new AppletFormatAdapter().formatSequences(
1151             e.getActionCommand(), viewport.getAlignment(),
1152             viewport.showJVSuffix));
1153   }
1154
1155   public void loadAnnotations()
1156   {
1157     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1158     cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
1159     cap.setAnnotationImport();
1160     Frame frame = new Frame();
1161     frame.add(cap);
1162     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
1163
1164   }
1165
1166   public String outputAnnotations(boolean displayTextbox)
1167   {
1168     String annotation = new AnnotationFile().printAnnotations(
1169             viewport.showAnnotation ? viewport.getAlignment()
1170                     .getAlignmentAnnotation() : null, viewport
1171                     .getAlignment().getGroups(), ((Alignment) viewport
1172                     .getAlignment()).alignmentProperties);
1173
1174     if (displayTextbox)
1175     {
1176       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1177       Frame frame = new Frame();
1178       frame.add(cap);
1179       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
1180       cap.setText(annotation);
1181     }
1182
1183     return annotation;
1184   }
1185
1186   private Hashtable getDisplayedFeatureCols()
1187   {
1188     if (alignPanel.getFeatureRenderer() != null
1189             && viewport.featuresDisplayed != null)
1190     {
1191       FeatureRenderer fr = alignPanel.getFeatureRenderer();
1192       Hashtable fcols = new Hashtable();
1193       Enumeration en = viewport.featuresDisplayed.keys();
1194       while (en.hasMoreElements())
1195       {
1196         Object col = en.nextElement();
1197         fcols.put(col, fr.featureColours.get(col));
1198       }
1199       return fcols;
1200     }
1201     return null;
1202   }
1203
1204   public String outputFeatures(boolean displayTextbox, String format)
1205   {
1206     String features;
1207     if (format.equalsIgnoreCase("Jalview"))
1208     {
1209       features = new FeaturesFile().printJalviewFormat(viewport
1210               .getAlignment().getSequencesArray(),
1211               getDisplayedFeatureCols());
1212     }
1213     else
1214     {
1215       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1216               .getSequencesArray(), getDisplayedFeatureCols());
1217     }
1218
1219     if (displayTextbox)
1220     {
1221       boolean frimport = false;
1222       if (features == null || features.equals("No Features Visible"))
1223       {
1224         features = "# No features visible - paste some and import them here.";
1225         frimport = true;
1226       }
1227
1228       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1229       if (frimport)
1230       {
1231         cap.setAnnotationImport();
1232       }
1233       Frame frame = new Frame();
1234       frame.add(cap);
1235       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
1236       cap.setText(features);
1237     }
1238     else
1239     {
1240       if (features == null)
1241         features = "";
1242     }
1243
1244     return features;
1245   }
1246
1247   void launchFullApplication()
1248   {
1249     StringBuffer url = new StringBuffer(jalviewServletURL);
1250
1251     url.append("?open="
1252             + appendProtocol(viewport.applet.getParameter("file")));
1253
1254     if (viewport.applet.getParameter("features") != null)
1255     {
1256       url.append("&features=");
1257       url.append(appendProtocol(viewport.applet.getParameter("features")));
1258     }
1259
1260     if (viewport.applet.getParameter("annotations") != null)
1261     {
1262       url.append("&annotations=");
1263       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1264     }
1265
1266     if (viewport.applet.getParameter("jnetfile") != null)
1267     {
1268       url.append("&annotations=");
1269       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1270     }
1271
1272     if (viewport.applet.getParameter("defaultColour") != null)
1273     {
1274       url.append("&colour="
1275               + removeWhiteSpace(viewport.applet
1276                       .getParameter("defaultColour")));
1277     }
1278
1279     if (viewport.applet.getParameter("userDefinedColour") != null)
1280     {
1281       url.append("&colour="
1282               + removeWhiteSpace(viewport.applet
1283                       .getParameter("userDefinedColour")));
1284     }
1285     if (viewport.applet.getParameter("tree") != null)
1286     {
1287       url.append("&tree="
1288               + appendProtocol(viewport.applet.getParameter("tree")));
1289     }
1290     if (viewport.applet.getParameter("treeFile") != null)
1291     {
1292       url.append("&tree="
1293               + appendProtocol(viewport.applet.getParameter("treeFile")));
1294     }
1295
1296     showURL(url.toString(), "FULL_APP");
1297   }
1298
1299   String removeWhiteSpace(String colour)
1300   {
1301     StringBuffer sb = new StringBuffer();
1302     for (int i = 0; i < colour.length(); i++)
1303     {
1304       if (Character.isWhitespace(colour.charAt(i)))
1305       {
1306         sb.append("%20");
1307       }
1308       else
1309       {
1310         sb.append(colour.charAt(i));
1311       }
1312     }
1313
1314     return sb.toString();
1315   }
1316
1317   String appendProtocol(String url)
1318   {
1319     try
1320     {
1321       new URL(url);
1322       url = URLEncoder.encode(url);
1323     }
1324     /*
1325      * When we finally deprecate 1.1 compatibility, we can start to use
1326      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1327      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1328      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1329      * ex.printStackTrace(); }
1330      */
1331     catch (java.net.MalformedURLException ex)
1332     {
1333       url = viewport.applet.getCodeBase() + url;
1334     }
1335     return url;
1336   }
1337
1338   public void closeMenuItem_actionPerformed()
1339   {
1340     PaintRefresher.RemoveComponent(alignPanel);
1341     if (alignPanel.seqPanel != null
1342             && alignPanel.seqPanel.seqCanvas != null)
1343     {
1344       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1345     }
1346     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1347     {
1348       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1349     }
1350
1351     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1352     {
1353       System.exit(0);
1354     }
1355     else
1356     {
1357     }
1358     viewport = null;
1359     alignPanel = null;
1360     this.dispose();
1361   }
1362
1363   /**
1364    * TODO: JAL-1104
1365    */
1366   void updateEditMenuBar()
1367   {
1368
1369     if (viewport.historyList.size() > 0)
1370     {
1371       undoMenuItem.setEnabled(true);
1372       CommandI command = (CommandI) viewport.historyList.peek();
1373       undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1374     }
1375     else
1376     {
1377       undoMenuItem.setEnabled(false);
1378       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1379     }
1380
1381     if (viewport.redoList.size() > 0)
1382     {
1383       redoMenuItem.setEnabled(true);
1384
1385       CommandI command = (CommandI) viewport.redoList.peek();
1386       redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1387     }
1388     else
1389     {
1390       redoMenuItem.setEnabled(false);
1391       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1392     }
1393   }
1394
1395   /**
1396    * TODO: JAL-1104
1397    */
1398   public void addHistoryItem(CommandI command)
1399   {
1400     if (command.getSize() > 0)
1401     {
1402       viewport.historyList.push(command);
1403       viewport.redoList.removeAllElements();
1404       updateEditMenuBar();
1405       viewport.updateHiddenColumns();
1406     }
1407   }
1408
1409   /**
1410    * TODO: JAL-1104 DOCUMENT ME!
1411    *
1412    * @param e
1413    *          DOCUMENT ME!
1414    */
1415   protected void undoMenuItem_actionPerformed()
1416   {
1417     if (viewport.historyList.size() < 1)
1418     {
1419       return;
1420     }
1421
1422     CommandI command = (CommandI) viewport.historyList.pop();
1423     viewport.redoList.push(command);
1424     command.undoCommand(null);
1425
1426     AlignViewport originalSource = getOriginatingSource(command);
1427     // JBPNote Test
1428     if (originalSource != viewport)
1429     {
1430       System.err
1431               .println("Warning: Viewport object mismatch whilst undoing");
1432     }
1433     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1434                                           // viewport.getColumnSelection().getHiddenColumns()
1435                                           // != null;
1436     updateEditMenuBar();
1437     originalSource.firePropertyChange("alignment", null, originalSource
1438             .getAlignment().getSequences());
1439   }
1440
1441   /**
1442    * TODO: JAL-1104 DOCUMENT ME!
1443    *
1444    * @param e
1445    *          DOCUMENT ME!
