src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.FeatureRenderer;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.EditCommand.Action;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.ColumnSelection;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.io.AnnotationFile;
  46 import jalview.io.AppletFormatAdapter;
  47 import jalview.io.FeaturesFile;
  48 import jalview.io.TCoffeeScoreFile;
  49 import jalview.schemes.Blosum62ColourScheme;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.ClustalxColourScheme;
  52 import jalview.schemes.ColourSchemeI;
  53 import jalview.schemes.HelixColourScheme;
  54 import jalview.schemes.HydrophobicColourScheme;
  55 import jalview.schemes.NucleotideColourScheme;
  56 import jalview.schemes.PIDColourScheme;
  57 import jalview.schemes.PurinePyrimidineColourScheme;
  58 import jalview.schemes.RNAHelicesColourChooser;
  59 import jalview.schemes.RNAInteractionColourScheme;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.structures.models.AAStructureBindingModel;
  67 import jalview.util.MessageManager;
  68
  69 import java.awt.BorderLayout;
  70 import java.awt.Canvas;
  71 import java.awt.CheckboxMenuItem;
  72 import java.awt.Color;
  73 import java.awt.Font;
  74 import java.awt.FontMetrics;
  75 import java.awt.Frame;
  76 import java.awt.Graphics;
  77 import java.awt.Label;
  78 import java.awt.Menu;
  79 import java.awt.MenuBar;
  80 import java.awt.MenuItem;
  81 import java.awt.event.ActionEvent;
  82 import java.awt.event.ActionListener;
  83 import java.awt.event.FocusEvent;
  84 import java.awt.event.FocusListener;
  85 import java.awt.event.ItemEvent;
  86 import java.awt.event.ItemListener;
  87 import java.awt.event.KeyEvent;
  88 import java.awt.event.KeyListener;
  89 import java.awt.event.WindowAdapter;
  90 import java.awt.event.WindowEvent;
  91 import java.io.IOException;
  92 import java.net.URL;
  93 import java.net.URLEncoder;
  94 import java.util.Arrays;
  95 import java.util.Hashtable;
  96 import java.util.List;
  97 import java.util.Map;
  98 import java.util.StringTokenizer;
  99 import java.util.Vector;
 100
 101 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 102         ItemListener, KeyListener, AlignViewControllerGuiI
 103 {
 104   public AlignViewControllerI avc;
 105
 106   public AlignmentPanel alignPanel;
 107
 108   public AlignViewport viewport;
 109
 110   int DEFAULT_WIDTH = 700;
 111
 112   int DEFAULT_HEIGHT = 500;
 113
 114   String jalviewServletURL;
 115
 116   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 117           String title, boolean embedded)
 118   {
 119     if (applet != null)
 120     {
 121       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 122     }
 123
 124     try
 125     {
 126       jbInit();
 127     } catch (Exception ex)
 128     {
 129       ex.printStackTrace();
 130     }
 131     // need to get window geometry before we calculate alignment layout
 132     if (applet != null)
 133     {
 134       String param;
 135       try
 136       {
 137         param = applet.getParameter("windowWidth");
 138         if (param != null)
 139         {
 140           int width = Integer.parseInt(param);
 141           DEFAULT_WIDTH = width;
 142         }
 143         param = applet.getParameter("windowHeight");
 144         if (param != null)
 145         {
 146           int height = Integer.parseInt(param);
 147           DEFAULT_HEIGHT = height;
 148         }
 149       } catch (Exception ex)
 150       {
 151       }
 152     }
 153     viewport = new AlignViewport(al, applet);
 154     alignPanel = new AlignmentPanel(this, viewport);
 155     avc = new jalview.controller.AlignViewController(this, viewport,
 156             alignPanel);
 157     viewport.updateConservation(alignPanel);
 158     viewport.updateConsensus(alignPanel);
 159
 160     annotationPanelMenuItem.setState(viewport.showAnnotation);
 161     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 162     followMouseOverFlag.setState(viewport.getFollowHighlight());
 163     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 164     showGroupConservation.setState(viewport.isShowGroupConservation());
 165     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 166     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 167     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 168     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 169
 170     seqLimits.setState(viewport.showJVSuffix);
 171
 172     if (applet != null)
 173     {
 174       String param = applet.getParameter("sortBy");
 175       if (param != null)
 176       {
 177         if (param.equalsIgnoreCase("Id"))
 178         {
 179           sortIDMenuItem_actionPerformed();
 180         }
 181         else if (param.equalsIgnoreCase("Pairwise Identity"))
 182         {
 183           sortPairwiseMenuItem_actionPerformed();
 184         }
 185         else if (param.equalsIgnoreCase("Length"))
 186         {
 187           sortLengthMenuItem_actionPerformed();
 188         }
 189       }
 190
 191       param = applet.getParameter("wrap");
 192       if (param != null)
 193       {
 194         if (param.equalsIgnoreCase("true"))
 195         {
 196           wrapMenuItem.setState(true);
 197           wrapMenuItem_actionPerformed();
 198         }
 199       }
 200       param = applet.getParameter("centrecolumnlabels");
 201       if (param != null)
 202       {
 203         centreColumnLabelFlag.setState(true);
 204         centreColumnLabelFlag_stateChanged();
 205       }
 206
 207     }
 208     if (viewport.getAlignment().isNucleotide())
 209     {
 210       viewport.updateStrucConsensus(alignPanel);
 211       if (viewport.getAlignment().hasRNAStructure())
 212       {
 213         RNAHelixColour.setEnabled(true);
 214       }
 215       else
 216       {
 217         RNAHelixColour.setEnabled(false);
 218       }
 219     }
 220     else
 221     {
 222       RNAHelixColour.setEnabled(false);
 223       purinePyrimidineColour.setEnabled(false);
 224     }
 225     // Some JVMS send keyevents to Top frame or lowest panel,
 226     // Havent worked out why yet. So add to both this frame and seqCanvas for
 227     // now
 228     this.addKeyListener(this);
 229     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 230     alignPanel.idPanel.idCanvas.addKeyListener(this);
 231     alignPanel.scalePanel.addKeyListener(this);
 232     alignPanel.annotationPanel.addKeyListener(this);
 233     alignPanel.annotationPanelHolder.addKeyListener(this);
 234     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 235     alignPanel.alabels.addKeyListener(this);
 236     createAlignFrameWindow(embedded, title);
 237
 238     validate();
 239     alignPanel.adjustAnnotationHeight();
 240     alignPanel.paintAlignment(true);
 241   }
 242
 243   public AlignViewport getAlignViewport()
 244   {
 245     return viewport;
 246   }
 247
 248   public SeqCanvas getSeqcanvas()
 249   {
 250     return alignPanel.seqPanel.seqCanvas;
 251   }
 252
 253   /**
 254    * Load a features file onto the alignment
 255    *
 256    * @param file
 257    *          file URL, content, or other resolvable path
 258    * @param type
 259    *          is protocol for accessing data referred to by file
 260    */
 261
 262   public boolean parseFeaturesFile(String file, String type)
 263   {
 264     return parseFeaturesFile(file, type, true);
 265   }
 266
 267   /**
 268    * Load a features file onto the alignment
 269    *
 270    * @param file
 271    *          file URL, content, or other resolvable path
 272    * @param type
 273    *          is protocol for accessing data referred to by file
 274    * @param autoenabledisplay
 275    *          when true, display features flag will be automatically enabled if
 276    *          features are loaded
 277    * @return true if data parsed as a features file
 278    */
 279   public boolean parseFeaturesFile(String file, String type,
 280           boolean autoenabledisplay)
 281   {
 282     // TODO: test if importing a features file onto an alignment which already
 283     // has features with links overwrites the original links.
