src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.FeatureRenderer;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.EditCommand.Action;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.ColumnSelection;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.io.AnnotationFile;
  46 import jalview.io.AppletFormatAdapter;
  47 import jalview.io.FeaturesFile;
  48 import jalview.io.TCoffeeScoreFile;
  49 import jalview.schemes.Blosum62ColourScheme;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.ClustalxColourScheme;
  52 import jalview.schemes.ColourSchemeI;
  53 import jalview.schemes.HelixColourScheme;
  54 import jalview.schemes.HydrophobicColourScheme;
  55 import jalview.schemes.NucleotideColourScheme;
  56 import jalview.schemes.PIDColourScheme;
  57 import jalview.schemes.PurinePyrimidineColourScheme;
  58 import jalview.schemes.RNAHelicesColourChooser;
  59 import jalview.schemes.RNAInteractionColourScheme;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.util.MessageManager;
  67
  68 import java.awt.BorderLayout;
  69 import java.awt.Canvas;
  70 import java.awt.CheckboxMenuItem;
  71 import java.awt.Color;
  72 import java.awt.Font;
  73 import java.awt.FontMetrics;
  74 import java.awt.Frame;
  75 import java.awt.Graphics;
  76 import java.awt.Label;
  77 import java.awt.Menu;
  78 import java.awt.MenuBar;
  79 import java.awt.MenuItem;
  80 import java.awt.event.ActionEvent;
  81 import java.awt.event.ActionListener;
  82 import java.awt.event.FocusEvent;
  83 import java.awt.event.FocusListener;
  84 import java.awt.event.ItemEvent;
  85 import java.awt.event.ItemListener;
  86 import java.awt.event.KeyEvent;
  87 import java.awt.event.KeyListener;
  88 import java.awt.event.WindowAdapter;
  89 import java.awt.event.WindowEvent;
  90 import java.io.IOException;
  91 import java.net.URL;
  92 import java.net.URLEncoder;
  93 import java.util.Arrays;
  94 import java.util.Hashtable;
  95 import java.util.List;
  96 import java.util.Map;
  97 import java.util.StringTokenizer;
  98 import java.util.Vector;
  99
 100 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 101         ItemListener, KeyListener, AlignViewControllerGuiI
 102 {
 103   public AlignViewControllerI avc;
 104
 105   public AlignmentPanel alignPanel;
 106
 107   public AlignViewport viewport;
 108
 109   int DEFAULT_WIDTH = 700;
 110
 111   int DEFAULT_HEIGHT = 500;
 112
 113   String jalviewServletURL;
 114
 115   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 116           String title, boolean embedded)
 117   {
 118     if (applet != null)
 119     {
 120       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 121     }
 122
 123     try
 124     {
 125       jbInit();
 126     } catch (Exception ex)
 127     {
 128       ex.printStackTrace();
 129     }
 130     // need to get window geometry before we calculate alignment layout
 131     if (applet != null)
 132     {
 133       String param;
 134       try
 135       {
 136         param = applet.getParameter("windowWidth");
 137         if (param != null)
 138         {
 139           int width = Integer.parseInt(param);
 140           DEFAULT_WIDTH = width;
 141         }
 142         param = applet.getParameter("windowHeight");
 143         if (param != null)
 144         {
 145           int height = Integer.parseInt(param);
 146           DEFAULT_HEIGHT = height;
 147         }
 148       } catch (Exception ex)
 149       {
 150       }
 151     }
 152     viewport = new AlignViewport(al, applet);
 153     alignPanel = new AlignmentPanel(this, viewport);
 154     avc = new jalview.controller.AlignViewController(this, viewport,
 155             alignPanel);
 156     viewport.updateConservation(alignPanel);
 157     viewport.updateConsensus(alignPanel);
 158
 159     annotationPanelMenuItem.setState(viewport.showAnnotation);
 160     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 161     followMouseOverFlag.setState(viewport.getFollowHighlight());
 162     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 163     showGroupConservation.setState(viewport.isShowGroupConservation());
 164     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 165     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 166     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 167     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 168
 169     seqLimits.setState(viewport.showJVSuffix);
 170
 171     if (applet != null)
 172     {
 173       String param = applet.getParameter("sortBy");
 174       if (param != null)
 175       {
 176         if (param.equalsIgnoreCase("Id"))
 177         {
 178           sortIDMenuItem_actionPerformed();
 179         }
 180         else if (param.equalsIgnoreCase("Pairwise Identity"))
 181         {
 182           sortPairwiseMenuItem_actionPerformed();
 183         }
 184         else if (param.equalsIgnoreCase("Length"))
 185         {
 186           sortLengthMenuItem_actionPerformed();
 187         }
 188       }
 189
 190       param = applet.getParameter("wrap");
 191       if (param != null)
 192       {
 193         if (param.equalsIgnoreCase("true"))
 194         {
 195           wrapMenuItem.setState(true);
 196           wrapMenuItem_actionPerformed();
 197         }
 198       }
 199       param = applet.getParameter("centrecolumnlabels");
 200       if (param != null)
 201       {
 202         centreColumnLabelFlag.setState(true);
 203         centreColumnLabelFlag_stateChanged();
 204       }
 205
 206     }
 207     if (viewport.getAlignment().isNucleotide())
 208     {
 209       viewport.updateStrucConsensus(alignPanel);
 210       if (viewport.getAlignment().hasRNAStructure())
 211       {
 212         RNAHelixColour.setEnabled(true);
 213       }
 214       else
 215       {
 216         RNAHelixColour.setEnabled(false);
 217       }
 218     }
 219     else
 220     {
 221       RNAHelixColour.setEnabled(false);
 222       purinePyrimidineColour.setEnabled(false);
 223     }
 224     // Some JVMS send keyevents to Top frame or lowest panel,
 225     // Havent worked out why yet. So add to both this frame and seqCanvas for
 226     // now
 227     this.addKeyListener(this);
 228     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 229     alignPanel.idPanel.idCanvas.addKeyListener(this);
 230     alignPanel.scalePanel.addKeyListener(this);
 231     alignPanel.annotationPanel.addKeyListener(this);
 232     alignPanel.annotationPanelHolder.addKeyListener(this);
 233     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 234     alignPanel.alabels.addKeyListener(this);
 235     createAlignFrameWindow(embedded, title);
 236
 237     validate();
 238     alignPanel.adjustAnnotationHeight();
 239     alignPanel.paintAlignment(true);
 240   }
 241
 242   public AlignViewport getAlignViewport()
 243   {
 244     return viewport;
 245   }
 246
 247   public SeqCanvas getSeqcanvas()
 248   {
 249     return alignPanel.seqPanel.seqCanvas;
 250   }
 251
 252   /**
 253    * Load a features file onto the alignment
 254    *
 255    * @param file
 256    *          file URL, content, or other resolvable path
 257    * @param type
 258    *          is protocol for accessing data referred to by file
 259    */
 260
 261   public boolean parseFeaturesFile(String file, String type)
 262   {
 263     return parseFeaturesFile(file, type, true);
 264   }
 265
 266   /**
 267    * Load a features file onto the alignment
 268    *
 269    * @param file
 270    *          file URL, content, or other resolvable path
 271    * @param type
 272    *          is protocol for accessing data referred to by file
 273    * @param autoenabledisplay
 274    *          when true, display features flag will be automatically enabled if
 275    *          features are loaded
 276    * @return true if data parsed as a features file
 277    */
 278   public boolean parseFeaturesFile(String file, String type,
 279           boolean autoenabledisplay)
 280   {
 281     // TODO: test if importing a features file onto an alignment which already
 282     // has features with links overwrites the original links.
 283
 284     Hashtable featureLinks = new Hashtable();
 285     boolean featuresFile = false;
 286     try
 287     {
 288       featuresFile = new jalview.io.FeaturesFile(file, type)
 289               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 290                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 291                       true, viewport.applet.getDefaultParameter(
 292                               "relaxedidmatch", false));
 293     } catch (Exception ex)
 294     {
 295       ex.printStackTrace();
 296     }
 297
 298     if (featuresFile)
 299     {
 300       if (featureLinks.size() > 0)
 301       {
 302         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 303       }
 304       if (autoenabledisplay)
 305       {
 306         viewport.setShowSequenceFeatures(true);
 307         sequenceFeatures.setState(true);
 308       }
 309       if (alignPanel.seqPanel.seqCanvas.fr != null)
 310       {
 311         // update the min/max ranges where necessary
 312         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 313       }
 314       if (viewport.featureSettings != null)
 315       {
 316         viewport.featureSettings.refreshTable();
 317       }
 318       alignPanel.paintAlignment(true);
 319       statusBar.setText(MessageManager
 320               .getString("label.successfully_added_features_alignment"));
 321     }
 322     return featuresFile;
 323   }
 324
 325   @Override
 326   public void keyPressed(KeyEvent evt)
 327   {
 328     if (viewport.cursorMode
 329             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 330                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 331                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 332             && Character.isDigit(evt.getKeyChar()))
 333     {
 334       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 335     }
 336
 337     switch (evt.getKeyCode())
 338     {
 339     case 27: // escape key
 340       deselectAllSequenceMenuItem_actionPerformed();
 341
 342       alignPanel.alabels.cancelDrag();
 343       break;
 344     case KeyEvent.VK_X:
 345       if (evt.isControlDown() || evt.isMetaDown())
 346       {
 347         cut_actionPerformed();
 348       }
 349       break;
 350     case KeyEvent.VK_C:
 351       if (viewport.cursorMode && !evt.isControlDown())
 352       {
 353         alignPanel.seqPanel.setCursorColumn();
 354       }
 355       if (evt.isControlDown() || evt.isMetaDown())
 356       {
 357         copy_actionPerformed();
 358       }
 359       break;
 360     case KeyEvent.VK_V:
 361       if (evt.isControlDown())
 362       {
 363         paste(evt.isShiftDown());
 364       }
 365       break;
 366     case KeyEvent.VK_A:
 367       if (evt.isControlDown() || evt.isMetaDown())
 368       {
 369         selectAllSequenceMenuItem_actionPerformed();
 370       }
 371       break;
 372     case KeyEvent.VK_DOWN:
 373       if (viewport.cursorMode)
 374       {
 375         alignPanel.seqPanel.moveCursor(0, 1);
 376       }
 377       else
 378       {
 379         moveSelectedSequences(false);
 380       }
 381       break;
 382
 383     case KeyEvent.VK_UP:
 384       if (viewport.cursorMode)
 385       {
 386         alignPanel.seqPanel.moveCursor(0, -1);
 387       }
 388       else
 389       {
 390         moveSelectedSequences(true);
 391       }
 392       break;
 393
 394     case KeyEvent.VK_LEFT:
 395       if (evt.isAltDown() || !viewport.cursorMode)
 396       {
 397         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 398       }
 399       else
 400       {
 401         alignPanel.seqPanel.moveCursor(-1, 0);
 402       }
 403       break;
 404
 405     case KeyEvent.VK_RIGHT:
 406       if (evt.isAltDown() || !viewport.cursorMode)
 407       {
 408         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 409       }
 410       else
 411       {
 412         alignPanel.seqPanel.moveCursor(1, 0);
 413       }
 414       break;
 415
 416     case KeyEvent.VK_SPACE:
 417       if (viewport.cursorMode)
 418       {
 419         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 420                 || evt.isShiftDown() || evt.isAltDown());
 421       }
 422       break;
 423
 424     case KeyEvent.VK_DELETE:
 425     case KeyEvent.VK_BACK_SPACE:
 426       if (viewport.cursorMode)
 427       {
 428         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 429                 || evt.isShiftDown() || evt.isAltDown());
 430       }
 431       else
 432       {
 433         cut_actionPerformed();
 434         alignPanel.seqPanel.seqCanvas.repaint();
 435       }
 436       break;
 437
 438     case KeyEvent.VK_S:
 439       if (viewport.cursorMode)
 440       {
 441         alignPanel.seqPanel.setCursorRow();
 442       }
 443       break;
 444     case KeyEvent.VK_P:
 445       if (viewport.cursorMode)
 446       {
 447         alignPanel.seqPanel.setCursorPosition();
 448       }
 449       break;
 450
 451     case KeyEvent.VK_ENTER:
 452     case KeyEvent.VK_COMMA:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.setCursorRowAndColumn();
 456       }
 457       break;
 458
 459     case KeyEvent.VK_Q:
 460       if (viewport.cursorMode)
 461       {
 462         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 463       }
 464       break;
 465     case KeyEvent.VK_M:
 466       if (viewport.cursorMode)
 467       {
 468         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 469       }
 470       break;
 471
 472     case KeyEvent.VK_F2:
 473       viewport.cursorMode = !viewport.cursorMode;
 474       statusBar.setText(MessageManager.formatMessage(
 475               "label.keyboard_editing_mode", new String[]
 476               { (viewport.cursorMode ? "on" : "off") }));
 477       if (viewport.cursorMode)
 478       {
 479         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 480         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 481       }
 482       break;
 483
 484     case KeyEvent.VK_F:
 485       if (evt.isControlDown())
 486       {
 487         findMenuItem_actionPerformed();
 488       }
 489       break;
 490
 491     case KeyEvent.VK_H:
 492     {
 493       boolean toggleSeqs = !evt.isControlDown();
 494       boolean toggleCols = !evt.isShiftDown();
 495       toggleHiddenRegions(toggleSeqs, toggleCols);
 496       break;
 497     }
 498
 499     case KeyEvent.VK_PAGE_UP:
 500       if (viewport.wrapAlignment)
 501       {
 502         alignPanel.scrollUp(true);
 503       }
 504       else
 505       {
 506         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 507                 - viewport.endSeq + viewport.startSeq);
 508       }
 509       break;
 510
 511     case KeyEvent.VK_PAGE_DOWN:
 512       if (viewport.wrapAlignment)
 513       {
 514         alignPanel.scrollUp(false);
 515       }
 516       else
 517       {
 518         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 519                 + viewport.endSeq - viewport.startSeq);
 520       }
 521       break;
 522
 523     case KeyEvent.VK_Z:
 524       if (evt.isControlDown())
 525       {
 526         undoMenuItem_actionPerformed();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_Y:
 531       if (evt.isControlDown())
 532       {
 533         redoMenuItem_actionPerformed();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_L:
 538       if (evt.isControlDown())
 539       {
 540         trimAlignment(true);
 541       }
 542       break;
 543
 544     case KeyEvent.VK_R:
 545       if (evt.isControlDown())
 546       {
 547         trimAlignment(false);
 548       }
 549       break;
 550
 551     case KeyEvent.VK_E:
 552       if (evt.isControlDown())
 553       {
 554         if (evt.isShiftDown())
 555         {
 556           this.removeAllGapsMenuItem_actionPerformed();
 557         }
 558         else
 559         {
 560           removeGappedColumnMenuItem_actionPerformed();
 561         }
 562       }
 563       break;
 564     case KeyEvent.VK_I:
 565       if (evt.isControlDown())
 566       {
 567         if (evt.isAltDown())
 568         {
 569           invertColSel_actionPerformed();
 570         }
 571         else
 572         {
 573           invertSequenceMenuItem_actionPerformed();
 574         }
 575       }
 576       break;
 577
 578     case KeyEvent.VK_G:
 579       if (evt.isControlDown())
 580       {
 581         if (evt.isShiftDown())
 582         {
 583           this.unGroup_actionPerformed();
 584         }
 585         else
 586         {
 587           this.createGroup_actionPerformed();
 588         }
 589       }
 590       break;
 591
 592     case KeyEvent.VK_U:
 593       if (evt.isControlDown())
 594       {
 595         this.deleteGroups_actionPerformed();
 596       }
 597       break;
 598
 599     case KeyEvent.VK_T:
 600       if (evt.isControlDown())
 601       {
 602         newView(null);
 603       }
 604       break;
 605
 606     }
 607     alignPanel.paintAlignment(true);
 608   }
 609
 610   /**
 611    * called by key handler and the hide all/show all menu items
 612    *
 613    * @param toggleSeqs
 614    * @param toggleCols
 615    */
 616   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 617   {
 618     boolean hide = false;
 619     SequenceGroup sg = viewport.getSelectionGroup();
 620     if (!toggleSeqs && !toggleCols)
 621     {
 622       // Hide everything by the current selection - this is a hack - we do the
 623       // invert and then hide
 624       // first check that there will be visible columns after the invert.
