src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.SequenceStructureBinding;
  27 import jalview.bin.JalviewLite;
  28 import jalview.commands.CommandI;
  29 import jalview.commands.EditCommand;
  30 import jalview.commands.EditCommand.Action;
  31 import jalview.commands.OrderCommand;
  32 import jalview.commands.RemoveGapColCommand;
  33 import jalview.commands.RemoveGapsCommand;
  34 import jalview.commands.SlideSequencesCommand;
  35 import jalview.commands.TrimRegionCommand;
  36 import jalview.datamodel.Alignment;
  37 import jalview.datamodel.AlignmentI;
  38 import jalview.datamodel.AlignmentOrder;
  39 import jalview.datamodel.ColumnSelection;
  40 import jalview.datamodel.PDBEntry;
  41 import jalview.datamodel.Sequence;
  42 import jalview.datamodel.SequenceGroup;
  43 import jalview.datamodel.SequenceI;
  44 import jalview.io.AnnotationFile;
  45 import jalview.io.AppletFormatAdapter;
  46 import jalview.io.FeaturesFile;
  47 import jalview.io.TCoffeeScoreFile;
  48 import jalview.schemes.Blosum62ColourScheme;
  49 import jalview.schemes.BuriedColourScheme;
  50 import jalview.schemes.ClustalxColourScheme;
  51 import jalview.schemes.ColourSchemeI;
  52 import jalview.schemes.HelixColourScheme;
  53 import jalview.schemes.HydrophobicColourScheme;
  54 import jalview.schemes.NucleotideColourScheme;
  55 import jalview.schemes.PIDColourScheme;
  56 import jalview.schemes.PurinePyrimidineColourScheme;
  57 import jalview.schemes.RNAHelicesColourChooser;
  58 import jalview.schemes.RNAInteractionColourScheme;
  59 import jalview.schemes.StrandColourScheme;
  60 import jalview.schemes.TCoffeeColourScheme;
  61 import jalview.schemes.TaylorColourScheme;
  62 import jalview.schemes.TurnColourScheme;
  63 import jalview.schemes.ZappoColourScheme;
  64 import jalview.structure.StructureSelectionManager;
  65 import jalview.util.MessageManager;
  66
  67 import java.awt.BorderLayout;
  68 import java.awt.Canvas;
  69 import java.awt.CheckboxMenuItem;
  70 import java.awt.Color;
  71 import java.awt.Font;
  72 import java.awt.FontMetrics;
  73 import java.awt.Frame;
  74 import java.awt.Graphics;
  75 import java.awt.Label;
  76 import java.awt.Menu;
  77 import java.awt.MenuBar;
  78 import java.awt.MenuItem;
  79 import java.awt.event.ActionEvent;
  80 import java.awt.event.ActionListener;
  81 import java.awt.event.FocusEvent;
  82 import java.awt.event.FocusListener;
  83 import java.awt.event.ItemEvent;
  84 import java.awt.event.ItemListener;
  85 import java.awt.event.KeyEvent;
  86 import java.awt.event.KeyListener;
  87 import java.awt.event.WindowAdapter;
  88 import java.awt.event.WindowEvent;
  89 import java.io.IOException;
  90 import java.net.URL;
  91 import java.net.URLEncoder;
  92 import java.util.Enumeration;
  93 import java.util.Hashtable;
  94 import java.util.List;
  95 import java.util.StringTokenizer;
  96 import java.util.Vector;
  97
  98 public class AlignFrame extends EmbmenuFrame implements ActionListener,
  99         ItemListener, KeyListener, AlignViewControllerGuiI
 100 {
 101   public AlignViewControllerI avc;
 102
 103   public AlignmentPanel alignPanel;
 104
 105   public AlignViewport viewport;
 106
 107   int DEFAULT_WIDTH = 700;
 108
 109   int DEFAULT_HEIGHT = 500;
 110
 111   String jalviewServletURL;
 112
 113   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 114           String title, boolean embedded)
 115   {
 116     if (applet != null)
 117     {
 118       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 119     }
 120
 121     try
 122     {
 123       jbInit();
 124     } catch (Exception ex)
 125     {
 126       ex.printStackTrace();
 127     }
 128     // need to get window geometry before we calculate alignment layout
 129     if (applet != null)
 130     {
 131       String param;
 132       try
 133       {
 134         param = applet.getParameter("windowWidth");
 135         if (param != null)
 136         {
 137           int width = Integer.parseInt(param);
 138           DEFAULT_WIDTH = width;
 139         }
 140         param = applet.getParameter("windowHeight");
 141         if (param != null)
 142         {
 143           int height = Integer.parseInt(param);
 144           DEFAULT_HEIGHT = height;
 145         }
 146       } catch (Exception ex)
 147       {
 148       }
 149     }
 150     viewport = new AlignViewport(al, applet);
 151     alignPanel = new AlignmentPanel(this, viewport);
 152     avc = new jalview.controller.AlignViewController(this, viewport,
 153             alignPanel);
 154     viewport.updateConservation(alignPanel);
 155     viewport.updateConsensus(alignPanel);
 156
 157     annotationPanelMenuItem.setState(viewport.showAnnotation);
 158     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 159     followMouseOverFlag.setState(viewport.getFollowHighlight());
 160     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 161     showGroupConservation.setState(viewport.isShowGroupConservation());
 162     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 163     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 164     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 165     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 166
 167     seqLimits.setState(viewport.showJVSuffix);
 168
 169     if (applet != null)
 170     {
 171       String param = applet.getParameter("sortBy");
 172       if (param != null)
 173       {
 174         if (param.equalsIgnoreCase("Id"))
 175         {
 176           sortIDMenuItem_actionPerformed();
 177         }
 178         else if (param.equalsIgnoreCase("Pairwise Identity"))
 179         {
 180           sortPairwiseMenuItem_actionPerformed();
 181         }
 182         else if (param.equalsIgnoreCase("Length"))
 183         {
 184           sortLengthMenuItem_actionPerformed();
 185         }
 186       }
 187
 188       param = applet.getParameter("wrap");
 189       if (param != null)
 190       {
 191         if (param.equalsIgnoreCase("true"))
 192         {
 193           wrapMenuItem.setState(true);
 194           wrapMenuItem_actionPerformed();
 195         }
 196       }
 197       param = applet.getParameter("centrecolumnlabels");
 198       if (param != null)
 199       {
 200         centreColumnLabelFlag.setState(true);
 201         centreColumnLabelFlag_stateChanged();
 202       }
 203
 204     }
 205     if (viewport.getAlignment().isNucleotide())
 206     {
 207       viewport.updateStrucConsensus(alignPanel);
 208       if (viewport.getAlignment().hasRNAStructure())
 209       {
 210         RNAHelixColour.setEnabled(true);
 211       }
 212       else
 213       {
 214         RNAHelixColour.setEnabled(false);
 215       }
 216     }
 217     else
 218     {
 219       RNAHelixColour.setEnabled(false);
 220       purinePyrimidineColour.setEnabled(false);
 221     }
 222     // Some JVMS send keyevents to Top frame or lowest panel,
 223     // Havent worked out why yet. So add to both this frame and seqCanvas for
 224     // now
 225     this.addKeyListener(this);
 226     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 227     alignPanel.idPanel.idCanvas.addKeyListener(this);
 228     alignPanel.scalePanel.addKeyListener(this);
 229     alignPanel.annotationPanel.addKeyListener(this);
 230     alignPanel.annotationPanelHolder.addKeyListener(this);
 231     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 232     alignPanel.alabels.addKeyListener(this);
 233     createAlignFrameWindow(embedded, title);
 234
 235     validate();
 236     alignPanel.adjustAnnotationHeight();
 237     alignPanel.paintAlignment(true);
 238   }
 239
 240   public AlignViewport getAlignViewport()
 241   {
 242     return viewport;
 243   }
 244
 245   public SeqCanvas getSeqcanvas()
 246   {
 247     return alignPanel.seqPanel.seqCanvas;
 248   }
 249
 250   /**
 251    * Load a features file onto the alignment
 252    *
 253    * @param file
 254    *          file URL, content, or other resolvable path
 255    * @param type
 256    *          is protocol for accessing data referred to by file
 257    */
 258
 259   public boolean parseFeaturesFile(String file, String type)
 260   {
 261     return parseFeaturesFile(file, type, true);
 262   }
 263
 264   /**
 265    * Load a features file onto the alignment
 266    *
 267    * @param file
 268    *          file URL, content, or other resolvable path
 269    * @param type
 270    *          is protocol for accessing data referred to by file
 271    * @param autoenabledisplay
 272    *          when true, display features flag will be automatically enabled if
 273    *          features are loaded
 274    * @return true if data parsed as a features file
 275    */
 276   public boolean parseFeaturesFile(String file, String type,
 277           boolean autoenabledisplay)
 278   {
 279     // TODO: test if importing a features file onto an alignment which already
 280     // has features with links overwrites the original links.
 281
 282     Hashtable featureLinks = new Hashtable();
 283     boolean featuresFile = false;
 284     try
 285     {
 286       featuresFile = new jalview.io.FeaturesFile(file, type)
 287               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 288                       .getFeatureRenderer().featureColours, featureLinks,
 289                       true, viewport.applet.getDefaultParameter(
 290                               "relaxedidmatch", false));
 291     } catch (Exception ex)
 292     {
 293       ex.printStackTrace();
 294     }
 295
 296     if (featuresFile)
 297     {
 298       if (featureLinks.size() > 0)
 299       {
 300         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 301       }
 302       if (autoenabledisplay)
 303       {
 304         viewport.showSequenceFeatures = true;
 305         sequenceFeatures.setState(true);
 306       }
 307       if (viewport.featureSettings != null)
 308       {
 309         viewport.featureSettings.refreshTable();
 310       }
 311       alignPanel.paintAlignment(true);
 312       statusBar.setText(MessageManager
 313               .getString("label.successfully_added_features_alignment"));
 314     }
 315     return featuresFile;
 316   }
 317
 318   @Override
 319   public void keyPressed(KeyEvent evt)
 320   {
 321     if (viewport.cursorMode
 322             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 323                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 324                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 325             && Character.isDigit(evt.getKeyChar()))
 326     {
 327       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 328     }
 329
 330     switch (evt.getKeyCode())
 331     {
 332     case 27: // escape key
 333       deselectAllSequenceMenuItem_actionPerformed();
 334
 335       alignPanel.alabels.cancelDrag();
 336       break;
 337     case KeyEvent.VK_X:
 338       if (evt.isControlDown() || evt.isMetaDown())
 339       {
 340         cut_actionPerformed();
 341       }
 342       break;
 343     case KeyEvent.VK_C:
 344       if (viewport.cursorMode && !evt.isControlDown())
 345       {
 346         alignPanel.seqPanel.setCursorColumn();
 347       }
 348       if (evt.isControlDown() || evt.isMetaDown())
 349       {
 350         copy_actionPerformed();
 351       }
 352       break;
 353     case KeyEvent.VK_V:
 354       if (evt.isControlDown())
 355       {
 356         paste(evt.isShiftDown());
 357       }
 358       break;
 359     case KeyEvent.VK_A:
 360       if (evt.isControlDown() || evt.isMetaDown())
 361       {
 362         selectAllSequenceMenuItem_actionPerformed();
 363       }
 364       break;
 365     case KeyEvent.VK_DOWN:
 366       if (viewport.cursorMode)
 367       {
 368         alignPanel.seqPanel.moveCursor(0, 1);
 369       }
 370       else
 371       {
 372         moveSelectedSequences(false);
 373       }
 374       break;
 375
 376     case KeyEvent.VK_UP:
 377       if (viewport.cursorMode)
 378       {
 379         alignPanel.seqPanel.moveCursor(0, -1);
 380       }
 381       else
 382       {
 383         moveSelectedSequences(true);
 384       }
 385       break;
 386
 387     case KeyEvent.VK_LEFT:
 388       if (evt.isAltDown() || !viewport.cursorMode)
 389       {
 390         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 391       }
 392       else
 393       {
 394         alignPanel.seqPanel.moveCursor(-1, 0);
 395       }
 396       break;
 397
 398     case KeyEvent.VK_RIGHT:
 399       if (evt.isAltDown() || !viewport.cursorMode)
 400       {
 401         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 402       }
 403       else
 404       {
 405         alignPanel.seqPanel.moveCursor(1, 0);
 406       }
 407       break;
 408
 409     case KeyEvent.VK_SPACE:
 410       if (viewport.cursorMode)
 411       {
 412         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 413                 || evt.isShiftDown() || evt.isAltDown());
 414       }
 415       break;
 416
 417     case KeyEvent.VK_DELETE:
 418     case KeyEvent.VK_BACK_SPACE:
 419       if (viewport.cursorMode)
 420       {
 421         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 422                 || evt.isShiftDown() || evt.isAltDown());
 423       }
 424       else
 425       {
 426         cut_actionPerformed();
 427         alignPanel.seqPanel.seqCanvas.repaint();
 428       }
 429       break;
 430
 431     case KeyEvent.VK_S:
 432       if (viewport.cursorMode)
 433       {
 434         alignPanel.seqPanel.setCursorRow();
 435       }
 436       break;
 437     case KeyEvent.VK_P:
 438       if (viewport.cursorMode)
 439       {
 440         alignPanel.seqPanel.setCursorPosition();
 441       }
 442       break;
 443
 444     case KeyEvent.VK_ENTER:
 445     case KeyEvent.VK_COMMA:
 446       if (viewport.cursorMode)
 447       {
 448         alignPanel.seqPanel.setCursorRowAndColumn();
 449       }
 450       break;
 451
 452     case KeyEvent.VK_Q:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 456       }
 457       break;
 458     case KeyEvent.VK_M:
 459       if (viewport.cursorMode)
 460       {
 461         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 462       }
 463       break;
 464
 465     case KeyEvent.VK_F2:
 466       viewport.cursorMode = !viewport.cursorMode;
 467       statusBar.setText(MessageManager.formatMessage(
 468               "label.keyboard_editing_mode", new String[]
 469               { (viewport.cursorMode ? "on" : "off") }));
 470       if (viewport.cursorMode)
 471       {
 472         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 473         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 474       }
 475       break;
 476
 477     case KeyEvent.VK_F:
 478       if (evt.isControlDown())
 479       {
 480         findMenuItem_actionPerformed();
 481       }
 482       break;
 483
 484     case KeyEvent.VK_H:
 485     {
 486       boolean toggleSeqs = !evt.isControlDown();
 487       boolean toggleCols = !evt.isShiftDown();
 488       toggleHiddenRegions(toggleSeqs, toggleCols);
 489       break;
 490     }
 491
 492     case KeyEvent.VK_PAGE_UP:
 493       if (viewport.wrapAlignment)
 494       {
 495         alignPanel.scrollUp(true);
 496       }
 497       else
 498       {
 499         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 500                 - viewport.endSeq + viewport.startSeq);
 501       }
 502       break;
 503
 504     case KeyEvent.VK_PAGE_DOWN:
 505       if (viewport.wrapAlignment)
 506       {
 507         alignPanel.scrollUp(false);
 508       }
 509       else
 510       {
 511         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 512                 + viewport.endSeq - viewport.startSeq);
 513       }
 514       break;
 515
 516     case KeyEvent.VK_Z:
 517       if (evt.isControlDown())
 518       {
 519         undoMenuItem_actionPerformed();
 520       }
 521       break;
 522
 523     case KeyEvent.VK_Y:
 524       if (evt.isControlDown())
 525       {
 526         redoMenuItem_actionPerformed();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_L:
 531       if (evt.isControlDown())
 532       {
 533         trimAlignment(true);
 534       }
 535       break;
 536
 537     case KeyEvent.VK_R:
 538       if (evt.isControlDown())
 539       {
 540         trimAlignment(false);
 541       }
 542       break;
 543
 544     case KeyEvent.VK_E:
 545       if (evt.isControlDown())
 546       {
 547         if (evt.isShiftDown())
 548         {
 549           this.removeAllGapsMenuItem_actionPerformed();
 550         }
 551         else
 552         {
 553           removeGappedColumnMenuItem_actionPerformed();
 554         }
 555       }
 556       break;
 557     case KeyEvent.VK_I:
 558       if (evt.isControlDown())
 559       {
 560         if (evt.isAltDown())
 561         {
 562           invertColSel_actionPerformed();
 563         }
 564         else
 565         {
 566           invertSequenceMenuItem_actionPerformed();
 567         }
 568       }
 569       break;
 570
 571     case KeyEvent.VK_G:
 572       if (evt.isControlDown())
 573       {
 574         if (evt.isShiftDown())
 575         {
 576           this.unGroup_actionPerformed();
 577         }
 578         else
 579         {
 580           this.createGroup_actionPerformed();
 581         }
 582       }
 583       break;
 584
 585     case KeyEvent.VK_U:
 586       if (evt.isControlDown())
 587       {
 588         this.deleteGroups_actionPerformed();
 589       }
 590       break;
 591
 592     case KeyEvent.VK_T:
 593       if (evt.isControlDown())
 594       {
 595         newView(null);
 596       }
 597       break;
 598
 599     }
 600     alignPanel.paintAlignment(true);
 601   }
 602
 603   /**
 604    * called by key handler and the hide all/show all menu items
 605    *
 606    * @param toggleSeqs
 607    * @param toggleCols
 608    */
 609   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 610   {
 611     boolean hide = false;
 612     SequenceGroup sg = viewport.getSelectionGroup();
 613     if (!toggleSeqs && !toggleCols)
 614     {
 615       // Hide everything by the current selection - this is a hack - we do the
 616       // invert and then hide
 617       // first check that there will be visible columns after the invert.