1446    */
1447   protected void redoMenuItem_actionPerformed()
1448   {
1449     if (viewport.redoList.size() < 1)
1450     {
1451       return;
1452     }
1453
1454     CommandI command = (CommandI) viewport.redoList.pop();
1455     viewport.historyList.push(command);
1456     command.doCommand(null);
1457
1458     AlignViewport originalSource = getOriginatingSource(command);
1459     // JBPNote Test
1460     if (originalSource != viewport)
1461     {
1462       System.err
1463               .println("Warning: Viewport object mismatch whilst re-doing");
1464     }
1465     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1466                                           // viewport.getColumnSelection().getHiddenColumns()
1467                                           // != null;
1468
1469     updateEditMenuBar();
1470     originalSource.firePropertyChange("alignment", null, originalSource
1471             .getAlignment().getSequences());
1472   }
1473
1474   AlignViewport getOriginatingSource(CommandI command)
1475   {
1476     AlignViewport originalSource = null;
1477     // For sequence removal and addition, we need to fire
1478     // the property change event FROM the viewport where the
1479     // original alignment was altered
1480     AlignmentI al = null;
1481     if (command instanceof EditCommand)
1482     {
1483       EditCommand editCommand = (EditCommand) command;
1484       al = editCommand.getAlignment();
1485       Vector comps = (Vector) PaintRefresher.components.get(viewport
1486               .getSequenceSetId());
1487       for (int i = 0; i < comps.size(); i++)
1488       {
1489         if (comps.elementAt(i) instanceof AlignmentPanel)
1490         {
1491           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1492           {
1493             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1494             break;
1495           }
1496         }
1497       }
1498     }
1499
1500     if (originalSource == null)
1501     {
1502       // The original view is closed, we must validate
1503       // the current view against the closed view first
1504       if (al != null)
1505       {
1506         PaintRefresher.validateSequences(al, viewport.getAlignment());
1507       }
1508
1509       originalSource = viewport;
1510     }
1511
1512     return originalSource;
1513   }
1514
1515   public void moveSelectedSequences(boolean up)
1516   {
1517     SequenceGroup sg = viewport.getSelectionGroup();
1518     if (sg == null)
1519     {
1520       return;
1521     }
1522     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1523             up ? null : viewport.getHiddenRepSequences(), up);
1524     alignPanel.paintAlignment(true);
1525   }
1526
1527   synchronized void slideSequences(boolean right, int size)
1528   {
1529     List<SequenceI> sg = new Vector<SequenceI>();
1530     if (viewport.cursorMode)
1531     {
1532       sg.add(viewport.getAlignment().getSequenceAt(
1533               alignPanel.seqPanel.seqCanvas.cursorY));
1534     }
1535     else if (viewport.getSelectionGroup() != null
1536             && viewport.getSelectionGroup().getSize() != viewport
1537                     .getAlignment().getHeight())
1538     {
1539       sg = viewport.getSelectionGroup().getSequences(
1540               viewport.getHiddenRepSequences());
1541     }
1542
1543     if (sg.size() < 1)
1544     {
1545       return;
1546     }
1547
1548     Vector<SequenceI> invertGroup = new Vector();
1549
1550     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1551     {
1552       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1553         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1554     }
1555
1556     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1557
1558     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1559             .size()]);
1560     for (int i = 0; i < invertGroup.size(); i++)
1561       seqs2[i] = invertGroup.elementAt(i);
1562
1563     SlideSequencesCommand ssc;
1564     if (right)
1565       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1566               size, viewport.getGapCharacter());
1567     else
1568       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1569               size, viewport.getGapCharacter());
1570
1571     int groupAdjustment = 0;
1572     if (ssc.getGapsInsertedBegin() && right)
1573     {
1574       if (viewport.cursorMode)
1575         alignPanel.seqPanel.moveCursor(size, 0);
1576       else
1577         groupAdjustment = size;
1578     }
1579     else if (!ssc.getGapsInsertedBegin() && !right)
1580     {
1581       if (viewport.cursorMode)
1582         alignPanel.seqPanel.moveCursor(-size, 0);
1583       else
1584         groupAdjustment = -size;
1585     }
1586
1587     if (groupAdjustment != 0)
1588     {
1589       viewport.getSelectionGroup().setStartRes(
1590               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1591       viewport.getSelectionGroup().setEndRes(
1592               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1593     }
1594
1595     boolean appendHistoryItem = false;
1596     if (viewport.historyList != null && viewport.historyList.size() > 0
1597             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1598     {
1599       appendHistoryItem = ssc
1600               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1601                       .peek());
1602     }
1603
1604     if (!appendHistoryItem)
1605       addHistoryItem(ssc);
1606
1607     repaint();
1608   }
1609
1610   static StringBuffer copiedSequences;
1611
1612   static Vector copiedHiddenColumns;
1613
1614   protected void copy_actionPerformed()
1615   {
1616     if (viewport.getSelectionGroup() == null)
1617     {
1618       return;
1619     }
1620
1621     SequenceGroup sg = viewport.getSelectionGroup();
1622     copiedSequences = new StringBuffer();
1623     Hashtable orderedSeqs = new Hashtable();
1624     for (int i = 0; i < sg.getSize(); i++)
1625     {
1626       SequenceI seq = sg.getSequenceAt(i);
1627       int index = viewport.getAlignment().findIndex(seq);
1628       orderedSeqs.put(index + "", seq);
1629     }
1630
1631     int index = 0, startRes, endRes;
1632     char ch;
1633
1634     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1635     {
1636       copiedHiddenColumns = new Vector();
1637       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1638       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1639               .size(); i++)
1640       {
1641         int[] region = (int[]) viewport.getColumnSelection()
1642                 .getHiddenColumns().elementAt(i);
1643
1644         copiedHiddenColumns.addElement(new int[]
1645         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1646       }
1647     }
1648     else
1649     {
1650       copiedHiddenColumns = null;
1651     }
1652
1653     for (int i = 0; i < sg.getSize(); i++)
1654     {
1655       SequenceI seq = null;
1656
1657       while (seq == null)
1658       {
1659         if (orderedSeqs.containsKey(index + ""))
1660         {
1661           seq = (SequenceI) orderedSeqs.get(index + "");
1662           index++;
1663
1664           break;
1665         }
1666         else
1667         {
1668           index++;
1669         }
1670       }
1671
1672       // FIND START RES
1673       // Returns residue following index if gap
1674       startRes = seq.findPosition(sg.getStartRes());
1675
1676       // FIND END RES
1677       // Need to find the residue preceeding index if gap
1678       endRes = 0;
1679
1680       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1681       {
1682         ch = seq.getCharAt(j);
1683         if (!jalview.util.Comparison.isGap((ch)))
1684         {
1685           endRes++;
1686         }
1687       }
1688
1689       if (endRes > 0)
1690       {
1691         endRes += seq.getStart() - 1;
1692       }
1693
1694       copiedSequences.append(seq.getName()
1695               + "\t"
1696               + startRes
1697               + "\t"
1698               + endRes
1699               + "\t"
1700               + seq.getSequenceAsString(sg.getStartRes(),
1701                       sg.getEndRes() + 1) + "\n");
1702     }
1703
1704   }
1705
1706   protected void pasteNew_actionPerformed()
1707   {
1708     paste(true);
1709   }
1710
1711   protected void pasteThis_actionPerformed()
1712   {
1713     paste(false);
1714   }
1715
1716   void paste(boolean newAlignment)
1717   {
1718     try
1719     {
1720
1721       if (copiedSequences == null)
1722       {
1723         return;
1724       }
1725
1726       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1727       Vector seqs = new Vector();
1728       while (st.hasMoreElements())
1729       {
1730         String name = st.nextToken();
1731         int start = Integer.parseInt(st.nextToken());
1732         int end = Integer.parseInt(st.nextToken());
1733         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1734       }
1735       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1736       for (int i = 0; i < seqs.size(); i++)
1737       {
1738         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1739       }
1740
1741       if (newAlignment)
1742       {
1743         String newtitle = new String("Copied sequences");
1744         if (getTitle().startsWith("Copied sequences"))
1745         {
1746           newtitle = getTitle();
1747         }
1748         else
1749         {
1750           newtitle = newtitle.concat("- from " + getTitle());
1751         }
1752         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1753                 viewport.applet, newtitle, false);
1754         if (copiedHiddenColumns != null)
1755         {
1756           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1757           {
1758             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1759             af.viewport.hideColumns(region[0], region[1]);
1760           }
1761         }
1762
1763         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1764                 DEFAULT_HEIGHT);
1765       }
1766       else
1767       {
1768         addSequences(newSeqs);
1769       }
1770
1771     } catch (Exception ex)
1772     {
1773     } // could be anything being pasted in here
1774
1775   }
1776
1777   void addSequences(SequenceI[] seqs)
1778   {
1779     for (int i = 0; i < seqs.length; i++)
1780     {
1781       viewport.getAlignment().addSequence(seqs[i]);
1782     }
1783
1784     // !newAlignment
1785     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1786             seqs, 0, viewport.getAlignment().getWidth(),
1787             viewport.getAlignment()));
1788
1789     viewport.setEndSeq(viewport.getAlignment().getHeight());
1790     viewport.getAlignment().getWidth();
1791     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1792             .getSequences());
1793
1794   }
1795
1796   protected void cut_actionPerformed()
1797   {
1798     copy_actionPerformed();
1799     delete_actionPerformed();
1800   }
1801
1802   protected void delete_actionPerformed()
1803   {
1804
1805     SequenceGroup sg = viewport.getSelectionGroup();
1806     if (sg == null)
1807     {
1808       return;
1809     }
1810
1811     Vector seqs = new Vector();
1812     SequenceI seq;
1813     for (int i = 0; i < sg.getSize(); i++)
1814     {
1815       seq = sg.getSequenceAt(i);
1816       seqs.addElement(seq);
1817     }
1818
1819     // If the cut affects all sequences, remove highlighted columns
1820     if (sg.getSize() == viewport.getAlignment().getHeight())
1821     {
1822       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1823               sg.getEndRes() + 1);
1824     }
1825
1826     SequenceI[] cut = new SequenceI[seqs.size()];
1827     for (int i = 0; i < seqs.size(); i++)
1828     {
1829       cut[i] = (SequenceI) seqs.elementAt(i);
1830     }
1831
1832     /*
1833      * //ADD HISTORY ITEM
1834      */
1835     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1836             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1837             viewport.getAlignment()));
1838
1839     viewport.setSelectionGroup(null);
1840     viewport.getAlignment().deleteGroup(sg);
1841
1842     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1843             .getSequences());
1844
1845     if (viewport.getAlignment().getHeight() < 1)
1846     {
1847       this.setVisible(false);
1848     }
1849     viewport.sendSelection();
1850   }
1851
1852   /**
1853    * group consensus toggled
1854    *
1855    */
1856   protected void showGroupConsensus_actionPerformed()
1857   {
1858     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1859     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1860
1861   }
1862
1863   /**
1864    * group conservation toggled.