 625       if ((viewport.getColumnSelection() != null
 626               && viewport.getColumnSelection().getSelected() != null && viewport
 627               .getColumnSelection().getSelected().size() > 0)
 628               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 629                       .getEndRes()))
 630       {
 631         // now invert the sequence set, if required - empty selection implies
 632         // that no hiding is required.
 633         if (sg != null)
 634         {
 635           invertSequenceMenuItem_actionPerformed();
 636           sg = viewport.getSelectionGroup();
 637           toggleSeqs = true;
 638
 639         }
 640         viewport.expandColSelection(sg, true);
 641         // finally invert the column selection and get the new sequence
 642         // selection and indicate it should be hidden.
 643         invertColSel_actionPerformed();
 644         toggleCols = true;
 645       }
 646     }
 647
 648     if (toggleSeqs)
 649     {
 650       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 651       {
 652         hide = true;
 653         viewport.hideAllSelectedSeqs();
 654       }
 655       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 656               .size() > 0))
 657       {
 658         viewport.showAllHiddenSeqs();
 659       }
 660     }
 661
 662     if (toggleCols)
 663     {
 664       if (viewport.getColumnSelection().getSelected().size() > 0)
 665       {
 666         viewport.hideSelectedColumns();
 667         if (!toggleSeqs)
 668         {
 669           viewport.setSelectionGroup(sg);
 670         }
 671       }
 672       else if (!hide)
 673       {
 674         viewport.showAllHiddenColumns();
 675       }
 676     }
 677   }
 678
 679   @Override
 680   public void keyReleased(KeyEvent evt)
 681   {
 682   }
 683
 684   @Override
 685   public void keyTyped(KeyEvent evt)
 686   {
 687   }
 688
 689   @Override
 690   public void itemStateChanged(ItemEvent evt)
 691   {
 692     if (evt.getSource() == displayNonconservedMenuItem)
 693     {
 694       displayNonconservedMenuItem_actionPerformed();
 695     }
 696     else if (evt.getSource() == colourTextMenuItem)
 697     {
 698       colourTextMenuItem_actionPerformed();
 699     }
 700     else if (evt.getSource() == wrapMenuItem)
 701     {
 702       wrapMenuItem_actionPerformed();
 703     }
 704     else if (evt.getSource() == scaleAbove)
 705     {
 706       viewport.setScaleAboveWrapped(scaleAbove.getState());
 707     }
 708     else if (evt.getSource() == scaleLeft)
 709     {
 710       viewport.setScaleLeftWrapped(scaleLeft.getState());
 711     }
 712     else if (evt.getSource() == scaleRight)
 713     {
 714       viewport.setScaleRightWrapped(scaleRight.getState());
 715     }
 716     else if (evt.getSource() == seqLimits)
 717     {
 718       seqLimits_itemStateChanged();
 719     }
 720     else if (evt.getSource() == viewBoxesMenuItem)
 721     {
 722       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 723     }
 724     else if (evt.getSource() == viewTextMenuItem)
 725     {
 726       viewport.setShowText(viewTextMenuItem.getState());
 727     }
 728     else if (evt.getSource() == renderGapsMenuItem)
 729     {
 730       viewport.setRenderGaps(renderGapsMenuItem.getState());
 731     }
 732     else if (evt.getSource() == annotationPanelMenuItem)
 733     {
 734       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 735       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 736     }
 737     else if (evt.getSource() == sequenceFeatures)
 738     {
 739       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 740       alignPanel.seqPanel.seqCanvas.repaint();
 741     }
 742     else if (evt.getSource() == conservationMenuItem)
 743     {
 744       conservationMenuItem_actionPerformed();
 745     }
 746     else if (evt.getSource() == abovePIDThreshold)
 747     {
 748       abovePIDThreshold_actionPerformed();
 749     }
 750     else if (evt.getSource() == applyToAllGroups)
 751     {
 752       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 753     }
 754     else if (evt.getSource() == autoCalculate)
 755     {
 756       viewport.autoCalculateConsensus = autoCalculate.getState();
 757     }
 758     else if (evt.getSource() == sortByTree)
 759     {
 760       viewport.sortByTree = sortByTree.getState();
 761     }
 762     else if (evt.getSource() == this.centreColumnLabelFlag)
 763     {
 764       centreColumnLabelFlag_stateChanged();
 765     }
 766     else if (evt.getSource() == this.followMouseOverFlag)
 767     {
 768       mouseOverFlag_stateChanged();
 769     }
 770     else if (evt.getSource() == showGroupConsensus)
 771     {
 772       showGroupConsensus_actionPerformed();
 773     }
 774     else if (evt.getSource() == showGroupConservation)
 775     {
 776       showGroupConservation_actionPerformed();
 777     }
 778     else if (evt.getSource() == showSequenceLogo)
 779     {
 780       showSequenceLogo_actionPerformed();
 781     }
 782     else if (evt.getSource() == normSequenceLogo)
 783     {
 784       normSequenceLogo_actionPerformed();
 785     }
 786     else if (evt.getSource() == showConsensusHistogram)
 787     {
 788       showConsensusHistogram_actionPerformed();
 789     }
 790     else if (evt.getSource() == applyAutoAnnotationSettings)
 791     {
 792       applyAutoAnnotationSettings_actionPerformed();
 793     }
 794     alignPanel.paintAlignment(true);
 795   }
 796
 797   private void mouseOverFlag_stateChanged()
 798   {
 799     viewport.followHighlight = followMouseOverFlag.getState();
 800     // TODO: could kick the scrollTo mechanism to reset view for current
 801     // searchresults.
 802   }
 803
 804   private void centreColumnLabelFlag_stateChanged()
 805   {
 806     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 807     this.alignPanel.annotationPanel.repaint();
 808   }
 809
 810   @Override
 811   public void actionPerformed(ActionEvent evt)
 812   {
 813     Object source = evt.getSource();
 814
 815     if (source == inputText)
 816     {
 817       inputText_actionPerformed();
 818     }
 819     else if (source == loadTree)
 820     {
 821       loadTree_actionPerformed();
 822     }
 823     else if (source == loadApplication)
 824     {
 825       launchFullApplication();
 826     }
 827     else if (source == loadAnnotations)
 828     {
 829       loadAnnotations();
 830     }
 831     else if (source == outputAnnotations)
 832     {
 833       outputAnnotations(true);
 834     }
 835     else if (source == outputFeatures)
 836     {
 837       outputFeatures(true, "Jalview");
 838     }
 839     else if (source == closeMenuItem)
 840     {
 841       closeMenuItem_actionPerformed();
 842     }
 843     else if (source == copy)
 844     {
 845       copy_actionPerformed();
 846     }
 847     else if (source == undoMenuItem)
 848     {
 849       undoMenuItem_actionPerformed();
 850     }
 851     else if (source == redoMenuItem)
 852     {
 853       redoMenuItem_actionPerformed();
 854     }
 855     else if (source == inputText)
 856     {
 857       inputText_actionPerformed();
 858     }
 859     else if (source == closeMenuItem)
 860     {
 861       closeMenuItem_actionPerformed();
 862     }
 863     else if (source == undoMenuItem)
 864     {
 865       undoMenuItem_actionPerformed();
 866     }
 867     else if (source == redoMenuItem)
 868     {
 869       redoMenuItem_actionPerformed();
 870     }
 871     else if (source == copy)
 872     {
 873       copy_actionPerformed();
 874     }
 875     else if (source == pasteNew)
 876     {
 877       pasteNew_actionPerformed();
 878     }
 879     else if (source == pasteThis)
 880     {
 881       pasteThis_actionPerformed();
 882     }
 883     else if (source == cut)
 884     {
 885       cut_actionPerformed();
 886     }
 887     else if (source == delete)
 888     {
 889       delete_actionPerformed();
 890     }
 891     else if (source == grpsFromSelection)
 892     {
 893       makeGrpsFromSelection_actionPerformed();
 894     }
 895     else if (source == deleteGroups)
 896     {
 897       deleteGroups_actionPerformed();
 898     }
 899     else if (source == selectAllSequenceMenuItem)
 900     {
 901       selectAllSequenceMenuItem_actionPerformed();
 902     }
 903     else if (source == deselectAllSequenceMenuItem)
 904     {
 905       deselectAllSequenceMenuItem_actionPerformed();
 906     }
 907     else if (source == invertSequenceMenuItem)
 908     {
 909       invertSequenceMenuItem_actionPerformed();
 910     }
 911     else if (source == invertColSel)
 912     {
 913       viewport.invertColumnSelection();
 914       alignPanel.paintAlignment(true);
 915     }
 916     else if (source == remove2LeftMenuItem)
 917     {
 918       trimAlignment(true);
 919     }
 920     else if (source == remove2RightMenuItem)
 921     {
 922       trimAlignment(false);
 923     }
 924     else if (source == removeGappedColumnMenuItem)
 925     {
 926       removeGappedColumnMenuItem_actionPerformed();
 927     }
 928     else if (source == removeAllGapsMenuItem)
 929     {
 930       removeAllGapsMenuItem_actionPerformed();
 931     }
 932     else if (source == findMenuItem)
 933     {
 934       findMenuItem_actionPerformed();
 935     }
 936     else if (source == font)
 937     {
 938       new FontChooser(alignPanel);
 939     }
 940     else if (source == newView)
 941     {
 942       newView(null);
 943     }
 944     else if (source == showColumns)
 945     {
 946       viewport.showAllHiddenColumns();
 947       alignPanel.paintAlignment(true);
 948     }
 949     else if (source == showSeqs)
 950     {
 951       viewport.showAllHiddenSeqs();
 952       alignPanel.paintAlignment(true);
 953     }
 954     else if (source == hideColumns)
 955     {
 956       viewport.hideSelectedColumns();
 957       alignPanel.paintAlignment(true);
 958     }
 959     else if (source == hideSequences
 960             && viewport.getSelectionGroup() != null)
 961     {
 962       viewport.hideAllSelectedSeqs();
 963       alignPanel.paintAlignment(true);
 964     }
 965     else if (source == hideAllButSelection)
 966     {
 967       toggleHiddenRegions(false, false);
 968       alignPanel.paintAlignment(true);
 969     }
 970     else if (source == hideAllSelection)
 971     {
 972       SequenceGroup sg = viewport.getSelectionGroup();
 973       viewport.expandColSelection(sg, false);
 974       viewport.hideAllSelectedSeqs();
 975       viewport.hideSelectedColumns();
 976       alignPanel.paintAlignment(true);
 977     }
 978     else if (source == showAllHidden)
 979     {
 980       viewport.showAllHiddenColumns();
 981       viewport.showAllHiddenSeqs();
 982       alignPanel.paintAlignment(true);
 983     }
 984     else if (source == showGroupConsensus)
 985     {
 986       showGroupConsensus_actionPerformed();
 987     }
 988     else if (source == showGroupConservation)
 989     {
 990       showGroupConservation_actionPerformed();
 991     }
 992     else if (source == showSequenceLogo)
 993     {
 994       showSequenceLogo_actionPerformed();
 995     }
 996     else if (source == normSequenceLogo)
 997     {
 998       normSequenceLogo_actionPerformed();
 999     }
1000     else if (source == showConsensusHistogram)
1001     {
1002       showConsensusHistogram_actionPerformed();
1003     }
1004     else if (source == applyAutoAnnotationSettings)
1005     {
1006       applyAutoAnnotationSettings_actionPerformed();
1007     }
1008     else if (source == featureSettings)
1009     {
1010       new FeatureSettings(alignPanel);
1011     }
1012     else if (source == alProperties)
1013     {
1014       StringBuffer contents = new jalview.io.AlignmentProperties(
1015               viewport.getAlignment()).formatAsString();
1016       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1017       cap.setText(contents.toString());
1018       Frame frame = new Frame();
1019       frame.add(cap);
1020       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1021               "label.alignment_properties", new String[]
1022               { getTitle() }), 400, 250);
1023     }
1024     else if (source == overviewMenuItem)
1025     {
1026       overviewMenuItem_actionPerformed();
1027     }
1028     else if (source == noColourmenuItem)
1029     {
1030       changeColour(null);
1031     }
1032     else if (source == clustalColour)
1033     {
1034       abovePIDThreshold.setState(false);
1035       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1036     }
1037     else if (source == zappoColour)
1038     {
1039       changeColour(new ZappoColourScheme());
1040     }
1041     else if (source == taylorColour)
1042     {
1043       changeColour(new TaylorColourScheme());
1044     }
1045     else if (source == hydrophobicityColour)
1046     {
1047       changeColour(new HydrophobicColourScheme());