 618       if ((viewport.getColumnSelection() != null
 619               && viewport.getColumnSelection().getSelected() != null && viewport
 620               .getColumnSelection().getSelected().size() > 0)
 621               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 622                       .getEndRes()))
 623       {
 624         // now invert the sequence set, if required - empty selection implies
 625         // that no hiding is required.
 626         if (sg != null)
 627         {
 628           invertSequenceMenuItem_actionPerformed();
 629           sg = viewport.getSelectionGroup();
 630           toggleSeqs = true;
 631
 632         }
 633         viewport.expandColSelection(sg, true);
 634         // finally invert the column selection and get the new sequence
 635         // selection and indicate it should be hidden.
 636         invertColSel_actionPerformed();
 637         toggleCols = true;
 638       }
 639     }
 640
 641     if (toggleSeqs)
 642     {
 643       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 644       {
 645         hide = true;
 646         viewport.hideAllSelectedSeqs();
 647       }
 648       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 649               .size() > 0))
 650       {
 651         viewport.showAllHiddenSeqs();
 652       }
 653     }
 654
 655     if (toggleCols)
 656     {
 657       if (viewport.getColumnSelection().getSelected().size() > 0)
 658       {
 659         viewport.hideSelectedColumns();
 660         if (!toggleSeqs)
 661         {
 662           viewport.setSelectionGroup(sg);
 663         }
 664       }
 665       else if (!hide)
 666       {
 667         viewport.showAllHiddenColumns();
 668       }
 669     }
 670   }
 671
 672   @Override
 673   public void keyReleased(KeyEvent evt)
 674   {
 675   }
 676
 677   @Override
 678   public void keyTyped(KeyEvent evt)
 679   {
 680   }
 681
 682   @Override
 683   public void itemStateChanged(ItemEvent evt)
 684   {
 685     if (evt.getSource() == displayNonconservedMenuItem)
 686     {
 687       displayNonconservedMenuItem_actionPerformed();
 688     }
 689     else if (evt.getSource() == colourTextMenuItem)
 690     {
 691       colourTextMenuItem_actionPerformed();
 692     }
 693     else if (evt.getSource() == wrapMenuItem)
 694     {
 695       wrapMenuItem_actionPerformed();
 696     }
 697     else if (evt.getSource() == scaleAbove)
 698     {
 699       viewport.setScaleAboveWrapped(scaleAbove.getState());
 700     }
 701     else if (evt.getSource() == scaleLeft)
 702     {
 703       viewport.setScaleLeftWrapped(scaleLeft.getState());
 704     }
 705     else if (evt.getSource() == scaleRight)
 706     {
 707       viewport.setScaleRightWrapped(scaleRight.getState());
 708     }
 709     else if (evt.getSource() == seqLimits)
 710     {
 711       seqLimits_itemStateChanged();
 712     }
 713     else if (evt.getSource() == viewBoxesMenuItem)
 714     {
 715       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 716     }
 717     else if (evt.getSource() == viewTextMenuItem)
 718     {
 719       viewport.setShowText(viewTextMenuItem.getState());
 720     }
 721     else if (evt.getSource() == renderGapsMenuItem)
 722     {
 723       viewport.setRenderGaps(renderGapsMenuItem.getState());
 724     }
 725     else if (evt.getSource() == annotationPanelMenuItem)
 726     {
 727       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 728       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 729     }
 730     else if (evt.getSource() == sequenceFeatures)
 731     {
 732       viewport.showSequenceFeatures(sequenceFeatures.getState());
 733       alignPanel.seqPanel.seqCanvas.repaint();
 734     }
 735     else if (evt.getSource() == conservationMenuItem)
 736     {
 737       conservationMenuItem_actionPerformed();
 738     }
 739     else if (evt.getSource() == abovePIDThreshold)
 740     {
 741       abovePIDThreshold_actionPerformed();
 742     }
 743     else if (evt.getSource() == applyToAllGroups)
 744     {
 745       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 746     }
 747     else if (evt.getSource() == autoCalculate)
 748     {
 749       viewport.autoCalculateConsensus = autoCalculate.getState();
 750     }
 751     else if (evt.getSource() == sortByTree)
 752     {
 753       viewport.sortByTree = sortByTree.getState();
 754     }
 755     else if (evt.getSource() == this.centreColumnLabelFlag)
 756     {
 757       centreColumnLabelFlag_stateChanged();
 758     }
 759     else if (evt.getSource() == this.followMouseOverFlag)
 760     {
 761       mouseOverFlag_stateChanged();
 762     }
 763     else if (evt.getSource() == showGroupConsensus)
 764     {
 765       showGroupConsensus_actionPerformed();
 766     }
 767     else if (evt.getSource() == showGroupConservation)
 768     {
 769       showGroupConservation_actionPerformed();
 770     }
 771     else if (evt.getSource() == showSequenceLogo)
 772     {
 773       showSequenceLogo_actionPerformed();
 774     }
 775     else if (evt.getSource() == normSequenceLogo)
 776     {
 777       normSequenceLogo_actionPerformed();
 778     }
 779     else if (evt.getSource() == showConsensusHistogram)
 780     {
 781       showConsensusHistogram_actionPerformed();
 782     }
 783     else if (evt.getSource() == applyAutoAnnotationSettings)
 784     {
 785       applyAutoAnnotationSettings_actionPerformed();
 786     }
 787     alignPanel.paintAlignment(true);
 788   }
 789
 790   private void mouseOverFlag_stateChanged()
 791   {
 792     viewport.followHighlight = followMouseOverFlag.getState();
 793     // TODO: could kick the scrollTo mechanism to reset view for current
 794     // searchresults.
 795   }
 796
 797   private void centreColumnLabelFlag_stateChanged()
 798   {
 799     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 800     this.alignPanel.annotationPanel.repaint();
 801   }
 802
 803   @Override
 804   public void actionPerformed(ActionEvent evt)
 805   {
 806     Object source = evt.getSource();
 807
 808     if (source == inputText)
 809     {
 810       inputText_actionPerformed();
 811     }
 812     else if (source == loadTree)
 813     {
 814       loadTree_actionPerformed();
 815     }
 816     else if (source == loadApplication)
 817     {
 818       launchFullApplication();
 819     }
 820     else if (source == loadAnnotations)
 821     {
 822       loadAnnotations();
 823     }
 824     else if (source == outputAnnotations)
 825     {
 826       outputAnnotations(true);
 827     }
 828     else if (source == outputFeatures)
 829     {
 830       outputFeatures(true, "Jalview");
 831     }
 832     else if (source == closeMenuItem)
 833     {
 834       closeMenuItem_actionPerformed();
 835     }
 836     else if (source == copy)
 837     {
 838       copy_actionPerformed();
 839     }
 840     else if (source == undoMenuItem)
 841     {
 842       undoMenuItem_actionPerformed();
 843     }
 844     else if (source == redoMenuItem)
 845     {
 846       redoMenuItem_actionPerformed();
 847     }
 848     else if (source == inputText)
 849     {
 850       inputText_actionPerformed();
 851     }
 852     else if (source == closeMenuItem)
 853     {
 854       closeMenuItem_actionPerformed();
 855     }
 856     else if (source == undoMenuItem)
 857     {
 858       undoMenuItem_actionPerformed();
 859     }
 860     else if (source == redoMenuItem)
 861     {
 862       redoMenuItem_actionPerformed();
 863     }
 864     else if (source == copy)
 865     {
 866       copy_actionPerformed();
 867     }
 868     else if (source == pasteNew)
 869     {
 870       pasteNew_actionPerformed();
 871     }
 872     else if (source == pasteThis)
 873     {
 874       pasteThis_actionPerformed();
 875     }
 876     else if (source == cut)
 877     {
 878       cut_actionPerformed();
 879     }
 880     else if (source == delete)
 881     {
 882       delete_actionPerformed();
 883     }
 884     else if (source == grpsFromSelection)
 885     {
 886       makeGrpsFromSelection_actionPerformed();
 887     }
 888     else if (source == deleteGroups)
 889     {
 890       deleteGroups_actionPerformed();
 891     }
 892     else if (source == selectAllSequenceMenuItem)
 893     {
 894       selectAllSequenceMenuItem_actionPerformed();
 895     }
 896     else if (source == deselectAllSequenceMenuItem)
 897     {
 898       deselectAllSequenceMenuItem_actionPerformed();
 899     }
 900     else if (source == invertSequenceMenuItem)
 901     {
 902       invertSequenceMenuItem_actionPerformed();
 903     }
 904     else if (source == invertColSel)
 905     {
 906       viewport.invertColumnSelection();
 907       alignPanel.paintAlignment(true);
 908     }
 909     else if (source == remove2LeftMenuItem)
 910     {
 911       trimAlignment(true);
 912     }
 913     else if (source == remove2RightMenuItem)
 914     {
 915       trimAlignment(false);
 916     }
 917     else if (source == removeGappedColumnMenuItem)
 918     {
 919       removeGappedColumnMenuItem_actionPerformed();
 920     }
 921     else if (source == removeAllGapsMenuItem)
 922     {
 923       removeAllGapsMenuItem_actionPerformed();
 924     }
 925     else if (source == findMenuItem)
 926     {
 927       findMenuItem_actionPerformed();
 928     }
 929     else if (source == font)
 930     {
 931       new FontChooser(alignPanel);
 932     }
 933     else if (source == newView)
 934     {
 935       newView(null);
 936     }
 937     else if (source == showColumns)
 938     {
 939       viewport.showAllHiddenColumns();
 940       alignPanel.paintAlignment(true);
 941     }
 942     else if (source == showSeqs)
 943     {
 944       viewport.showAllHiddenSeqs();
 945       alignPanel.paintAlignment(true);
 946     }
 947     else if (source == hideColumns)
 948     {
 949       viewport.hideSelectedColumns();
 950       alignPanel.paintAlignment(true);
 951     }
 952     else if (source == hideSequences
 953             && viewport.getSelectionGroup() != null)
 954     {
 955       viewport.hideAllSelectedSeqs();
 956       alignPanel.paintAlignment(true);
 957     }
 958     else if (source == hideAllButSelection)
 959     {
 960       toggleHiddenRegions(false, false);
 961       alignPanel.paintAlignment(true);
 962     }
 963     else if (source == hideAllSelection)
 964     {
 965       SequenceGroup sg = viewport.getSelectionGroup();
 966       viewport.expandColSelection(sg, false);
 967       viewport.hideAllSelectedSeqs();
 968       viewport.hideSelectedColumns();
 969       alignPanel.paintAlignment(true);
 970     }
 971     else if (source == showAllHidden)
 972     {
 973       viewport.showAllHiddenColumns();
 974       viewport.showAllHiddenSeqs();
 975       alignPanel.paintAlignment(true);
 976     }
 977     else if (source == showGroupConsensus)
 978     {
 979       showGroupConsensus_actionPerformed();
 980     }
 981     else if (source == showGroupConservation)
 982     {
 983       showGroupConservation_actionPerformed();
 984     }
 985     else if (source == showSequenceLogo)
 986     {
 987       showSequenceLogo_actionPerformed();
 988     }
 989     else if (source == normSequenceLogo)
 990     {
 991       normSequenceLogo_actionPerformed();
 992     }
 993     else if (source == showConsensusHistogram)
 994     {
 995       showConsensusHistogram_actionPerformed();
 996     }
 997     else if (source == applyAutoAnnotationSettings)
 998     {
 999       applyAutoAnnotationSettings_actionPerformed();
1000     }
1001     else if (source == featureSettings)
1002     {
1003       new FeatureSettings(alignPanel);
1004     }
1005     else if (source == alProperties)
1006     {
1007       StringBuffer contents = new jalview.io.AlignmentProperties(
1008               viewport.getAlignment()).formatAsString();
1009       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1010       cap.setText(contents.toString());
1011       Frame frame = new Frame();
1012       frame.add(cap);
1013       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1014               "label.alignment_properties", new String[]
1015               { getTitle() }), 400, 250);
1016     }
1017     else if (source == overviewMenuItem)
1018     {
1019       overviewMenuItem_actionPerformed();
1020     }
1021     else if (source == noColourmenuItem)
1022     {
1023       changeColour(null);
1024     }
1025     else if (source == clustalColour)
1026     {
1027       abovePIDThreshold.setState(false);
1028       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1029     }
1030     else if (source == zappoColour)
1031     {
1032       changeColour(new ZappoColourScheme());
1033     }
1034     else if (source == taylorColour)
1035     {
1036       changeColour(new TaylorColourScheme());
1037     }
1038     else if (source == hydrophobicityColour)
1039     {
1040       changeColour(new HydrophobicColourScheme());
1041     }
1042     else if (source == helixColour)
1043     {
1044       changeColour(new HelixColourScheme());
1045     }
1046     else if (source == strandColour)
1047     {
1048       changeColour(new StrandColourScheme());
1049     }
1050     else if (source == turnColour)
1051     {
1052       changeColour(new TurnColourScheme());
1053     }