1865    */
1866   protected void showGroupConservation_actionPerformed()
1867   {
1868     viewport.setShowGroupConservation(showGroupConservation.getState());
1869     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1870   }
1871
1872   /*
1873    * (non-Javadoc)
1874    *
1875    * @see
1876    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1877    * .event.ActionEvent)
1878    */
1879   protected void showConsensusHistogram_actionPerformed()
1880   {
1881     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1882     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1883   }
1884
1885   /*
1886    * (non-Javadoc)
1887    *
1888    * @see
1889    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1890    * .event.ActionEvent)
1891    */
1892   protected void showSequenceLogo_actionPerformed()
1893   {
1894     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1895     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1896   }
1897
1898   protected void normSequenceLogo_actionPerformed()
1899   {
1900     showSequenceLogo.setState(true);
1901     viewport.setShowSequenceLogo(true);
1902     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1903     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1904   }
1905
1906   protected void applyAutoAnnotationSettings_actionPerformed()
1907   {
1908     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1909   }
1910
1911   protected void makeGrpsFromSelection_actionPerformed()
1912   {
1913     if (avc.makeGroupsFromSelection()) {
1914       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1915       alignPanel.updateAnnotation();
1916       alignPanel.paintAlignment(true);
1917     }
1918   }
1919
1920   protected void createGroup_actionPerformed()
1921   {
1922     avc.createGroup();
1923   }
1924   protected void unGroup_actionPerformed()
1925   {
1926     if (avc.unGroup())
1927     {
1928       alignPanel.alignmentChanged();
1929     }
1930   }
1931   protected void deleteGroups_actionPerformed()
1932   {
1933     if (avc.deleteGroups())
1934     {
1935       alignPanel.alignmentChanged();
1936     }
1937   }
1938
1939   public void selectAllSequenceMenuItem_actionPerformed()
1940   {
1941     SequenceGroup sg = new SequenceGroup();
1942     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1943     {
1944       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1945     }
1946     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1947     viewport.setSelectionGroup(sg);
1948     alignPanel.paintAlignment(true);
1949     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1950     viewport.sendSelection();
1951   }
1952
1953   public void deselectAllSequenceMenuItem_actionPerformed()
1954   {
1955     if (viewport.cursorMode)
1956     {
1957       alignPanel.seqPanel.keyboardNo1 = null;
1958       alignPanel.seqPanel.keyboardNo2 = null;
1959     }
1960     viewport.setSelectionGroup(null);
1961     viewport.getColumnSelection().clear();
1962     viewport.setSelectionGroup(null);
1963     alignPanel.idPanel.idCanvas.searchResults = null;
1964     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1965     alignPanel.paintAlignment(true);
1966     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1967     viewport.sendSelection();
1968   }
1969
1970   public void invertSequenceMenuItem_actionPerformed()
1971   {
1972     SequenceGroup sg = viewport.getSelectionGroup();
1973     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1974     {
1975       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1976     }
1977
1978     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1979     viewport.sendSelection();
1980   }
1981
1982   public void invertColSel_actionPerformed()
1983   {
1984     viewport.invertColumnSelection();
1985     alignPanel.paintAlignment(true);
1986     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1987     viewport.sendSelection();
1988   }
1989
1990   void trimAlignment(boolean trimLeft)
1991   {
1992     ColumnSelection colSel = viewport.getColumnSelection();
1993     int column;
1994
1995     if (colSel.size() > 0)
1996     {
1997       if (trimLeft)
1998       {
1999         column = colSel.getMin();
2000       }
2001       else
2002       {
2003         column = colSel.getMax();
2004       }
2005
2006       SequenceI[] seqs;
2007       if (viewport.getSelectionGroup() != null)
2008       {
2009         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2010                 viewport.getHiddenRepSequences());
2011       }
2012       else
2013       {
2014         seqs = viewport.getAlignment().getSequencesArray();
2015       }
2016
2017       TrimRegionCommand trimRegion;
2018       if (trimLeft)
2019       {
2020         trimRegion = new TrimRegionCommand("Remove Left",
2021                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2022                 viewport.getAlignment(), viewport.getColumnSelection(),
2023                 viewport.getSelectionGroup());
2024         viewport.setStartRes(0);
2025       }
2026       else
2027       {
2028         trimRegion = new TrimRegionCommand("Remove Right",
2029                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2030                 viewport.getAlignment(), viewport.getColumnSelection(),
2031                 viewport.getSelectionGroup());
2032       }
2033
2034       statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2035       addHistoryItem(trimRegion);
2036
2037       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2038       {
2039         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2040                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2041         {
2042           viewport.getAlignment().deleteGroup(sg);
2043         }
2044       }
2045
2046       viewport.firePropertyChange("alignment", null, viewport
2047               .getAlignment().getSequences());
2048     }
2049   }
2050
2051   public void removeGappedColumnMenuItem_actionPerformed()
2052   {
2053     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2054
2055     SequenceI[] seqs;
2056     if (viewport.getSelectionGroup() != null)
2057     {
2058       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2059               viewport.getHiddenRepSequences());
2060       start = viewport.getSelectionGroup().getStartRes();
2061       end = viewport.getSelectionGroup().getEndRes();
2062     }
2063     else
2064     {
2065       seqs = viewport.getAlignment().getSequencesArray();
2066     }
2067
2068     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2069             "Remove Gapped Columns", seqs, start, end,
2070             viewport.getAlignment());
2071
2072     addHistoryItem(removeGapCols);
2073
2074     statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2075
2076     // This is to maintain viewport position on first residue
2077     // of first sequence
2078     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2079     int startRes = seq.findPosition(viewport.startRes);
2080     // ShiftList shifts;
2081     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2082     // edit.alColumnChanges=shifts.getInverse();
2083     // if (viewport.hasHiddenColumns)
2084     // viewport.getColumnSelection().compensateForEdits(shifts);
2085     viewport.setStartRes(seq.findIndex(startRes) - 1);
2086     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2087             .getSequences());
2088
2089   }
2090
2091   public void removeAllGapsMenuItem_actionPerformed()
2092   {
2093     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2094
2095     SequenceI[] seqs;
2096     if (viewport.getSelectionGroup() != null)
2097     {
2098       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2099               viewport.getHiddenRepSequences());
2100       start = viewport.getSelectionGroup().getStartRes();
2101       end = viewport.getSelectionGroup().getEndRes();
2102     }
2103     else
2104     {
2105       seqs = viewport.getAlignment().getSequencesArray();
2106     }
2107
2108     // This is to maintain viewport position on first residue
2109     // of first sequence
2110     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2111     int startRes = seq.findPosition(viewport.startRes);
2112
2113     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2114             viewport.getAlignment()));
2115
2116     viewport.setStartRes(seq.findIndex(startRes) - 1);
2117
2118     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2119             .getSequences());
2120
2121   }
2122
2123   public void findMenuItem_actionPerformed()
2124   {
2125     new Finder(alignPanel);
2126   }
2127
2128   /**
2129    * create a new view derived from the current view
2130    *
2131    * @param viewtitle
2132    * @return frame for the new view
2133    */
2134   public AlignFrame newView(String viewtitle)
2135   {
2136     AlignmentI newal;
2137     if (viewport.hasHiddenRows())
2138     {
2139       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2140               .getFullAlignment().getSequencesArray());
2141     }
2142     else
2143     {
2144       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2145     }
2146
2147     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2148     {
2149       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2150       {
2151         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2152         {
2153           newal.addAnnotation(viewport.getAlignment()
2154                   .getAlignmentAnnotation()[i]);
2155         }
2156       }
2157     }
2158
2159     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2160
2161     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2162     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2163     PaintRefresher.Register(newaf.alignPanel,
2164             newaf.alignPanel.av.getSequenceSetId());
2165
2166     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2167             newaf.alignPanel.av.getSequenceSetId());
2168     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2169             newaf.alignPanel.av.getSequenceSetId());
2170
2171     Vector comps = (Vector) PaintRefresher.components.get(viewport
2172             .getSequenceSetId());
2173     int viewSize = -1;
2174     for (int i = 0; i < comps.size(); i++)
2175     {
2176       if (comps.elementAt(i) instanceof AlignmentPanel)
2177       {
2178         viewSize++;
2179       }
2180     }
2181