1048     }
1049     else if (source == helixColour)
1050     {
1051       changeColour(new HelixColourScheme());
1052     }
1053     else if (source == strandColour)
1054     {
1055       changeColour(new StrandColourScheme());
1056     }
1057     else if (source == turnColour)
1058     {
1059       changeColour(new TurnColourScheme());
1060     }
1061     else if (source == buriedColour)
1062     {
1063       changeColour(new BuriedColourScheme());
1064     }
1065     else if (source == nucleotideColour)
1066     {
1067       changeColour(new NucleotideColourScheme());
1068     }
1069     else if (source == purinePyrimidineColour)
1070     {
1071       changeColour(new PurinePyrimidineColourScheme());
1072     }
1073     else if (source == RNAInteractionColour)
1074     {
1075       changeColour(new RNAInteractionColourScheme());
1076     }
1077     else if (source == RNAHelixColour)
1078     {
1079       new RNAHelicesColourChooser(viewport, alignPanel);
1080     }
1081     else if (source == modifyPID)
1082     {
1083       modifyPID_actionPerformed();
1084     }
1085     else if (source == modifyConservation)
1086     {
1087       modifyConservation_actionPerformed();
1088     }
1089     else if (source == userDefinedColour)
1090     {
1091       new UserDefinedColours(alignPanel, null);
1092     }
1093     else if (source == PIDColour)
1094     {
1095       changeColour(new PIDColourScheme());
1096     }
1097     else if (source == BLOSUM62Colour)
1098     {
1099       changeColour(new Blosum62ColourScheme());
1100     }
1101     else if (source == tcoffeeColour)
1102     {
1103       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1104     }
1105     else if (source == annotationColour)
1106     {
1107       new AnnotationColourChooser(viewport, alignPanel);
1108     }
1109     else if (source == sortPairwiseMenuItem)
1110     {
1111       sortPairwiseMenuItem_actionPerformed();
1112     }
1113     else if (source == sortIDMenuItem)
1114     {
1115       sortIDMenuItem_actionPerformed();
1116     }
1117     else if (source == sortLengthMenuItem)
1118     {
1119       sortLengthMenuItem_actionPerformed();
1120     }
1121     else if (source == sortGroupMenuItem)
1122     {
1123       sortGroupMenuItem_actionPerformed();
1124     }
1125     else if (source == removeRedundancyMenuItem)
1126     {
1127       removeRedundancyMenuItem_actionPerformed();
1128     }
1129     else if (source == pairwiseAlignmentMenuItem)
1130     {
1131       pairwiseAlignmentMenuItem_actionPerformed();
1132     }
1133     else if (source == PCAMenuItem)
1134     {
1135       PCAMenuItem_actionPerformed();
1136     }
1137     else if (source == averageDistanceTreeMenuItem)
1138     {
1139       averageDistanceTreeMenuItem_actionPerformed();
1140     }
1141     else if (source == neighbourTreeMenuItem)
1142     {
1143       neighbourTreeMenuItem_actionPerformed();
1144     }
1145     else if (source == njTreeBlosumMenuItem)
1146     {
1147       njTreeBlosumMenuItem_actionPerformed();
1148     }
1149     else if (source == avDistanceTreeBlosumMenuItem)
1150     {
1151       avTreeBlosumMenuItem_actionPerformed();
1152     }
1153     else if (source == documentation)
1154     {
1155       documentation_actionPerformed();
1156     }
1157     else if (source == about)
1158     {
1159       about_actionPerformed();
1160     }
1161
1162   }
1163
1164   public void inputText_actionPerformed()
1165   {
1166     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1167     Frame frame = new Frame();
1168     frame.add(cap);
1169     jalview.bin.JalviewLite.addFrame(frame,
1170             MessageManager.getString("label.input_cut_paste"), 500, 500);
1171   }
1172
1173   protected void outputText_actionPerformed(ActionEvent e)
1174   {
1175     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1176     Frame frame = new Frame();
1177     frame.add(cap);
1178     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1179             "label.alignment_output_command", new String[]
1180             { e.getActionCommand() }), 600, 500);
1181     cap.setText(new AppletFormatAdapter().formatSequences(
1182             e.getActionCommand(), viewport.getAlignment(),
1183             viewport.showJVSuffix));
1184   }
1185
1186   public void loadAnnotations()
1187   {
1188     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1189     cap.setText(MessageManager
1190             .getString("label.paste_features_annotations_Tcoffee_here"));
1191     cap.setAnnotationImport();
1192     Frame frame = new Frame();
1193     frame.add(cap);
1194     jalview.bin.JalviewLite.addFrame(frame,
1195             MessageManager.getString("action.paste_annotations"), 400, 300);
1196
1197   }
1198
1199   public String outputAnnotations(boolean displayTextbox)
1200   {
1201     String annotation = new AnnotationFile()
1202             .printAnnotationsForView(viewport);
1203
1204     if (displayTextbox)
1205     {
1206       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1207       Frame frame = new Frame();
1208       frame.add(cap);
1209       jalview.bin.JalviewLite.addFrame(frame,
1210               MessageManager.getString("label.annotations"), 600, 500);
1211       cap.setText(annotation);
1212     }
1213
1214     return annotation;
1215   }
1216
1217   private Map<String,Object> getDisplayedFeatureCols()
1218   {
1219     if (alignPanel.getFeatureRenderer() != null
1220             && viewport.getFeaturesDisplayed()!= null)
1221     {
1222       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1223
1224     }
1225     return null;
1226   }
1227
1228   public String outputFeatures(boolean displayTextbox, String format)
1229   {
1230     String features;
1231     if (format.equalsIgnoreCase("Jalview"))
1232     {
1233       features = new FeaturesFile().printJalviewFormat(viewport
1234               .getAlignment().getSequencesArray(),
1235               getDisplayedFeatureCols());
1236     }
1237     else
1238     {
1239       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1240               .getSequencesArray(), getDisplayedFeatureCols());
1241     }
1242
1243     if (displayTextbox)
1244     {
1245       boolean frimport = false;
1246       if (features == null || features.equals("No Features Visible"))
1247       {
1248         features = "# No features visible - paste some and import them here.";
1249         frimport = true;
1250       }
1251
1252       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1253       if (frimport)
1254       {
1255         cap.setAnnotationImport();
1256       }
1257       Frame frame = new Frame();
1258       frame.add(cap);
1259       jalview.bin.JalviewLite.addFrame(frame,
1260               MessageManager.getString("label.features"), 600, 500);
1261       cap.setText(features);
1262     }
1263     else
1264     {
1265       if (features == null)
1266       {
1267         features = "";
1268       }
1269     }
1270
1271     return features;
1272   }
1273
1274   void launchFullApplication()
1275   {
1276     StringBuffer url = new StringBuffer(jalviewServletURL);
1277
1278     url.append("?open="
1279             + appendProtocol(viewport.applet.getParameter("file")));
1280
1281     if (viewport.applet.getParameter("features") != null)
1282     {
1283       url.append("&features=");
1284       url.append(appendProtocol(viewport.applet.getParameter("features")));
1285     }
1286
1287     if (viewport.applet.getParameter("annotations") != null)
1288     {
1289       url.append("&annotations=");
1290       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1291     }
1292
1293     if (viewport.applet.getParameter("jnetfile") != null)
1294     {
1295       url.append("&annotations=");
1296       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1297     }
1298
1299     if (viewport.applet.getParameter("defaultColour") != null)
1300     {
1301       url.append("&colour="
1302               + removeWhiteSpace(viewport.applet
1303                       .getParameter("defaultColour")));
1304     }
1305
1306     if (viewport.applet.getParameter("userDefinedColour") != null)
1307     {
1308       url.append("&colour="
1309               + removeWhiteSpace(viewport.applet
1310                       .getParameter("userDefinedColour")));
1311     }
1312     if (viewport.applet.getParameter("tree") != null)
1313     {
1314       url.append("&tree="
1315               + appendProtocol(viewport.applet.getParameter("tree")));
1316     }
1317     if (viewport.applet.getParameter("treeFile") != null)
1318     {
1319       url.append("&tree="
1320               + appendProtocol(viewport.applet.getParameter("treeFile")));
1321     }
1322
1323     showURL(url.toString(), "FULL_APP");
1324   }
1325
1326   String removeWhiteSpace(String colour)
1327   {
1328     StringBuffer sb = new StringBuffer();
1329     for (int i = 0; i < colour.length(); i++)
1330     {
1331       if (Character.isWhitespace(colour.charAt(i)))
1332       {
1333         sb.append("%20");
1334       }
1335       else
1336       {
1337         sb.append(colour.charAt(i));
1338       }
1339     }
1340
1341     return sb.toString();
1342   }
1343
1344   String appendProtocol(String url)
1345   {
1346     try
1347     {
1348       new URL(url);
1349       url = URLEncoder.encode(url);
1350     }
1351     /*
1352      * When we finally deprecate 1.1 compatibility, we can start to use
1353      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1354      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1355      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1356      * ex.printStackTrace(); }
1357      */
1358     catch (java.net.MalformedURLException ex)
1359     {
1360       url = viewport.applet.getCodeBase() + url;
1361     }
1362     return url;
1363   }
1364
1365   public void closeMenuItem_actionPerformed()
1366   {
1367     PaintRefresher.RemoveComponent(alignPanel);
1368     if (alignPanel.seqPanel != null
1369             && alignPanel.seqPanel.seqCanvas != null)
1370     {
1371       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1372     }
1373     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1374     {
1375       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1376     }
1377
1378     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1379     {
1380       System.exit(0);
1381     }
1382     else
1383     {
1384     }
1385     viewport = null;
1386     alignPanel = null;
1387     this.dispose();
1388   }
1389
1390   /**
1391    * TODO: JAL-1104
1392    */
1393   void updateEditMenuBar()
1394   {
1395
1396     if (viewport.historyList.size() > 0)
1397     {
1398       undoMenuItem.setEnabled(true);
1399       CommandI command = (CommandI) viewport.historyList.peek();
1400       undoMenuItem.setLabel(MessageManager.formatMessage(
1401               "label.undo_command", new String[]
1402               { command.getDescription() }));
1403     }
1404     else
1405     {
1406       undoMenuItem.setEnabled(false);
1407       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1408     }
1409
1410     if (viewport.redoList.size() > 0)
1411     {
1412       redoMenuItem.setEnabled(true);
1413
1414       CommandI command = (CommandI) viewport.redoList.peek();
1415       redoMenuItem.setLabel(MessageManager.formatMessage(
1416               "label.redo_command", new String[]
1417               { command.getDescription() }));
1418     }
1419     else
1420     {
1421       redoMenuItem.setEnabled(false);
1422       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1423     }
1424   }
1425
1426   /**
1427    * TODO: JAL-1104
1428    */
1429   @Override
1430   public void addHistoryItem(CommandI command)
1431   {
1432     if (command.getSize() > 0)
1433     {
1434       viewport.historyList.push(command);
1435       viewport.redoList.removeAllElements();
1436       updateEditMenuBar();
1437       viewport.updateHiddenColumns();
1438     }
1439   }
1440
1441   /**
1442    * TODO: JAL-1104 DOCUMENT ME!
1443    *
1444    * @param e
1445    *          DOCUMENT ME!
1446    */
1447   protected void undoMenuItem_actionPerformed()
1448   {
1449     if (viewport.historyList.size() < 1)
1450     {
1451       return;
1452     }
1453
1454     CommandI command = (CommandI) viewport.historyList.pop();
1455     viewport.redoList.push(command);
1456     command.undoCommand(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 undoing");
1464     }
1465     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1466                                           // viewport.getColumnSelection().getHiddenColumns()
1467                                           // != null;
1468     updateEditMenuBar();
1469     originalSource.firePropertyChange("alignment", null, originalSource
1470             .getAlignment().getSequences());
1471   }
1472
1473   /**
1474    * TODO: JAL-1104 DOCUMENT ME!
1475    *
1476    * @param e
1477    *          DOCUMENT ME!