1054     else if (source == buriedColour)
1055     {
1056       changeColour(new BuriedColourScheme());
1057     }
1058     else if (source == nucleotideColour)
1059     {
1060       changeColour(new NucleotideColourScheme());
1061     }
1062     else if (source == purinePyrimidineColour)
1063     {
1064       changeColour(new PurinePyrimidineColourScheme());
1065     }
1066     else if (source == RNAInteractionColour)
1067     {
1068       changeColour(new RNAInteractionColourScheme());
1069     }
1070     else if (source == RNAHelixColour)
1071     {
1072       new RNAHelicesColourChooser(viewport, alignPanel);
1073     }
1074     else if (source == modifyPID)
1075     {
1076       modifyPID_actionPerformed();
1077     }
1078     else if (source == modifyConservation)
1079     {
1080       modifyConservation_actionPerformed();
1081     }
1082     else if (source == userDefinedColour)
1083     {
1084       new UserDefinedColours(alignPanel, null);
1085     }
1086     else if (source == PIDColour)
1087     {
1088       changeColour(new PIDColourScheme());
1089     }
1090     else if (source == BLOSUM62Colour)
1091     {
1092       changeColour(new Blosum62ColourScheme());
1093     }
1094     else if (source == tcoffeeColour)
1095     {
1096       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1097     }
1098     else if (source == annotationColour)
1099     {
1100       new AnnotationColourChooser(viewport, alignPanel);
1101     }
1102     else if (source == sortPairwiseMenuItem)
1103     {
1104       sortPairwiseMenuItem_actionPerformed();
1105     }
1106     else if (source == sortIDMenuItem)
1107     {
1108       sortIDMenuItem_actionPerformed();
1109     }
1110     else if (source == sortLengthMenuItem)
1111     {
1112       sortLengthMenuItem_actionPerformed();
1113     }
1114     else if (source == sortGroupMenuItem)
1115     {
1116       sortGroupMenuItem_actionPerformed();
1117     }
1118     else if (source == removeRedundancyMenuItem)
1119     {
1120       removeRedundancyMenuItem_actionPerformed();
1121     }
1122     else if (source == pairwiseAlignmentMenuItem)
1123     {
1124       pairwiseAlignmentMenuItem_actionPerformed();
1125     }
1126     else if (source == PCAMenuItem)
1127     {
1128       PCAMenuItem_actionPerformed();
1129     }
1130     else if (source == averageDistanceTreeMenuItem)
1131     {
1132       averageDistanceTreeMenuItem_actionPerformed();
1133     }
1134     else if (source == neighbourTreeMenuItem)
1135     {
1136       neighbourTreeMenuItem_actionPerformed();
1137     }
1138     else if (source == njTreeBlosumMenuItem)
1139     {
1140       njTreeBlosumMenuItem_actionPerformed();
1141     }
1142     else if (source == avDistanceTreeBlosumMenuItem)
1143     {
1144       avTreeBlosumMenuItem_actionPerformed();
1145     }
1146     else if (source == documentation)
1147     {
1148       documentation_actionPerformed();
1149     }
1150     else if (source == about)
1151     {
1152       about_actionPerformed();
1153     }
1154
1155   }
1156
1157   public void inputText_actionPerformed()
1158   {
1159     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1160     Frame frame = new Frame();
1161     frame.add(cap);
1162     jalview.bin.JalviewLite.addFrame(frame,
1163             MessageManager.getString("label.input_cut_paste"), 500, 500);
1164   }
1165
1166   protected void outputText_actionPerformed(ActionEvent e)
1167   {
1168     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1169     Frame frame = new Frame();
1170     frame.add(cap);
1171     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1172             "label.alignment_output_command", new String[]
1173             { e.getActionCommand() }), 600, 500);
1174     cap.setText(new AppletFormatAdapter().formatSequences(
1175             e.getActionCommand(), viewport.getAlignment(),
1176             viewport.showJVSuffix));
1177   }
1178
1179   public void loadAnnotations()
1180   {
1181     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1182     cap.setText(MessageManager
1183             .getString("label.paste_features_annotations_Tcoffee_here"));
1184     cap.setAnnotationImport();
1185     Frame frame = new Frame();
1186     frame.add(cap);
1187     jalview.bin.JalviewLite.addFrame(frame,
1188             MessageManager.getString("action.paste_annotations"), 400, 300);
1189
1190   }
1191
1192   public String outputAnnotations(boolean displayTextbox)
1193   {
1194     String annotation = new AnnotationFile().printAnnotations(
1195             viewport.showAnnotation ? viewport.getAlignment()
1196                     .getAlignmentAnnotation() : null, viewport
1197                     .getAlignment().getGroups(), ((Alignment) viewport
1198                     .getAlignment()).alignmentProperties);
1199
1200     if (displayTextbox)
1201     {
1202       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1203       Frame frame = new Frame();
1204       frame.add(cap);
1205       jalview.bin.JalviewLite.addFrame(frame,
1206               MessageManager.getString("label.annotations"), 600, 500);
1207       cap.setText(annotation);
1208     }
1209
1210     return annotation;
1211   }
1212
1213   private Hashtable getDisplayedFeatureCols()
1214   {
1215     if (alignPanel.getFeatureRenderer() != null
1216             && viewport.featuresDisplayed != null)
1217     {
1218       FeatureRenderer fr = alignPanel.getFeatureRenderer();
1219       Hashtable fcols = new Hashtable();
1220       Enumeration en = viewport.featuresDisplayed.keys();
1221       while (en.hasMoreElements())
1222       {
1223         Object col = en.nextElement();
1224         fcols.put(col, fr.featureColours.get(col));
1225       }
1226       return fcols;
1227     }
1228     return null;
1229   }
1230
1231   public String outputFeatures(boolean displayTextbox, String format)
1232   {
1233     String features;
1234     if (format.equalsIgnoreCase("Jalview"))
1235     {
1236       features = new FeaturesFile().printJalviewFormat(viewport
1237               .getAlignment().getSequencesArray(),
1238               getDisplayedFeatureCols());
1239     }
1240     else
1241     {
1242       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1243               .getSequencesArray(), getDisplayedFeatureCols());
1244     }
1245
1246     if (displayTextbox)
1247     {
1248       boolean frimport = false;
1249       if (features == null || features.equals("No Features Visible"))
1250       {
1251         features = "# No features visible - paste some and import them here.";
1252         frimport = true;
1253       }
1254
1255       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1256       if (frimport)
1257       {
1258         cap.setAnnotationImport();
1259       }
1260       Frame frame = new Frame();
1261       frame.add(cap);
1262       jalview.bin.JalviewLite.addFrame(frame,
1263               MessageManager.getString("label.features"), 600, 500);
1264       cap.setText(features);
1265     }
1266     else
1267     {
1268       if (features == null)
1269       {
1270         features = "";
1271       }
1272     }
1273
1274     return features;
1275   }
1276
1277   void launchFullApplication()
1278   {
1279     StringBuffer url = new StringBuffer(jalviewServletURL);
1280
1281     url.append("?open="
1282             + appendProtocol(viewport.applet.getParameter("file")));
1283
1284     if (viewport.applet.getParameter("features") != null)
1285     {
1286       url.append("&features=");
1287       url.append(appendProtocol(viewport.applet.getParameter("features")));
1288     }
1289
1290     if (viewport.applet.getParameter("annotations") != null)
1291     {
1292       url.append("&annotations=");
1293       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1294     }
1295
1296     if (viewport.applet.getParameter("jnetfile") != null)
1297     {
1298       url.append("&annotations=");
1299       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1300     }
1301
1302     if (viewport.applet.getParameter("defaultColour") != null)
1303     {
1304       url.append("&colour="
1305               + removeWhiteSpace(viewport.applet
1306                       .getParameter("defaultColour")));
1307     }
1308
1309     if (viewport.applet.getParameter("userDefinedColour") != null)
1310     {
1311       url.append("&colour="
1312               + removeWhiteSpace(viewport.applet
1313                       .getParameter("userDefinedColour")));
1314     }
1315     if (viewport.applet.getParameter("tree") != null)
1316     {
1317       url.append("&tree="
1318               + appendProtocol(viewport.applet.getParameter("tree")));
1319     }
1320     if (viewport.applet.getParameter("treeFile") != null)
1321     {
1322       url.append("&tree="
1323               + appendProtocol(viewport.applet.getParameter("treeFile")));
1324     }
1325
1326     showURL(url.toString(), "FULL_APP");
1327   }
1328
1329   String removeWhiteSpace(String colour)
1330   {
1331     StringBuffer sb = new StringBuffer();
1332     for (int i = 0; i < colour.length(); i++)
1333     {
1334       if (Character.isWhitespace(colour.charAt(i)))
1335       {
1336         sb.append("%20");
1337       }
1338       else
1339       {
1340         sb.append(colour.charAt(i));
1341       }
1342     }
1343
1344     return sb.toString();
1345   }
1346
1347   String appendProtocol(String url)
1348   {
1349     try
1350     {
1351       new URL(url);
1352       url = URLEncoder.encode(url);
1353     }
1354     /*
1355      * When we finally deprecate 1.1 compatibility, we can start to use
1356      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1357      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1358      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1359      * ex.printStackTrace(); }
1360      */
1361     catch (java.net.MalformedURLException ex)
1362     {
1363       url = viewport.applet.getCodeBase() + url;
1364     }
1365     return url;
1366   }
1367
1368   public void closeMenuItem_actionPerformed()
1369   {
1370     PaintRefresher.RemoveComponent(alignPanel);
1371     if (alignPanel.seqPanel != null
1372             && alignPanel.seqPanel.seqCanvas != null)
1373     {
1374       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1375     }
1376     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1377     {
1378       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1379     }
1380
1381     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1382     {
1383       System.exit(0);
1384     }
1385     else
1386     {
1387     }
1388     viewport = null;
1389     alignPanel = null;
1390     this.dispose();
1391   }
1392
1393   /**
1394    * TODO: JAL-1104
1395    */
1396   void updateEditMenuBar()
1397   {
1398
1399     if (viewport.historyList.size() > 0)
1400     {
1401       undoMenuItem.setEnabled(true);
1402       CommandI command = (CommandI) viewport.historyList.peek();
1403       undoMenuItem.setLabel(MessageManager.formatMessage(
1404               "label.undo_command", new String[]
1405               { command.getDescription() }));
1406     }
1407     else
1408     {
1409       undoMenuItem.setEnabled(false);
1410       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1411     }
1412
1413     if (viewport.redoList.size() > 0)
1414     {
1415       redoMenuItem.setEnabled(true);
1416
1417       CommandI command = (CommandI) viewport.redoList.peek();
1418       redoMenuItem.setLabel(MessageManager.formatMessage(
1419               "label.redo_command", new String[]
1420               { command.getDescription() }));
1421     }
1422     else
1423     {
1424       redoMenuItem.setEnabled(false);
1425       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1426     }
1427   }
1428
1429   /**
1430    * TODO: JAL-1104
1431    */
1432   public void addHistoryItem(CommandI command)
1433   {
1434     if (command.getSize() > 0)
1435     {
1436       viewport.historyList.push(command);
1437       viewport.redoList.removeAllElements();
1438       updateEditMenuBar();
1439       viewport.updateHiddenColumns();
1440     }
1441   }
1442
1443   /**
1444    * TODO: JAL-1104 DOCUMENT ME!
1445    *
1446    * @param e
1447    *          DOCUMENT ME!
1448    */
1449   protected void undoMenuItem_actionPerformed()
1450   {
1451     if (viewport.historyList.size() < 1)
1452     {
1453       return;
1454     }
1455
1456     CommandI command = (CommandI) viewport.historyList.pop();
1457     viewport.redoList.push(command);
1458     command.undoCommand(null);
1459
1460     AlignViewport originalSource = getOriginatingSource(command);
1461     // JBPNote Test
1462     if (originalSource != viewport)
1463     {
1464       System.err
1465               .println("Warning: Viewport object mismatch whilst undoing");
1466     }
1467     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1468                                           // viewport.getColumnSelection().getHiddenColumns()
1469                                           // != null;
1470     updateEditMenuBar();
1471     originalSource.firePropertyChange("alignment", null, originalSource
1472             .getAlignment().getSequences());
1473   }
1474
1475   /**
1476    * TODO: JAL-1104 DOCUMENT ME!
1477    *
1478    * @param e
1479    *          DOCUMENT ME!