 284
 285     Hashtable featureLinks = new Hashtable();
 286     boolean featuresFile = false;
 287     try
 288     {
 289       featuresFile = new jalview.io.FeaturesFile(file, type)
 290               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 291                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 292                       true, viewport.applet.getDefaultParameter(
 293                               "relaxedidmatch", false));
 294     } catch (Exception ex)
 295     {
 296       ex.printStackTrace();
 297     }
 298
 299     if (featuresFile)
 300     {
 301       if (featureLinks.size() > 0)
 302       {
 303         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 304       }
 305       if (autoenabledisplay)
 306       {
 307         viewport.setShowSequenceFeatures(true);
 308         sequenceFeatures.setState(true);
 309       }
 310       if (alignPanel.seqPanel.seqCanvas.fr != null)
 311       {
 312         // update the min/max ranges where necessary
 313         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 314       }
 315       if (viewport.featureSettings != null)
 316       {
 317         viewport.featureSettings.refreshTable();
 318       }
 319       alignPanel.paintAlignment(true);
 320       statusBar.setText(MessageManager
 321               .getString("label.successfully_added_features_alignment"));
 322     }
 323     return featuresFile;
 324   }
 325
 326   @Override
 327   public void keyPressed(KeyEvent evt)
 328   {
 329     if (viewport.cursorMode
 330             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 331                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 332                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 333             && Character.isDigit(evt.getKeyChar()))
 334     {
 335       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 336     }
 337
 338     switch (evt.getKeyCode())
 339     {
 340     case 27: // escape key
 341       deselectAllSequenceMenuItem_actionPerformed();
 342
 343       alignPanel.alabels.cancelDrag();
 344       break;
 345     case KeyEvent.VK_X:
 346       if (evt.isControlDown() || evt.isMetaDown())
 347       {
 348         cut_actionPerformed();
 349       }
 350       break;
 351     case KeyEvent.VK_C:
 352       if (viewport.cursorMode && !evt.isControlDown())
 353       {
 354         alignPanel.seqPanel.setCursorColumn();
 355       }
 356       if (evt.isControlDown() || evt.isMetaDown())
 357       {
 358         copy_actionPerformed();
 359       }
 360       break;
 361     case KeyEvent.VK_V:
 362       if (evt.isControlDown())
 363       {
 364         paste(evt.isShiftDown());
 365       }
 366       break;
 367     case KeyEvent.VK_A:
 368       if (evt.isControlDown() || evt.isMetaDown())
 369       {
 370         selectAllSequenceMenuItem_actionPerformed();
 371       }
 372       break;
 373     case KeyEvent.VK_DOWN:
 374       if (viewport.cursorMode)
 375       {
 376         alignPanel.seqPanel.moveCursor(0, 1);
 377       }
 378       else
 379       {
 380         moveSelectedSequences(false);
 381       }
 382       break;
 383
 384     case KeyEvent.VK_UP:
 385       if (viewport.cursorMode)
 386       {
 387         alignPanel.seqPanel.moveCursor(0, -1);
 388       }
 389       else
 390       {
 391         moveSelectedSequences(true);
 392       }
 393       break;
 394
 395     case KeyEvent.VK_LEFT:
 396       if (evt.isAltDown() || !viewport.cursorMode)
 397       {
 398         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 399       }
 400       else
 401       {
 402         alignPanel.seqPanel.moveCursor(-1, 0);
 403       }
 404       break;
 405
 406     case KeyEvent.VK_RIGHT:
 407       if (evt.isAltDown() || !viewport.cursorMode)
 408       {
 409         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 410       }
 411       else
 412       {
 413         alignPanel.seqPanel.moveCursor(1, 0);
 414       }
 415       break;
 416
 417     case KeyEvent.VK_SPACE:
 418       if (viewport.cursorMode)
 419       {
 420         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 421                 || evt.isShiftDown() || evt.isAltDown());
 422       }
 423       break;
 424
 425     case KeyEvent.VK_DELETE:
 426     case KeyEvent.VK_BACK_SPACE:
 427       if (viewport.cursorMode)
 428       {
 429         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 430                 || evt.isShiftDown() || evt.isAltDown());
 431       }
 432       else
 433       {
 434         cut_actionPerformed();
 435         alignPanel.seqPanel.seqCanvas.repaint();
 436       }
 437       break;
 438
 439     case KeyEvent.VK_S:
 440       if (viewport.cursorMode)
 441       {
 442         alignPanel.seqPanel.setCursorRow();
 443       }
 444       break;
 445     case KeyEvent.VK_P:
 446       if (viewport.cursorMode)
 447       {
 448         alignPanel.seqPanel.setCursorPosition();
 449       }
 450       break;
 451
 452     case KeyEvent.VK_ENTER:
 453     case KeyEvent.VK_COMMA:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.setCursorRowAndColumn();
 457       }
 458       break;
 459
 460     case KeyEvent.VK_Q:
 461       if (viewport.cursorMode)
 462       {
 463         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 464       }
 465       break;
 466     case KeyEvent.VK_M:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_F2:
 474       viewport.cursorMode = !viewport.cursorMode;
 475       statusBar.setText(MessageManager.formatMessage(
 476               "label.keyboard_editing_mode", new String[]
 477               { (viewport.cursorMode ? "on" : "off") }));
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 481         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 482       }
 483       break;
 484
 485     case KeyEvent.VK_F:
 486       if (evt.isControlDown())
 487       {
 488         findMenuItem_actionPerformed();
 489       }
 490       break;
 491
 492     case KeyEvent.VK_H:
 493     {
 494       boolean toggleSeqs = !evt.isControlDown();
 495       boolean toggleCols = !evt.isShiftDown();
 496       toggleHiddenRegions(toggleSeqs, toggleCols);
 497       break;
 498     }
 499
 500     case KeyEvent.VK_PAGE_UP:
 501       if (viewport.wrapAlignment)
 502       {
 503         alignPanel.scrollUp(true);
 504       }
 505       else
 506       {
 507         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 508                 - viewport.endSeq + viewport.startSeq);
 509       }
 510       break;
 511
 512     case KeyEvent.VK_PAGE_DOWN:
 513       if (viewport.wrapAlignment)
 514       {
 515         alignPanel.scrollUp(false);
 516       }
 517       else
 518       {
 519         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 520                 + viewport.endSeq - viewport.startSeq);
 521       }
 522       break;
 523
 524     case KeyEvent.VK_Z:
 525       if (evt.isControlDown())
 526       {
 527         undoMenuItem_actionPerformed();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_Y:
 532       if (evt.isControlDown())
 533       {
 534         redoMenuItem_actionPerformed();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_L:
 539       if (evt.isControlDown())
 540       {
 541         trimAlignment(true);
 542       }
 543       break;
 544
 545     case KeyEvent.VK_R:
 546       if (evt.isControlDown())
 547       {
 548         trimAlignment(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_E:
 553       if (evt.isControlDown())
 554       {
 555         if (evt.isShiftDown())
 556         {
 557           this.removeAllGapsMenuItem_actionPerformed();
 558         }
 559         else
 560         {
 561           removeGappedColumnMenuItem_actionPerformed();
 562         }
 563       }
 564       break;
 565     case KeyEvent.VK_I:
 566       if (evt.isControlDown())
 567       {
 568         if (evt.isAltDown())
 569         {
 570           invertColSel_actionPerformed();
 571         }
 572         else
 573         {
 574           invertSequenceMenuItem_actionPerformed();
 575         }
 576       }
 577       break;
 578
 579     case KeyEvent.VK_G:
 580       if (evt.isControlDown())
 581       {
 582         if (evt.isShiftDown())
 583         {
 584           this.unGroup_actionPerformed();
 585         }
 586         else
 587         {
 588           this.createGroup_actionPerformed();
 589         }
 590       }
 591       break;
 592
 593     case KeyEvent.VK_U:
 594       if (evt.isControlDown())
 595       {
 596         this.deleteGroups_actionPerformed();
 597       }
 598       break;
 599
 600     case KeyEvent.VK_T:
 601       if (evt.isControlDown())
 602       {
 603         newView(null);
 604       }
 605       break;
 606
 607     }
 608     alignPanel.paintAlignment(true);
 609   }
 610
 611   /**
 612    * called by key handler and the hide all/show all menu items
 613    *
 614    * @param toggleSeqs
 615    * @param toggleCols
 616    */
 617   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 618   {
 619     boolean hide = false;
 620     SequenceGroup sg = viewport.getSelectionGroup();
 621     if (!toggleSeqs && !toggleCols)
 622     {
 623       // Hide everything by the current selection - this is a hack - we do the
 624       // invert and then hide
 625       // first check that there will be visible columns after the invert.