1478    */
1479   protected void redoMenuItem_actionPerformed()
1480   {
1481     if (viewport.redoList.size() < 1)
1482     {
1483       return;
1484     }
1485
1486     CommandI command = (CommandI) viewport.redoList.pop();
1487     viewport.historyList.push(command);
1488     command.doCommand(null);
1489
1490     AlignViewport originalSource = getOriginatingSource(command);
1491     // JBPNote Test
1492     if (originalSource != viewport)
1493     {
1494       System.err
1495               .println("Warning: Viewport object mismatch whilst re-doing");
1496     }
1497     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1498                                           // viewport.getColumnSelection().getHiddenColumns()
1499                                           // != null;
1500
1501     updateEditMenuBar();
1502     originalSource.firePropertyChange("alignment", null, originalSource
1503             .getAlignment().getSequences());
1504   }
1505
1506   AlignViewport getOriginatingSource(CommandI command)
1507   {
1508     AlignViewport originalSource = null;
1509     // For sequence removal and addition, we need to fire
1510     // the property change event FROM the viewport where the
1511     // original alignment was altered
1512     AlignmentI al = null;
1513     if (command instanceof EditCommand)
1514     {
1515       EditCommand editCommand = (EditCommand) command;
1516       al = editCommand.getAlignment();
1517       Vector comps = (Vector) PaintRefresher.components.get(viewport
1518               .getSequenceSetId());
1519       for (int i = 0; i < comps.size(); i++)
1520       {
1521         if (comps.elementAt(i) instanceof AlignmentPanel)
1522         {
1523           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1524           {
1525             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1526             break;
1527           }
1528         }
1529       }
1530     }
1531
1532     if (originalSource == null)
1533     {
1534       // The original view is closed, we must validate
1535       // the current view against the closed view first
1536       if (al != null)
1537       {
1538         PaintRefresher.validateSequences(al, viewport.getAlignment());
1539       }
1540
1541       originalSource = viewport;
1542     }
1543
1544     return originalSource;
1545   }
1546
1547   public void moveSelectedSequences(boolean up)
1548   {
1549     SequenceGroup sg = viewport.getSelectionGroup();
1550     if (sg == null)
1551     {
1552       return;
1553     }
1554     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1555             up ? null : viewport.getHiddenRepSequences(), up);
1556     alignPanel.paintAlignment(true);
1557   }
1558
1559   synchronized void slideSequences(boolean right, int size)
1560   {
1561     List<SequenceI> sg = new Vector<SequenceI>();
1562     if (viewport.cursorMode)
1563     {
1564       sg.add(viewport.getAlignment().getSequenceAt(
1565               alignPanel.seqPanel.seqCanvas.cursorY));
1566     }
1567     else if (viewport.getSelectionGroup() != null
1568             && viewport.getSelectionGroup().getSize() != viewport
1569                     .getAlignment().getHeight())
1570     {
1571       sg = viewport.getSelectionGroup().getSequences(
1572               viewport.getHiddenRepSequences());
1573     }
1574
1575     if (sg.size() < 1)
1576     {
1577       return;
1578     }
1579
1580     Vector<SequenceI> invertGroup = new Vector();
1581
1582     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1583     {
1584       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1585       {
1586         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1587       }
1588     }
1589
1590     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1591
1592     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1593             .size()]);
1594     for (int i = 0; i < invertGroup.size(); i++)
1595     {
1596       seqs2[i] = invertGroup.elementAt(i);
1597     }
1598
1599     SlideSequencesCommand ssc;
1600     if (right)
1601     {
1602       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1603               size, viewport.getGapCharacter());
1604     }
1605     else
1606     {
1607       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1608               size, viewport.getGapCharacter());
1609     }
1610
1611     int groupAdjustment = 0;
1612     if (ssc.getGapsInsertedBegin() && right)
1613     {
1614       if (viewport.cursorMode)
1615       {
1616         alignPanel.seqPanel.moveCursor(size, 0);
1617       }
1618       else
1619       {
1620         groupAdjustment = size;
1621       }
1622     }
1623     else if (!ssc.getGapsInsertedBegin() && !right)
1624     {
1625       if (viewport.cursorMode)
1626       {
1627         alignPanel.seqPanel.moveCursor(-size, 0);
1628       }
1629       else
1630       {
1631         groupAdjustment = -size;
1632       }
1633     }
1634
1635     if (groupAdjustment != 0)
1636     {
1637       viewport.getSelectionGroup().setStartRes(
1638               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1639       viewport.getSelectionGroup().setEndRes(
1640               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1641     }
1642
1643     boolean appendHistoryItem = false;
1644     if (viewport.historyList != null && viewport.historyList.size() > 0
1645             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1646     {
1647       appendHistoryItem = ssc
1648               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1649                       .peek());
1650     }
1651
1652     if (!appendHistoryItem)
1653     {
1654       addHistoryItem(ssc);
1655     }
1656
1657     repaint();
1658   }
1659
1660   static StringBuffer copiedSequences;
1661
1662   static Vector copiedHiddenColumns;
1663
1664   protected void copy_actionPerformed()
1665   {
1666     if (viewport.getSelectionGroup() == null)
1667     {
1668       return;
1669     }
1670
1671     SequenceGroup sg = viewport.getSelectionGroup();
1672     copiedSequences = new StringBuffer();
1673     Hashtable orderedSeqs = new Hashtable();
1674     for (int i = 0; i < sg.getSize(); i++)
1675     {
1676       SequenceI seq = sg.getSequenceAt(i);
1677       int index = viewport.getAlignment().findIndex(seq);
1678       orderedSeqs.put(index + "", seq);
1679     }
1680
1681     int index = 0, startRes, endRes;
1682     char ch;
1683
1684     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1685     {
1686       copiedHiddenColumns = new Vector();
1687       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1688       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1689               .size(); i++)
1690       {
1691         int[] region = (int[]) viewport.getColumnSelection()
1692                 .getHiddenColumns().elementAt(i);
1693
1694         copiedHiddenColumns.addElement(new int[]
1695         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1696       }
1697     }
1698     else
1699     {
1700       copiedHiddenColumns = null;
1701     }
1702
1703     for (int i = 0; i < sg.getSize(); i++)
1704     {
1705       SequenceI seq = null;
1706
1707       while (seq == null)
1708       {
1709         if (orderedSeqs.containsKey(index + ""))
1710         {
1711           seq = (SequenceI) orderedSeqs.get(index + "");
1712           index++;
1713
1714           break;
1715         }
1716         else
1717         {
1718           index++;
1719         }
1720       }
1721
1722       // FIND START RES
1723       // Returns residue following index if gap
1724       startRes = seq.findPosition(sg.getStartRes());
1725
1726       // FIND END RES
1727       // Need to find the residue preceeding index if gap
1728       endRes = 0;
1729
1730       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1731       {
1732         ch = seq.getCharAt(j);
1733         if (!jalview.util.Comparison.isGap((ch)))
1734         {
1735           endRes++;
1736         }
1737       }
1738
1739       if (endRes > 0)
1740       {
1741         endRes += seq.getStart() - 1;
1742       }
1743
1744       copiedSequences.append(seq.getName()
1745               + "\t"
1746               + startRes
1747               + "\t"
1748               + endRes
1749               + "\t"
1750               + seq.getSequenceAsString(sg.getStartRes(),
1751                       sg.getEndRes() + 1) + "\n");
1752     }
1753
1754   }
1755
1756   protected void pasteNew_actionPerformed()
1757   {
1758     paste(true);
1759   }
1760
1761   protected void pasteThis_actionPerformed()
1762   {
1763     paste(false);
1764   }
1765
1766   void paste(boolean newAlignment)
1767   {
1768     try
1769     {
1770
1771       if (copiedSequences == null)
1772       {
1773         return;
1774       }
1775
1776       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1777       Vector seqs = new Vector();
1778       while (st.hasMoreElements())
1779       {
1780         String name = st.nextToken();
1781         int start = Integer.parseInt(st.nextToken());
1782         int end = Integer.parseInt(st.nextToken());
1783         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1784       }
1785       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1786       for (int i = 0; i < seqs.size(); i++)
1787       {
1788         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1789       }
1790
1791       if (newAlignment)
1792       {
1793         String newtitle = MessageManager.getString("label.copied_sequences");
1794         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1795         {
1796           newtitle = getTitle();
1797         }
1798         else
1799         {
1800           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1801         }
1802         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1803                 viewport.applet, newtitle, false);
1804         if (copiedHiddenColumns != null)
1805         {
1806           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1807           {
1808             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1809             af.viewport.hideColumns(region[0], region[1]);
1810           }
1811         }
1812
1813         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1814                 DEFAULT_HEIGHT);
1815       }
1816       else
1817       {
1818         addSequences(newSeqs);
1819       }
1820
1821     } catch (Exception ex)
1822     {
1823     } // could be anything being pasted in here
1824
1825   }
1826
1827   void addSequences(SequenceI[] seqs)
1828   {
1829     for (int i = 0; i < seqs.length; i++)
1830     {
1831       viewport.getAlignment().addSequence(seqs[i]);
1832     }
1833
1834     // !newAlignment
1835     addHistoryItem(new EditCommand(
1836             MessageManager.getString("label.add_sequences"), Action.PASTE,
1837             seqs, 0, viewport.getAlignment().getWidth(),
1838             viewport.getAlignment()));
1839
1840     viewport.setEndSeq(viewport.getAlignment().getHeight());
1841     viewport.getAlignment().getWidth();
1842     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1843             .getSequences());
1844
1845   }
1846
1847   protected void cut_actionPerformed()
1848   {
1849     copy_actionPerformed();
1850     delete_actionPerformed();
1851   }
1852
1853   protected void delete_actionPerformed()
1854   {
1855
1856     SequenceGroup sg = viewport.getSelectionGroup();
1857     if (sg == null)
1858     {
1859       return;
1860     }
1861
1862     Vector seqs = new Vector();
1863     SequenceI seq;
1864     for (int i = 0; i < sg.getSize(); i++)
1865     {
1866       seq = sg.getSequenceAt(i);
1867       seqs.addElement(seq);
1868     }
1869
1870     // If the cut affects all sequences, remove highlighted columns
1871     if (sg.getSize() == viewport.getAlignment().getHeight())
1872     {
1873       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1874               sg.getEndRes() + 1);
1875     }
1876
1877     SequenceI[] cut = new SequenceI[seqs.size()];
1878     for (int i = 0; i < seqs.size(); i++)
1879     {
1880       cut[i] = (SequenceI) seqs.elementAt(i);
1881     }
1882
1883     /*
1884      * //ADD HISTORY ITEM
1885      */
1886     addHistoryItem(new EditCommand(
1887             MessageManager.getString("label.cut_sequences"), Action.CUT,
1888             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1889             viewport.getAlignment()));
1890
1891     viewport.setSelectionGroup(null);
1892     viewport.getAlignment().deleteGroup(sg);
1893
1894     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1895             .getSequences());
1896
1897     if (viewport.getAlignment().getHeight() < 1)
1898     {
1899       this.setVisible(false);
1900     }
1901     viewport.sendSelection();
1902   }
1903
1904   /**
1905    * group consensus toggled
1906    *
1907    */
1908   protected void showGroupConsensus_actionPerformed()
1909   {
1910     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1911     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1912
1913   }
1914
1915   /**
1916    * group conservation toggled.
1917    */
1918   protected void showGroupConservation_actionPerformed()
1919   {
1920     viewport.setShowGroupConservation(showGroupConservation.getState());
1921     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1922   }
1923
1924   /*
1925    * (non-Javadoc)
1926    *
1927    * @see
1928    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1929    * .event.ActionEvent)
1930    */
1931   protected void showConsensusHistogram_actionPerformed()
1932   {
1933     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1934     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1935   }
1936
1937   /*
1938    * (non-Javadoc)
1939    *
1940    * @see
1941    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1942    * .event.ActionEvent)
1943    */
1944   protected void showSequenceLogo_actionPerformed()
1945   {
1946     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1947     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1948   }
1949
1950   protected void normSequenceLogo_actionPerformed()
1951   {
1952     showSequenceLogo.setState(true);
1953     viewport.setShowSequenceLogo(true);
1954     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1955     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1956   }
1957
1958   protected void applyAutoAnnotationSettings_actionPerformed()
1959   {
1960     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1961   }
1962
1963   protected void makeGrpsFromSelection_actionPerformed()
1964   {
1965     if (avc.makeGroupsFromSelection())
1966     {
1967       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1968       alignPanel.updateAnnotation();
1969       alignPanel.paintAlignment(true);
1970     }
1971   }
1972
1973   protected void createGroup_actionPerformed()
1974   {
1975     avc.createGroup();
1976   }
1977
1978   protected void unGroup_actionPerformed()
1979   {
1980     if (avc.unGroup())
1981     {
1982       alignPanel.alignmentChanged();
1983     }
1984   }
1985
1986   protected void deleteGroups_actionPerformed()
1987   {
1988     if (avc.deleteGroups())
1989     {
1990       alignPanel.alignmentChanged();
1991     }
1992   }
1993
1994   public void selectAllSequenceMenuItem_actionPerformed()
1995   {
1996     SequenceGroup sg = new SequenceGroup();
1997     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1998     {
1999       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2000     }
2001     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2002     viewport.setSelectionGroup(sg);
2003     alignPanel.paintAlignment(true);
2004     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2005     viewport.sendSelection();
2006   }
2007
2008   public void deselectAllSequenceMenuItem_actionPerformed()
2009   {
2010     if (viewport.cursorMode)
2011     {
2012       alignPanel.seqPanel.keyboardNo1 = null;
2013       alignPanel.seqPanel.keyboardNo2 = null;
2014     }
2015     viewport.setSelectionGroup(null);
2016     viewport.getColumnSelection().clear();
2017     viewport.setSelectionGroup(null);
2018     alignPanel.idPanel.idCanvas.searchResults = null;
2019     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2020     alignPanel.paintAlignment(true);
2021     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2022     viewport.sendSelection();
2023   }
2024
2025   public void invertSequenceMenuItem_actionPerformed()
2026   {
2027     SequenceGroup sg = viewport.getSelectionGroup();
2028     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2029     {
2030       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2031     }
2032
2033     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2034     viewport.sendSelection();
2035   }
2036
2037   public void invertColSel_actionPerformed()
2038   {
2039     viewport.invertColumnSelection();
2040     alignPanel.paintAlignment(true);
2041     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2042     viewport.sendSelection();
2043   }
2044
2045   void trimAlignment(boolean trimLeft)
2046   {
2047     ColumnSelection colSel = viewport.getColumnSelection();
2048     int column;
2049
2050     if (colSel.size() > 0)
2051     {
2052       if (trimLeft)
2053       {
2054         column = colSel.getMin();
2055       }
2056       else
2057       {
2058         column = colSel.getMax();