1480    */
1481   protected void redoMenuItem_actionPerformed()
1482   {
1483     if (viewport.redoList.size() < 1)
1484     {
1485       return;
1486     }
1487
1488     CommandI command = (CommandI) viewport.redoList.pop();
1489     viewport.historyList.push(command);
1490     command.doCommand(null);
1491
1492     AlignViewport originalSource = getOriginatingSource(command);
1493     // JBPNote Test
1494     if (originalSource != viewport)
1495     {
1496       System.err
1497               .println("Warning: Viewport object mismatch whilst re-doing");
1498     }
1499     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1500                                           // viewport.getColumnSelection().getHiddenColumns()
1501                                           // != null;
1502
1503     updateEditMenuBar();
1504     originalSource.firePropertyChange("alignment", null, originalSource
1505             .getAlignment().getSequences());
1506   }
1507
1508   AlignViewport getOriginatingSource(CommandI command)
1509   {
1510     AlignViewport originalSource = null;
1511     // For sequence removal and addition, we need to fire
1512     // the property change event FROM the viewport where the
1513     // original alignment was altered
1514     AlignmentI al = null;
1515     if (command instanceof EditCommand)
1516     {
1517       EditCommand editCommand = (EditCommand) command;
1518       al = editCommand.getAlignment();
1519       Vector comps = (Vector) PaintRefresher.components.get(viewport
1520               .getSequenceSetId());
1521       for (int i = 0; i < comps.size(); i++)
1522       {
1523         if (comps.elementAt(i) instanceof AlignmentPanel)
1524         {
1525           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1526           {
1527             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1528             break;
1529           }
1530         }
1531       }
1532     }
1533
1534     if (originalSource == null)
1535     {
1536       // The original view is closed, we must validate
1537       // the current view against the closed view first
1538       if (al != null)
1539       {
1540         PaintRefresher.validateSequences(al, viewport.getAlignment());
1541       }
1542
1543       originalSource = viewport;
1544     }
1545
1546     return originalSource;
1547   }
1548
1549   public void moveSelectedSequences(boolean up)
1550   {
1551     SequenceGroup sg = viewport.getSelectionGroup();
1552     if (sg == null)
1553     {
1554       return;
1555     }
1556     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1557             up ? null : viewport.getHiddenRepSequences(), up);
1558     alignPanel.paintAlignment(true);
1559   }
1560
1561   synchronized void slideSequences(boolean right, int size)
1562   {
1563     List<SequenceI> sg = new Vector<SequenceI>();
1564     if (viewport.cursorMode)
1565     {
1566       sg.add(viewport.getAlignment().getSequenceAt(
1567               alignPanel.seqPanel.seqCanvas.cursorY));
1568     }
1569     else if (viewport.getSelectionGroup() != null
1570             && viewport.getSelectionGroup().getSize() != viewport
1571                     .getAlignment().getHeight())
1572     {
1573       sg = viewport.getSelectionGroup().getSequences(
1574               viewport.getHiddenRepSequences());
1575     }
1576
1577     if (sg.size() < 1)
1578     {
1579       return;
1580     }
1581
1582     Vector<SequenceI> invertGroup = new Vector();
1583
1584     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1585     {
1586       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1587       {
1588         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1589       }
1590     }
1591
1592     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1593
1594     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1595             .size()]);
1596     for (int i = 0; i < invertGroup.size(); i++)
1597     {
1598       seqs2[i] = invertGroup.elementAt(i);
1599     }
1600
1601     SlideSequencesCommand ssc;
1602     if (right)
1603     {
1604       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1605               size, viewport.getGapCharacter());
1606     }
1607     else
1608     {
1609       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1610               size, viewport.getGapCharacter());
1611     }
1612
1613     int groupAdjustment = 0;
1614     if (ssc.getGapsInsertedBegin() && right)
1615     {
1616       if (viewport.cursorMode)
1617       {
1618         alignPanel.seqPanel.moveCursor(size, 0);
1619       }
1620       else
1621       {
1622         groupAdjustment = size;
1623       }
1624     }
1625     else if (!ssc.getGapsInsertedBegin() && !right)
1626     {
1627       if (viewport.cursorMode)
1628       {
1629         alignPanel.seqPanel.moveCursor(-size, 0);
1630       }
1631       else
1632       {
1633         groupAdjustment = -size;
1634       }
1635     }
1636
1637     if (groupAdjustment != 0)
1638     {
1639       viewport.getSelectionGroup().setStartRes(
1640               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1641       viewport.getSelectionGroup().setEndRes(
1642               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1643     }
1644
1645     boolean appendHistoryItem = false;
1646     if (viewport.historyList != null && viewport.historyList.size() > 0
1647             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1648     {
1649       appendHistoryItem = ssc
1650               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1651                       .peek());
1652     }
1653
1654     if (!appendHistoryItem)
1655     {
1656       addHistoryItem(ssc);
1657     }
1658
1659     repaint();
1660   }
1661
1662   static StringBuffer copiedSequences;
1663
1664   static Vector copiedHiddenColumns;
1665
1666   protected void copy_actionPerformed()
1667   {
1668     if (viewport.getSelectionGroup() == null)
1669     {
1670       return;
1671     }
1672
1673     SequenceGroup sg = viewport.getSelectionGroup();
1674     copiedSequences = new StringBuffer();
1675     Hashtable orderedSeqs = new Hashtable();
1676     for (int i = 0; i < sg.getSize(); i++)
1677     {
1678       SequenceI seq = sg.getSequenceAt(i);
1679       int index = viewport.getAlignment().findIndex(seq);
1680       orderedSeqs.put(index + "", seq);
1681     }
1682
1683     int index = 0, startRes, endRes;
1684     char ch;
1685
1686     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1687     {
1688       copiedHiddenColumns = new Vector();
1689       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1690       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1691               .size(); i++)
1692       {
1693         int[] region = (int[]) viewport.getColumnSelection()
1694                 .getHiddenColumns().elementAt(i);
1695
1696         copiedHiddenColumns.addElement(new int[]
1697         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1698       }
1699     }
1700     else
1701     {
1702       copiedHiddenColumns = null;
1703     }
1704
1705     for (int i = 0; i < sg.getSize(); i++)
1706     {
1707       SequenceI seq = null;
1708
1709       while (seq == null)
1710       {
1711         if (orderedSeqs.containsKey(index + ""))
1712         {
1713           seq = (SequenceI) orderedSeqs.get(index + "");
1714           index++;
1715
1716           break;
1717         }
1718         else
1719         {
1720           index++;
1721         }
1722       }
1723
1724       // FIND START RES
1725       // Returns residue following index if gap
1726       startRes = seq.findPosition(sg.getStartRes());
1727
1728       // FIND END RES
1729       // Need to find the residue preceeding index if gap
1730       endRes = 0;
1731
1732       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1733       {
1734         ch = seq.getCharAt(j);
1735         if (!jalview.util.Comparison.isGap((ch)))
1736         {
1737           endRes++;
1738         }
1739       }
1740
1741       if (endRes > 0)
1742       {
1743         endRes += seq.getStart() - 1;
1744       }
1745
1746       copiedSequences.append(seq.getName()
1747               + "\t"
1748               + startRes
1749               + "\t"
1750               + endRes
1751               + "\t"
1752               + seq.getSequenceAsString(sg.getStartRes(),
1753                       sg.getEndRes() + 1) + "\n");
1754     }
1755
1756   }
1757
1758   protected void pasteNew_actionPerformed()
1759   {
1760     paste(true);
1761   }
1762
1763   protected void pasteThis_actionPerformed()
1764   {
1765     paste(false);
1766   }
1767
1768   void paste(boolean newAlignment)
1769   {
1770     try
1771     {
1772
1773       if (copiedSequences == null)
1774       {
1775         return;
1776       }
1777
1778       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1779       Vector seqs = new Vector();
1780       while (st.hasMoreElements())
1781       {
1782         String name = st.nextToken();
1783         int start = Integer.parseInt(st.nextToken());
1784         int end = Integer.parseInt(st.nextToken());
1785         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1786       }
1787       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1788       for (int i = 0; i < seqs.size(); i++)
1789       {
1790         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1791       }
1792
1793       if (newAlignment)
1794       {
1795         String newtitle = MessageManager.getString("label.copied_sequences");
1796         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1797         {
1798           newtitle = getTitle();
1799         }
1800         else
1801         {
1802           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1803         }
1804         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1805                 viewport.applet, newtitle, false);
1806         if (copiedHiddenColumns != null)
1807         {
1808           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1809           {
1810             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1811             af.viewport.hideColumns(region[0], region[1]);
1812           }
1813         }
1814
1815         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1816                 DEFAULT_HEIGHT);
1817       }
1818       else
1819       {
1820         addSequences(newSeqs);
1821       }
1822
1823     } catch (Exception ex)
1824     {
1825     } // could be anything being pasted in here
1826
1827   }
1828
1829   void addSequences(SequenceI[] seqs)
1830   {
1831     for (int i = 0; i < seqs.length; i++)
1832     {
1833       viewport.getAlignment().addSequence(seqs[i]);
1834     }
1835
1836     // !newAlignment
1837     addHistoryItem(new EditCommand(
1838             MessageManager.getString("label.add_sequences"), Action.PASTE,
1839             seqs, 0, viewport.getAlignment().getWidth(),
1840             viewport.getAlignment()));
1841
1842     viewport.setEndSeq(viewport.getAlignment().getHeight());
1843     viewport.getAlignment().getWidth();
1844     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1845             .getSequences());
1846
1847   }
1848
1849   protected void cut_actionPerformed()
1850   {
1851     copy_actionPerformed();
1852     delete_actionPerformed();
1853   }
1854
1855   protected void delete_actionPerformed()
1856   {
1857
1858     SequenceGroup sg = viewport.getSelectionGroup();
1859     if (sg == null)
1860     {
1861       return;
1862     }
1863
1864     Vector seqs = new Vector();
1865     SequenceI seq;
1866     for (int i = 0; i < sg.getSize(); i++)
1867     {
1868       seq = sg.getSequenceAt(i);
1869       seqs.addElement(seq);
1870     }
1871
1872     // If the cut affects all sequences, remove highlighted columns
1873     if (sg.getSize() == viewport.getAlignment().getHeight())
1874     {
1875       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1876               sg.getEndRes() + 1);
1877     }
1878
1879     SequenceI[] cut = new SequenceI[seqs.size()];
1880     for (int i = 0; i < seqs.size(); i++)
1881     {
1882       cut[i] = (SequenceI) seqs.elementAt(i);
1883     }
1884
1885     /*
1886      * //ADD HISTORY ITEM
1887      */
1888     addHistoryItem(new EditCommand(
1889             MessageManager.getString("label.cut_sequences"), Action.CUT,
1890             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1891             viewport.getAlignment()));
1892
1893     viewport.setSelectionGroup(null);
1894     viewport.getAlignment().deleteGroup(sg);
1895
1896     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1897             .getSequences());
1898
1899     if (viewport.getAlignment().getHeight() < 1)
1900     {
1901       this.setVisible(false);
1902     }
1903     viewport.sendSelection();
1904   }
1905
1906   /**
1907    * group consensus toggled
1908    *
1909    */
1910   protected void showGroupConsensus_actionPerformed()
1911   {
1912     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1913     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1914
1915   }
1916
1917   /**
1918    * group conservation toggled.