2182     String title = new String(this.getTitle());
2183     if (viewtitle != null)
2184     {
2185       title = viewtitle + " ( " + title + ")";
2186     }
2187     else
2188     {
2189       if (title.indexOf("(View") > -1)
2190       {
2191         title = title.substring(0, title.indexOf("(View"));
2192       }
2193       title += "(View " + viewSize + ")";
2194     }
2195
2196     newaf.setTitle(title.toString());
2197
2198     newaf.viewport.historyList = viewport.historyList;
2199     newaf.viewport.redoList = viewport.redoList;
2200     return newaf;
2201   }
2202
2203   /**
2204    *
2205    * @return list of feature groups on the view
2206    */
2207   public String[] getFeatureGroups()
2208   {
2209     FeatureRenderer fr = null;
2210     if (alignPanel != null
2211             && (fr = alignPanel.getFeatureRenderer()) != null)
2212     {
2213       return fr.getGroups();
2214     }
2215     return null;
2216   }
2217
2218   /**
2219    * get sequence feature groups that are hidden or shown
2220    *
2221    * @param visible
2222    *          true is visible
2223    * @return list
2224    */
2225   public String[] getFeatureGroupsOfState(boolean visible)
2226   {
2227     FeatureRenderer fr = null;
2228     if (alignPanel != null
2229             && (fr = alignPanel.getFeatureRenderer()) != null)
2230     {
2231       return fr.getGroups(visible);
2232     }
2233     return null;
2234   }
2235
2236   /**
2237    * Change the display state for the given feature groups
2238    *
2239    * @param groups
2240    *          list of group strings
2241    * @param state
2242    *          visible or invisible
2243    */
2244   public void setFeatureGroupState(String[] groups, boolean state)
2245   {
2246     FeatureRenderer fr = null;
2247     this.sequenceFeatures.setState(true);
2248     viewport.showSequenceFeatures(true);
2249     if (alignPanel != null
2250             && (fr = alignPanel.getFeatureRenderer()) != null)
2251     {
2252       fr.setGroupState(groups, state);
2253       alignPanel.seqPanel.seqCanvas.repaint();
2254       if (alignPanel.overviewPanel != null)
2255       {
2256         alignPanel.overviewPanel.updateOverviewImage();
2257       }
2258     }
2259   }
2260
2261   public void seqLimits_itemStateChanged()
2262   {
2263     viewport.setShowJVSuffix(seqLimits.getState());
2264     alignPanel.fontChanged();
2265     alignPanel.paintAlignment(true);
2266   }
2267
2268   protected void colourTextMenuItem_actionPerformed()
2269   {
2270     viewport.setColourText(colourTextMenuItem.getState());
2271     alignPanel.paintAlignment(true);
2272   }
2273
2274   protected void displayNonconservedMenuItem_actionPerformed()
2275   {
2276     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2277     alignPanel.paintAlignment(true);
2278   }
2279
2280   protected void wrapMenuItem_actionPerformed()
2281   {
2282     viewport.setWrapAlignment(wrapMenuItem.getState());
2283     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2284     scaleAbove.setEnabled(wrapMenuItem.getState());
2285     scaleLeft.setEnabled(wrapMenuItem.getState());
2286     scaleRight.setEnabled(wrapMenuItem.getState());
2287     alignPanel.paintAlignment(true);
2288   }
2289
2290   public void overviewMenuItem_actionPerformed()
2291   {
2292     if (alignPanel.overviewPanel != null)
2293     {
2294       return;
2295     }
2296
2297     Frame frame = new Frame();
2298     OverviewPanel overview = new OverviewPanel(alignPanel);
2299     frame.add(overview);
2300     // +50 must allow for applet frame window
2301     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
2302             overview.getPreferredSize().width,
2303             overview.getPreferredSize().height + 50);
2304
2305     frame.pack();
2306     final AlignmentPanel ap = alignPanel;
2307     frame.addWindowListener(new WindowAdapter()
2308     {
2309       @Override
2310       public void windowClosing(WindowEvent e)
2311       {
2312         if (ap != null)
2313         {
2314           ap.setOverviewPanel(null);
2315         }
2316       };
2317     });
2318
2319     alignPanel.setOverviewPanel(overview);
2320
2321   }
2322
2323   void changeColour(ColourSchemeI cs)
2324   {
2325     int threshold = 0;
2326
2327     if (cs != null)
2328     {
2329       if (viewport.getAbovePIDThreshold())
2330       {
2331         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
2332                 "Background"));
2333       }
2334
2335       if (viewport.getConservationSelected())
2336       {
2337         cs.setConservationApplied(true);
2338         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2339                 cs, "Background"));
2340       }
2341       else
2342       {
2343         cs.setConservationApplied(false);
2344       }
2345     }
2346     viewport.setGlobalColourScheme(cs);
2347
2348     if (alignPanel.getOverviewPanel() != null)
2349     {
2350       alignPanel.getOverviewPanel().updateOverviewImage();
2351     }
2352
2353     jalview.structure.StructureSelectionManager
2354             .getStructureSelectionManager(viewport.applet)
2355             .sequenceColoursChanged(alignPanel);
2356
2357     alignPanel.paintAlignment(true);
2358   }
2359
2360   protected void modifyPID_actionPerformed()
2361   {
2362     if (viewport.getAbovePIDThreshold()
2363             && viewport.getGlobalColourScheme() != null)
2364     {
2365       SliderPanel.setPIDSliderSource(alignPanel,
2366               viewport.getGlobalColourScheme(), "Background");
2367       SliderPanel.showPIDSlider();
2368     }
2369   }
2370
2371   protected void modifyConservation_actionPerformed()
2372   {
2373     if (viewport.getConservationSelected()
2374             && viewport.getGlobalColourScheme() != null)
2375     {
2376       SliderPanel.setConservationSlider(alignPanel,
2377               viewport.getGlobalColourScheme(), "Background");
2378       SliderPanel.showConservationSlider();
2379     }
2380   }
2381
2382   protected void conservationMenuItem_actionPerformed()
2383   {
2384     viewport.setConservationSelected(conservationMenuItem.getState());
2385
2386     viewport.setAbovePIDThreshold(false);
2387     abovePIDThreshold.setState(false);
2388
2389     changeColour(viewport.getGlobalColourScheme());
2390
2391     modifyConservation_actionPerformed();
2392   }
2393
2394   public void abovePIDThreshold_actionPerformed()
2395   {
2396     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2397
2398     conservationMenuItem.setState(false);
2399     viewport.setConservationSelected(false);
2400
2401     changeColour(viewport.getGlobalColourScheme());
2402
2403     modifyPID_actionPerformed();
2404   }
2405
2406   public void sortPairwiseMenuItem_actionPerformed()
2407   {
2408     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2409     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2410             .getAlignment().getSequenceAt(0), null);
2411
2412     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2413             viewport.getAlignment()));
2414     alignPanel.paintAlignment(true);
2415   }
2416
2417   public void sortIDMenuItem_actionPerformed()
2418   {
2419     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2420     AlignmentSorter.sortByID(viewport.getAlignment());
2421     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2422             viewport.getAlignment()));
2423     alignPanel.paintAlignment(true);
2424   }
2425
2426   public void sortLengthMenuItem_actionPerformed()
2427   {
2428     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2429     AlignmentSorter.sortByLength(viewport.getAlignment());
2430     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2431             viewport.getAlignment()));
2432     alignPanel.paintAlignment(true);
2433   }
2434
2435   public void sortGroupMenuItem_actionPerformed()
2436   {
2437     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2438     AlignmentSorter.sortByGroup(viewport.getAlignment());
2439     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2440             viewport.getAlignment()));
2441     alignPanel.paintAlignment(true);
2442
2443   }
2444
2445   public void removeRedundancyMenuItem_actionPerformed()
2446   {
2447     new RedundancyPanel(alignPanel);
2448   }
2449
2450   public void pairwiseAlignmentMenuItem_actionPerformed()
2451   {
2452     if (viewport.getSelectionGroup() != null
2453             && viewport.getSelectionGroup().getSize() > 1)
2454     {
2455       Frame frame = new Frame();
2456       frame.add(new PairwiseAlignPanel(alignPanel));
2457       jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
2458               500);
2459     }
2460   }
2461
2462   public void PCAMenuItem_actionPerformed()
2463   {
2464     // are the sequences aligned?
2465     if (!viewport.getAlignment().isAligned(false))
2466     {
2467       SequenceI current;
2468       int Width = viewport.getAlignment().getWidth();
2469
2470       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2471       {
2472         current = viewport.getAlignment().getSequenceAt(i);
2473
2474         if (current.getLength() < Width)
2475         {
2476           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2477         }
2478       }
2479       alignPanel.paintAlignment(true);
2480     }
2481
2482     if ((viewport.getSelectionGroup() != null
2483             && viewport.getSelectionGroup().getSize() < 4 && viewport
2484             .getSelectionGroup().getSize() > 0)
2485             || viewport.getAlignment().getHeight() < 4)
2486     {
2487       return;
2488     }
2489
2490     try
2491     {
2492       new PCAPanel(viewport);
2493     } catch (java.lang.OutOfMemoryError ex)
2494     {
2495     }
2496
2497   }
2498
2499   public void averageDistanceTreeMenuItem_actionPerformed()
2500   {
2501     NewTreePanel("AV", "PID", "Average distance tree using PID");
2502   }
2503
2504   public void neighbourTreeMenuItem_actionPerformed()
2505   {
2506     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2507   }
2508
2509   protected void njTreeBlosumMenuItem_actionPerformed()
2510   {
2511     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2512   }
2513
2514   protected void avTreeBlosumMenuItem_actionPerformed()
2515   {
2516     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2517   }
2518
2519   void NewTreePanel(String type, String pwType, String title)
2520   {
2521     // are the sequences aligned?