2059       }
2060
2061       SequenceI[] seqs;
2062       if (viewport.getSelectionGroup() != null)
2063       {
2064         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2065                 viewport.getHiddenRepSequences());
2066       }
2067       else
2068       {
2069         seqs = viewport.getAlignment().getSequencesArray();
2070       }
2071
2072       TrimRegionCommand trimRegion;
2073       if (trimLeft)
2074       {
2075         trimRegion = new TrimRegionCommand("Remove Left",
2076                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2077                 viewport.getAlignment(), viewport.getColumnSelection(),
2078                 viewport.getSelectionGroup());
2079         viewport.setStartRes(0);
2080       }
2081       else
2082       {
2083         trimRegion = new TrimRegionCommand("Remove Right",
2084                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2085                 viewport.getAlignment(), viewport.getColumnSelection(),
2086                 viewport.getSelectionGroup());
2087       }
2088
2089       statusBar.setText(MessageManager.formatMessage(
2090               "label.removed_columns", new String[]
2091               { Integer.valueOf(trimRegion.getSize()).toString() }));
2092       addHistoryItem(trimRegion);
2093
2094       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2095       {
2096         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2097                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2098         {
2099           viewport.getAlignment().deleteGroup(sg);
2100         }
2101       }
2102
2103       viewport.firePropertyChange("alignment", null, viewport
2104               .getAlignment().getSequences());
2105     }
2106   }
2107
2108   public void removeGappedColumnMenuItem_actionPerformed()
2109   {
2110     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2111
2112     SequenceI[] seqs;
2113     if (viewport.getSelectionGroup() != null)
2114     {
2115       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2116               viewport.getHiddenRepSequences());
2117       start = viewport.getSelectionGroup().getStartRes();
2118       end = viewport.getSelectionGroup().getEndRes();
2119     }
2120     else
2121     {
2122       seqs = viewport.getAlignment().getSequencesArray();
2123     }
2124
2125     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2126             "Remove Gapped Columns", seqs, start, end,
2127             viewport.getAlignment());
2128
2129     addHistoryItem(removeGapCols);
2130
2131     statusBar.setText(MessageManager.formatMessage(
2132             "label.removed_empty_columns", new String[]
2133             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2134
2135     // This is to maintain viewport position on first residue
2136     // of first sequence
2137     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2138     int startRes = seq.findPosition(viewport.startRes);
2139     // ShiftList shifts;
2140     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2141     // edit.alColumnChanges=shifts.getInverse();
2142     // if (viewport.hasHiddenColumns)
2143     // viewport.getColumnSelection().compensateForEdits(shifts);
2144     viewport.setStartRes(seq.findIndex(startRes) - 1);
2145     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2146             .getSequences());
2147
2148   }
2149
2150   public void removeAllGapsMenuItem_actionPerformed()
2151   {
2152     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2153
2154     SequenceI[] seqs;
2155     if (viewport.getSelectionGroup() != null)
2156     {
2157       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2158               viewport.getHiddenRepSequences());
2159       start = viewport.getSelectionGroup().getStartRes();
2160       end = viewport.getSelectionGroup().getEndRes();
2161     }
2162     else
2163     {
2164       seqs = viewport.getAlignment().getSequencesArray();
2165     }
2166
2167     // This is to maintain viewport position on first residue
2168     // of first sequence
2169     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2170     int startRes = seq.findPosition(viewport.startRes);
2171
2172     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2173             viewport.getAlignment()));
2174
2175     viewport.setStartRes(seq.findIndex(startRes) - 1);
2176
2177     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2178             .getSequences());
2179
2180   }
2181
2182   public void findMenuItem_actionPerformed()
2183   {
2184     new Finder(alignPanel);
2185   }
2186
2187   /**
2188    * create a new view derived from the current view
2189    *
2190    * @param viewtitle
2191    * @return frame for the new view
2192    */
2193   public AlignFrame newView(String viewtitle)
2194   {
2195     AlignmentI newal;
2196     if (viewport.hasHiddenRows())
2197     {
2198       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2199               .getFullAlignment().getSequencesArray());
2200     }
2201     else
2202     {
2203       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2204     }
2205
2206     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2207     {
2208       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2209       {
2210         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2211         {
2212           newal.addAnnotation(viewport.getAlignment()
2213                   .getAlignmentAnnotation()[i]);
2214         }
2215       }
2216     }
2217
2218     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2219
2220     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2221     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2222     PaintRefresher.Register(newaf.alignPanel,
2223             newaf.alignPanel.av.getSequenceSetId());
2224
2225     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2226             newaf.alignPanel.av.getSequenceSetId());
2227     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2228             newaf.alignPanel.av.getSequenceSetId());
2229
2230     Vector comps = (Vector) PaintRefresher.components.get(viewport
2231             .getSequenceSetId());
2232     int viewSize = -1;
2233     for (int i = 0; i < comps.size(); i++)
2234     {
2235       if (comps.elementAt(i) instanceof AlignmentPanel)
2236       {
2237         viewSize++;
2238       }
2239     }
2240
2241     String title = new String(this.getTitle());
2242     if (viewtitle != null)
2243     {
2244       title = viewtitle + " ( " + title + ")";
2245     }
2246     else
2247     {
2248       if (title.indexOf("(View") > -1)
2249       {
2250         title = title.substring(0, title.indexOf("(View"));
2251       }
2252       title += "(View " + viewSize + ")";
2253     }
2254
2255     newaf.setTitle(title.toString());
2256
2257     newaf.viewport.historyList = viewport.historyList;
2258     newaf.viewport.redoList = viewport.redoList;
2259     return newaf;
2260   }
2261
2262   /**
2263    *
2264    * @return list of feature groups on the view
2265    */
2266   public String[] getFeatureGroups()
2267   {
2268     FeatureRenderer fr = null;
2269     if (alignPanel != null
2270             && (fr = alignPanel.getFeatureRenderer()) != null)
2271     {
2272       List gps = fr.getFeatureGroups();
2273       int p=0;
2274       String[] _gps = new String[gps.size()];
2275       for (Object gp:gps)
2276       {
2277         _gps[p++] = gp.toString();
2278       }
2279       return _gps;
2280     }
2281     return null;
2282   }
2283
2284   /**
2285    * get sequence feature groups that are hidden or shown
2286    *
2287    * @param visible
2288    *          true is visible
2289    * @return list
2290    */
2291   public String[] getFeatureGroupsOfState(boolean visible)
2292   {
2293     FeatureRenderer fr = null;
2294     if (alignPanel != null
2295             && (fr = alignPanel.getFeatureRenderer()) != null)
2296     {
2297       List gps = fr.getGroups(visible);
2298       int p=0;
2299       String[] _gps = new String[gps.size()];
2300       for (Object gp:gps)
2301       {
2302         _gps[p++] = gp.toString();
2303       }
2304       return _gps;
2305     }
2306     return null;
2307   }
2308
2309   /**
2310    * Change the display state for the given feature groups
2311    *
2312    * @param groups
2313    *          list of group strings
2314    * @param state
2315    *          visible or invisible
2316    */
2317   public void setFeatureGroupState(String[] groups, boolean state)
2318   {
2319     FeatureRenderer fr = null;
2320     this.sequenceFeatures.setState(true);
2321     viewport.setShowSequenceFeatures(true);
2322     if (alignPanel != null
2323             && (fr = alignPanel.getFeatureRenderer()) != null)
2324     {
2325
2326       fr.setGroupVisibility(Arrays.asList(groups), state);
2327       alignPanel.seqPanel.seqCanvas.repaint();
2328       if (alignPanel.overviewPanel != null)
2329       {
2330         alignPanel.overviewPanel.updateOverviewImage();
2331       }
2332     }
2333   }
2334
2335   public void seqLimits_itemStateChanged()
2336   {
2337     viewport.setShowJVSuffix(seqLimits.getState());
2338     alignPanel.fontChanged();
2339     alignPanel.paintAlignment(true);
2340   }
2341
2342   protected void colourTextMenuItem_actionPerformed()
2343   {
2344     viewport.setColourText(colourTextMenuItem.getState());
2345     alignPanel.paintAlignment(true);
2346   }
2347
2348   protected void displayNonconservedMenuItem_actionPerformed()
2349   {
2350     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2351     alignPanel.paintAlignment(true);
2352   }
2353
2354   protected void wrapMenuItem_actionPerformed()
2355   {
2356     viewport.setWrapAlignment(wrapMenuItem.getState());
2357     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2358     scaleAbove.setEnabled(wrapMenuItem.getState());
2359     scaleLeft.setEnabled(wrapMenuItem.getState());
2360     scaleRight.setEnabled(wrapMenuItem.getState());
2361     alignPanel.paintAlignment(true);
2362   }
2363
2364   public void overviewMenuItem_actionPerformed()
2365   {
2366     if (alignPanel.overviewPanel != null)
2367     {
2368       return;
2369     }
2370
2371     Frame frame = new Frame();
2372     OverviewPanel overview = new OverviewPanel(alignPanel);
2373     frame.add(overview);
2374     // +50 must allow for applet frame window
2375     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2376             "label.overview_params", new String[]
2377             { this.getTitle() }), overview.getPreferredSize().width,
2378             overview.getPreferredSize().height + 50);
2379
2380     frame.pack();
2381     final AlignmentPanel ap = alignPanel;
2382     frame.addWindowListener(new WindowAdapter()
2383     {
2384       @Override
2385       public void windowClosing(WindowEvent e)
2386       {
2387         if (ap != null)
2388         {
2389           ap.setOverviewPanel(null);
2390         }
2391       };
2392     });
2393
2394     alignPanel.setOverviewPanel(overview);
2395
2396   }
2397
2398   void changeColour(ColourSchemeI cs)
2399   {
2400     int threshold = 0;
2401
2402     if (cs != null)
2403     {
2404       if (viewport.getAbovePIDThreshold())
2405       {
2406         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2407                 cs, "Background"));
2408       }
2409
2410       if (viewport.getConservationSelected())
2411       {
2412         cs.setConservationApplied(true);
2413         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2414                 cs, "Background"));
2415       }
2416       else
2417       {
2418         cs.setConservationApplied(false);
2419       }
2420     }
2421     viewport.setGlobalColourScheme(cs);
2422
2423     if (alignPanel.getOverviewPanel() != null)
2424     {
2425       alignPanel.getOverviewPanel().updateOverviewImage();
2426     }
2427
2428     jalview.structure.StructureSelectionManager
2429             .getStructureSelectionManager(viewport.applet)
2430             .sequenceColoursChanged(alignPanel);
2431
2432     alignPanel.paintAlignment(true);
2433   }
2434
2435   protected void modifyPID_actionPerformed()
2436   {
2437     if (viewport.getAbovePIDThreshold()
2438             && viewport.getGlobalColourScheme() != null)
2439     {
2440       SliderPanel.setPIDSliderSource(alignPanel,
2441               viewport.getGlobalColourScheme(), "Background");
2442       SliderPanel.showPIDSlider();
2443     }
2444   }
2445
2446   protected void modifyConservation_actionPerformed()
2447   {
2448     if (viewport.getConservationSelected()
2449             && viewport.getGlobalColourScheme() != null)
2450     {
2451       SliderPanel.setConservationSlider(alignPanel,
2452               viewport.getGlobalColourScheme(), "Background");
2453       SliderPanel.showConservationSlider();
2454     }
2455   }
2456
2457   protected void conservationMenuItem_actionPerformed()
2458   {
2459     viewport.setConservationSelected(conservationMenuItem.getState());
2460
2461     viewport.setAbovePIDThreshold(false);
2462     abovePIDThreshold.setState(false);
2463
2464     changeColour(viewport.getGlobalColourScheme());
2465
2466     modifyConservation_actionPerformed();
2467   }
2468
2469   public void abovePIDThreshold_actionPerformed()
2470   {
2471     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2472
2473     conservationMenuItem.setState(false);
2474     viewport.setConservationSelected(false);
2475
2476     changeColour(viewport.getGlobalColourScheme());
2477
2478     modifyPID_actionPerformed();
2479   }
2480
2481   public void sortPairwiseMenuItem_actionPerformed()
2482   {
2483     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2484     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2485             .getAlignment().getSequenceAt(0), null);
2486
2487     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2488             viewport.getAlignment()));
2489     alignPanel.paintAlignment(true);
2490   }
2491
2492   public void sortIDMenuItem_actionPerformed()
2493   {
2494     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2495     AlignmentSorter.sortByID(viewport.getAlignment());
2496     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2497             viewport.getAlignment()));
2498     alignPanel.paintAlignment(true);
2499   }
2500
2501   public void sortLengthMenuItem_actionPerformed()
2502   {
2503     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2504     AlignmentSorter.sortByLength(viewport.getAlignment());
2505     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2506             viewport.getAlignment()));
2507     alignPanel.paintAlignment(true);
2508   }
2509
2510   public void sortGroupMenuItem_actionPerformed()
2511   {
2512     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2513     AlignmentSorter.sortByGroup(viewport.getAlignment());
2514     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2515             viewport.getAlignment()));
2516     alignPanel.paintAlignment(true);
2517
2518   }
2519
2520   public void removeRedundancyMenuItem_actionPerformed()
2521   {
2522     new RedundancyPanel(alignPanel);
2523   }
2524
2525   public void pairwiseAlignmentMenuItem_actionPerformed()
2526   {
2527     if (viewport.getSelectionGroup() != null
2528             && viewport.getSelectionGroup().getSize() > 1)
2529     {
2530       Frame frame = new Frame();
2531       frame.add(new PairwiseAlignPanel(alignPanel));
2532       jalview.bin.JalviewLite.addFrame(frame,
2533               MessageManager.getString("action.pairwise_alignment"), 600,
2534               500);
2535     }
2536   }
2537
2538   public void PCAMenuItem_actionPerformed()
2539   {
2540     // are the sequences aligned?
2541     if (!viewport.getAlignment().isAligned(false))
2542     {
2543       SequenceI current;
2544       int Width = viewport.getAlignment().getWidth();
2545
2546       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2547       {
2548         current = viewport.getAlignment().getSequenceAt(i);
2549
2550         if (current.getLength() < Width)
2551         {
2552           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2553         }
2554       }
2555       alignPanel.paintAlignment(true);
2556     }
2557
2558     if ((viewport.getSelectionGroup() != null
2559             && viewport.getSelectionGroup().getSize() < 4 && viewport
2560             .getSelectionGroup().getSize() > 0)
2561             || viewport.getAlignment().getHeight() < 4)
2562     {
2563       return;
2564     }
2565
2566     try
2567     {
2568       new PCAPanel(viewport);
2569     } catch (java.lang.OutOfMemoryError ex)
2570     {
2571     }
2572
2573   }
2574
2575   public void averageDistanceTreeMenuItem_actionPerformed()
2576   {
2577     NewTreePanel("AV", "PID", "Average distance tree using PID");
2578   }
2579
2580   public void neighbourTreeMenuItem_actionPerformed()
2581   {
2582     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2583   }
2584
2585   protected void njTreeBlosumMenuItem_actionPerformed()
2586   {
2587     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2588   }
2589
2590   protected void avTreeBlosumMenuItem_actionPerformed()
2591   {
2592     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2593   }
2594
2595   void NewTreePanel(String type, String pwType, String title)
2596   {
2597     // are the sequences aligned?