1919    */
1920   protected void showGroupConservation_actionPerformed()
1921   {
1922     viewport.setShowGroupConservation(showGroupConservation.getState());
1923     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1924   }
1925
1926   /*
1927    * (non-Javadoc)
1928    *
1929    * @see
1930    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1931    * .event.ActionEvent)
1932    */
1933   protected void showConsensusHistogram_actionPerformed()
1934   {
1935     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1936     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1937   }
1938
1939   /*
1940    * (non-Javadoc)
1941    *
1942    * @see
1943    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1944    * .event.ActionEvent)
1945    */
1946   protected void showSequenceLogo_actionPerformed()
1947   {
1948     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1949     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1950   }
1951
1952   protected void normSequenceLogo_actionPerformed()
1953   {
1954     showSequenceLogo.setState(true);
1955     viewport.setShowSequenceLogo(true);
1956     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1957     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1958   }
1959
1960   protected void applyAutoAnnotationSettings_actionPerformed()
1961   {
1962     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1963   }
1964
1965   protected void makeGrpsFromSelection_actionPerformed()
1966   {
1967     if (avc.makeGroupsFromSelection())
1968     {
1969       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1970       alignPanel.updateAnnotation();
1971       alignPanel.paintAlignment(true);
1972     }
1973   }
1974
1975   protected void createGroup_actionPerformed()
1976   {
1977     avc.createGroup();
1978   }
1979
1980   protected void unGroup_actionPerformed()
1981   {
1982     if (avc.unGroup())
1983     {
1984       alignPanel.alignmentChanged();
1985     }
1986   }
1987
1988   protected void deleteGroups_actionPerformed()
1989   {
1990     if (avc.deleteGroups())
1991     {
1992       alignPanel.alignmentChanged();
1993     }
1994   }
1995
1996   public void selectAllSequenceMenuItem_actionPerformed()
1997   {
1998     SequenceGroup sg = new SequenceGroup();
1999     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2000     {
2001       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2002     }
2003     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2004     viewport.setSelectionGroup(sg);
2005     alignPanel.paintAlignment(true);
2006     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2007     viewport.sendSelection();
2008   }
2009
2010   public void deselectAllSequenceMenuItem_actionPerformed()
2011   {
2012     if (viewport.cursorMode)
2013     {
2014       alignPanel.seqPanel.keyboardNo1 = null;
2015       alignPanel.seqPanel.keyboardNo2 = null;
2016     }
2017     viewport.setSelectionGroup(null);
2018     viewport.getColumnSelection().clear();
2019     viewport.setSelectionGroup(null);
2020     alignPanel.idPanel.idCanvas.searchResults = null;
2021     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2022     alignPanel.paintAlignment(true);
2023     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2024     viewport.sendSelection();
2025   }
2026
2027   public void invertSequenceMenuItem_actionPerformed()
2028   {
2029     SequenceGroup sg = viewport.getSelectionGroup();
2030     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2031     {
2032       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2033     }
2034
2035     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2036     viewport.sendSelection();
2037   }
2038
2039   public void invertColSel_actionPerformed()
2040   {
2041     viewport.invertColumnSelection();
2042     alignPanel.paintAlignment(true);
2043     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2044     viewport.sendSelection();
2045   }
2046
2047   void trimAlignment(boolean trimLeft)
2048   {
2049     ColumnSelection colSel = viewport.getColumnSelection();
2050     int column;
2051
2052     if (colSel.size() > 0)
2053     {
2054       if (trimLeft)
2055       {
2056         column = colSel.getMin();
2057       }
2058       else
2059       {
2060         column = colSel.getMax();
2061       }
2062
2063       SequenceI[] seqs;
2064       if (viewport.getSelectionGroup() != null)
2065       {
2066         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2067                 viewport.getHiddenRepSequences());
2068       }
2069       else
2070       {
2071         seqs = viewport.getAlignment().getSequencesArray();
2072       }
2073
2074       TrimRegionCommand trimRegion;
2075       if (trimLeft)
2076       {
2077         trimRegion = new TrimRegionCommand("Remove Left",
2078                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2079                 viewport.getAlignment(), viewport.getColumnSelection(),
2080                 viewport.getSelectionGroup());
2081         viewport.setStartRes(0);
2082       }
2083       else
2084       {
2085         trimRegion = new TrimRegionCommand("Remove Right",
2086                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2087                 viewport.getAlignment(), viewport.getColumnSelection(),
2088                 viewport.getSelectionGroup());
2089       }
2090
2091       statusBar.setText(MessageManager.formatMessage(
2092               "label.removed_columns", new String[]
2093               { Integer.valueOf(trimRegion.getSize()).toString() }));
2094       addHistoryItem(trimRegion);
2095
2096       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2097       {
2098         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2099                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2100         {
2101           viewport.getAlignment().deleteGroup(sg);
2102         }
2103       }
2104
2105       viewport.firePropertyChange("alignment", null, viewport
2106               .getAlignment().getSequences());
2107     }
2108   }
2109
2110   public void removeGappedColumnMenuItem_actionPerformed()
2111   {
2112     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2113
2114     SequenceI[] seqs;
2115     if (viewport.getSelectionGroup() != null)
2116     {
2117       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2118               viewport.getHiddenRepSequences());
2119       start = viewport.getSelectionGroup().getStartRes();
2120       end = viewport.getSelectionGroup().getEndRes();
2121     }
2122     else
2123     {
2124       seqs = viewport.getAlignment().getSequencesArray();
2125     }
2126
2127     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2128             "Remove Gapped Columns", seqs, start, end,
2129             viewport.getAlignment());
2130
2131     addHistoryItem(removeGapCols);
2132
2133     statusBar.setText(MessageManager.formatMessage(
2134             "label.removed_empty_columns", new String[]
2135             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2136
2137     // This is to maintain viewport position on first residue
2138     // of first sequence
2139     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2140     int startRes = seq.findPosition(viewport.startRes);
2141     // ShiftList shifts;
2142     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2143     // edit.alColumnChanges=shifts.getInverse();
2144     // if (viewport.hasHiddenColumns)
2145     // viewport.getColumnSelection().compensateForEdits(shifts);
2146     viewport.setStartRes(seq.findIndex(startRes) - 1);
2147     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2148             .getSequences());
2149
2150   }
2151
2152   public void removeAllGapsMenuItem_actionPerformed()
2153   {
2154     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2155
2156     SequenceI[] seqs;
2157     if (viewport.getSelectionGroup() != null)
2158     {
2159       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2160               viewport.getHiddenRepSequences());
2161       start = viewport.getSelectionGroup().getStartRes();
2162       end = viewport.getSelectionGroup().getEndRes();
2163     }
2164     else
2165     {
2166       seqs = viewport.getAlignment().getSequencesArray();
2167     }
2168
2169     // This is to maintain viewport position on first residue
2170     // of first sequence
2171     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2172     int startRes = seq.findPosition(viewport.startRes);
2173
2174     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2175             viewport.getAlignment()));
2176
2177     viewport.setStartRes(seq.findIndex(startRes) - 1);
2178
2179     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2180             .getSequences());
2181
2182   }
2183
2184   public void findMenuItem_actionPerformed()
2185   {
2186     new Finder(alignPanel);
2187   }
2188
2189   /**
2190    * create a new view derived from the current view
2191    *
2192    * @param viewtitle
2193    * @return frame for the new view
2194    */
2195   public AlignFrame newView(String viewtitle)
2196   {
2197     AlignmentI newal;
2198     if (viewport.hasHiddenRows())
2199     {
2200       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2201               .getFullAlignment().getSequencesArray());
2202     }
2203     else
2204     {
2205       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2206     }
2207
2208     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2209     {
2210       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2211       {
2212         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2213         {
2214           newal.addAnnotation(viewport.getAlignment()
2215                   .getAlignmentAnnotation()[i]);
2216         }
2217       }
2218     }
2219
2220     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2221
2222     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2223     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2224     PaintRefresher.Register(newaf.alignPanel,
2225             newaf.alignPanel.av.getSequenceSetId());
2226
2227     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2228             newaf.alignPanel.av.getSequenceSetId());
2229     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2230             newaf.alignPanel.av.getSequenceSetId());
2231
2232     Vector comps = (Vector) PaintRefresher.components.get(viewport
2233             .getSequenceSetId());
2234     int viewSize = -1;
2235     for (int i = 0; i < comps.size(); i++)
2236     {
2237       if (comps.elementAt(i) instanceof AlignmentPanel)
2238       {
2239         viewSize++;
2240       }
2241     }
2242
2243     String title = new String(this.getTitle());
2244     if (viewtitle != null)
2245     {
2246       title = viewtitle + " ( " + title + ")";
2247     }
2248     else
2249     {
2250       if (title.indexOf("(View") > -1)
2251       {
2252         title = title.substring(0, title.indexOf("(View"));
2253       }
2254       title += "(View " + viewSize + ")";
2255     }
2256
2257     newaf.setTitle(title.toString());
2258
2259     newaf.viewport.historyList = viewport.historyList;
2260     newaf.viewport.redoList = viewport.redoList;
2261     return newaf;
2262   }
2263
2264   /**
2265    *
2266    * @return list of feature groups on the view
2267    */
2268   public String[] getFeatureGroups()
2269   {
2270     FeatureRenderer fr = null;
2271     if (alignPanel != null
2272             && (fr = alignPanel.getFeatureRenderer()) != null)
2273     {
2274       return fr.getGroups();
2275     }
2276     return null;
2277   }
2278
2279   /**
2280    * get sequence feature groups that are hidden or shown
2281    *
2282    * @param visible
2283    *          true is visible
2284    * @return list
2285    */
2286   public String[] getFeatureGroupsOfState(boolean visible)
2287   {
2288     FeatureRenderer fr = null;
2289     if (alignPanel != null
2290             && (fr = alignPanel.getFeatureRenderer()) != null)
2291     {
2292       return fr.getGroups(visible);
2293     }
2294     return null;
2295   }
2296
2297   /**
2298    * Change the display state for the given feature groups
2299    *
2300    * @param groups
2301    *          list of group strings
2302    * @param state
2303    *          visible or invisible
2304    */
2305   public void setFeatureGroupState(String[] groups, boolean state)
2306   {
2307     FeatureRenderer fr = null;
2308     this.sequenceFeatures.setState(true);
2309     viewport.showSequenceFeatures(true);
2310     if (alignPanel != null
2311             && (fr = alignPanel.getFeatureRenderer()) != null)
2312     {
2313       fr.setGroupState(groups, state);
2314       alignPanel.seqPanel.seqCanvas.repaint();
2315       if (alignPanel.overviewPanel != null)
2316       {
2317         alignPanel.overviewPanel.updateOverviewImage();
2318       }
2319     }
2320   }
2321
2322   public void seqLimits_itemStateChanged()
2323   {
2324     viewport.setShowJVSuffix(seqLimits.getState());
2325     alignPanel.fontChanged();
2326     alignPanel.paintAlignment(true);
2327   }
2328
2329   protected void colourTextMenuItem_actionPerformed()
2330   {
2331     viewport.setColourText(colourTextMenuItem.getState());
2332     alignPanel.paintAlignment(true);
2333   }
2334
2335   protected void displayNonconservedMenuItem_actionPerformed()
2336   {
2337     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2338     alignPanel.paintAlignment(true);
2339   }
2340
2341   protected void wrapMenuItem_actionPerformed()
2342   {
2343     viewport.setWrapAlignment(wrapMenuItem.getState());
2344     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2345     scaleAbove.setEnabled(wrapMenuItem.getState());
2346     scaleLeft.setEnabled(wrapMenuItem.getState());
2347     scaleRight.setEnabled(wrapMenuItem.getState());
2348     alignPanel.paintAlignment(true);
2349   }
2350
2351   public void overviewMenuItem_actionPerformed()
2352   {
2353     if (alignPanel.overviewPanel != null)
2354     {
2355       return;
2356     }
2357
2358     Frame frame = new Frame();
2359     OverviewPanel overview = new OverviewPanel(alignPanel);
2360     frame.add(overview);
2361     // +50 must allow for applet frame window
2362     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2363             "label.overview_params", new String[]
2364             { this.getTitle() }), overview.getPreferredSize().width,
2365             overview.getPreferredSize().height + 50);
2366
2367     frame.pack();
2368     final AlignmentPanel ap = alignPanel;
2369     frame.addWindowListener(new WindowAdapter()
2370     {
2371       @Override
2372       public void windowClosing(WindowEvent e)
2373       {
2374         if (ap != null)
2375         {
2376           ap.setOverviewPanel(null);
2377         }
2378       };
2379     });
2380
2381     alignPanel.setOverviewPanel(overview);
2382
2383   }
2384
2385   void changeColour(ColourSchemeI cs)
2386   {
2387     int threshold = 0;
2388
2389     if (cs != null)
2390     {
2391       if (viewport.getAbovePIDThreshold())
2392       {
2393         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2394                 cs, "Background"));
2395       }
2396
2397       if (viewport.getConservationSelected())
2398       {
2399         cs.setConservationApplied(true);
2400         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2401                 cs, "Background"));
2402       }
2403       else
2404       {
2405         cs.setConservationApplied(false);
2406       }
2407     }
2408     viewport.setGlobalColourScheme(cs);
2409
2410     if (alignPanel.getOverviewPanel() != null)
2411     {
2412       alignPanel.getOverviewPanel().updateOverviewImage();
2413     }
2414
2415     jalview.structure.StructureSelectionManager
2416             .getStructureSelectionManager(viewport.applet)
2417             .sequenceColoursChanged(alignPanel);
2418
2419     alignPanel.paintAlignment(true);
2420   }
2421
2422   protected void modifyPID_actionPerformed()
2423   {
2424     if (viewport.getAbovePIDThreshold()
2425             && viewport.getGlobalColourScheme() != null)
2426     {
2427       SliderPanel.setPIDSliderSource(alignPanel,
2428               viewport.getGlobalColourScheme(), "Background");
2429       SliderPanel.showPIDSlider();
2430     }
2431   }
2432
2433   protected void modifyConservation_actionPerformed()
2434   {
2435     if (viewport.getConservationSelected()
2436             && viewport.getGlobalColourScheme() != null)
2437     {
2438       SliderPanel.setConservationSlider(alignPanel,
2439               viewport.getGlobalColourScheme(), "Background");
2440       SliderPanel.showConservationSlider();
2441     }
2442   }
2443
2444   protected void conservationMenuItem_actionPerformed()
2445   {
2446     viewport.setConservationSelected(conservationMenuItem.getState());
2447
2448     viewport.setAbovePIDThreshold(false);
2449     abovePIDThreshold.setState(false);
2450
2451     changeColour(viewport.getGlobalColourScheme());
2452
2453     modifyConservation_actionPerformed();
2454   }
2455
2456   public void abovePIDThreshold_actionPerformed()
2457   {
2458     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2459
2460     conservationMenuItem.setState(false);
2461     viewport.setConservationSelected(false);
2462
2463     changeColour(viewport.getGlobalColourScheme());
2464
2465     modifyPID_actionPerformed();
2466   }
2467
2468   public void sortPairwiseMenuItem_actionPerformed()
2469   {
2470     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2471     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2472             .getAlignment().getSequenceAt(0), null);
2473
2474     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2475             viewport.getAlignment()));
2476     alignPanel.paintAlignment(true);
2477   }
2478
2479   public void sortIDMenuItem_actionPerformed()
2480   {
2481     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2482     AlignmentSorter.sortByID(viewport.getAlignment());
2483     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2484             viewport.getAlignment()));
2485     alignPanel.paintAlignment(true);
2486   }
2487
2488   public void sortLengthMenuItem_actionPerformed()
2489   {
2490     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2491     AlignmentSorter.sortByLength(viewport.getAlignment());
2492     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2493             viewport.getAlignment()));
2494     alignPanel.paintAlignment(true);
2495   }
2496
2497   public void sortGroupMenuItem_actionPerformed()
2498   {
2499     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2500     AlignmentSorter.sortByGroup(viewport.getAlignment());
2501     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2502             viewport.getAlignment()));
2503     alignPanel.paintAlignment(true);
2504
2505   }
2506
2507   public void removeRedundancyMenuItem_actionPerformed()
2508   {
2509     new RedundancyPanel(alignPanel);
2510   }
2511
2512   public void pairwiseAlignmentMenuItem_actionPerformed()
2513   {
2514     if (viewport.getSelectionGroup() != null
2515             && viewport.getSelectionGroup().getSize() > 1)
2516     {
2517       Frame frame = new Frame();
2518       frame.add(new PairwiseAlignPanel(alignPanel));
2519       jalview.bin.JalviewLite.addFrame(frame,
2520               MessageManager.getString("action.pairwise_alignment"), 600,
2521               500);
2522     }
2523   }
2524
2525   public void PCAMenuItem_actionPerformed()
2526   {
2527     // are the sequences aligned?
2528     if (!viewport.getAlignment().isAligned(false))
2529     {
2530       SequenceI current;
2531       int Width = viewport.getAlignment().getWidth();
2532
2533       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2534       {
2535         current = viewport.getAlignment().getSequenceAt(i);
2536
2537         if (current.getLength() < Width)
2538         {
2539           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2540         }
2541       }
2542       alignPanel.paintAlignment(true);
2543     }
2544
2545     if ((viewport.getSelectionGroup() != null
2546             && viewport.getSelectionGroup().getSize() < 4 && viewport
2547             .getSelectionGroup().getSize() > 0)
2548             || viewport.getAlignment().getHeight() < 4)
2549     {
2550       return;
2551     }
2552
2553     try
2554     {
2555       new PCAPanel(viewport);
2556     } catch (java.lang.OutOfMemoryError ex)
2557     {
2558     }
2559
2560   }
2561
2562   public void averageDistanceTreeMenuItem_actionPerformed()
2563   {
2564     NewTreePanel("AV", "PID", "Average distance tree using PID");
2565   }
2566
2567   public void neighbourTreeMenuItem_actionPerformed()
2568   {
2569     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2570   }
2571
2572   protected void njTreeBlosumMenuItem_actionPerformed()
2573   {
2574     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2575   }
2576
2577   protected void avTreeBlosumMenuItem_actionPerformed()
2578   {
2579     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2580   }
2581
2582   void NewTreePanel(String type, String pwType, String title)
2583   {
2584     // are the sequences aligned?