2522     if (!viewport.getAlignment().isAligned(false))
2523     {
2524       SequenceI current;
2525       int Width = viewport.getAlignment().getWidth();
2526
2527       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2528       {
2529         current = viewport.getAlignment().getSequenceAt(i);
2530
2531         if (current.getLength() < Width)
2532         {
2533           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2534         }
2535       }
2536       alignPanel.paintAlignment(true);
2537
2538     }
2539
2540     if ((viewport.getSelectionGroup() != null && viewport
2541             .getSelectionGroup().getSize() > 1)
2542             || (viewport.getAlignment().getHeight() > 1))
2543     {
2544       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2545
2546       addTreeMenuItem(tp, title);
2547
2548       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2549     }
2550   }
2551
2552   void loadTree_actionPerformed()
2553   {
2554     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2555     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2556     cap.setTreeImport();
2557     Frame frame = new Frame();
2558     frame.add(cap);
2559     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
2560   }
2561
2562   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2563   {
2564     TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
2565     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2566     addTreeMenuItem(tp, treeFile);
2567   }
2568
2569   /**
2570    * sort the alignment using the given treePanel
2571    *
2572    * @param treePanel
2573    *          tree used to sort view
2574    * @param title
2575    *          string used for undo event name
2576    */
2577   public void sortByTree(TreePanel treePanel, String title)
2578   {
2579     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2580     AlignmentSorter
2581             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2582     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2583     // HistoryItem.SORT));
2584     addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
2585             viewport.getAlignment()));
2586     alignPanel.paintAlignment(true);
2587   }
2588
2589   /**
2590    * Do any automatic reordering of the alignment and add the necessary bits to
2591    * the menu structure for the new tree
2592    *
2593    * @param treePanel
2594    * @param title
2595    */
2596   protected void addTreeMenuItem(final TreePanel treePanel,
2597           final String title)
2598   {
2599     final MenuItem item = new MenuItem(title);
2600     sortByTreeMenu.add(item);
2601     item.addActionListener(new java.awt.event.ActionListener()
2602     {
2603       @Override
2604       public void actionPerformed(ActionEvent evt)
2605       {
2606         sortByTree(treePanel, title); // treePanel.getTitle());
2607       }
2608     });
2609
2610     treePanel.addWindowListener(new WindowAdapter()
2611     {
2612       @Override
2613       public void windowOpened(WindowEvent e)
2614       {
2615         if (viewport.sortByTree)
2616         {
2617           sortByTree(treePanel, title);
2618         }
2619         super.windowOpened(e);
2620       }
2621
2622       @Override
2623       public void windowClosing(WindowEvent e)
2624       {
2625         sortByTreeMenu.remove(item);
2626       };
2627     });
2628   }
2629
2630   public boolean sortBy(AlignmentOrder alorder, String undoname)
2631   {
2632     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2633     if (viewport.applet.debug)
2634     {
2635       System.err.println("Sorting " + alorder.getOrder().size()
2636               + " in alignment '" + getTitle() + "'");
2637     }
2638     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2639     if (undoname != null)
2640     {
2641       addHistoryItem(new OrderCommand(undoname, oldOrder,
2642               viewport.getAlignment()));
2643     }
2644     alignPanel.paintAlignment(true);
2645     return true;
2646   }
2647
2648   protected void documentation_actionPerformed()
2649   {
2650     alignPanel.av.applet.openJalviewHelpUrl();
2651   }
2652
2653   protected void about_actionPerformed()
2654   {
2655
2656     class AboutPanel extends Canvas
2657     {
2658       String version;
2659
2660       String builddate;
2661
2662       public AboutPanel(String version, String builddate)
2663       {
2664         this.version = version;
2665         this.builddate = builddate;
2666       }
2667
2668       @Override
2669       public void paint(Graphics g)
2670       {
2671         g.setColor(Color.white);
2672         g.fillRect(0, 0, getSize().width, getSize().height);
2673         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2674         FontMetrics fm = g.getFontMetrics();
2675         int fh = fm.getHeight();
2676         int y = 5, x = 7;
2677         g.setColor(Color.black);
2678         // TODO: update this text for each release or centrally store it for
2679         // lite and application
2680         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2681         g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
2682         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2683         g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
2684         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2685         g.drawString(
2686                 MessageManager.getString("label.jalview_authors_1"),
2687                 x, y += fh * 1.5);
2688         g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
2689         g.drawString(
2690                 MessageManager.getString("label.jalview_dev_managers"),
2691                 x, y += fh);
2692         g.drawString(
2693                 MessageManager.getString("label.jalview_distribution_lists"),
2694                 x, y += fh);
2695         g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
2696         g.drawString(
2697                 MessageManager.getString("label.jalview_cite_1_authors"),
2698                 x, y += fh);
2699         g.drawString(
2700                 MessageManager.getString("label.jalview_cite_1_title"),
2701                 x, y += fh);
2702         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2703                 x, y += fh);
2704       }
2705     }
2706
2707     Frame frame = new Frame();
2708     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2709             .getBuildDate()));
2710     jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
2711
2712   }
2713
2714   public void showURL(String url, String target)
2715   {
2716     if (viewport.applet == null)
2717     {
2718       System.out.println("Not running as applet - no browser available.");
2719     }
2720     else
2721     {
2722       viewport.applet.showURL(url, target);
2723     }
2724   }
2725
2726   // ////////////////////////////////////////////////////////////////////////////////
2727   // JBuilder Graphics here
2728
2729   MenuBar alignFrameMenuBar = new MenuBar();
2730
2731   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2732
2733   MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
2734
2735   MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
2736
2737   MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
2738
2739   MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
2740
2741   MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
2742
2743   MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
2744
2745   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2746
2747   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2748
2749   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2750
2751   Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
2752
2753   MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
2754
2755   MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
2756
2757   MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
2758
2759   MenuItem remove2LeftMenuItem = new MenuItem();
2760
2761   MenuItem remove2RightMenuItem = new MenuItem();
2762
2763   MenuItem removeGappedColumnMenuItem = new MenuItem();
2764
2765   MenuItem removeAllGapsMenuItem = new MenuItem();
2766
2767   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2768
2769   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2770
2771   MenuItem sortPairwiseMenuItem = new MenuItem();
2772
2773   MenuItem sortIDMenuItem = new MenuItem();
2774
2775   MenuItem sortLengthMenuItem = new MenuItem();
2776
2777   MenuItem sortGroupMenuItem = new MenuItem();
2778
2779   MenuItem removeRedundancyMenuItem = new MenuItem();
2780
2781   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2782
2783   MenuItem PCAMenuItem = new MenuItem();
2784
2785   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2786
2787   MenuItem neighbourTreeMenuItem = new MenuItem();
2788
2789   BorderLayout borderLayout1 = new BorderLayout();
2790
2791   public Label statusBar = new Label();
2792
2793   Menu outputTextboxMenu = new Menu();
2794
2795   MenuItem clustalColour = new MenuItem();
2796
2797   MenuItem zappoColour = new MenuItem();
2798
2799   MenuItem taylorColour = new MenuItem();
2800
2801   MenuItem hydrophobicityColour = new MenuItem();
2802
2803   MenuItem helixColour = new MenuItem();
2804
2805   MenuItem strandColour = new MenuItem();
2806
2807   MenuItem turnColour = new MenuItem();
2808
2809   MenuItem buriedColour = new MenuItem();
2810
2811   MenuItem purinePyrimidineColour = new MenuItem();
2812
2813   MenuItem RNAHelixColour = new MenuItem();
2814
2815   MenuItem userDefinedColour = new MenuItem();
2816
2817   MenuItem PIDColour = new MenuItem();
2818
2819   MenuItem BLOSUM62Colour = new MenuItem();
2820
2821   MenuItem tcoffeeColour = new MenuItem();
2822
2823   MenuItem njTreeBlosumMenuItem = new MenuItem();
2824
2825   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2826
2827   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2828
2829   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2830
2831   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2832
2833   MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
2834
2835   MenuItem overviewMenuItem = new MenuItem();
2836
2837   MenuItem undoMenuItem = new MenuItem();
2838
2839   MenuItem redoMenuItem = new MenuItem();
2840
2841   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2842
2843   MenuItem noColourmenuItem = new MenuItem();
2844
2845   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2846
2847   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2848
2849   MenuItem findMenuItem = new MenuItem();
2850
2851   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2852
2853   MenuItem nucleotideColour = new MenuItem();
2854
2855   MenuItem deleteGroups = new MenuItem();
2856
2857   MenuItem grpsFromSelection = new MenuItem();
2858
2859   MenuItem createGroup = new MenuItem();
2860
2861   MenuItem unGroup = new MenuItem();
2862
2863   MenuItem delete = new MenuItem();
2864
2865   MenuItem copy = new MenuItem();
2866
2867   MenuItem cut = new MenuItem();
2868
2869   Menu pasteMenu = new Menu();
2870
2871   MenuItem pasteNew = new MenuItem();
2872
2873   MenuItem pasteThis = new MenuItem();
2874