2598     if (!viewport.getAlignment().isAligned(false))
2599     {
2600       SequenceI current;
2601       int Width = viewport.getAlignment().getWidth();
2602
2603       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2604       {
2605         current = viewport.getAlignment().getSequenceAt(i);
2606
2607         if (current.getLength() < Width)
2608         {
2609           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2610         }
2611       }
2612       alignPanel.paintAlignment(true);
2613
2614     }
2615
2616     if ((viewport.getSelectionGroup() != null && viewport
2617             .getSelectionGroup().getSize() > 1)
2618             || (viewport.getAlignment().getHeight() > 1))
2619     {
2620       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2621
2622       addTreeMenuItem(tp, title);
2623
2624       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2625     }
2626   }
2627
2628   void loadTree_actionPerformed()
2629   {
2630     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2631     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2632     cap.setTreeImport();
2633     Frame frame = new Frame();
2634     frame.add(cap);
2635     jalview.bin.JalviewLite.addFrame(frame,
2636             MessageManager.getString("label.paste_newick_file"), 400, 300);
2637   }
2638
2639   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2640   {
2641     TreePanel tp = new TreePanel(alignPanel, treeFile,
2642             MessageManager.getString("label.load_tree_from_file"), tree);
2643     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2644     addTreeMenuItem(tp, treeFile);
2645   }
2646
2647   /**
2648    * sort the alignment using the given treePanel
2649    *
2650    * @param treePanel
2651    *          tree used to sort view
2652    * @param title
2653    *          string used for undo event name
2654    */
2655   public void sortByTree(TreePanel treePanel, String title)
2656   {
2657     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2658     AlignmentSorter
2659             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2660     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2661     // HistoryItem.SORT));
2662     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2663             "label.order_by_params", new String[]
2664             { title }), oldOrder, viewport.getAlignment()));
2665     alignPanel.paintAlignment(true);
2666   }
2667
2668   /**
2669    * Do any automatic reordering of the alignment and add the necessary bits to
2670    * the menu structure for the new tree
2671    *
2672    * @param treePanel
2673    * @param title
2674    */
2675   protected void addTreeMenuItem(final TreePanel treePanel,
2676           final String title)
2677   {
2678     final MenuItem item = new MenuItem(title);
2679     sortByTreeMenu.add(item);
2680     item.addActionListener(new java.awt.event.ActionListener()
2681     {
2682       @Override
2683       public void actionPerformed(ActionEvent evt)
2684       {
2685         sortByTree(treePanel, title); // treePanel.getTitle());
2686       }
2687     });
2688
2689     treePanel.addWindowListener(new WindowAdapter()
2690     {
2691       @Override
2692       public void windowOpened(WindowEvent e)
2693       {
2694         if (viewport.sortByTree)
2695         {
2696           sortByTree(treePanel, title);
2697         }
2698         super.windowOpened(e);
2699       }
2700
2701       @Override
2702       public void windowClosing(WindowEvent e)
2703       {
2704         sortByTreeMenu.remove(item);
2705       };
2706     });
2707   }
2708
2709   public boolean sortBy(AlignmentOrder alorder, String undoname)
2710   {
2711     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2712     if (viewport.applet.debug)
2713     {
2714       System.err.println("Sorting " + alorder.getOrder().size()
2715               + " in alignment '" + getTitle() + "'");
2716     }
2717     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2718     if (undoname != null)
2719     {
2720       addHistoryItem(new OrderCommand(undoname, oldOrder,
2721               viewport.getAlignment()));
2722     }
2723     alignPanel.paintAlignment(true);
2724     return true;
2725   }
2726
2727   protected void documentation_actionPerformed()
2728   {
2729     alignPanel.av.applet.openJalviewHelpUrl();
2730   }
2731
2732   protected void about_actionPerformed()
2733   {
2734
2735     class AboutPanel extends Canvas
2736     {
2737       String version;
2738
2739       String builddate;
2740
2741       public AboutPanel(String version, String builddate)
2742       {
2743         this.version = version;
2744         this.builddate = builddate;
2745       }
2746
2747       @Override
2748       public void paint(Graphics g)
2749       {
2750         g.setColor(Color.white);
2751         g.fillRect(0, 0, getSize().width, getSize().height);
2752         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2753         FontMetrics fm = g.getFontMetrics();
2754         int fh = fm.getHeight();
2755         int y = 5, x = 7;
2756         g.setColor(Color.black);
2757         // TODO: update this text for each release or centrally store it for
2758         // lite and application
2759         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2760         g.drawString(MessageManager.formatMessage(
2761                 "label.jalviewLite_release", new String[]
2762                 { version }), x, y += fh);
2763         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2764         g.drawString(MessageManager.formatMessage(
2765                 "label.jaview_build_date", new String[]
2766                 { builddate }), x, y += fh);
2767         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2768         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2769                 x, y += fh * 1.5);
2770         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2771                 x + 50, y += fh + 8);
2772         g.drawString(
2773                 MessageManager.getString("label.jalview_dev_managers"), x,
2774                 y += fh);
2775         g.drawString(MessageManager
2776                 .getString("label.jalview_distribution_lists"), x, y += fh);
2777         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2778                 x, y += fh + 8);
2779         g.drawString(
2780                 MessageManager.getString("label.jalview_cite_1_authors"),
2781                 x, y += fh);
2782         g.drawString(
2783                 MessageManager.getString("label.jalview_cite_1_title"), x,
2784                 y += fh);
2785         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2786                 x, y += fh);
2787       }
2788     }
2789
2790     Frame frame = new Frame();
2791     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2792             .getBuildDate()));
2793     jalview.bin.JalviewLite.addFrame(frame,
2794             MessageManager.getString("label.jalview"), 580, 220);
2795
2796   }
2797
2798   public void showURL(String url, String target)
2799   {
2800     if (viewport.applet == null)
2801     {
2802       System.out.println("Not running as applet - no browser available.");
2803     }
2804     else
2805     {
2806       viewport.applet.showURL(url, target);
2807     }
2808   }
2809
2810   // ////////////////////////////////////////////////////////////////////////////////
2811   // JBuilder Graphics here
2812
2813   MenuBar alignFrameMenuBar = new MenuBar();
2814
2815   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2816
2817   MenuItem loadApplication = new MenuItem(
2818           MessageManager.getString("label.view_full_application"));
2819
2820   MenuItem loadTree = new MenuItem(
2821           MessageManager.getString("label.load_associated_tree"));
2822
2823   MenuItem loadAnnotations = new MenuItem(
2824           MessageManager.getString("label.load_features_annotations"));
2825
2826   MenuItem outputFeatures = new MenuItem(
2827           MessageManager.getString("label.export_features").concat("..."));
2828
2829   MenuItem outputAnnotations = new MenuItem(
2830           MessageManager.getString("label.export_annotations").concat("..."));
2831
2832   MenuItem closeMenuItem = new MenuItem(
2833           MessageManager.getString("action.close"));
2834
2835   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2836
2837   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2838
2839   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2840
2841   Menu calculateMenu = new Menu(
2842           MessageManager.getString("action.calculate"));
2843
2844   MenuItem selectAllSequenceMenuItem = new MenuItem(
2845           MessageManager.getString("action.select_all"));
2846
2847   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2848           MessageManager.getString("action.deselect_all"));
2849
2850   MenuItem invertSequenceMenuItem = new MenuItem(
2851           MessageManager.getString("action.invert_selection"));
2852
2853   MenuItem remove2LeftMenuItem = new MenuItem();
2854
2855   MenuItem remove2RightMenuItem = new MenuItem();
2856
2857   MenuItem removeGappedColumnMenuItem = new MenuItem();
2858
2859   MenuItem removeAllGapsMenuItem = new MenuItem();
2860
2861   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2862
2863   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2864
2865   MenuItem sortPairwiseMenuItem = new MenuItem();
2866
2867   MenuItem sortIDMenuItem = new MenuItem();
2868
2869   MenuItem sortLengthMenuItem = new MenuItem();
2870
2871   MenuItem sortGroupMenuItem = new MenuItem();
2872
2873   MenuItem removeRedundancyMenuItem = new MenuItem();
2874
2875   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2876
2877   MenuItem PCAMenuItem = new MenuItem();
2878
2879   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2880
2881   MenuItem neighbourTreeMenuItem = new MenuItem();
2882
2883   BorderLayout borderLayout1 = new BorderLayout();
2884
2885   public Label statusBar = new Label();
2886
2887   Menu outputTextboxMenu = new Menu();
2888
2889   MenuItem clustalColour = new MenuItem();
2890
2891   MenuItem zappoColour = new MenuItem();
2892
2893   MenuItem taylorColour = new MenuItem();
2894
2895   MenuItem hydrophobicityColour = new MenuItem();
2896
2897   MenuItem helixColour = new MenuItem();
2898
2899   MenuItem strandColour = new MenuItem();
2900
2901   MenuItem turnColour = new MenuItem();
2902
2903   MenuItem buriedColour = new MenuItem();
2904
2905   MenuItem purinePyrimidineColour = new MenuItem();
2906
2907   MenuItem RNAInteractionColour = new MenuItem();
2908
2909   MenuItem RNAHelixColour = new MenuItem();
2910
2911   MenuItem userDefinedColour = new MenuItem();
2912
2913   MenuItem PIDColour = new MenuItem();
2914
2915   MenuItem BLOSUM62Colour = new MenuItem();
2916
2917   MenuItem tcoffeeColour = new MenuItem();
2918
2919   MenuItem njTreeBlosumMenuItem = new MenuItem();
2920
2921   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2922
2923   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2924
2925   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2926
2927   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2928
2929   MenuItem alProperties = new MenuItem(
2930           MessageManager.getString("label.alignment_props"));
2931
2932   MenuItem overviewMenuItem = new MenuItem();
2933
2934   MenuItem undoMenuItem = new MenuItem();
2935
2936   MenuItem redoMenuItem = new MenuItem();
2937
2938   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2939
2940   MenuItem noColourmenuItem = new MenuItem();
2941
2942   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2943
2944   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2945
2946   MenuItem findMenuItem = new MenuItem();
2947
2948   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2949
2950   MenuItem nucleotideColour = new MenuItem();
2951
2952   MenuItem deleteGroups = new MenuItem();
2953
2954   MenuItem grpsFromSelection = new MenuItem();
2955
2956   MenuItem createGroup = new MenuItem();
2957
2958   MenuItem unGroup = new MenuItem();
2959
2960   MenuItem delete = new MenuItem();
2961
2962   MenuItem copy = new MenuItem();
2963
2964   MenuItem cut = new MenuItem();
2965
2966   Menu pasteMenu = new Menu();
2967
2968   MenuItem pasteNew = new MenuItem();
2969
2970   MenuItem pasteThis = new MenuItem();
2971
2972   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2973
2974   MenuItem font = new MenuItem();
2975
2976   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2977
2978   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2979
2980   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2981
2982   MenuItem modifyPID = new MenuItem();
2983
2984   MenuItem modifyConservation = new MenuItem();
2985
2986   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2987           "Autocalculate Consensus", true);
2988
2989   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2990           "Sort Alignment With New Tree", true);
2991
2992   Menu sortByTreeMenu = new Menu();
2993
2994   Menu sort = new Menu();
2995
2996   Menu calculate = new Menu();
2997
2998   MenuItem inputText = new MenuItem();
2999
3000   Menu helpMenu = new Menu();
3001
3002   MenuItem documentation = new MenuItem();
3003
3004   MenuItem about = new MenuItem();
3005
3006   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3007
3008   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3009
3010   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3011
3012   Menu autoAnnMenu = new Menu();
3013
3014   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3015
3016   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3017
3018   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3019
3020   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3021
3022   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3023
3024   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3025
3026   private void jbInit() throws Exception
3027   {
3028
3029     setMenuBar(alignFrameMenuBar);
3030
3031     MenuItem item;
3032
3033     // dynamically fill save as menu with available formats
3034     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3035     {
3036
3037       item = new MenuItem(
3038               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3039
3040       item.addActionListener(new java.awt.event.ActionListener()
3041       {
3042         @Override
3043         public void actionPerformed(ActionEvent e)
3044         {
3045           outputText_actionPerformed(e);
3046         }
3047       });
3048
3049       outputTextboxMenu.add(item);
3050     }
3051     closeMenuItem.addActionListener(this);
3052     loadApplication.addActionListener(this);
3053
3054     loadTree.addActionListener(this);
3055     loadAnnotations.addActionListener(this);
3056     outputFeatures.addActionListener(this);
3057     outputAnnotations.addActionListener(this);
3058     selectAllSequenceMenuItem.addActionListener(this);
3059     deselectAllSequenceMenuItem.addActionListener(this);
3060     invertSequenceMenuItem.addActionListener(this);
3061     remove2LeftMenuItem.setLabel(MessageManager
3062             .getString("action.remove_left"));
3063     remove2LeftMenuItem.addActionListener(this);
3064     remove2RightMenuItem.setLabel(MessageManager
3065             .getString("action.remove_right"));
3066     remove2RightMenuItem.addActionListener(this);
3067     removeGappedColumnMenuItem.setLabel(MessageManager
3068             .getString("action.remove_empty_columns"));
3069     removeGappedColumnMenuItem.addActionListener(this);
3070     removeAllGapsMenuItem.setLabel(MessageManager
3071             .getString("action.remove_all_gaps"));
3072     removeAllGapsMenuItem.addActionListener(this);
3073     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3074     viewBoxesMenuItem.setState(true);
3075     viewBoxesMenuItem.addItemListener(this);
3076     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3077     viewTextMenuItem.setState(true);
3078     viewTextMenuItem.addItemListener(this);
3079     sortPairwiseMenuItem.setLabel(MessageManager
3080             .getString("action.by_pairwise_id"));
3081     sortPairwiseMenuItem.addActionListener(this);
3082     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3083     sortIDMenuItem.addActionListener(this);
3084     sortLengthMenuItem.setLabel(MessageManager
3085             .getString("action.by_length"));
3086     sortLengthMenuItem.addActionListener(this);
3087     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3088     sortGroupMenuItem.addActionListener(this);
3089     removeRedundancyMenuItem.setLabel(MessageManager
3090             .getString("action.remove_redundancy").concat("..."));
3091     removeRedundancyMenuItem.addActionListener(this);
3092     pairwiseAlignmentMenuItem.setLabel(MessageManager
3093             .getString("action.pairwise_alignment"));
3094     pairwiseAlignmentMenuItem.addActionListener(this);
3095     PCAMenuItem.setLabel(MessageManager
3096             .getString("label.principal_component_analysis"));
3097     PCAMenuItem.addActionListener(this);
3098     averageDistanceTreeMenuItem.setLabel(MessageManager
3099             .getString("label.average_distance_identity"));
3100     averageDistanceTreeMenuItem.addActionListener(this);
3101     neighbourTreeMenuItem.setLabel(MessageManager
3102             .getString("label.neighbour_joining_identity"));
3103     neighbourTreeMenuItem.addActionListener(this);
3104     statusBar.setBackground(Color.white);
3105     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3106     statusBar.setText(MessageManager.getString("label.status_bar"));
3107     outputTextboxMenu.setLabel(MessageManager
3108             .getString("label.out_to_textbox"));
3109     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3110
3111     clustalColour.addActionListener(this);
3112     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3113     zappoColour.addActionListener(this);
3114     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3115     taylorColour.addActionListener(this);