2585     if (!viewport.getAlignment().isAligned(false))
2586     {
2587       SequenceI current;
2588       int Width = viewport.getAlignment().getWidth();
2589
2590       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2591       {
2592         current = viewport.getAlignment().getSequenceAt(i);
2593
2594         if (current.getLength() < Width)
2595         {
2596           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2597         }
2598       }
2599       alignPanel.paintAlignment(true);
2600
2601     }
2602
2603     if ((viewport.getSelectionGroup() != null && viewport
2604             .getSelectionGroup().getSize() > 1)
2605             || (viewport.getAlignment().getHeight() > 1))
2606     {
2607       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2608
2609       addTreeMenuItem(tp, title);
2610
2611       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2612     }
2613   }
2614
2615   void loadTree_actionPerformed()
2616   {
2617     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2618     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2619     cap.setTreeImport();
2620     Frame frame = new Frame();
2621     frame.add(cap);
2622     jalview.bin.JalviewLite.addFrame(frame,
2623             MessageManager.getString("label.paste_newick_file"), 400, 300);
2624   }
2625
2626   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2627   {
2628     TreePanel tp = new TreePanel(alignPanel, treeFile,
2629             MessageManager.getString("label.load_tree_from_file"), tree);
2630     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2631     addTreeMenuItem(tp, treeFile);
2632   }
2633
2634   /**
2635    * sort the alignment using the given treePanel
2636    *
2637    * @param treePanel
2638    *          tree used to sort view
2639    * @param title
2640    *          string used for undo event name
2641    */
2642   public void sortByTree(TreePanel treePanel, String title)
2643   {
2644     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2645     AlignmentSorter
2646             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2647     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2648     // HistoryItem.SORT));
2649     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2650             "label.order_by_params", new String[]
2651             { title }), oldOrder, viewport.getAlignment()));
2652     alignPanel.paintAlignment(true);
2653   }
2654
2655   /**
2656    * Do any automatic reordering of the alignment and add the necessary bits to
2657    * the menu structure for the new tree
2658    *
2659    * @param treePanel
2660    * @param title
2661    */
2662   protected void addTreeMenuItem(final TreePanel treePanel,
2663           final String title)
2664   {
2665     final MenuItem item = new MenuItem(title);
2666     sortByTreeMenu.add(item);
2667     item.addActionListener(new java.awt.event.ActionListener()
2668     {
2669       @Override
2670       public void actionPerformed(ActionEvent evt)
2671       {
2672         sortByTree(treePanel, title); // treePanel.getTitle());
2673       }
2674     });
2675
2676     treePanel.addWindowListener(new WindowAdapter()
2677     {
2678       @Override
2679       public void windowOpened(WindowEvent e)
2680       {
2681         if (viewport.sortByTree)
2682         {
2683           sortByTree(treePanel, title);
2684         }
2685         super.windowOpened(e);
2686       }
2687
2688       @Override
2689       public void windowClosing(WindowEvent e)
2690       {
2691         sortByTreeMenu.remove(item);
2692       };
2693     });
2694   }
2695
2696   public boolean sortBy(AlignmentOrder alorder, String undoname)
2697   {
2698     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699     if (viewport.applet.debug)
2700     {
2701       System.err.println("Sorting " + alorder.getOrder().size()
2702               + " in alignment '" + getTitle() + "'");
2703     }
2704     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2705     if (undoname != null)
2706     {
2707       addHistoryItem(new OrderCommand(undoname, oldOrder,
2708               viewport.getAlignment()));
2709     }
2710     alignPanel.paintAlignment(true);
2711     return true;
2712   }
2713
2714   protected void documentation_actionPerformed()
2715   {
2716     alignPanel.av.applet.openJalviewHelpUrl();
2717   }
2718
2719   protected void about_actionPerformed()
2720   {
2721
2722     class AboutPanel extends Canvas
2723     {
2724       String version;
2725
2726       String builddate;
2727
2728       public AboutPanel(String version, String builddate)
2729       {
2730         this.version = version;
2731         this.builddate = builddate;
2732       }
2733
2734       @Override
2735       public void paint(Graphics g)
2736       {
2737         g.setColor(Color.white);
2738         g.fillRect(0, 0, getSize().width, getSize().height);
2739         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2740         FontMetrics fm = g.getFontMetrics();
2741         int fh = fm.getHeight();
2742         int y = 5, x = 7;
2743         g.setColor(Color.black);
2744         // TODO: update this text for each release or centrally store it for
2745         // lite and application
2746         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2747         g.drawString(MessageManager.formatMessage(
2748                 "label.jalviewLite_release", new String[]
2749                 { version }), x, y += fh);
2750         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2751         g.drawString(MessageManager.formatMessage(
2752                 "label.jaview_build_date", new String[]
2753                 { builddate }), x, y += fh);
2754         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2755         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2756                 x, y += fh * 1.5);
2757         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2758                 x + 50, y += fh + 8);
2759         g.drawString(
2760                 MessageManager.getString("label.jalview_dev_managers"), x,
2761                 y += fh);
2762         g.drawString(MessageManager
2763                 .getString("label.jalview_distribution_lists"), x, y += fh);
2764         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2765                 x, y += fh + 8);
2766         g.drawString(
2767                 MessageManager.getString("label.jalview_cite_1_authors"),
2768                 x, y += fh);
2769         g.drawString(
2770                 MessageManager.getString("label.jalview_cite_1_title"), x,
2771                 y += fh);
2772         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2773                 x, y += fh);
2774       }
2775     }
2776
2777     Frame frame = new Frame();
2778     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2779             .getBuildDate()));
2780     jalview.bin.JalviewLite.addFrame(frame,
2781             MessageManager.getString("label.jalview"), 580, 220);
2782
2783   }
2784
2785   public void showURL(String url, String target)
2786   {
2787     if (viewport.applet == null)
2788     {
2789       System.out.println("Not running as applet - no browser available.");
2790     }
2791     else
2792     {
2793       viewport.applet.showURL(url, target);
2794     }
2795   }
2796
2797   // ////////////////////////////////////////////////////////////////////////////////
2798   // JBuilder Graphics here
2799
2800   MenuBar alignFrameMenuBar = new MenuBar();
2801
2802   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2803
2804   MenuItem loadApplication = new MenuItem(
2805           MessageManager.getString("label.view_full_application"));
2806
2807   MenuItem loadTree = new MenuItem(
2808           MessageManager.getString("label.load_associated_tree"));
2809
2810   MenuItem loadAnnotations = new MenuItem(
2811           MessageManager.getString("label.load_features_annotations"));
2812
2813   MenuItem outputFeatures = new MenuItem(
2814           MessageManager.getString("label.export_features").concat("..."));
2815
2816   MenuItem outputAnnotations = new MenuItem(
2817           MessageManager.getString("label.export_annotations").concat("..."));
2818
2819   MenuItem closeMenuItem = new MenuItem(
2820           MessageManager.getString("action.close"));
2821
2822   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2823
2824   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2825
2826   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2827
2828   Menu calculateMenu = new Menu(
2829           MessageManager.getString("action.calculate"));
2830
2831   MenuItem selectAllSequenceMenuItem = new MenuItem(
2832           MessageManager.getString("action.select_all"));
2833
2834   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2835           MessageManager.getString("action.deselect_all"));
2836
2837   MenuItem invertSequenceMenuItem = new MenuItem(
2838           MessageManager.getString("action.invert_selection"));
2839
2840   MenuItem remove2LeftMenuItem = new MenuItem();
2841
2842   MenuItem remove2RightMenuItem = new MenuItem();
2843
2844   MenuItem removeGappedColumnMenuItem = new MenuItem();
2845
2846   MenuItem removeAllGapsMenuItem = new MenuItem();
2847
2848   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2849
2850   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2851
2852   MenuItem sortPairwiseMenuItem = new MenuItem();
2853
2854   MenuItem sortIDMenuItem = new MenuItem();
2855
2856   MenuItem sortLengthMenuItem = new MenuItem();
2857
2858   MenuItem sortGroupMenuItem = new MenuItem();
2859
2860   MenuItem removeRedundancyMenuItem = new MenuItem();
2861
2862   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2863
2864   MenuItem PCAMenuItem = new MenuItem();
2865
2866   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2867
2868   MenuItem neighbourTreeMenuItem = new MenuItem();
2869
2870   BorderLayout borderLayout1 = new BorderLayout();
2871
2872   public Label statusBar = new Label();
2873
2874   Menu outputTextboxMenu = new Menu();
2875
2876   MenuItem clustalColour = new MenuItem();
2877
2878   MenuItem zappoColour = new MenuItem();
2879
2880   MenuItem taylorColour = new MenuItem();
2881
2882   MenuItem hydrophobicityColour = new MenuItem();
2883
2884   MenuItem helixColour = new MenuItem();
2885
2886   MenuItem strandColour = new MenuItem();
2887
2888   MenuItem turnColour = new MenuItem();
2889
2890   MenuItem buriedColour = new MenuItem();
2891
2892   MenuItem purinePyrimidineColour = new MenuItem();
2893
2894   MenuItem RNAInteractionColour = new MenuItem();
2895
2896   MenuItem RNAHelixColour = new MenuItem();
2897
2898   MenuItem userDefinedColour = new MenuItem();
2899
2900   MenuItem PIDColour = new MenuItem();
2901
2902   MenuItem BLOSUM62Colour = new MenuItem();
2903
2904   MenuItem tcoffeeColour = new MenuItem();
2905
2906   MenuItem njTreeBlosumMenuItem = new MenuItem();
2907
2908   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2909
2910   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2911
2912   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2913
2914   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2915
2916   MenuItem alProperties = new MenuItem(
2917           MessageManager.getString("label.alignment_props"));
2918
2919   MenuItem overviewMenuItem = new MenuItem();
2920
2921   MenuItem undoMenuItem = new MenuItem();
2922
2923   MenuItem redoMenuItem = new MenuItem();
2924
2925   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2926
2927   MenuItem noColourmenuItem = new MenuItem();
2928
2929   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2930
2931   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2932
2933   MenuItem findMenuItem = new MenuItem();
2934
2935   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2936
2937   MenuItem nucleotideColour = new MenuItem();
2938
2939   MenuItem deleteGroups = new MenuItem();
2940
2941   MenuItem grpsFromSelection = new MenuItem();
2942
2943   MenuItem createGroup = new MenuItem();
2944
2945   MenuItem unGroup = new MenuItem();
2946
2947   MenuItem delete = new MenuItem();
2948
2949   MenuItem copy = new MenuItem();
2950
2951   MenuItem cut = new MenuItem();
2952
2953   Menu pasteMenu = new Menu();
2954
2955   MenuItem pasteNew = new MenuItem();
2956
2957   MenuItem pasteThis = new MenuItem();
2958
2959   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2960
2961   MenuItem font = new MenuItem();
2962
2963   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2964
2965   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2966
2967   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2968
2969   MenuItem modifyPID = new MenuItem();
2970
2971   MenuItem modifyConservation = new MenuItem();
2972
2973   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2974           "Autocalculate Consensus", true);
2975
2976   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2977           "Sort Alignment With New Tree", true);
2978
2979   Menu sortByTreeMenu = new Menu();
2980
2981   Menu sort = new Menu();
2982
2983   Menu calculate = new Menu();
2984
2985   MenuItem inputText = new MenuItem();
2986
2987   Menu helpMenu = new Menu();
2988
2989   MenuItem documentation = new MenuItem();
2990
2991   MenuItem about = new MenuItem();
2992
2993   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2994
2995   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2996
2997   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2998
2999   Menu autoAnnMenu = new Menu();
3000
3001   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3002
3003   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3004
3005   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3006
3007   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3008
3009   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3010
3011   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3012
3013   private void jbInit() throws Exception
3014   {
3015
3016     setMenuBar(alignFrameMenuBar);
3017
3018     MenuItem item;
3019
3020     // dynamically fill save as menu with available formats
3021     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3022     {
3023
3024       item = new MenuItem(
3025               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3026
3027       item.addActionListener(new java.awt.event.ActionListener()
3028       {
3029         @Override
3030         public void actionPerformed(ActionEvent e)
3031         {
3032           outputText_actionPerformed(e);
3033         }
3034       });
3035
3036       outputTextboxMenu.add(item);
3037     }
3038     closeMenuItem.addActionListener(this);
3039     loadApplication.addActionListener(this);
3040
3041     loadTree.addActionListener(this);
3042     loadAnnotations.addActionListener(this);
3043     outputFeatures.addActionListener(this);
3044     outputAnnotations.addActionListener(this);
3045     selectAllSequenceMenuItem.addActionListener(this);
3046     deselectAllSequenceMenuItem.addActionListener(this);
3047     invertSequenceMenuItem.addActionListener(this);
3048     remove2LeftMenuItem.setLabel(MessageManager
3049             .getString("action.remove_left"));
3050     remove2LeftMenuItem.addActionListener(this);
3051     remove2RightMenuItem.setLabel(MessageManager
3052             .getString("action.remove_right"));
3053     remove2RightMenuItem.addActionListener(this);
3054     removeGappedColumnMenuItem.setLabel(MessageManager
3055             .getString("action.remove_empty_columns"));
3056     removeGappedColumnMenuItem.addActionListener(this);
3057     removeAllGapsMenuItem.setLabel(MessageManager
3058             .getString("action.remove_all_gaps"));
3059     removeAllGapsMenuItem.addActionListener(this);
3060     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3061     viewBoxesMenuItem.setState(true);
3062     viewBoxesMenuItem.addItemListener(this);
3063     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3064     viewTextMenuItem.setState(true);
3065     viewTextMenuItem.addItemListener(this);
3066     sortPairwiseMenuItem.setLabel(MessageManager
3067             .getString("action.by_pairwise_id"));
3068     sortPairwiseMenuItem.addActionListener(this);
3069     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3070     sortIDMenuItem.addActionListener(this);
3071     sortLengthMenuItem.setLabel(MessageManager
3072             .getString("action.by_length"));
3073     sortLengthMenuItem.addActionListener(this);
3074     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3075     sortGroupMenuItem.addActionListener(this);
3076     removeRedundancyMenuItem.setLabel(MessageManager
3077             .getString("action.remove_redundancy").concat("..."));
3078     removeRedundancyMenuItem.addActionListener(this);
3079     pairwiseAlignmentMenuItem.setLabel(MessageManager
3080             .getString("action.pairwise_alignment"));
3081     pairwiseAlignmentMenuItem.addActionListener(this);
3082     PCAMenuItem.setLabel(MessageManager
3083             .getString("label.principal_component_analysis"));
3084     PCAMenuItem.addActionListener(this);
3085     averageDistanceTreeMenuItem.setLabel(MessageManager
3086             .getString("label.average_distance_identity"));
3087     averageDistanceTreeMenuItem.addActionListener(this);
3088     neighbourTreeMenuItem.setLabel(MessageManager
3089             .getString("label.neighbour_joining_identity"));
3090     neighbourTreeMenuItem.addActionListener(this);
3091     statusBar.setBackground(Color.white);
3092     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3093     statusBar.setText(MessageManager.getString("label.status_bar"));
3094     outputTextboxMenu.setLabel(MessageManager
3095             .getString("label.out_to_textbox"));
3096     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3097
3098     clustalColour.addActionListener(this);
3099     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3100     zappoColour.addActionListener(this);
3101     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3102     taylorColour.addActionListener(this);