 626       if ((viewport.getColumnSelection() != null
 627               && viewport.getColumnSelection().getSelected() != null && viewport
 628               .getColumnSelection().getSelected().size() > 0)
 629               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 630                       .getEndRes()))
 631       {
 632         // now invert the sequence set, if required - empty selection implies
 633         // that no hiding is required.
 634         if (sg != null)
 635         {
 636           invertSequenceMenuItem_actionPerformed();
 637           sg = viewport.getSelectionGroup();
 638           toggleSeqs = true;
 639
 640         }
 641         viewport.expandColSelection(sg, true);
 642         // finally invert the column selection and get the new sequence
 643         // selection and indicate it should be hidden.
 644         invertColSel_actionPerformed();
 645         toggleCols = true;
 646       }
 647     }
 648
 649     if (toggleSeqs)
 650     {
 651       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 652       {
 653         hide = true;
 654         viewport.hideAllSelectedSeqs();
 655       }
 656       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 657               .size() > 0))
 658       {
 659         viewport.showAllHiddenSeqs();
 660       }
 661     }
 662
 663     if (toggleCols)
 664     {
 665       if (viewport.getColumnSelection().getSelected().size() > 0)
 666       {
 667         viewport.hideSelectedColumns();
 668         if (!toggleSeqs)
 669         {
 670           viewport.setSelectionGroup(sg);
 671         }
 672       }
 673       else if (!hide)
 674       {
 675         viewport.showAllHiddenColumns();
 676       }
 677     }
 678   }
 679
 680   @Override
 681   public void keyReleased(KeyEvent evt)
 682   {
 683   }
 684
 685   @Override
 686   public void keyTyped(KeyEvent evt)
 687   {
 688   }
 689
 690   @Override
 691   public void itemStateChanged(ItemEvent evt)
 692   {
 693     if (evt.getSource() == displayNonconservedMenuItem)
 694     {
 695       displayNonconservedMenuItem_actionPerformed();
 696     }
 697     else if (evt.getSource() == colourTextMenuItem)
 698     {
 699       colourTextMenuItem_actionPerformed();
 700     }
 701     else if (evt.getSource() == wrapMenuItem)
 702     {
 703       wrapMenuItem_actionPerformed();
 704     }
 705     else if (evt.getSource() == scaleAbove)
 706     {
 707       viewport.setScaleAboveWrapped(scaleAbove.getState());
 708     }
 709     else if (evt.getSource() == scaleLeft)
 710     {
 711       viewport.setScaleLeftWrapped(scaleLeft.getState());
 712     }
 713     else if (evt.getSource() == scaleRight)
 714     {
 715       viewport.setScaleRightWrapped(scaleRight.getState());
 716     }
 717     else if (evt.getSource() == seqLimits)
 718     {
 719       seqLimits_itemStateChanged();
 720     }
 721     else if (evt.getSource() == viewBoxesMenuItem)
 722     {
 723       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 724     }
 725     else if (evt.getSource() == viewTextMenuItem)
 726     {
 727       viewport.setShowText(viewTextMenuItem.getState());
 728     }
 729     else if (evt.getSource() == renderGapsMenuItem)
 730     {
 731       viewport.setRenderGaps(renderGapsMenuItem.getState());
 732     }
 733     else if (evt.getSource() == annotationPanelMenuItem)
 734     {
 735       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 736       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 737     }
 738     else if (evt.getSource() == sequenceFeatures)
 739     {
 740       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 741       alignPanel.seqPanel.seqCanvas.repaint();
 742     }
 743     else if (evt.getSource() == conservationMenuItem)
 744     {
 745       conservationMenuItem_actionPerformed();
 746     }
 747     else if (evt.getSource() == abovePIDThreshold)
 748     {
 749       abovePIDThreshold_actionPerformed();
 750     }
 751     else if (evt.getSource() == applyToAllGroups)
 752     {
 753       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 754     }
 755     else if (evt.getSource() == autoCalculate)
 756     {
 757       viewport.autoCalculateConsensus = autoCalculate.getState();
 758     }
 759     else if (evt.getSource() == sortByTree)
 760     {
 761       viewport.sortByTree = sortByTree.getState();
 762     }
 763     else if (evt.getSource() == this.centreColumnLabelFlag)
 764     {
 765       centreColumnLabelFlag_stateChanged();
 766     }
 767     else if (evt.getSource() == this.followMouseOverFlag)
 768     {
 769       mouseOverFlag_stateChanged();
 770     }
 771     else if (evt.getSource() == showGroupConsensus)
 772     {
 773       showGroupConsensus_actionPerformed();
 774     }
 775     else if (evt.getSource() == showGroupConservation)
 776     {
 777       showGroupConservation_actionPerformed();
 778     }
 779     else if (evt.getSource() == showSequenceLogo)
 780     {
 781       showSequenceLogo_actionPerformed();
 782     }
 783     else if (evt.getSource() == normSequenceLogo)
 784     {
 785       normSequenceLogo_actionPerformed();
 786     }
 787     else if (evt.getSource() == showConsensusHistogram)
 788     {
 789       showConsensusHistogram_actionPerformed();
 790     }
 791     else if (evt.getSource() == applyAutoAnnotationSettings)
 792     {
 793       applyAutoAnnotationSettings_actionPerformed();
 794     }
 795     alignPanel.paintAlignment(true);
 796   }
 797
 798   private void mouseOverFlag_stateChanged()
 799   {
 800     viewport.followHighlight = followMouseOverFlag.getState();
 801     // TODO: could kick the scrollTo mechanism to reset view for current
 802     // searchresults.