2875   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2876
2877   MenuItem font = new MenuItem();
2878
2879   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2880
2881   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2882
2883   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2884
2885   MenuItem modifyPID = new MenuItem();
2886
2887   MenuItem modifyConservation = new MenuItem();
2888
2889   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2890           "Autocalculate Consensus", true);
2891
2892   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2893           "Sort Alignment With New Tree", true);
2894
2895   Menu sortByTreeMenu = new Menu();
2896
2897   Menu sort = new Menu();
2898
2899   Menu calculate = new Menu();
2900
2901   MenuItem inputText = new MenuItem();
2902
2903   Menu helpMenu = new Menu();
2904
2905   MenuItem documentation = new MenuItem();
2906
2907   MenuItem about = new MenuItem();
2908
2909   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2910
2911   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2912
2913   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2914
2915   Menu autoAnnMenu = new Menu();
2916
2917   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2918
2919   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2920
2921   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2922
2923   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2924
2925   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2926
2927   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2928
2929   private void jbInit() throws Exception
2930   {
2931
2932     setMenuBar(alignFrameMenuBar);
2933
2934     MenuItem item;
2935
2936     // dynamically fill save as menu with available formats
2937     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2938     {
2939
2940       item = new MenuItem(
2941               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2942
2943       item.addActionListener(new java.awt.event.ActionListener()
2944       {
2945         @Override
2946         public void actionPerformed(ActionEvent e)
2947         {
2948           outputText_actionPerformed(e);
2949         }
2950       });
2951
2952       outputTextboxMenu.add(item);
2953     }
2954     closeMenuItem.addActionListener(this);
2955     loadApplication.addActionListener(this);
2956
2957     loadTree.addActionListener(this);
2958     loadAnnotations.addActionListener(this);
2959     outputFeatures.addActionListener(this);
2960     outputAnnotations.addActionListener(this);
2961     selectAllSequenceMenuItem.addActionListener(this);
2962     deselectAllSequenceMenuItem.addActionListener(this);
2963     invertSequenceMenuItem.addActionListener(this);
2964     remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
2965     remove2LeftMenuItem.addActionListener(this);
2966     remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
2967     remove2RightMenuItem.addActionListener(this);
2968     removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
2969     removeGappedColumnMenuItem.addActionListener(this);
2970     removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
2971     removeAllGapsMenuItem.addActionListener(this);
2972     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
2973     viewBoxesMenuItem.setState(true);
2974     viewBoxesMenuItem.addItemListener(this);
2975     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
2976     viewTextMenuItem.setState(true);
2977     viewTextMenuItem.addItemListener(this);
2978     sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
2979     sortPairwiseMenuItem.addActionListener(this);
2980     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
2981     sortIDMenuItem.addActionListener(this);
2982     sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
2983     sortLengthMenuItem.addActionListener(this);
2984     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
2985     sortGroupMenuItem.addActionListener(this);
2986     removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
2987     removeRedundancyMenuItem.addActionListener(this);
2988     pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
2989     pairwiseAlignmentMenuItem.addActionListener(this);
2990     PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
2991     PCAMenuItem.addActionListener(this);
2992     averageDistanceTreeMenuItem
2993             .setLabel(MessageManager.getString("label.average_distance_identity"));
2994     averageDistanceTreeMenuItem.addActionListener(this);
2995     neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
2996     neighbourTreeMenuItem.addActionListener(this);
2997     statusBar.setBackground(Color.white);
2998     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2999     statusBar.setText(MessageManager.getString("label.status_bar"));
3000     outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
3001     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3002
3003     clustalColour.addActionListener(this);
3004     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3005     zappoColour.addActionListener(this);
3006     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3007     taylorColour.addActionListener(this);
3008     hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
3009     hydrophobicityColour.addActionListener(this);
3010     helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
3011     helixColour.addActionListener(this);
3012     strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
3013     strandColour.addActionListener(this);
3014     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3015     turnColour.addActionListener(this);
3016     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3017     buriedColour.addActionListener(this);
3018     purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
3019     purinePyrimidineColour.addActionListener(this);
3020     RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
3021     RNAHelixColour.addActionListener(this);
3022     userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
3023     userDefinedColour.addActionListener(this);
3024     PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
3025     PIDColour.addActionListener(this);
3026     BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
3027     BLOSUM62Colour.addActionListener(this);
3028     tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
3029     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3030                                      // provided
3031     tcoffeeColour.addActionListener(this);
3032     avDistanceTreeBlosumMenuItem
3033             .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
3034     avDistanceTreeBlosumMenuItem.addActionListener(this);
3035     njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
3036     njTreeBlosumMenuItem.addActionListener(this);
3037     annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
3038     annotationPanelMenuItem.addItemListener(this);
3039     colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
3040     colourTextMenuItem.addItemListener(this);
3041     displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
3042     displayNonconservedMenuItem.addItemListener(this);
3043     alProperties.addActionListener(this);
3044     overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
3045     overviewMenuItem.addActionListener(this);
3046     undoMenuItem.setEnabled(false);
3047     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3048     undoMenuItem.addActionListener(this);
3049     redoMenuItem.setEnabled(false);
3050     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3051     redoMenuItem.addActionListener(this);
3052     conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
3053     conservationMenuItem.addItemListener(this);
3054     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3055     noColourmenuItem.addActionListener(this);
3056     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3057     wrapMenuItem.addItemListener(this);
3058     renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
3059     renderGapsMenuItem.setState(true);
3060     renderGapsMenuItem.addItemListener(this);
3061     findMenuItem.setLabel(MessageManager.getString("action.find"));
3062     findMenuItem.addActionListener(this);
3063     abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
3064     abovePIDThreshold.addItemListener(this);
3065     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3066     nucleotideColour.addActionListener(this);
3067     deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
3068     deleteGroups.addActionListener(this);
3069     grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
3070     grpsFromSelection.addActionListener(this);
3071     createGroup.setLabel(MessageManager.getString("action.create_group"));
3072     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3073     copy.setLabel(MessageManager.getString("action.copy"));
3074     copy.addActionListener(this);
3075     cut.setLabel(MessageManager.getString("action.cut"));
3076     cut.addActionListener(this);
3077     delete.setLabel(MessageManager.getString("action.delete"));
3078     delete.addActionListener(this);
3079     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3080     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3081     pasteNew.addActionListener(this);
3082     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3083     pasteThis.addActionListener(this);
3084     applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
3085     applyToAllGroups.setState(true);
3086     applyToAllGroups.addItemListener(this);
3087     font.setLabel(MessageManager.getString("action.font"));
3088     font.addActionListener(this);
3089     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3090     scaleAbove.setState(true);
3091     scaleAbove.setEnabled(false);
3092     scaleAbove.addItemListener(this);
3093     scaleLeft.setEnabled(false);
3094     scaleLeft.setState(true);
3095     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3096     scaleLeft.addItemListener(this);
3097     scaleRight.setEnabled(false);
3098     scaleRight.setState(true);
3099     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3100     scaleRight.addItemListener(this);
3101     modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
3102     modifyPID.addActionListener(this);
3103     modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
3104     modifyConservation.addActionListener(this);
3105     sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
3106     sort.setLabel(MessageManager.getString("action.sort"));
3107     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3108     autoCalculate.addItemListener(this);
3109     sortByTree.addItemListener(this);
3110     inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
3111     inputText.addActionListener(this);
3112     centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
3113     centreColumnLabelFlag.addItemListener(this);
3114     followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
3115     followMouseOverFlag.addItemListener(this);