3116     hydrophobicityColour.setLabel(MessageManager
3117             .getString("label.hydrophobicity"));
3118     hydrophobicityColour.addActionListener(this);
3119     helixColour
3120             .setLabel(MessageManager.getString("label.helix_propensity"));
3121     helixColour.addActionListener(this);
3122     strandColour.setLabel(MessageManager
3123             .getString("label.strand_propensity"));
3124     strandColour.addActionListener(this);
3125     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3126     turnColour.addActionListener(this);
3127     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3128     buriedColour.addActionListener(this);
3129     purinePyrimidineColour.setLabel(MessageManager
3130             .getString("label.purine_pyrimidine"));
3131     purinePyrimidineColour.addActionListener(this);
3132     RNAInteractionColour.setLabel(MessageManager
3133             .getString("label.rna_interaction"));
3134     RNAInteractionColour.addActionListener(this);
3135     RNAHelixColour.setLabel(MessageManager
3136             .getString("action.by_rna_helixes"));
3137     RNAHelixColour.addActionListener(this);
3138     userDefinedColour.setLabel(MessageManager
3139             .getString("action.user_defined"));
3140     userDefinedColour.addActionListener(this);
3141     PIDColour.setLabel(MessageManager
3142             .getString("label.percentage_identity"));
3143     PIDColour.addActionListener(this);
3144     BLOSUM62Colour.setLabel(MessageManager
3145             .getString("label.blosum62_score"));
3146     BLOSUM62Colour.addActionListener(this);
3147     tcoffeeColour
3148             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3149     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3150                                      // provided
3151     tcoffeeColour.addActionListener(this);
3152     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3153             .getString("label.average_distance_bloslum62"));
3154     avDistanceTreeBlosumMenuItem.addActionListener(this);
3155     njTreeBlosumMenuItem.setLabel(MessageManager
3156             .getString("label.neighbour_blosum62"));
3157     njTreeBlosumMenuItem.addActionListener(this);
3158     annotationPanelMenuItem.setLabel(MessageManager
3159             .getString("label.show_annotations"));
3160     annotationPanelMenuItem.addItemListener(this);
3161     colourTextMenuItem.setLabel(MessageManager
3162             .getString("label.colour_text"));
3163     colourTextMenuItem.addItemListener(this);
3164     displayNonconservedMenuItem.setLabel(MessageManager
3165             .getString("label.show_non_conversed"));
3166     displayNonconservedMenuItem.addItemListener(this);
3167     alProperties.addActionListener(this);
3168     overviewMenuItem.setLabel(MessageManager
3169             .getString("label.overview_window"));
3170     overviewMenuItem.addActionListener(this);
3171     undoMenuItem.setEnabled(false);
3172     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3173     undoMenuItem.addActionListener(this);
3174     redoMenuItem.setEnabled(false);
3175     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3176     redoMenuItem.addActionListener(this);
3177     conservationMenuItem.setLabel(MessageManager
3178             .getString("action.by_conservation"));
3179     conservationMenuItem.addItemListener(this);
3180     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3181     noColourmenuItem.addActionListener(this);
3182     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3183     wrapMenuItem.addItemListener(this);
3184     renderGapsMenuItem.setLabel(MessageManager
3185             .getString("action.show_gaps"));
3186     renderGapsMenuItem.setState(true);
3187     renderGapsMenuItem.addItemListener(this);
3188     findMenuItem.setLabel(MessageManager.getString("action.find"));
3189     findMenuItem.addActionListener(this);
3190     abovePIDThreshold.setLabel(MessageManager
3191             .getString("label.above_identity_threshold"));
3192     abovePIDThreshold.addItemListener(this);
3193     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3194     nucleotideColour.addActionListener(this);
3195     deleteGroups.setLabel(MessageManager
3196             .getString("action.undefine_groups"));
3197     deleteGroups.addActionListener(this);
3198     grpsFromSelection.setLabel(MessageManager
3199             .getString("action.make_groups_selection"));
3200     grpsFromSelection.addActionListener(this);
3201     createGroup.setLabel(MessageManager.getString("action.create_group"));
3202     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3203     copy.setLabel(MessageManager.getString("action.copy"));
3204     copy.addActionListener(this);
3205     cut.setLabel(MessageManager.getString("action.cut"));
3206     cut.addActionListener(this);
3207     delete.setLabel(MessageManager.getString("action.delete"));
3208     delete.addActionListener(this);
3209     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3210     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3211     pasteNew.addActionListener(this);
3212     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3213     pasteThis.addActionListener(this);
3214     applyToAllGroups.setLabel(MessageManager
3215             .getString("label.apply_colour_to_all_groups"));
3216     applyToAllGroups.setState(true);
3217     applyToAllGroups.addItemListener(this);
3218     font.setLabel(MessageManager.getString("action.font"));
3219     font.addActionListener(this);
3220     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3221     scaleAbove.setState(true);
3222     scaleAbove.setEnabled(false);
3223     scaleAbove.addItemListener(this);
3224     scaleLeft.setEnabled(false);
3225     scaleLeft.setState(true);
3226     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3227     scaleLeft.addItemListener(this);
3228     scaleRight.setEnabled(false);
3229     scaleRight.setState(true);
3230     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3231     scaleRight.addItemListener(this);
3232     modifyPID.setLabel(MessageManager
3233             .getString("label.modify_identity_thereshold"));
3234     modifyPID.addActionListener(this);
3235     modifyConservation.setLabel(MessageManager
3236             .getString("label.modify_conservation_thereshold"));
3237     modifyConservation.addActionListener(this);
3238     sortByTreeMenu.setLabel(MessageManager
3239             .getString("action.by_tree_order"));
3240     sort.setLabel(MessageManager.getString("action.sort"));
3241     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3242     autoCalculate.addItemListener(this);
3243     sortByTree.addItemListener(this);
3244     inputText
3245             .setLabel(MessageManager.getString("label.input_from_textbox"));
3246     inputText.addActionListener(this);
3247     centreColumnLabelFlag.setLabel(MessageManager
3248             .getString("label.centre_column_labels"));
3249     centreColumnLabelFlag.addItemListener(this);
3250     followMouseOverFlag.setLabel(MessageManager
3251             .getString("label.automatic_scrolling"));
3252     followMouseOverFlag.addItemListener(this);
3253     helpMenu.setLabel(MessageManager.getString("action.help"));
3254     documentation.setLabel(MessageManager.getString("label.documentation"));
3255     documentation.addActionListener(this);
3256
3257     about.setLabel(MessageManager.getString("label.about"));
3258     about.addActionListener(this);
3259     seqLimits.setState(true);
3260     seqLimits.setLabel(MessageManager
3261             .getString("label.show_sequence_limits"));
3262     seqLimits.addItemListener(this);
3263     featureSettings.setLabel(MessageManager
3264             .getString("label.feature_settings"));
3265     featureSettings.addActionListener(this);
3266     sequenceFeatures.setLabel(MessageManager
3267             .getString("label.sequence_features"));
3268     sequenceFeatures.addItemListener(this);
3269     sequenceFeatures.setState(false);
3270     annotationColour.setLabel(MessageManager
3271             .getString("action.by_annotation"));
3272     annotationColour.addActionListener(this);
3273     invertSequenceMenuItem.setLabel(MessageManager
3274             .getString("action.invert_sequence_selection"));
3275     invertColSel.setLabel(MessageManager
3276             .getString("action.invert_column_selection"));
3277     menu1.setLabel(MessageManager.getString("action.show"));
3278     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3279     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3280     menu2.setLabel(MessageManager.getString("action.hide"));
3281     hideColumns
3282             .setLabel(MessageManager.getString("label.selected_columns"));
3283     hideSequences.setLabel(MessageManager
3284             .getString("label.selected_sequences"));
3285     hideAllButSelection.setLabel(MessageManager
3286             .getString("label.all_but_selected_region"));
3287     hideAllSelection.setLabel(MessageManager
3288             .getString("label.selected_region"));
3289     showAllHidden.setLabel(MessageManager
3290             .getString("label.all_sequences_columns"));
3291     showGroupConsensus.setLabel(MessageManager
3292             .getString("label.group_consensus"));
3293     showGroupConservation.setLabel(MessageManager
3294             .getString("label.group_conservation"));
3295     showConsensusHistogram.setLabel(MessageManager
3296             .getString("label.show_consensus_histogram"));
3297     showSequenceLogo.setLabel(MessageManager
3298             .getString("label.show_consensus_logo"));
3299     normSequenceLogo.setLabel(MessageManager
3300             .getString("label.norm_consensus_logo"));
3301     applyAutoAnnotationSettings.setLabel(MessageManager
3302             .getString("label.apply_all_groups"));
3303     applyAutoAnnotationSettings.setState(true);
3304     autoAnnMenu.setLabel(MessageManager
3305             .getString("label.autocalculated_annotation"));
3306
3307     invertColSel.addActionListener(this);
3308     showColumns.addActionListener(this);
3309     showSeqs.addActionListener(this);
3310     hideColumns.addActionListener(this);
3311     hideSequences.addActionListener(this);
3312     hideAllButSelection.addActionListener(this);
3313     hideAllSelection.addActionListener(this);
3314     showAllHidden.addActionListener(this);
3315     showGroupConsensus.addItemListener(this);
3316     showGroupConservation.addItemListener(this);
3317     showConsensusHistogram.addItemListener(this);
3318     showSequenceLogo.addItemListener(this);
3319     normSequenceLogo.addItemListener(this);
3320
3321     applyAutoAnnotationSettings.addItemListener(this);
3322     formatMenu.setLabel(MessageManager.getString("action.format"));
3323     selectMenu.setLabel(MessageManager.getString("action.select"));
3324     newView.setLabel(MessageManager.getString("action.new_view"));
3325     newView.addActionListener(this);
3326     alignFrameMenuBar.add(fileMenu);
3327     alignFrameMenuBar.add(editMenu);
3328     alignFrameMenuBar.add(selectMenu);
3329     alignFrameMenuBar.add(viewMenu);
3330     alignFrameMenuBar.add(formatMenu);
3331     alignFrameMenuBar.add(colourMenu);
3332     alignFrameMenuBar.add(calculateMenu);
3333     alignFrameMenuBar.add(helpMenu);
3334
3335     fileMenu.add(inputText);
3336     fileMenu.add(loadTree);
3337     fileMenu.add(loadAnnotations);
3338
3339     fileMenu.addSeparator();
3340     fileMenu.add(outputTextboxMenu);
3341     fileMenu.add(outputFeatures);
3342     fileMenu.add(outputAnnotations);
3343
3344     if (jalviewServletURL != null)
3345     {
3346       fileMenu.add(loadApplication);
3347     }
3348
3349     fileMenu.addSeparator();
3350     fileMenu.add(closeMenuItem);
3351
3352     editMenu.add(undoMenuItem);
3353     editMenu.add(redoMenuItem);
3354     editMenu.add(cut);
3355     editMenu.add(copy);
3356     editMenu.add(pasteMenu);
3357     editMenu.add(delete);
3358     editMenu.addSeparator();
3359     editMenu.add(remove2LeftMenuItem);
3360     editMenu.add(remove2RightMenuItem);
3361     editMenu.add(removeGappedColumnMenuItem);
3362     editMenu.add(removeAllGapsMenuItem);
3363     editMenu.add(removeRedundancyMenuItem);
3364     viewMenu.add(newView);
3365     viewMenu.addSeparator();
3366     viewMenu.add(menu1);
3367     viewMenu.add(menu2);
3368     viewMenu.addSeparator();
3369     viewMenu.add(followMouseOverFlag);
3370     viewMenu.add(annotationPanelMenuItem);
3371     autoAnnMenu.add(applyAutoAnnotationSettings);
3372     autoAnnMenu.add(showConsensusHistogram);
3373     autoAnnMenu.add(showSequenceLogo);
3374     autoAnnMenu.add(normSequenceLogo);
3375     autoAnnMenu.addSeparator();
3376     autoAnnMenu.add(showGroupConservation);
3377     autoAnnMenu.add(showGroupConsensus);
3378     viewMenu.add(autoAnnMenu);
3379     viewMenu.addSeparator();
3380     viewMenu.add(sequenceFeatures);
3381     viewMenu.add(featureSettings);
3382     viewMenu.addSeparator();
3383     viewMenu.add(alProperties);
3384     viewMenu.addSeparator();
3385     viewMenu.add(overviewMenuItem);
3386     colourMenu.add(applyToAllGroups);
3387     colourMenu.addSeparator();
3388     colourMenu.add(noColourmenuItem);
3389     colourMenu.add(clustalColour);
3390     colourMenu.add(BLOSUM62Colour);
3391     colourMenu.add(PIDColour);
3392     colourMenu.add(zappoColour);
3393     colourMenu.add(taylorColour);
3394     colourMenu.add(hydrophobicityColour);
3395     colourMenu.add(helixColour);
3396     colourMenu.add(strandColour);
3397     colourMenu.add(turnColour);
3398     colourMenu.add(buriedColour);
3399     colourMenu.add(nucleotideColour);
3400     colourMenu.add(purinePyrimidineColour);
3401     // colourMenu.add(RNAInteractionColour);
3402     colourMenu.add(tcoffeeColour);
3403     colourMenu.add(userDefinedColour);
3404     colourMenu.addSeparator();
3405     colourMenu.add(conservationMenuItem);
3406     colourMenu.add(modifyConservation);
3407     colourMenu.add(abovePIDThreshold);
3408     colourMenu.add(modifyPID);
3409     colourMenu.add(annotationColour);
3410     colourMenu.add(RNAHelixColour);
3411     calculateMenu.add(sort);
3412     calculateMenu.add(calculate);
3413     calculateMenu.addSeparator();
3414     calculateMenu.add(pairwiseAlignmentMenuItem);
3415     calculateMenu.add(PCAMenuItem);
3416     calculateMenu.add(autoCalculate);
3417     calculateMenu.add(sortByTree);
3418     this.add(statusBar, BorderLayout.SOUTH);
3419     pasteMenu.add(pasteNew);
3420     pasteMenu.add(pasteThis);
3421     sort.add(sortIDMenuItem);
3422     sort.add(sortLengthMenuItem);
3423     sort.add(sortByTreeMenu);
3424     sort.add(sortGroupMenuItem);
3425     sort.add(sortPairwiseMenuItem);
3426     calculate.add(averageDistanceTreeMenuItem);
3427     calculate.add(neighbourTreeMenuItem);
3428     calculate.add(avDistanceTreeBlosumMenuItem);
3429     calculate.add(njTreeBlosumMenuItem);
3430     helpMenu.add(documentation);
3431     helpMenu.add(about);
3432     menu1.add(showColumns);
3433     menu1.add(showSeqs);
3434     menu1.add(showAllHidden);
3435     menu2.add(hideColumns);
3436     menu2.add(hideSequences);
3437     menu2.add(hideAllSelection);
3438     menu2.add(hideAllButSelection);
3439     formatMenu.add(font);
3440     formatMenu.add(seqLimits);
3441     formatMenu.add(wrapMenuItem);
3442     formatMenu.add(scaleAbove);
3443     formatMenu.add(scaleLeft);
3444     formatMenu.add(scaleRight);
3445     formatMenu.add(viewBoxesMenuItem);
3446     formatMenu.add(viewTextMenuItem);
3447     formatMenu.add(colourTextMenuItem);
3448     formatMenu.add(displayNonconservedMenuItem);
3449     formatMenu.add(renderGapsMenuItem);
3450     formatMenu.add(centreColumnLabelFlag);
3451     selectMenu.add(findMenuItem);
3452     selectMenu.addSeparator();
3453     selectMenu.add(selectAllSequenceMenuItem);
3454     selectMenu.add(deselectAllSequenceMenuItem);
3455     selectMenu.add(invertSequenceMenuItem);
3456     selectMenu.add(invertColSel);
3457     selectMenu.add(createGroup);
3458     selectMenu.add(unGroup);
3459     selectMenu.add(grpsFromSelection);
3460     selectMenu.add(deleteGroups);
3461
3462   }
3463
3464   public void setStatus(String string)
3465   {
3466     statusBar.setText(string);
3467   };
3468
3469   MenuItem featureSettings = new MenuItem();
3470
3471   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3472
3473   MenuItem annotationColour = new MenuItem();
3474
3475   MenuItem invertColSel = new MenuItem();
3476
3477   Menu menu1 = new Menu();
3478
3479   MenuItem showColumns = new MenuItem();
3480
3481   MenuItem showSeqs = new MenuItem();
3482
3483   Menu menu2 = new Menu();
3484
3485   MenuItem hideColumns = new MenuItem();
3486
3487   MenuItem hideSequences = new MenuItem();
3488
3489   MenuItem hideAllButSelection = new MenuItem();
3490
3491   MenuItem hideAllSelection = new MenuItem();
3492
3493   MenuItem showAllHidden = new MenuItem();
3494
3495   Menu formatMenu = new Menu();
3496
3497   Menu selectMenu = new Menu();
3498
3499   MenuItem newView = new MenuItem();
3500
3501   /**
3502    * Attach the alignFrame panels after embedding menus, if necessary. This used
3503    * to be called setEmbedded, but is now creates the dropdown menus in a
3504    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3505    *
3506    * @param reallyEmbedded
3507    *          true to attach the view to the applet area on the page rather than
3508    *          in a new window
3509    */
3510   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3511   {
3512     if (reallyEmbedded)
3513     {
3514       // ////
3515       // Explicly build the embedded menu panel for the on-page applet
3516       //
3517       // view cannot be closed if its actually on the page
3518       fileMenu.remove(closeMenuItem);
3519       fileMenu.remove(3); // Remove Seperator
3520       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3521               Font.PLAIN, 11, false); // use our own fonts.