 803   }
 804
 805   private void centreColumnLabelFlag_stateChanged()
 806   {
 807     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 808     this.alignPanel.annotationPanel.repaint();
 809   }
 810
 811   @Override
 812   public void actionPerformed(ActionEvent evt)
 813   {
 814     Object source = evt.getSource();
 815
 816     if (source == inputText)
 817     {
 818       inputText_actionPerformed();
 819     }
 820     else if (source == loadTree)
 821     {
 822       loadTree_actionPerformed();
 823     }
 824     else if (source == loadApplication)
 825     {
 826       launchFullApplication();
 827     }
 828     else if (source == loadAnnotations)
 829     {
 830       loadAnnotations();
 831     }
 832     else if (source == outputAnnotations)
 833     {
 834       outputAnnotations(true);
 835     }
 836     else if (source == outputFeatures)
 837     {
 838       outputFeatures(true, "Jalview");
 839     }
 840     else if (source == closeMenuItem)
 841     {
 842       closeMenuItem_actionPerformed();
 843     }
 844     else if (source == copy)
 845     {
 846       copy_actionPerformed();
 847     }
 848     else if (source == undoMenuItem)
 849     {
 850       undoMenuItem_actionPerformed();
 851     }
 852     else if (source == redoMenuItem)
 853     {
 854       redoMenuItem_actionPerformed();
 855     }
 856     else if (source == inputText)
 857     {
 858       inputText_actionPerformed();
 859     }
 860     else if (source == closeMenuItem)
 861     {
 862       closeMenuItem_actionPerformed();
 863     }
 864     else if (source == undoMenuItem)
 865     {
 866       undoMenuItem_actionPerformed();
 867     }
 868     else if (source == redoMenuItem)
 869     {
 870       redoMenuItem_actionPerformed();
 871     }
 872     else if (source == copy)
 873     {
 874       copy_actionPerformed();
 875     }
 876     else if (source == pasteNew)
 877     {
 878       pasteNew_actionPerformed();
 879     }
 880     else if (source == pasteThis)
 881     {
 882       pasteThis_actionPerformed();
 883     }
 884     else if (source == cut)
 885     {
 886       cut_actionPerformed();
 887     }
 888     else if (source == delete)
 889     {
 890       delete_actionPerformed();
 891     }
 892     else if (source == grpsFromSelection)
 893     {
 894       makeGrpsFromSelection_actionPerformed();
 895     }
 896     else if (source == deleteGroups)
 897     {
 898       deleteGroups_actionPerformed();
 899     }
 900     else if (source == selectAllSequenceMenuItem)
 901     {
 902       selectAllSequenceMenuItem_actionPerformed();
 903     }
 904     else if (source == deselectAllSequenceMenuItem)
 905     {
 906       deselectAllSequenceMenuItem_actionPerformed();
 907     }
 908     else if (source == invertSequenceMenuItem)
 909     {
 910       invertSequenceMenuItem_actionPerformed();
 911     }
 912     else if (source == invertColSel)
 913     {
 914       viewport.invertColumnSelection();
 915       alignPanel.paintAlignment(true);
 916     }
 917     else if (source == remove2LeftMenuItem)
 918     {
 919       trimAlignment(true);
 920     }
 921     else if (source == remove2RightMenuItem)
 922     {
 923       trimAlignment(false);
 924     }
 925     else if (source == removeGappedColumnMenuItem)
 926     {
 927       removeGappedColumnMenuItem_actionPerformed();
 928     }
 929     else if (source == removeAllGapsMenuItem)
 930     {
 931       removeAllGapsMenuItem_actionPerformed();
 932     }
 933     else if (source == findMenuItem)
 934     {
 935       findMenuItem_actionPerformed();
 936     }
 937     else if (source == font)
 938     {
 939       new FontChooser(alignPanel);
 940     }
 941     else if (source == newView)
 942     {
 943       newView(null);
 944     }
 945     else if (source == showColumns)
 946     {
 947       viewport.showAllHiddenColumns();
 948       alignPanel.paintAlignment(true);
 949     }
 950     else if (source == showSeqs)
 951     {
 952       viewport.showAllHiddenSeqs();
 953       alignPanel.paintAlignment(true);
 954     }
 955     else if (source == hideColumns)
 956     {
 957       viewport.hideSelectedColumns();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == hideSequences
 961             && viewport.getSelectionGroup() != null)
 962     {
 963       viewport.hideAllSelectedSeqs();
 964       alignPanel.paintAlignment(true);
 965     }
 966     else if (source == hideAllButSelection)
 967     {
 968       toggleHiddenRegions(false, false);
 969       alignPanel.paintAlignment(true);
 970     }
 971     else if (source == hideAllSelection)
 972     {
 973       SequenceGroup sg = viewport.getSelectionGroup();
 974       viewport.expandColSelection(sg, false);
 975       viewport.hideAllSelectedSeqs();
 976       viewport.hideSelectedColumns();
 977       alignPanel.paintAlignment(true);
 978     }
 979     else if (source == showAllHidden)
 980     {
 981       viewport.showAllHiddenColumns();
 982       viewport.showAllHiddenSeqs();
 983       alignPanel.paintAlignment(true);
 984     }
 985     else if (source == showGroupConsensus)
 986     {
 987       showGroupConsensus_actionPerformed();
 988     }
 989     else if (source == showGroupConservation)
 990     {
 991       showGroupConservation_actionPerformed();
 992     }
 993     else if (source == showSequenceLogo)
 994     {
 995       showSequenceLogo_actionPerformed();
 996     }
 997     else if (source == normSequenceLogo)
 998     {
 999       normSequenceLogo_actionPerformed();
1000     }
1001     else if (source == showConsensusHistogram)
1002     {
1003       showConsensusHistogram_actionPerformed();
1004     }
1005     else if (source == applyAutoAnnotationSettings)
1006     {
1007       applyAutoAnnotationSettings_actionPerformed();
1008     }
1009     else if (source == featureSettings)
1010     {
1011       new FeatureSettings(alignPanel);
1012     }
1013     else if (source == alProperties)
1014     {
1015       StringBuffer contents = new jalview.io.AlignmentProperties(
1016               viewport.getAlignment()).formatAsString();
1017       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1018       cap.setText(contents.toString());
1019       Frame frame = new Frame();
1020       frame.add(cap);
1021       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1022               "label.alignment_properties", new String[]
1023               { getTitle() }), 400, 250);
1024     }
1025     else if (source == overviewMenuItem)
1026     {
1027       overviewMenuItem_actionPerformed();
1028     }
1029     else if (source == noColourmenuItem)
1030     {
1031       changeColour(null);
1032     }
1033     else if (source == clustalColour)
1034     {
1035       abovePIDThreshold.setState(false);
1036       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1037     }
1038     else if (source == zappoColour)