3116     helpMenu.setLabel(MessageManager.getString("action.help"));
3117     documentation.setLabel(MessageManager.getString("label.documentation"));
3118     documentation.addActionListener(this);
3119
3120     about.setLabel(MessageManager.getString("label.about"));
3121     about.addActionListener(this);
3122     seqLimits.setState(true);
3123     seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
3124     seqLimits.addItemListener(this);
3125     featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
3126     featureSettings.addActionListener(this);
3127     sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
3128     sequenceFeatures.addItemListener(this);
3129     sequenceFeatures.setState(false);
3130     annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
3131     annotationColour.addActionListener(this);
3132     invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
3133     invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
3134     menu1.setLabel(MessageManager.getString("action.show"));
3135     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3136     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3137     menu2.setLabel(MessageManager.getString("action.hide"));
3138     hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
3139     hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
3140     hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
3141     hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
3142     showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
3143     showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
3144     showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
3145     showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
3146     showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
3147     normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
3148     applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
3149     applyAutoAnnotationSettings.setState(true);
3150     autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
3151
3152     invertColSel.addActionListener(this);
3153     showColumns.addActionListener(this);
3154     showSeqs.addActionListener(this);
3155     hideColumns.addActionListener(this);
3156     hideSequences.addActionListener(this);
3157     hideAllButSelection.addActionListener(this);
3158     hideAllSelection.addActionListener(this);
3159     showAllHidden.addActionListener(this);
3160     showGroupConsensus.addItemListener(this);
3161     showGroupConservation.addItemListener(this);
3162     showConsensusHistogram.addItemListener(this);
3163     showSequenceLogo.addItemListener(this);
3164     normSequenceLogo.addItemListener(this);
3165
3166     applyAutoAnnotationSettings.addItemListener(this);
3167     formatMenu.setLabel(MessageManager.getString("action.format"));
3168     selectMenu.setLabel(MessageManager.getString("action.select"));
3169     newView.setLabel(MessageManager.getString("action.new_view"));
3170     newView.addActionListener(this);
3171     alignFrameMenuBar.add(fileMenu);
3172     alignFrameMenuBar.add(editMenu);
3173     alignFrameMenuBar.add(selectMenu);
3174     alignFrameMenuBar.add(viewMenu);
3175     alignFrameMenuBar.add(formatMenu);
3176     alignFrameMenuBar.add(colourMenu);
3177     alignFrameMenuBar.add(calculateMenu);
3178     alignFrameMenuBar.add(helpMenu);
3179
3180     fileMenu.add(inputText);
3181     fileMenu.add(loadTree);
3182     fileMenu.add(loadAnnotations);
3183
3184     fileMenu.addSeparator();
3185     fileMenu.add(outputTextboxMenu);
3186     fileMenu.add(outputFeatures);
3187     fileMenu.add(outputAnnotations);
3188
3189     if (jalviewServletURL != null)
3190     {
3191       fileMenu.add(loadApplication);
3192     }
3193
3194     fileMenu.addSeparator();
3195     fileMenu.add(closeMenuItem);
3196
3197     editMenu.add(undoMenuItem);
3198     editMenu.add(redoMenuItem);
3199     editMenu.add(cut);
3200     editMenu.add(copy);
3201     editMenu.add(pasteMenu);
3202     editMenu.add(delete);
3203     editMenu.addSeparator();
3204     editMenu.add(remove2LeftMenuItem);
3205     editMenu.add(remove2RightMenuItem);
3206     editMenu.add(removeGappedColumnMenuItem);
3207     editMenu.add(removeAllGapsMenuItem);
3208     editMenu.add(removeRedundancyMenuItem);
3209     viewMenu.add(newView);
3210     viewMenu.addSeparator();
3211     viewMenu.add(menu1);
3212     viewMenu.add(menu2);
3213     viewMenu.addSeparator();
3214     viewMenu.add(followMouseOverFlag);
3215     viewMenu.add(annotationPanelMenuItem);
3216     autoAnnMenu.add(applyAutoAnnotationSettings);
3217     autoAnnMenu.add(showConsensusHistogram);
3218     autoAnnMenu.add(showSequenceLogo);
3219     autoAnnMenu.add(normSequenceLogo);
3220     autoAnnMenu.addSeparator();
3221     autoAnnMenu.add(showGroupConservation);
3222     autoAnnMenu.add(showGroupConsensus);
3223     viewMenu.add(autoAnnMenu);
3224     viewMenu.addSeparator();
3225     viewMenu.add(sequenceFeatures);
3226     viewMenu.add(featureSettings);
3227     viewMenu.addSeparator();
3228     viewMenu.add(alProperties);
3229     viewMenu.addSeparator();
3230     viewMenu.add(overviewMenuItem);
3231     colourMenu.add(applyToAllGroups);
3232     colourMenu.addSeparator();
3233     colourMenu.add(noColourmenuItem);
3234     colourMenu.add(clustalColour);
3235     colourMenu.add(BLOSUM62Colour);
3236     colourMenu.add(PIDColour);
3237     colourMenu.add(zappoColour);
3238     colourMenu.add(taylorColour);
3239     colourMenu.add(hydrophobicityColour);
3240     colourMenu.add(helixColour);
3241     colourMenu.add(strandColour);
3242     colourMenu.add(turnColour);
3243     colourMenu.add(buriedColour);
3244     colourMenu.add(nucleotideColour);
3245     colourMenu.add(purinePyrimidineColour);
3246     colourMenu.add(tcoffeeColour);
3247     colourMenu.add(userDefinedColour);
3248     colourMenu.addSeparator();
3249     colourMenu.add(conservationMenuItem);
3250     colourMenu.add(modifyConservation);
3251     colourMenu.add(abovePIDThreshold);
3252     colourMenu.add(modifyPID);
3253     colourMenu.add(annotationColour);
3254     colourMenu.add(RNAHelixColour);
3255     calculateMenu.add(sort);
3256     calculateMenu.add(calculate);
3257     calculateMenu.addSeparator();
3258     calculateMenu.add(pairwiseAlignmentMenuItem);
3259     calculateMenu.add(PCAMenuItem);
3260     calculateMenu.add(autoCalculate);
3261     calculateMenu.add(sortByTree);
3262     this.add(statusBar, BorderLayout.SOUTH);
3263     pasteMenu.add(pasteNew);
3264     pasteMenu.add(pasteThis);
3265     sort.add(sortIDMenuItem);
3266     sort.add(sortLengthMenuItem);
3267     sort.add(sortByTreeMenu);
3268     sort.add(sortGroupMenuItem);
3269     sort.add(sortPairwiseMenuItem);
3270     calculate.add(averageDistanceTreeMenuItem);
3271     calculate.add(neighbourTreeMenuItem);
3272     calculate.add(avDistanceTreeBlosumMenuItem);
3273     calculate.add(njTreeBlosumMenuItem);
3274     helpMenu.add(documentation);
3275     helpMenu.add(about);
3276     menu1.add(showColumns);
3277     menu1.add(showSeqs);
3278     menu1.add(showAllHidden);
3279     menu2.add(hideColumns);
3280     menu2.add(hideSequences);
3281     menu2.add(hideAllSelection);
3282     menu2.add(hideAllButSelection);
3283     formatMenu.add(font);
3284     formatMenu.add(seqLimits);
3285     formatMenu.add(wrapMenuItem);
3286     formatMenu.add(scaleAbove);
3287     formatMenu.add(scaleLeft);
3288     formatMenu.add(scaleRight);
3289     formatMenu.add(viewBoxesMenuItem);
3290     formatMenu.add(viewTextMenuItem);
3291     formatMenu.add(colourTextMenuItem);
3292     formatMenu.add(displayNonconservedMenuItem);
3293     formatMenu.add(renderGapsMenuItem);
3294     formatMenu.add(centreColumnLabelFlag);
3295     selectMenu.add(findMenuItem);
3296     selectMenu.addSeparator();
3297     selectMenu.add(selectAllSequenceMenuItem);
3298     selectMenu.add(deselectAllSequenceMenuItem);
3299     selectMenu.add(invertSequenceMenuItem);
3300     selectMenu.add(invertColSel);
3301     selectMenu.add(createGroup);
3302     selectMenu.add(unGroup);
3303     selectMenu.add(grpsFromSelection);
3304     selectMenu.add(deleteGroups);
3305
3306   }
3307
3308
3309   public void setStatus(String string) {
3310     statusBar.setText(string);
3311   };
3312
3313   MenuItem featureSettings = new MenuItem();
3314
3315   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3316
3317   MenuItem annotationColour = new MenuItem();
3318
3319   MenuItem invertColSel = new MenuItem();
3320
3321   Menu menu1 = new Menu();
3322
3323   MenuItem showColumns = new MenuItem();
3324
3325   MenuItem showSeqs = new MenuItem();
3326
3327   Menu menu2 = new Menu();
3328
3329   MenuItem hideColumns = new MenuItem();
3330
3331   MenuItem hideSequences = new MenuItem();
3332
3333   MenuItem hideAllButSelection = new MenuItem();
3334
3335   MenuItem hideAllSelection = new MenuItem();
3336
3337   MenuItem showAllHidden = new MenuItem();
3338
3339   Menu formatMenu = new Menu();
3340
3341   Menu selectMenu = new Menu();
3342
3343   MenuItem newView = new MenuItem();
3344
3345   /**
3346    * Attach the alignFrame panels after embedding menus, if necessary. This used
3347    * to be called setEmbedded, but is now creates the dropdown menus in a
3348    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3349    *
3350    * @param reallyEmbedded
3351    *          true to attach the view to the applet area on the page rather than
3352    *          in a new window
3353    */
3354   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3355   {
3356     if (reallyEmbedded)
3357     {
3358       // ////
3359       // Explicly build the embedded menu panel for the on-page applet
3360       //
3361       // view cannot be closed if its actually on the page
3362       fileMenu.remove(closeMenuItem);
3363       fileMenu.remove(3); // Remove Seperator
3364       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3365               Font.PLAIN, 10, false); // use our own fonts.
3366       // and actually add the components to the applet area
3367       viewport.applet.setLayout(new BorderLayout());
3368       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3369       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3370       alignPanel.setSize(viewport.applet.getSize().width,
3371               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3372                       - statusBar.HEIGHT);
3373       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3374       final AlignFrame me = this;
3375       viewport.applet.addFocusListener(new FocusListener()
3376       {
3377
3378         @Override
3379         public void focusLost(FocusEvent e)
3380         {
3381           if (me.viewport.applet.currentAlignFrame == me)
3382           {
3383             me.viewport.applet.currentAlignFrame = null;
3384           }
3385         }
3386
3387         @Override
3388         public void focusGained(FocusEvent e)
3389         {
3390           me.viewport.applet.currentAlignFrame = me;
3391         }
3392       });
3393       viewport.applet.validate();
3394     }
3395     else
3396     {
3397       // //////
3398       // test and embed menu bar if necessary.