3103     hydrophobicityColour.setLabel(MessageManager
3104             .getString("label.hydrophobicity"));
3105     hydrophobicityColour.addActionListener(this);
3106     helixColour
3107             .setLabel(MessageManager.getString("label.helix_propensity"));
3108     helixColour.addActionListener(this);
3109     strandColour.setLabel(MessageManager
3110             .getString("label.strand_propensity"));
3111     strandColour.addActionListener(this);
3112     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3113     turnColour.addActionListener(this);
3114     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3115     buriedColour.addActionListener(this);
3116     purinePyrimidineColour.setLabel(MessageManager
3117             .getString("label.purine_pyrimidine"));
3118     purinePyrimidineColour.addActionListener(this);
3119     RNAInteractionColour.setLabel(MessageManager
3120             .getString("label.rna_interaction"));
3121     RNAInteractionColour.addActionListener(this);
3122     RNAHelixColour.setLabel(MessageManager
3123             .getString("action.by_rna_helixes"));
3124     RNAHelixColour.addActionListener(this);
3125     userDefinedColour.setLabel(MessageManager
3126             .getString("action.user_defined"));
3127     userDefinedColour.addActionListener(this);
3128     PIDColour.setLabel(MessageManager
3129             .getString("label.percentage_identity"));
3130     PIDColour.addActionListener(this);
3131     BLOSUM62Colour.setLabel(MessageManager
3132             .getString("label.blosum62_score"));
3133     BLOSUM62Colour.addActionListener(this);
3134     tcoffeeColour
3135             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3136     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3137                                      // provided
3138     tcoffeeColour.addActionListener(this);
3139     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3140             .getString("label.average_distance_bloslum62"));
3141     avDistanceTreeBlosumMenuItem.addActionListener(this);
3142     njTreeBlosumMenuItem.setLabel(MessageManager
3143             .getString("label.neighbour_blosum62"));
3144     njTreeBlosumMenuItem.addActionListener(this);
3145     annotationPanelMenuItem.setLabel(MessageManager
3146             .getString("label.show_annotations"));
3147     annotationPanelMenuItem.addItemListener(this);
3148     colourTextMenuItem.setLabel(MessageManager
3149             .getString("label.colour_text"));
3150     colourTextMenuItem.addItemListener(this);
3151     displayNonconservedMenuItem.setLabel(MessageManager
3152             .getString("label.show_non_conversed"));
3153     displayNonconservedMenuItem.addItemListener(this);
3154     alProperties.addActionListener(this);
3155     overviewMenuItem.setLabel(MessageManager
3156             .getString("label.overview_window"));
3157     overviewMenuItem.addActionListener(this);
3158     undoMenuItem.setEnabled(false);
3159     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3160     undoMenuItem.addActionListener(this);
3161     redoMenuItem.setEnabled(false);
3162     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3163     redoMenuItem.addActionListener(this);
3164     conservationMenuItem.setLabel(MessageManager
3165             .getString("action.by_conservation"));
3166     conservationMenuItem.addItemListener(this);
3167     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3168     noColourmenuItem.addActionListener(this);
3169     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3170     wrapMenuItem.addItemListener(this);
3171     renderGapsMenuItem.setLabel(MessageManager
3172             .getString("action.show_gaps"));
3173     renderGapsMenuItem.setState(true);
3174     renderGapsMenuItem.addItemListener(this);
3175     findMenuItem.setLabel(MessageManager.getString("action.find"));
3176     findMenuItem.addActionListener(this);
3177     abovePIDThreshold.setLabel(MessageManager
3178             .getString("label.above_identity_threshold"));
3179     abovePIDThreshold.addItemListener(this);
3180     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3181     nucleotideColour.addActionListener(this);
3182     deleteGroups.setLabel(MessageManager
3183             .getString("action.undefine_groups"));
3184     deleteGroups.addActionListener(this);
3185     grpsFromSelection.setLabel(MessageManager
3186             .getString("action.make_groups_selection"));
3187     grpsFromSelection.addActionListener(this);
3188     createGroup.setLabel(MessageManager.getString("action.create_group"));
3189     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3190     copy.setLabel(MessageManager.getString("action.copy"));
3191     copy.addActionListener(this);
3192     cut.setLabel(MessageManager.getString("action.cut"));
3193     cut.addActionListener(this);
3194     delete.setLabel(MessageManager.getString("action.delete"));
3195     delete.addActionListener(this);
3196     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3197     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3198     pasteNew.addActionListener(this);
3199     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3200     pasteThis.addActionListener(this);
3201     applyToAllGroups.setLabel(MessageManager
3202             .getString("label.apply_colour_to_all_groups"));
3203     applyToAllGroups.setState(true);
3204     applyToAllGroups.addItemListener(this);
3205     font.setLabel(MessageManager.getString("action.font"));
3206     font.addActionListener(this);
3207     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3208     scaleAbove.setState(true);
3209     scaleAbove.setEnabled(false);
3210     scaleAbove.addItemListener(this);
3211     scaleLeft.setEnabled(false);
3212     scaleLeft.setState(true);
3213     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3214     scaleLeft.addItemListener(this);
3215     scaleRight.setEnabled(false);
3216     scaleRight.setState(true);
3217     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3218     scaleRight.addItemListener(this);
3219     modifyPID.setLabel(MessageManager
3220             .getString("label.modify_identity_thereshold"));
3221     modifyPID.addActionListener(this);
3222     modifyConservation.setLabel(MessageManager
3223             .getString("label.modify_conservation_thereshold"));
3224     modifyConservation.addActionListener(this);
3225     sortByTreeMenu.setLabel(MessageManager
3226             .getString("action.by_tree_order"));
3227     sort.setLabel(MessageManager.getString("action.sort"));
3228     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3229     autoCalculate.addItemListener(this);
3230     sortByTree.addItemListener(this);
3231     inputText
3232             .setLabel(MessageManager.getString("label.input_from_textbox"));
3233     inputText.addActionListener(this);
3234     centreColumnLabelFlag.setLabel(MessageManager
3235             .getString("label.centre_column_labels"));
3236     centreColumnLabelFlag.addItemListener(this);
3237     followMouseOverFlag.setLabel(MessageManager
3238             .getString("label.automatic_scrolling"));
3239     followMouseOverFlag.addItemListener(this);
3240     helpMenu.setLabel(MessageManager.getString("action.help"));
3241     documentation.setLabel(MessageManager.getString("label.documentation"));
3242     documentation.addActionListener(this);
3243
3244     about.setLabel(MessageManager.getString("label.about"));
3245     about.addActionListener(this);
3246     seqLimits.setState(true);
3247     seqLimits.setLabel(MessageManager
3248             .getString("label.show_sequence_limits"));
3249     seqLimits.addItemListener(this);
3250     featureSettings.setLabel(MessageManager
3251             .getString("label.feature_settings"));
3252     featureSettings.addActionListener(this);
3253     sequenceFeatures.setLabel(MessageManager
3254             .getString("label.sequence_features"));
3255     sequenceFeatures.addItemListener(this);
3256     sequenceFeatures.setState(false);
3257     annotationColour.setLabel(MessageManager
3258             .getString("action.by_annotation"));
3259     annotationColour.addActionListener(this);
3260     invertSequenceMenuItem.setLabel(MessageManager
3261             .getString("action.invert_sequence_selection"));
3262     invertColSel.setLabel(MessageManager
3263             .getString("action.invert_column_selection"));
3264     menu1.setLabel(MessageManager.getString("action.show"));
3265     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3266     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3267     menu2.setLabel(MessageManager.getString("action.hide"));
3268     hideColumns
3269             .setLabel(MessageManager.getString("label.selected_columns"));
3270     hideSequences.setLabel(MessageManager
3271             .getString("label.selected_sequences"));
3272     hideAllButSelection.setLabel(MessageManager
3273             .getString("label.all_but_selected_region"));
3274     hideAllSelection.setLabel(MessageManager
3275             .getString("label.selected_region"));
3276     showAllHidden.setLabel(MessageManager
3277             .getString("label.all_sequences_columns"));
3278     showGroupConsensus.setLabel(MessageManager
3279             .getString("label.group_consensus"));
3280     showGroupConservation.setLabel(MessageManager
3281             .getString("label.group_conservation"));
3282     showConsensusHistogram.setLabel(MessageManager
3283             .getString("label.show_consensus_histogram"));
3284     showSequenceLogo.setLabel(MessageManager
3285             .getString("label.show_consensus_logo"));
3286     normSequenceLogo.setLabel(MessageManager
3287             .getString("label.norm_consensus_logo"));
3288     applyAutoAnnotationSettings.setLabel(MessageManager
3289             .getString("label.apply_all_groups"));
3290     applyAutoAnnotationSettings.setState(true);
3291     autoAnnMenu.setLabel(MessageManager
3292             .getString("label.autocalculated_annotation"));
3293
3294     invertColSel.addActionListener(this);
3295     showColumns.addActionListener(this);
3296     showSeqs.addActionListener(this);
3297     hideColumns.addActionListener(this);
3298     hideSequences.addActionListener(this);
3299     hideAllButSelection.addActionListener(this);
3300     hideAllSelection.addActionListener(this);
3301     showAllHidden.addActionListener(this);
3302     showGroupConsensus.addItemListener(this);
3303     showGroupConservation.addItemListener(this);
3304     showConsensusHistogram.addItemListener(this);
3305     showSequenceLogo.addItemListener(this);
3306     normSequenceLogo.addItemListener(this);
3307
3308     applyAutoAnnotationSettings.addItemListener(this);
3309     formatMenu.setLabel(MessageManager.getString("action.format"));
3310     selectMenu.setLabel(MessageManager.getString("action.select"));
3311     newView.setLabel(MessageManager.getString("action.new_view"));
3312     newView.addActionListener(this);
3313     alignFrameMenuBar.add(fileMenu);
3314     alignFrameMenuBar.add(editMenu);
3315     alignFrameMenuBar.add(selectMenu);
3316     alignFrameMenuBar.add(viewMenu);
3317     alignFrameMenuBar.add(formatMenu);
3318     alignFrameMenuBar.add(colourMenu);
3319     alignFrameMenuBar.add(calculateMenu);
3320     alignFrameMenuBar.add(helpMenu);
3321
3322     fileMenu.add(inputText);
3323     fileMenu.add(loadTree);
3324     fileMenu.add(loadAnnotations);
3325
3326     fileMenu.addSeparator();
3327     fileMenu.add(outputTextboxMenu);
3328     fileMenu.add(outputFeatures);
3329     fileMenu.add(outputAnnotations);
3330
3331     if (jalviewServletURL != null)
3332     {
3333       fileMenu.add(loadApplication);
3334     }
3335
3336     fileMenu.addSeparator();
3337     fileMenu.add(closeMenuItem);
3338
3339     editMenu.add(undoMenuItem);
3340     editMenu.add(redoMenuItem);
3341     editMenu.add(cut);
3342     editMenu.add(copy);
3343     editMenu.add(pasteMenu);
3344     editMenu.add(delete);
3345     editMenu.addSeparator();
3346     editMenu.add(remove2LeftMenuItem);
3347     editMenu.add(remove2RightMenuItem);
3348     editMenu.add(removeGappedColumnMenuItem);
3349     editMenu.add(removeAllGapsMenuItem);
3350     editMenu.add(removeRedundancyMenuItem);
3351     viewMenu.add(newView);
3352     viewMenu.addSeparator();
3353     viewMenu.add(menu1);
3354     viewMenu.add(menu2);
3355     viewMenu.addSeparator();
3356     viewMenu.add(followMouseOverFlag);
3357     viewMenu.add(annotationPanelMenuItem);
3358     autoAnnMenu.add(applyAutoAnnotationSettings);
3359     autoAnnMenu.add(showConsensusHistogram);
3360     autoAnnMenu.add(showSequenceLogo);
3361     autoAnnMenu.add(normSequenceLogo);
3362     autoAnnMenu.addSeparator();
3363     autoAnnMenu.add(showGroupConservation);
3364     autoAnnMenu.add(showGroupConsensus);
3365     viewMenu.add(autoAnnMenu);
3366     viewMenu.addSeparator();
3367     viewMenu.add(sequenceFeatures);
3368     viewMenu.add(featureSettings);
3369     viewMenu.addSeparator();
3370     viewMenu.add(alProperties);
3371     viewMenu.addSeparator();
3372     viewMenu.add(overviewMenuItem);
3373     colourMenu.add(applyToAllGroups);
3374     colourMenu.addSeparator();
3375     colourMenu.add(noColourmenuItem);
3376     colourMenu.add(clustalColour);
3377     colourMenu.add(BLOSUM62Colour);
3378     colourMenu.add(PIDColour);
3379     colourMenu.add(zappoColour);
3380     colourMenu.add(taylorColour);
3381     colourMenu.add(hydrophobicityColour);
3382     colourMenu.add(helixColour);
3383     colourMenu.add(strandColour);
3384     colourMenu.add(turnColour);
3385     colourMenu.add(buriedColour);
3386     colourMenu.add(nucleotideColour);
3387     colourMenu.add(purinePyrimidineColour);
3388     // colourMenu.add(RNAInteractionColour);
3389     colourMenu.add(tcoffeeColour);
3390     colourMenu.add(userDefinedColour);
3391     colourMenu.addSeparator();
3392     colourMenu.add(conservationMenuItem);
3393     colourMenu.add(modifyConservation);
3394     colourMenu.add(abovePIDThreshold);
3395     colourMenu.add(modifyPID);
3396     colourMenu.add(annotationColour);
3397     colourMenu.add(RNAHelixColour);
3398     calculateMenu.add(sort);
3399     calculateMenu.add(calculate);
3400     calculateMenu.addSeparator();
3401     calculateMenu.add(pairwiseAlignmentMenuItem);
3402     calculateMenu.add(PCAMenuItem);
3403     calculateMenu.add(autoCalculate);
3404     calculateMenu.add(sortByTree);
3405     this.add(statusBar, BorderLayout.SOUTH);
3406     pasteMenu.add(pasteNew);
3407     pasteMenu.add(pasteThis);
3408     sort.add(sortIDMenuItem);
3409     sort.add(sortLengthMenuItem);
3410     sort.add(sortByTreeMenu);
3411     sort.add(sortGroupMenuItem);
3412     sort.add(sortPairwiseMenuItem);
3413     calculate.add(averageDistanceTreeMenuItem);
3414     calculate.add(neighbourTreeMenuItem);
3415     calculate.add(avDistanceTreeBlosumMenuItem);
3416     calculate.add(njTreeBlosumMenuItem);
3417     helpMenu.add(documentation);
3418     helpMenu.add(about);
3419     menu1.add(showColumns);
3420     menu1.add(showSeqs);
3421     menu1.add(showAllHidden);
3422     menu2.add(hideColumns);
3423     menu2.add(hideSequences);
3424     menu2.add(hideAllSelection);
3425     menu2.add(hideAllButSelection);
3426     formatMenu.add(font);
3427     formatMenu.add(seqLimits);
3428     formatMenu.add(wrapMenuItem);
3429     formatMenu.add(scaleAbove);
3430     formatMenu.add(scaleLeft);
3431     formatMenu.add(scaleRight);
3432     formatMenu.add(viewBoxesMenuItem);
3433     formatMenu.add(viewTextMenuItem);
3434     formatMenu.add(colourTextMenuItem);
3435     formatMenu.add(displayNonconservedMenuItem);
3436     formatMenu.add(renderGapsMenuItem);
3437     formatMenu.add(centreColumnLabelFlag);
3438     selectMenu.add(findMenuItem);
3439     selectMenu.addSeparator();
3440     selectMenu.add(selectAllSequenceMenuItem);
3441     selectMenu.add(deselectAllSequenceMenuItem);
3442     selectMenu.add(invertSequenceMenuItem);
3443     selectMenu.add(invertColSel);
3444     selectMenu.add(createGroup);
3445     selectMenu.add(unGroup);
3446     selectMenu.add(grpsFromSelection);
3447     selectMenu.add(deleteGroups);
3448
3449   }
3450
3451   public void setStatus(String string)
3452   {
3453     statusBar.setText(string);
3454   };
3455
3456   MenuItem featureSettings = new MenuItem();
3457
3458   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3459
3460   MenuItem annotationColour = new MenuItem();
3461
3462   MenuItem invertColSel = new MenuItem();
3463
3464   Menu menu1 = new Menu();
3465
3466   MenuItem showColumns = new MenuItem();
3467
3468   MenuItem showSeqs = new MenuItem();
3469
3470   Menu menu2 = new Menu();
3471
3472   MenuItem hideColumns = new MenuItem();
3473
3474   MenuItem hideSequences = new MenuItem();
3475
3476   MenuItem hideAllButSelection = new MenuItem();
3477
3478   MenuItem hideAllSelection = new MenuItem();
3479
3480   MenuItem showAllHidden = new MenuItem();
3481
3482   Menu formatMenu = new Menu();
3483
3484   Menu selectMenu = new Menu();
3485
3486   MenuItem newView = new MenuItem();
3487
3488   /**
3489    * Attach the alignFrame panels after embedding menus, if necessary. This used
3490    * to be called setEmbedded, but is now creates the dropdown menus in a
3491    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3492    *
3493    * @param reallyEmbedded
3494    *          true to attach the view to the applet area on the page rather than
3495    *          in a new window
3496    */
3497   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3498   {
3499     if (reallyEmbedded)
3500     {
3501       // ////
3502       // Explicly build the embedded menu panel for the on-page applet
3503       //
3504       // view cannot be closed if its actually on the page
3505       fileMenu.remove(closeMenuItem);
3506       fileMenu.remove(3); // Remove Seperator
3507       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3508               Font.PLAIN, 11, false); // use our own fonts.