1039     {
1040       changeColour(new ZappoColourScheme());
1041     }
1042     else if (source == taylorColour)
1043     {
1044       changeColour(new TaylorColourScheme());
1045     }
1046     else if (source == hydrophobicityColour)
1047     {
1048       changeColour(new HydrophobicColourScheme());
1049     }
1050     else if (source == helixColour)
1051     {
1052       changeColour(new HelixColourScheme());
1053     }
1054     else if (source == strandColour)
1055     {
1056       changeColour(new StrandColourScheme());
1057     }
1058     else if (source == turnColour)
1059     {
1060       changeColour(new TurnColourScheme());
1061     }
1062     else if (source == buriedColour)
1063     {
1064       changeColour(new BuriedColourScheme());
1065     }
1066     else if (source == nucleotideColour)
1067     {
1068       changeColour(new NucleotideColourScheme());
1069     }
1070     else if (source == purinePyrimidineColour)
1071     {
1072       changeColour(new PurinePyrimidineColourScheme());
1073     }
1074     else if (source == RNAInteractionColour)
1075     {
1076       changeColour(new RNAInteractionColourScheme());
1077     }
1078     else if (source == RNAHelixColour)
1079     {
1080       new RNAHelicesColourChooser(viewport, alignPanel);
1081     }
1082     else if (source == modifyPID)
1083     {
1084       modifyPID_actionPerformed();
1085     }
1086     else if (source == modifyConservation)
1087     {
1088       modifyConservation_actionPerformed();
1089     }
1090     else if (source == userDefinedColour)
1091     {
1092       new UserDefinedColours(alignPanel, null);
1093     }
1094     else if (source == PIDColour)
1095     {
1096       changeColour(new PIDColourScheme());
1097     }
1098     else if (source == BLOSUM62Colour)
1099     {
1100       changeColour(new Blosum62ColourScheme());
1101     }
1102     else if (source == tcoffeeColour)
1103     {
1104       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1105     }
1106     else if (source == annotationColour)
1107     {
1108       new AnnotationColourChooser(viewport, alignPanel);
1109     }
1110     else if (source == annotationColumnSelection)
1111     {
1112       new AnnotationColumnChooser(viewport, alignPanel);
1113     }
1114     else if (source == sortPairwiseMenuItem)
1115     {
1116       sortPairwiseMenuItem_actionPerformed();
1117     }
1118     else if (source == sortIDMenuItem)
1119     {
1120       sortIDMenuItem_actionPerformed();
1121     }
1122     else if (source == sortLengthMenuItem)
1123     {
1124       sortLengthMenuItem_actionPerformed();
1125     }
1126     else if (source == sortGroupMenuItem)
1127     {
1128       sortGroupMenuItem_actionPerformed();
1129     }
1130     else if (source == removeRedundancyMenuItem)
1131     {
1132       removeRedundancyMenuItem_actionPerformed();
1133     }
1134     else if (source == pairwiseAlignmentMenuItem)
1135     {
1136       pairwiseAlignmentMenuItem_actionPerformed();
1137     }
1138     else if (source == PCAMenuItem)
1139     {
1140       PCAMenuItem_actionPerformed();
1141     }
1142     else if (source == averageDistanceTreeMenuItem)
1143     {
1144       averageDistanceTreeMenuItem_actionPerformed();
1145     }
1146     else if (source == neighbourTreeMenuItem)
1147     {
1148       neighbourTreeMenuItem_actionPerformed();
1149     }
1150     else if (source == njTreeBlosumMenuItem)
1151     {
1152       njTreeBlosumMenuItem_actionPerformed();
1153     }
1154     else if (source == avDistanceTreeBlosumMenuItem)
1155     {
1156       avTreeBlosumMenuItem_actionPerformed();
1157     }
1158     else if (source == documentation)
1159     {
1160       documentation_actionPerformed();
1161     }
1162     else if (source == about)
1163     {
1164       about_actionPerformed();
1165     }
1166
1167   }
1168
1169   public void inputText_actionPerformed()
1170   {
1171     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1172     Frame frame = new Frame();
1173     frame.add(cap);
1174     jalview.bin.JalviewLite.addFrame(frame,
1175             MessageManager.getString("label.input_cut_paste"), 500, 500);
1176   }
1177
1178   protected void outputText_actionPerformed(ActionEvent e)
1179   {
1180     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1181     Frame frame = new Frame();
1182     frame.add(cap);
1183     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184             "label.alignment_output_command", new String[]
1185             { e.getActionCommand() }), 600, 500);
1186     cap.setText(new AppletFormatAdapter().formatSequences(
1187             e.getActionCommand(), viewport.getAlignment(),
1188             viewport.showJVSuffix));
1189   }
1190
1191   public void loadAnnotations()
1192   {
1193     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1194     cap.setText(MessageManager
1195             .getString("label.paste_features_annotations_Tcoffee_here"));
1196     cap.setAnnotationImport();
1197     Frame frame = new Frame();
1198     frame.add(cap);
1199     jalview.bin.JalviewLite.addFrame(frame,
1200             MessageManager.getString("action.paste_annotations"), 400, 300);
1201
1202   }
1203
1204   public String outputAnnotations(boolean displayTextbox)
1205   {
1206     String annotation = new AnnotationFile()
1207             .printAnnotationsForView(viewport);
1208
1209     if (displayTextbox)
1210     {
1211       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212       Frame frame = new Frame();
1213       frame.add(cap);
1214       jalview.bin.JalviewLite.addFrame(frame,
1215               MessageManager.getString("label.annotations"), 600, 500);
1216       cap.setText(annotation);
1217     }
1218
1219     return annotation;
1220   }
1221
1222   private Map<String,Object> getDisplayedFeatureCols()
1223   {
1224     if (alignPanel.getFeatureRenderer() != null
1225             && viewport.getFeaturesDisplayed()!= null)
1226     {
1227       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1228
1229     }
1230     return null;
1231   }
1232
1233   public String outputFeatures(boolean displayTextbox, String format)
1234   {
1235     String features;
1236     if (format.equalsIgnoreCase("Jalview"))
1237     {
1238       features = new FeaturesFile().printJalviewFormat(viewport
1239               .getAlignment().getSequencesArray(),
1240               getDisplayedFeatureCols());
1241     }
1242     else
1243     {
1244       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1245               .getSequencesArray(), getDisplayedFeatureCols());
1246     }
1247
1248     if (displayTextbox)
1249     {
1250       boolean frimport = false;
1251       if (features == null || features.equals("No Features Visible"))
1252       {
1253         features = "# No features visible - paste some and import them here.";
1254         frimport = true;
1255       }
1256