3522       // and actually add the components to the applet area
3523       viewport.applet.setLayout(new BorderLayout());
3524       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3525       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3526       alignPanel.setSize(viewport.applet.getSize().width,
3527               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3528                       - statusBar.HEIGHT);
3529       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3530       final AlignFrame me = this;
3531       viewport.applet.addFocusListener(new FocusListener()
3532       {
3533
3534         @Override
3535         public void focusLost(FocusEvent e)
3536         {
3537           if (me.viewport.applet.currentAlignFrame == me)
3538           {
3539             me.viewport.applet.currentAlignFrame = null;
3540           }
3541         }
3542
3543         @Override
3544         public void focusGained(FocusEvent e)
3545         {
3546           me.viewport.applet.currentAlignFrame = me;
3547         }
3548       });
3549       viewport.applet.validate();
3550     }
3551     else
3552     {
3553       // //////
3554       // test and embed menu bar if necessary.
3555       //
3556       if (embedMenuIfNeeded(alignPanel))
3557       {
3558         // adjust for status bar height too
3559         alignPanel.setSize(getSize().width, getSize().height
3560                 - statusBar.HEIGHT);
3561       }
3562       add(statusBar, BorderLayout.SOUTH);
3563       add(alignPanel, BorderLayout.CENTER);
3564       // and register with the applet so it can pass external API calls to us
3565       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3566               DEFAULT_HEIGHT);
3567     }
3568   }
3569
3570   /**
3571    * create a new binding between structures in an existing jmol viewer instance
3572    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3573    * this does not open a new Jmol window, or modify the display of the
3574    * structures in the original jmol window. Note This method doesn't work
3575    * without an additional javascript library to exchange messages between the
3576    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3577    *
3578    * @param viewer
3579    *          JmolViewer instance
3580    * @param sequenceIds
3581    *          - sequence Ids to search for associations
3582    */
3583   public SequenceStructureBinding addStructureViewInstance(
3584           Object jmolviewer, String[] sequenceIds)
3585   {
3586     org.jmol.api.JmolViewer viewer = null;
3587     try
3588     {
3589       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3590     } catch (ClassCastException ex)
3591     {
3592       System.err.println("Unsupported viewer object :"
3593               + jmolviewer.getClass());
3594     }
3595     if (viewer == null)
3596     {
3597       System.err.println("Can't use this object as a structure viewer:"
3598               + jmolviewer.getClass());
3599       return null;
3600     }
3601     SequenceI[] seqs = null;
3602     if (sequenceIds == null || sequenceIds.length == 0)
3603     {
3604       seqs = viewport.getAlignment().getSequencesArray();
3605     }
3606     else
3607     {
3608       Vector sqi = new Vector();
3609       AlignmentI al = viewport.getAlignment();
3610       for (int sid = 0; sid < sequenceIds.length; sid++)
3611       {
3612         SequenceI sq = al.findName(sequenceIds[sid]);
3613         if (sq != null)
3614         {
3615           sqi.addElement(sq);
3616         }
3617       }
3618       if (sqi.size() > 0)
3619       {
3620         seqs = new SequenceI[sqi.size()];
3621         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3622         {
3623           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3624         }
3625       }
3626       else
3627       {
3628         return null;
3629       }
3630     }
3631     ExtJmol jmv = null;
3632     // TODO: search for a jmv that involves viewer
3633     if (jmv == null)
3634     { // create a new viewer/jalview binding.
3635       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3636       { seqs });
3637     }
3638     return jmv;
3639
3640   }
3641
3642   /**
3643    * bind a pdb file to a sequence in the current view
3644    *
3645    * @param sequenceId
3646    *          - sequenceId within the dataset.
3647    * @param pdbEntryString
3648    *          - the short name for the PDB file
3649    * @param pdbFile
3650    *          - pdb file - either a URL or a valid PDB file.
3651    * @return true if binding was as success TODO: consider making an exception
3652    *         structure for indicating when PDB parsing or sequenceId location
3653    *         fails.
3654    */
3655   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3656           String pdbFile)
3657   {
3658     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3659     boolean needtoadd = false;
3660     if (toaddpdb != null)
3661     {
3662       Vector pdbe = toaddpdb.getPDBId();
3663       PDBEntry pdbentry = null;
3664       if (pdbe != null && pdbe.size() > 0)
3665       {
3666         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3667         {
3668           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3669           if (!pdbentry.getId().equals(pdbEntryString)
3670                   && !pdbentry.getFile().equals(pdbFile))
3671           {
3672             pdbentry = null;
3673           }
3674           else
3675           {
3676             continue;
3677           }
3678         }
3679       }
3680       if (pdbentry == null)
3681       {
3682         pdbentry = new PDBEntry();
3683         pdbentry.setId(pdbEntryString);
3684         pdbentry.setFile(pdbFile);
3685         needtoadd = true; // add this new entry to sequence.
3686       }
3687       // resolve data source
3688       // TODO: this code should be a refactored to an io package
3689       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3690       if (protocol == null)
3691       {
3692         return false;
3693       }
3694       if (needtoadd)
3695       {
3696         // make a note of the access mode and add
3697         if (pdbentry.getProperty() == null)
3698         {
3699           pdbentry.setProperty(new Hashtable());
3700         }
3701         pdbentry.getProperty().put("protocol", protocol);
3702         toaddpdb.addPDBId(pdbentry);
3703         alignPanel.getStructureSelectionManager()
3704                 .registerPDBEntry(pdbentry);
3705       }
3706     }
3707     return true;
3708   }
3709
3710   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3711   {
3712     if (seqs != null)
3713     {
3714       Vector sequences = new Vector();
3715       for (int i = 0; i < seqs.length; i++)
3716       {
3717         if (seqs[i] != null)
3718         {
3719           sequences.addElement(new Object[]
3720           { seqs[i], (chains != null) ? chains[i] : null });
3721         }
3722       }
3723       seqs = new SequenceI[sequences.size()];
3724       chains = new String[sequences.size()];
3725       for (int i = 0, isize = sequences.size(); i < isize; i++)
3726       {
3727         Object[] oj = (Object[]) sequences.elementAt(i);
3728
3729         seqs[i] = (SequenceI) oj[0];
3730         chains[i] = (String) oj[1];
3731       }
3732     }
3733     return new Object[]
3734     { seqs, chains };
3735
3736   }
3737
3738   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3739           SequenceI[] seqs, String[] chains, String protocol)
3740   {
3741     // Scrub any null sequences from the array
3742     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3743     seqs = (SequenceI[]) sqch[0];
3744     chains = (String[]) sqch[1];
3745     if (seqs == null || seqs.length == 0)
3746     {
3747       System.err
3748               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3749     }
3750     if (protocol == null || protocol.trim().length() == 0
3751             || protocol.equals("null"))
3752     {
3753       protocol = (String) pdb.getProperty().get("protocol");
3754       if (protocol == null)
3755       {
3756         System.err.println("Couldn't work out protocol to open structure: "
3757                 + pdb.getId());
3758         return;
3759       }
3760     }
3761     if (applet.useXtrnalSviewer)
3762     {
3763       // register the association(s) and quit, don't create any windows.
3764       if (StructureSelectionManager.getStructureSelectionManager(applet)
3765               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3766       {
3767         System.err.println("Failed to map " + pdb.getFile() + " ("
3768                 + protocol + ") to any sequences");
3769       }
3770       return;
3771     }
3772     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3773     {
3774       // can only do alignments with Jmol
3775       // find the last jmol window assigned to this alignment
3776       jalview.appletgui.AppletJmol ajm = null, tajm;
3777       Vector jmols = applet
3778               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3779       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3780       {
3781         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3782         if (tajm.ap.alignFrame == this)
3783         {
3784           ajm = tajm;
3785           break;
3786         }
3787       }
3788       if (ajm != null)
3789       {
3790         System.err
3791                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3792         // try and add the pdb structure
3793         // ajm.addS
3794         ajm = null;
3795       }
3796     }
3797     // otherwise, create a new window
3798     if (applet.jmolAvailable)
3799     {
3800       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3801               protocol);
3802       applet.lastFrameX += 40;
3803       applet.lastFrameY += 40;
3804     }
3805     else
3806     {
3807       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3808     }
3809
3810   }
3811
3812   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3813           SequenceI[][] seqs, String[][] chains, String[] protocols)
3814   {
3815     // TODO Auto-generated method stub
3816     System.err.println("Aligned Structure View: Not yet implemented.");
3817   }
3818
3819   /**
3820    * modify the current selection, providing the user has not made a selection
3821    * already.
3822    *
3823    * @param sel
3824    *          - sequences from this alignment
3825    * @param csel
3826    *          - columns to be selected on the alignment
3827    */
3828   public void select(SequenceGroup sel, ColumnSelection csel)
3829   {
3830     alignPanel.seqPanel.selection(sel, csel, null);
3831   }
3832
3833   public void scrollTo(int row, int column)
3834   {
3835     alignPanel.seqPanel.scrollTo(row, column);
3836   }
3837
3838   public void scrollToRow(int row)
3839   {
3840     alignPanel.seqPanel.scrollToRow(row);
3841   }
3842
3843   public void scrollToColumn(int column)
3844   {
3845     alignPanel.seqPanel.scrollToColumn(column);
3846   }
3847
3848   /**
3849    * @return the alignments unique ID.
3850    */
3851   public String getSequenceSetId()
3852   {
3853     return viewport.getSequenceSetId();
3854   }
3855
3856   /**
3857    * Load the (T-Coffee) score file from the specified url
3858    *
3859    * @param source
3860    *          File/URL/T-COFFEE score file contents
3861    * @throws IOException
3862    * @return true if alignment was annotated with data from source
3863    */
3864   public boolean loadScoreFile(String source) throws IOException
3865   {
3866
3867     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3868             AppletFormatAdapter.checkProtocol(source));
3869     if (!file.isValid())
3870     {
3871       // TODO: raise dialog for gui
3872       System.err.println("Problems parsing T-Coffee scores: "
3873               + file.getWarningMessage());
3874       System.err.println("Origin was:\n" + source);
3875       return false;
3876     }
3877
3878     /*
3879      * check that the score matrix matches the alignment dimensions
3880      */
3881     AlignmentI aln;
3882     if ((aln = viewport.getAlignment()) != null
3883             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3884                     .getWidth()))
3885     {
3886       // TODO: raise a dialog box here rather than bomb out.
3887       System.err
3888               .println("The scores matrix does not match the alignment dimensions");
3889
3890     }
3891
3892     // TODO add parameter to indicate if matching should be done
3893     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3894     {
3895       alignPanel.fontChanged();
3896       tcoffeeColour.setEnabled(true);
3897       // switch to this color
3898       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3899       return true;
3900     }
3901     else
3902     {
3903       System.err.println("Problems resolving T-Coffee scores:");
3904       if (file.getWarningMessage() != null)
3905       {
3906         System.err.println(file.getWarningMessage());
3907       }
3908     }
3909     return false;
3910   }
3911
3912 }