3509       // and actually add the components to the applet area
3510       viewport.applet.setLayout(new BorderLayout());
3511       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3512       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3513       alignPanel.setSize(viewport.applet.getSize().width,
3514               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3515                       - statusBar.HEIGHT);
3516       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3517       final AlignFrame me = this;
3518       viewport.applet.addFocusListener(new FocusListener()
3519       {
3520
3521         @Override
3522         public void focusLost(FocusEvent e)
3523         {
3524           if (me.viewport.applet.currentAlignFrame == me)
3525           {
3526             me.viewport.applet.currentAlignFrame = null;
3527           }
3528         }
3529
3530         @Override
3531         public void focusGained(FocusEvent e)
3532         {
3533           me.viewport.applet.currentAlignFrame = me;
3534         }
3535       });
3536       viewport.applet.validate();
3537     }
3538     else
3539     {
3540       // //////
3541       // test and embed menu bar if necessary.
3542       //
3543       if (embedMenuIfNeeded(alignPanel))
3544       {
3545         // adjust for status bar height too
3546         alignPanel.setSize(getSize().width, getSize().height
3547                 - statusBar.HEIGHT);
3548       }
3549       add(statusBar, BorderLayout.SOUTH);
3550       add(alignPanel, BorderLayout.CENTER);
3551       // and register with the applet so it can pass external API calls to us
3552       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3553               DEFAULT_HEIGHT);
3554     }
3555   }
3556
3557   /**
3558    * create a new binding between structures in an existing jmol viewer instance
3559    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3560    * this does not open a new Jmol window, or modify the display of the
3561    * structures in the original jmol window. Note This method doesn't work
3562    * without an additional javascript library to exchange messages between the
3563    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3564    *
3565    * @param viewer
3566    *          JmolViewer instance
3567    * @param sequenceIds
3568    *          - sequence Ids to search for associations
3569    */
3570   public SequenceStructureBinding addStructureViewInstance(
3571           Object jmolviewer, String[] sequenceIds)
3572   {
3573     org.jmol.api.JmolViewer viewer = null;
3574     try
3575     {
3576       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3577     } catch (ClassCastException ex)
3578     {
3579       System.err.println("Unsupported viewer object :"
3580               + jmolviewer.getClass());
3581     }
3582     if (viewer == null)
3583     {
3584       System.err.println("Can't use this object as a structure viewer:"
3585               + jmolviewer.getClass());
3586       return null;
3587     }
3588     SequenceI[] seqs = null;
3589     if (sequenceIds == null || sequenceIds.length == 0)
3590     {
3591       seqs = viewport.getAlignment().getSequencesArray();
3592     }
3593     else
3594     {
3595       Vector sqi = new Vector();
3596       AlignmentI al = viewport.getAlignment();
3597       for (int sid = 0; sid < sequenceIds.length; sid++)
3598       {
3599         SequenceI sq = al.findName(sequenceIds[sid]);
3600         if (sq != null)
3601         {
3602           sqi.addElement(sq);
3603         }
3604       }
3605       if (sqi.size() > 0)
3606       {
3607         seqs = new SequenceI[sqi.size()];
3608         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3609         {
3610           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3611         }
3612       }
3613       else
3614       {
3615         return null;
3616       }
3617     }
3618     ExtJmol jmv = null;
3619     // TODO: search for a jmv that involves viewer
3620     if (jmv == null)
3621     { // create a new viewer/jalview binding.
3622       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3623       { seqs });
3624     }
3625     return jmv;
3626
3627   }
3628
3629   /**
3630    * bind a pdb file to a sequence in the current view
3631    *
3632    * @param sequenceId
3633    *          - sequenceId within the dataset.
3634    * @param pdbEntryString
3635    *          - the short name for the PDB file
3636    * @param pdbFile
3637    *          - pdb file - either a URL or a valid PDB file.
3638    * @return true if binding was as success TODO: consider making an exception
3639    *         structure for indicating when PDB parsing or sequenceId location
3640    *         fails.
3641    */
3642   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3643           String pdbFile)
3644   {
3645     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3646     boolean needtoadd = false;
3647     if (toaddpdb != null)
3648     {
3649       Vector pdbe = toaddpdb.getPDBId();
3650       PDBEntry pdbentry = null;
3651       if (pdbe != null && pdbe.size() > 0)
3652       {
3653         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3654         {
3655           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3656           if (!pdbentry.getId().equals(pdbEntryString)
3657                   && !pdbentry.getFile().equals(pdbFile))
3658           {
3659             pdbentry = null;
3660           }
3661           else
3662           {
3663             continue;
3664           }
3665         }
3666       }
3667       if (pdbentry == null)
3668       {
3669         pdbentry = new PDBEntry();
3670         pdbentry.setId(pdbEntryString);
3671         pdbentry.setFile(pdbFile);
3672         needtoadd = true; // add this new entry to sequence.
3673       }
3674       // resolve data source
3675       // TODO: this code should be a refactored to an io package
3676       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3677       if (protocol == null)
3678       {
3679         return false;
3680       }
3681       if (needtoadd)
3682       {
3683         // make a note of the access mode and add
3684         if (pdbentry.getProperty() == null)
3685         {
3686           pdbentry.setProperty(new Hashtable());
3687         }
3688         pdbentry.getProperty().put("protocol", protocol);
3689         toaddpdb.addPDBId(pdbentry);
3690         alignPanel.getStructureSelectionManager()
3691                 .registerPDBEntry(pdbentry);
3692       }
3693     }
3694     return true;
3695   }
3696
3697   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3698   {
3699     if (seqs != null)
3700     {
3701       Vector sequences = new Vector();
3702       for (int i = 0; i < seqs.length; i++)
3703       {
3704         if (seqs[i] != null)
3705         {
3706           sequences.addElement(new Object[]
3707           { seqs[i], (chains != null) ? chains[i] : null });
3708         }
3709       }
3710       seqs = new SequenceI[sequences.size()];
3711       chains = new String[sequences.size()];
3712       for (int i = 0, isize = sequences.size(); i < isize; i++)
3713       {
3714         Object[] oj = (Object[]) sequences.elementAt(i);
3715
3716         seqs[i] = (SequenceI) oj[0];
3717         chains[i] = (String) oj[1];
3718       }
3719     }
3720     return new Object[]
3721     { seqs, chains };
3722
3723   }
3724
3725   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3726           SequenceI[] seqs, String[] chains, String protocol)
3727   {
3728     // Scrub any null sequences from the array
3729     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3730     seqs = (SequenceI[]) sqch[0];
3731     chains = (String[]) sqch[1];
3732     if (seqs == null || seqs.length == 0)
3733     {
3734       System.err
3735               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3736     }
3737     if (protocol == null || protocol.trim().length() == 0
3738             || protocol.equals("null"))
3739     {
3740       protocol = (String) pdb.getProperty().get("protocol");
3741       if (protocol == null)
3742       {
3743         System.err.println("Couldn't work out protocol to open structure: "
3744                 + pdb.getId());
3745         return;
3746       }
3747     }
3748     if (applet.useXtrnalSviewer)
3749     {
3750       // register the association(s) and quit, don't create any windows.
3751       if (StructureSelectionManager.getStructureSelectionManager(applet)
3752               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3753       {
3754         System.err.println("Failed to map " + pdb.getFile() + " ("
3755                 + protocol + ") to any sequences");
3756       }
3757       return;
3758     }
3759     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3760     {
3761       // can only do alignments with Jmol
3762       // find the last jmol window assigned to this alignment
3763       jalview.appletgui.AppletJmol ajm = null, tajm;
3764       Vector jmols = applet
3765               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3766       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3767       {
3768         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3769         if (tajm.ap.alignFrame == this)
3770         {
3771           ajm = tajm;
3772           break;
3773         }
3774       }
3775       if (ajm != null)
3776       {
3777         System.err
3778                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3779         // try and add the pdb structure
3780         // ajm.addS
3781         ajm = null;
3782       }
3783     }
3784     // otherwise, create a new window
3785     if (applet.jmolAvailable)
3786     {
3787       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3788               protocol);
3789       applet.lastFrameX += 40;
3790       applet.lastFrameY += 40;
3791     }
3792     else
3793     {
3794       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3795     }
3796
3797   }
3798
3799   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3800           SequenceI[][] seqs, String[][] chains, String[] protocols)
3801   {
3802     // TODO Auto-generated method stub
3803     System.err.println("Aligned Structure View: Not yet implemented.");
3804   }
3805
3806   /**
3807    * modify the current selection, providing the user has not made a selection
3808    * already.
3809    *
3810    * @param sel
3811    *          - sequences from this alignment
3812    * @param csel
3813    *          - columns to be selected on the alignment
3814    */
3815   public void select(SequenceGroup sel, ColumnSelection csel)
3816   {
3817     alignPanel.seqPanel.selection(sel, csel, null);
3818   }
3819
3820   public void scrollTo(int row, int column)
3821   {
3822     alignPanel.seqPanel.scrollTo(row, column);
3823   }
3824
3825   public void scrollToRow(int row)
3826   {
3827     alignPanel.seqPanel.scrollToRow(row);
3828   }
3829
3830   public void scrollToColumn(int column)
3831   {
3832     alignPanel.seqPanel.scrollToColumn(column);
3833   }
3834
3835   /**
3836    * @return the alignments unique ID.
3837    */
3838   public String getSequenceSetId()
3839   {
3840     return viewport.getSequenceSetId();
3841   }
3842
3843   /**
3844    * Load the (T-Coffee) score file from the specified url
3845    *
3846    * @param source
3847    *          File/URL/T-COFFEE score file contents
3848    * @throws IOException
3849    * @return true if alignment was annotated with data from source
3850    */
3851   public boolean loadScoreFile(String source) throws IOException
3852   {
3853
3854     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3855             AppletFormatAdapter.checkProtocol(source));
3856     if (!file.isValid())
3857     {
3858       // TODO: raise dialog for gui
3859       System.err.println("Problems parsing T-Coffee scores: "
3860               + file.getWarningMessage());
3861       System.err.println("Origin was:\n" + source);
3862       return false;
3863     }
3864
3865     /*
3866      * check that the score matrix matches the alignment dimensions
3867      */
3868     AlignmentI aln;
3869     if ((aln = viewport.getAlignment()) != null
3870             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3871                     .getWidth()))
3872     {
3873       // TODO: raise a dialog box here rather than bomb out.
3874       System.err
3875               .println("The scores matrix does not match the alignment dimensions");
3876
3877     }
3878
3879     // TODO add parameter to indicate if matching should be done
3880     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3881     {
3882       alignPanel.fontChanged();
3883       tcoffeeColour.setEnabled(true);
3884       // switch to this color
3885       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3886       return true;
3887     }
3888     else
3889     {
3890       System.err.println("Problems resolving T-Coffee scores:");
3891       if (file.getWarningMessage() != null)
3892       {
3893         System.err.println(file.getWarningMessage());
3894       }
3895     }
3896     return false;
3897   }
3898
3899 }