1257       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1258       if (frimport)
1259       {
1260         cap.setAnnotationImport();
1261       }
1262       Frame frame = new Frame();
1263       frame.add(cap);
1264       jalview.bin.JalviewLite.addFrame(frame,
1265               MessageManager.getString("label.features"), 600, 500);
1266       cap.setText(features);
1267     }
1268     else
1269     {
1270       if (features == null)
1271       {
1272         features = "";
1273       }
1274     }
1275
1276     return features;
1277   }
1278
1279   void launchFullApplication()
1280   {
1281     StringBuffer url = new StringBuffer(jalviewServletURL);
1282
1283     // allow servlet parameters to be passed in applet parameter
1284     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1285             : "?";
1286     url.append(firstSep);
1287
1288     url.append("open="
1289             + appendProtocol(viewport.applet.getParameter("file")));
1290
1291     if (viewport.applet.getParameter("features") != null)
1292     {
1293       url.append("&features=");
1294       url.append(appendProtocol(viewport.applet.getParameter("features")));
1295     }
1296
1297     if (viewport.applet.getParameter("annotations") != null)
1298     {
1299       url.append("&annotations=");
1300       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1301     }
1302
1303     if (viewport.applet.getParameter("jnetfile") != null)
1304     {
1305       url.append("&annotations=");
1306       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1307     }
1308
1309     if (viewport.applet.getParameter("defaultColour") != null)
1310     {
1311       url.append("&colour="
1312               + removeWhiteSpace(viewport.applet
1313                       .getParameter("defaultColour")));
1314     }
1315
1316     if (viewport.applet.getParameter("userDefinedColour") != null)
1317     {
1318       url.append("&colour="
1319               + removeWhiteSpace(viewport.applet
1320                       .getParameter("userDefinedColour")));
1321     }
1322     if (viewport.applet.getParameter("tree") != null)
1323     {
1324       url.append("&tree="
1325               + appendProtocol(viewport.applet.getParameter("tree")));
1326     }
1327     if (viewport.applet.getParameter("treeFile") != null)
1328     {
1329       url.append("&tree="
1330               + appendProtocol(viewport.applet.getParameter("treeFile")));
1331     }
1332
1333     showURL(url.toString(), "FULL_APP");
1334   }
1335
1336   String removeWhiteSpace(String colour)
1337   {
1338     StringBuffer sb = new StringBuffer();
1339     for (int i = 0; i < colour.length(); i++)
1340     {
1341       if (Character.isWhitespace(colour.charAt(i)))
1342       {
1343         sb.append("%20");
1344       }
1345       else
1346       {
1347         sb.append(colour.charAt(i));
1348       }
1349     }
1350
1351     return sb.toString();
1352   }
1353
1354   String appendProtocol(String url)
1355   {
1356     try
1357     {
1358       new URL(url);
1359       url = URLEncoder.encode(url);
1360     }
1361     /*
1362      * When we finally deprecate 1.1 compatibility, we can start to use
1363      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1364      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1365      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1366      * ex.printStackTrace(); }
1367      */
1368     catch (java.net.MalformedURLException ex)
1369     {
1370       url = viewport.applet.getCodeBase() + url;
1371     }
1372     return url;
1373   }
1374
1375   public void closeMenuItem_actionPerformed()
1376   {
1377     PaintRefresher.RemoveComponent(alignPanel);
1378     if (alignPanel.seqPanel != null
1379             && alignPanel.seqPanel.seqCanvas != null)
1380     {
1381       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1382     }
1383     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1384     {
1385       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1386     }
1387
1388     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1389     {
1390       System.exit(0);
1391     }
1392     else
1393     {
1394     }
1395     viewport = null;
1396     alignPanel = null;
1397     this.dispose();
1398   }
1399
1400   /**
1401    * TODO: JAL-1104
1402    */
1403   void updateEditMenuBar()
1404   {
1405
1406     if (viewport.historyList.size() > 0)
1407     {
1408       undoMenuItem.setEnabled(true);
1409       CommandI command = (CommandI) viewport.historyList.peek();
1410       undoMenuItem.setLabel(MessageManager.formatMessage(
1411               "label.undo_command", new String[]
1412               { command.getDescription() }));
1413     }
1414     else
1415     {
1416       undoMenuItem.setEnabled(false);
1417       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1418     }
1419
1420     if (viewport.redoList.size() > 0)
1421     {
1422       redoMenuItem.setEnabled(true);
1423
1424       CommandI command = (CommandI) viewport.redoList.peek();
1425       redoMenuItem.setLabel(MessageManager.formatMessage(
1426               "label.redo_command", new String[]
1427               { command.getDescription() }));
1428     }
1429     else
1430     {
1431       redoMenuItem.setEnabled(false);
1432       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1433     }
1434   }
1435
1436   /**
1437    * TODO: JAL-1104
1438    */
1439   @Override
1440   public void addHistoryItem(CommandI command)
1441   {
1442     if (command.getSize() > 0)
1443     {
1444       viewport.historyList.push(command);
1445       viewport.redoList.removeAllElements();
1446       updateEditMenuBar();
1447       viewport.updateHiddenColumns();
1448     }
1449   }
1450
1451   /**
1452    * TODO: JAL-1104 DOCUMENT ME!
1453    *
1454    * @param e
1455    *          DOCUMENT ME!
1456    */
1457   protected void undoMenuItem_actionPerformed()
1458   {
1459     if (viewport.historyList.size() < 1)
1460     {
1461       return;
1462     }
1463
1464     CommandI command = (CommandI) viewport.historyList.pop();
1465     viewport.redoList.push(command);
1466     command.undoCommand(null);
1467
1468     AlignViewport originalSource = getOriginatingSource(command);
1469     // JBPNote Test
1470     if (originalSource != viewport)
1471     {
1472       System.err
1473               .println("Warning: Viewport object mismatch whilst undoing");
1474     }
1475     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1476                                           // viewport.getColumnSelection().getHiddenColumns()
1477                                           // != null;
1478     updateEditMenuBar();
1479     originalSource.firePropertyChange("alignment", null, originalSource
1480             .getAlignment().getSequences());
1481   }
1482
1483   /**
1484    * TODO: JAL-1104 DOCUMENT ME!
1485    *
1486    * @param e
1487    *          DOCUMENT ME!