3399       //
3400       if (embedMenuIfNeeded(alignPanel))
3401       {
3402         // adjust for status bar height too
3403         alignPanel.setSize(getSize().width, getSize().height
3404                 - statusBar.HEIGHT);
3405       }
3406       add(statusBar, BorderLayout.SOUTH);
3407       add(alignPanel, BorderLayout.CENTER);
3408       // and register with the applet so it can pass external API calls to us
3409       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3410               DEFAULT_HEIGHT);
3411     }
3412   }
3413
3414   /**
3415    * create a new binding between structures in an existing jmol viewer instance
3416    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3417    * this does not open a new Jmol window, or modify the display of the
3418    * structures in the original jmol window. Note This method doesn't work
3419    * without an additional javascript library to exchange messages between the
3420    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3421    *
3422    * @param viewer
3423    *          JmolViewer instance
3424    * @param sequenceIds
3425    *          - sequence Ids to search for associations
3426    */
3427   public SequenceStructureBinding addStructureViewInstance(
3428           Object jmolviewer, String[] sequenceIds)
3429   {
3430     org.jmol.api.JmolViewer viewer = null;
3431     try
3432     {
3433       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3434     } catch (ClassCastException ex)
3435     {
3436       System.err.println("Unsupported viewer object :"
3437               + jmolviewer.getClass());
3438     }
3439     if (viewer == null)
3440     {
3441       System.err.println("Can't use this object as a structure viewer:"
3442               + jmolviewer.getClass());
3443       return null;
3444     }
3445     SequenceI[] seqs = null;
3446     if (sequenceIds == null || sequenceIds.length == 0)
3447     {
3448       seqs = viewport.getAlignment().getSequencesArray();
3449     }
3450     else
3451     {
3452       Vector sqi = new Vector();
3453       AlignmentI al = viewport.getAlignment();
3454       for (int sid = 0; sid < sequenceIds.length; sid++)
3455       {
3456         SequenceI sq = al.findName(sequenceIds[sid]);
3457         if (sq != null)
3458         {
3459           sqi.addElement(sq);
3460         }
3461       }
3462       if (sqi.size() > 0)
3463       {
3464         seqs = new SequenceI[sqi.size()];
3465         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3466         {
3467           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3468         }
3469       }
3470       else
3471       {
3472         return null;
3473       }
3474     }
3475     ExtJmol jmv = null;
3476     // TODO: search for a jmv that involves viewer
3477     if (jmv == null)
3478     { // create a new viewer/jalview binding.
3479       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3480       { seqs });
3481     }
3482     return jmv;
3483
3484   }
3485
3486   /**
3487    * bind a pdb file to a sequence in the current view
3488    *
3489    * @param sequenceId
3490    *          - sequenceId within the dataset.
3491    * @param pdbEntryString
3492    *          - the short name for the PDB file
3493    * @param pdbFile
3494    *          - pdb file - either a URL or a valid PDB file.
3495    * @return true if binding was as success TODO: consider making an exception
3496    *         structure for indicating when PDB parsing or sequenceId location
3497    *         fails.
3498    */
3499   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3500           String pdbFile)
3501   {
3502     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3503     boolean needtoadd = false;
3504     if (toaddpdb != null)
3505     {
3506       Vector pdbe = toaddpdb.getPDBId();
3507       PDBEntry pdbentry = null;
3508       if (pdbe != null && pdbe.size() > 0)
3509       {
3510         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3511         {
3512           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3513           if (!pdbentry.getId().equals(pdbEntryString)
3514                   && !pdbentry.getFile().equals(pdbFile))
3515           {
3516             pdbentry = null;
3517           }
3518           else
3519           {
3520             continue;
3521           }
3522         }
3523       }
3524       if (pdbentry == null)
3525       {
3526         pdbentry = new PDBEntry();
3527         pdbentry.setId(pdbEntryString);
3528         pdbentry.setFile(pdbFile);
3529         needtoadd = true; // add this new entry to sequence.
3530       }
3531       // resolve data source
3532       // TODO: this code should be a refactored to an io package
3533       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3534       if (protocol == null)
3535       {
3536         return false;
3537       }
3538       if (needtoadd)
3539       {
3540         // make a note of the access mode and add
3541         if (pdbentry.getProperty() == null)
3542         {
3543           pdbentry.setProperty(new Hashtable());
3544         }
3545         pdbentry.getProperty().put("protocol", protocol);
3546         toaddpdb.addPDBId(pdbentry);
3547       }
3548     }
3549     return true;
3550   }
3551
3552   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3553   {
3554     if (seqs != null)
3555     {
3556       Vector sequences = new Vector();
3557       for (int i = 0; i < seqs.length; i++)
3558       {
3559         if (seqs[i] != null)
3560         {
3561           sequences.addElement(new Object[]
3562           { seqs[i], (chains != null) ? chains[i] : null });
3563         }
3564       }
3565       seqs = new SequenceI[sequences.size()];
3566       chains = new String[sequences.size()];
3567       for (int i = 0, isize = sequences.size(); i < isize; i++)
3568       {
3569         Object[] oj = (Object[]) sequences.elementAt(i);
3570
3571         seqs[i] = (SequenceI) oj[0];
3572         chains[i] = (String) oj[1];
3573       }
3574     }
3575     return new Object[]
3576     { seqs, chains };
3577
3578   }
3579
3580   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3581           SequenceI[] seqs, String[] chains, String protocol)
3582   {
3583     // Scrub any null sequences from the array
3584     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3585     seqs = (SequenceI[]) sqch[0];
3586     chains = (String[]) sqch[1];
3587     if (seqs == null || seqs.length == 0)
3588     {
3589       System.err
3590               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3591     }
3592     if (protocol == null || protocol.trim().length() == 0
3593             || protocol.equals("null"))
3594     {
3595       protocol = (String) pdb.getProperty().get("protocol");
3596       if (protocol == null)
3597       {
3598         System.err.println("Couldn't work out protocol to open structure: "
3599                 + pdb.getId());
3600         return;
3601       }
3602     }
3603     if (applet.useXtrnalSviewer)
3604     {
3605       // register the association(s) and quit, don't create any windows.
3606       if (StructureSelectionManager.getStructureSelectionManager(applet)
3607               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3608       {
3609         System.err.println("Failed to map " + pdb.getFile() + " ("
3610                 + protocol + ") to any sequences");
3611       }
3612       return;
3613     }
3614     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3615     {
3616       // can only do alignments with Jmol
3617       // find the last jmol window assigned to this alignment
3618       jalview.appletgui.AppletJmol ajm = null, tajm;
3619       Vector jmols = applet
3620               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3621       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3622       {
3623         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3624         if (tajm.ap.alignFrame == this)
3625         {
3626           ajm = tajm;
3627           break;
3628         }
3629       }
3630       if (ajm != null)
3631       {
3632         System.err
3633                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3634         // try and add the pdb structure
3635         // ajm.addS
3636         ajm = null;
3637       }
3638     }
3639     // otherwise, create a new window
3640     if (applet.jmolAvailable)
3641     {
3642       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3643               protocol);
3644       applet.lastFrameX += 40;
3645       applet.lastFrameY += 40;
3646     }
3647     else
3648     {
3649       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3650     }
3651
3652   }
3653
3654   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3655           SequenceI[][] seqs, String[][] chains, String[] protocols)
3656   {
3657     // TODO Auto-generated method stub
3658     System.err.println("Aligned Structure View: Not yet implemented.");
3659   }
3660
3661   /**
3662    * modify the current selection, providing the user has not made a selection
3663    * already.
3664    *
3665    * @param sel
3666    *          - sequences from this alignment
3667    * @param csel
3668    *          - columns to be selected on the alignment
3669    */
3670   public void select(SequenceGroup sel, ColumnSelection csel)
3671   {
3672     alignPanel.seqPanel.selection(sel, csel, null);
3673   }
3674
3675   public void scrollTo(int row, int column)
3676   {
3677     alignPanel.seqPanel.scrollTo(row, column);
3678   }
3679
3680   public void scrollToRow(int row)
3681   {
3682     alignPanel.seqPanel.scrollToRow(row);
3683   }
3684
3685   public void scrollToColumn(int column)
3686   {
3687     alignPanel.seqPanel.scrollToColumn(column);
3688   }
3689
3690   /**
3691    * @return the alignments unique ID.
3692    */
3693   public String getSequenceSetId()
3694   {
3695     return viewport.getSequenceSetId();
3696   }
3697
3698   /**
3699    * Load the (T-Coffee) score file from the specified url
3700    *
3701    * @param source
3702    *          File/URL/T-COFFEE score file contents
3703    * @throws IOException
3704    * @return true if alignment was annotated with data from source
3705    */
3706   public boolean loadScoreFile(String source) throws IOException
3707   {
3708
3709     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3710             AppletFormatAdapter.checkProtocol(source));
3711     if (!file.isValid())
3712     {
3713       // TODO: raise dialog for gui
3714       System.err.println("Problems parsing T-Coffee scores: "
3715               + file.getWarningMessage());
3716       System.err.println("Origin was:\n" + source);
3717       return false;
3718     }
3719
3720     /*
3721      * check that the score matrix matches the alignment dimensions
3722      */
3723     AlignmentI aln;
3724     if ((aln = viewport.getAlignment()) != null
3725             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3726                     .getWidth()))
3727     {
3728       // TODO: raise a dialog box here rather than bomb out.
3729       System.err
3730               .println("The scores matrix does not match the alignment dimensions");
3731
3732     }
3733
3734     // TODO add parameter to indicate if matching should be done
3735     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3736     {
3737       alignPanel.fontChanged();
3738       tcoffeeColour.setEnabled(true);
3739       // switch to this color
3740       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3741       return true;
3742     }
3743     else
3744     {
3745       System.err.println("Problems resolving T-Coffee scores:");
3746       if (file.getWarningMessage() != null)
3747       {
3748         System.err.println(file.getWarningMessage());
3749       }
3750     }
3751     return false;
3752   }
3753
3754 }