1488    */
1489   protected void redoMenuItem_actionPerformed()
1490   {
1491     if (viewport.redoList.size() < 1)
1492     {
1493       return;
1494     }
1495
1496     CommandI command = (CommandI) viewport.redoList.pop();
1497     viewport.historyList.push(command);
1498     command.doCommand(null);
1499
1500     AlignViewport originalSource = getOriginatingSource(command);
1501     // JBPNote Test
1502     if (originalSource != viewport)
1503     {
1504       System.err
1505               .println("Warning: Viewport object mismatch whilst re-doing");
1506     }
1507     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1508                                           // viewport.getColumnSelection().getHiddenColumns()
1509                                           // != null;
1510
1511     updateEditMenuBar();
1512     originalSource.firePropertyChange("alignment", null, originalSource
1513             .getAlignment().getSequences());
1514   }
1515
1516   AlignViewport getOriginatingSource(CommandI command)
1517   {
1518     AlignViewport originalSource = null;
1519     // For sequence removal and addition, we need to fire
1520     // the property change event FROM the viewport where the
1521     // original alignment was altered
1522     AlignmentI al = null;
1523     if (command instanceof EditCommand)
1524     {
1525       EditCommand editCommand = (EditCommand) command;
1526       al = editCommand.getAlignment();
1527       Vector comps = (Vector) PaintRefresher.components.get(viewport
1528               .getSequenceSetId());
1529       for (int i = 0; i < comps.size(); i++)
1530       {
1531         if (comps.elementAt(i) instanceof AlignmentPanel)
1532         {
1533           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1534           {
1535             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1536             break;
1537           }
1538         }
1539       }
1540     }
1541
1542     if (originalSource == null)
1543     {
1544       // The original view is closed, we must validate
1545       // the current view against the closed view first
1546       if (al != null)
1547       {
1548         PaintRefresher.validateSequences(al, viewport.getAlignment());
1549       }
1550
1551       originalSource = viewport;
1552     }
1553
1554     return originalSource;
1555   }
1556
1557   public void moveSelectedSequences(boolean up)
1558   {
1559     SequenceGroup sg = viewport.getSelectionGroup();
1560     if (sg == null)
1561     {
1562       return;
1563     }
1564     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1565             up ? null : viewport.getHiddenRepSequences(), up);
1566     alignPanel.paintAlignment(true);
1567   }
1568
1569   synchronized void slideSequences(boolean right, int size)
1570   {
1571     List<SequenceI> sg = new Vector<SequenceI>();
1572     if (viewport.cursorMode)
1573     {
1574       sg.add(viewport.getAlignment().getSequenceAt(
1575               alignPanel.seqPanel.seqCanvas.cursorY));
1576     }
1577     else if (viewport.getSelectionGroup() != null
1578             && viewport.getSelectionGroup().getSize() != viewport
1579                     .getAlignment().getHeight())
1580     {
1581       sg = viewport.getSelectionGroup().getSequences(
1582               viewport.getHiddenRepSequences());
1583     }
1584
1585     if (sg.size() < 1)
1586     {
1587       return;
1588     }
1589
1590     Vector<SequenceI> invertGroup = new Vector();
1591
1592     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1593     {
1594       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1595       {
1596         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1597       }
1598     }
1599
1600     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1601
1602     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1603             .size()]);
1604     for (int i = 0; i < invertGroup.size(); i++)
1605     {
1606       seqs2[i] = invertGroup.elementAt(i);
1607     }
1608
1609     SlideSequencesCommand ssc;
1610     if (right)
1611     {
1612       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1613               size, viewport.getGapCharacter());
1614     }
1615     else
1616     {
1617       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1618               size, viewport.getGapCharacter());
1619     }
1620
1621     int groupAdjustment = 0;
1622     if (ssc.getGapsInsertedBegin() && right)
1623     {
1624       if (viewport.cursorMode)
1625       {
1626         alignPanel.seqPanel.moveCursor(size, 0);
1627       }
1628       else
1629       {
1630         groupAdjustment = size;
1631       }
1632     }
1633     else if (!ssc.getGapsInsertedBegin() && !right)
1634     {
1635       if (viewport.cursorMode)
1636       {
1637         alignPanel.seqPanel.moveCursor(-size, 0);
1638       }
1639       else
1640       {
1641         groupAdjustment = -size;
1642       }
1643     }
1644
1645     if (groupAdjustment != 0)
1646     {
1647       viewport.getSelectionGroup().setStartRes(
1648               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1649       viewport.getSelectionGroup().setEndRes(
1650               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1651     }
1652
1653     boolean appendHistoryItem = false;
1654     if (viewport.historyList != null && viewport.historyList.size() > 0
1655             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1656     {
1657       appendHistoryItem = ssc
1658               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1659                       .peek());
1660     }
1661
1662     if (!appendHistoryItem)
1663     {
1664       addHistoryItem(ssc);
1665     }
1666
1667     repaint();
1668   }
1669
1670   static StringBuffer copiedSequences;
1671
1672   static Vector copiedHiddenColumns;
1673
1674   protected void copy_actionPerformed()
1675   {
1676     if (viewport.getSelectionGroup() == null)
1677     {
1678       return;
1679     }
1680
1681     SequenceGroup sg = viewport.getSelectionGroup();
1682     copiedSequences = new StringBuffer();
1683     Hashtable orderedSeqs = new Hashtable();
1684     for (int i = 0; i < sg.getSize(); i++)
1685     {
1686       SequenceI seq = sg.getSequenceAt(i);
1687       int index = viewport.getAlignment().findIndex(seq);
1688       orderedSeqs.put(index + "", seq);
1689     }
1690
1691     int index = 0, startRes, endRes;
1692     char ch;
1693
1694     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1695     {
1696       copiedHiddenColumns = new Vector();
1697       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1698       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1699       {
1700
1701         copiedHiddenColumns.addElement(new int[]
1702         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1703       }
1704     }
1705     else
1706     {
1707       copiedHiddenColumns = null;
1708     }
1709
1710     for (int i = 0; i < sg.getSize(); i++)
1711     {
1712       SequenceI seq = null;
1713
1714       while (seq == null)
1715       {
1716         if (orderedSeqs.containsKey(index + ""))
1717         {
1718           seq = (SequenceI) orderedSeqs.get(index + "");
1719           index++;
1720
1721           break;
1722         }
1723         else
1724         {
1725           index++;
1726         }
1727       }
1728
1729       // FIND START RES
1730       // Returns residue following index if gap
1731       startRes = seq.findPosition(sg.getStartRes());
1732
1733       // FIND END RES
1734       // Need to find the residue preceeding index if gap
1735       endRes = 0;
1736
1737       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1738       {
1739         ch = seq.getCharAt(j);
1740         if (!jalview.util.Comparison.isGap((ch)))
1741         {
1742           endRes++;
1743         }
1744       }
1745
1746       if (endRes > 0)
1747       {
1748         endRes += seq.getStart() - 1;
1749       }
1750
1751       copiedSequences.append(seq.getName()
1752               + "\t"
1753               + startRes
1754               + "\t"
1755               + endRes
1756               + "\t"
1757               + seq.getSequenceAsString(sg.getStartRes(),
1758                       sg.getEndRes() + 1) + "\n");
1759     }
1760
1761   }
1762
1763   protected void pasteNew_actionPerformed()
1764   {
1765     paste(true);
1766   }
1767
1768   protected void pasteThis_actionPerformed()
1769   {
1770     paste(false);
1771   }
1772
1773   void paste(boolean newAlignment)
1774   {
1775     try
1776     {
1777
1778       if (copiedSequences == null)
1779       {
1780         return;
1781       }
1782
1783       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1784       Vector seqs = new Vector();
1785       while (st.hasMoreElements())
1786       {
1787         String name = st.nextToken();
1788         int start = Integer.parseInt(st.nextToken());
1789         int end = Integer.parseInt(st.nextToken());
1790         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1791       }
1792       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1793       for (int i = 0; i < seqs.size(); i++)
1794       {
1795         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1796       }
1797
1798       if (newAlignment)
1799       {
1800         String newtitle = MessageManager.getString("label.copied_sequences");
1801         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1802         {
1803           newtitle = getTitle();
1804         }
1805         else
1806         {
1807           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1808         }
1809         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1810                 viewport.applet, newtitle, false);
1811         if (copiedHiddenColumns != null)
1812         {
1813           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1814           {
1815             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1816             af.viewport.hideColumns(region[0], region[1]);
1817           }
1818         }
1819
1820         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1821                 DEFAULT_HEIGHT);
1822       }
1823       else
1824       {
1825         addSequences(newSeqs);
1826       }
1827
1828     } catch (Exception ex)
1829     {
1830     } // could be anything being pasted in here
1831
1832   }
1833
1834   void addSequences(SequenceI[] seqs)
1835   {
1836     for (int i = 0; i < seqs.length; i++)
1837     {
1838       viewport.getAlignment().addSequence(seqs[i]);
1839     }
1840
1841     // !newAlignment
1842     addHistoryItem(new EditCommand(
1843             MessageManager.getString("label.add_sequences"), Action.PASTE,
1844             seqs, 0, viewport.getAlignment().getWidth(),
1845             viewport.getAlignment()));
1846
1847     viewport.setEndSeq(viewport.getAlignment().getHeight());
1848     viewport.getAlignment().getWidth();
1849     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1850             .getSequences());
1851
1852   }
1853
1854   protected void cut_actionPerformed()
1855   {
1856     copy_actionPerformed();
1857     delete_actionPerformed();
1858   }
1859
1860   protected void delete_actionPerformed()
1861   {
1862
1863     SequenceGroup sg = viewport.getSelectionGroup();
1864     if (sg == null)
1865     {
1866       return;
1867     }
1868
1869     Vector seqs = new Vector();
1870     SequenceI seq;
1871     for (int i = 0; i < sg.getSize(); i++)
1872     {
1873       seq = sg.getSequenceAt(i);
1874       seqs.addElement(seq);
1875     }
1876
1877     // If the cut affects all sequences, remove highlighted columns
1878     if (sg.getSize() == viewport.getAlignment().getHeight())
1879     {
1880       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1881               sg.getEndRes() + 1);
1882     }
1883
1884     SequenceI[] cut = new SequenceI[seqs.size()];
1885     for (int i = 0; i < seqs.size(); i++)
1886     {
1887       cut[i] = (SequenceI) seqs.elementAt(i);
1888     }
1889
1890     /*
1891      * //ADD HISTORY ITEM
1892      */
1893     addHistoryItem(new EditCommand(
1894             MessageManager.getString("label.cut_sequences"), Action.CUT,
1895             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1896             viewport.getAlignment()));
1897
1898     viewport.setSelectionGroup(null);
1899     viewport.getAlignment().deleteGroup(sg);
1900
1901     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1902             .getSequences());
1903
1904     if (viewport.getAlignment().getHeight() < 1)
1905     {
1906       this.setVisible(false);
1907     }
1908     viewport.sendSelection();
1909   }
1910
1911   /**
1912    * group consensus toggled
1913    *
1914    */
1915   protected void showGroupConsensus_actionPerformed()
1916   {
1917     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1918     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1919
1920   }
1921
1922   /**
1923    * group conservation toggled.
1924    */
1925   protected void showGroupConservation_actionPerformed()
1926   {
1927     viewport.setShowGroupConservation(showGroupConservation.getState());
1928     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1929   }
1930
1931   /*
1932    * (non-Javadoc)
1933    *
1934    * @see
1935    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1936    * .event.ActionEvent)
1937    */
1938   protected void showConsensusHistogram_actionPerformed()
1939   {
1940     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1941     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1942   }
1943
1944   /*
1945    * (non-Javadoc)
1946    *
1947    * @see
1948    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1949    * .event.ActionEvent)
1950    */
1951   protected void showSequenceLogo_actionPerformed()
1952   {
1953     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1954     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1955   }
1956
1957   protected void normSequenceLogo_actionPerformed()
1958   {
1959     showSequenceLogo.setState(true);
1960     viewport.setShowSequenceLogo(true);
1961     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1962     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1963   }
1964
1965   protected void applyAutoAnnotationSettings_actionPerformed()
1966   {
1967     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1968   }
1969
1970   protected void makeGrpsFromSelection_actionPerformed()
1971   {
1972     if (avc.makeGroupsFromSelection())
1973     {
1974       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1975       alignPanel.updateAnnotation();
1976       alignPanel.paintAlignment(true);
1977     }
1978   }
1979
1980   protected void createGroup_actionPerformed()
1981   {
1982     avc.createGroup();
1983   }
1984
1985   protected void unGroup_actionPerformed()
1986   {
1987     if (avc.unGroup())
1988     {
1989       alignPanel.alignmentChanged();
1990     }
1991   }
1992
1993   protected void deleteGroups_actionPerformed()
1994   {
1995     if (avc.deleteGroups())
1996     {
1997       alignPanel.alignmentChanged();
1998     }
1999   }
2000
2001   public void selectAllSequenceMenuItem_actionPerformed()
2002   {
2003     SequenceGroup sg = new SequenceGroup();
2004     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2005     {
2006       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2007     }
2008     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2009     viewport.setSelectionGroup(sg);
2010     alignPanel.paintAlignment(true);
2011     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2012     viewport.sendSelection();
2013   }
2014
2015   public void deselectAllSequenceMenuItem_actionPerformed()
2016   {
2017     if (viewport.cursorMode)
2018     {
2019       alignPanel.seqPanel.keyboardNo1 = null;
2020       alignPanel.seqPanel.keyboardNo2 = null;
2021     }
2022     viewport.setSelectionGroup(null);
2023     viewport.getColumnSelection().clear();
2024     viewport.setSelectionGroup(null);
2025     alignPanel.idPanel.idCanvas.searchResults = null;
2026     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2027     alignPanel.paintAlignment(true);
2028     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2029     viewport.sendSelection();
2030   }
2031
2032   public void invertSequenceMenuItem_actionPerformed()
2033   {
2034     SequenceGroup sg = viewport.getSelectionGroup();
2035     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2036     {
2037       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2038     }
2039
2040     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2041     viewport.sendSelection();
2042   }
2043
2044   public void invertColSel_actionPerformed()
2045   {
2046     viewport.invertColumnSelection();
2047     alignPanel.paintAlignment(true);
2048     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2049     viewport.sendSelection();
2050   }
2051
2052   void trimAlignment(boolean trimLeft)
2053   {
2054     ColumnSelection colSel = viewport.getColumnSelection();
2055     int column;
2056
2057     if (colSel.size() > 0)
2058     {
2059       if (trimLeft)
2060       {
2061         column = colSel.getMin();
2062       }
2063       else
2064       {
2065         column = colSel.getMax();
2066       }
2067
2068       SequenceI[] seqs;
2069       if (viewport.getSelectionGroup() != null)
2070       {
2071         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2072                 viewport.getHiddenRepSequences());
2073       }
2074       else
2075       {
2076         seqs = viewport.getAlignment().getSequencesArray();
2077       }
2078
2079       TrimRegionCommand trimRegion;
2080       if (trimLeft)
2081       {
2082         trimRegion = new TrimRegionCommand("Remove Left",
2083                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2084                 viewport.getAlignment(), viewport.getColumnSelection(),
2085                 viewport.getSelectionGroup());
2086         viewport.setStartRes(0);
2087       }
2088       else
2089       {
2090         trimRegion = new TrimRegionCommand("Remove Right",
2091                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2092                 viewport.getAlignment(), viewport.getColumnSelection(),
2093                 viewport.getSelectionGroup());
2094       }
2095
2096       statusBar.setText(MessageManager.formatMessage(
2097               "label.removed_columns", new String[]
2098               { Integer.valueOf(trimRegion.getSize()).toString() }));
2099       addHistoryItem(trimRegion);
2100
2101       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2102       {
2103         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2104                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2105         {
2106           viewport.getAlignment().deleteGroup(sg);
2107         }
2108       }
2109
2110       viewport.firePropertyChange("alignment", null, viewport
2111               .getAlignment().getSequences());
2112     }
2113   }
2114
2115   public void removeGappedColumnMenuItem_actionPerformed()
2116   {
2117     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2118
2119     SequenceI[] seqs;
2120     if (viewport.getSelectionGroup() != null)
2121     {
2122       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2123               viewport.getHiddenRepSequences());
2124       start = viewport.getSelectionGroup().getStartRes();
2125       end = viewport.getSelectionGroup().getEndRes();
2126     }
2127     else
2128     {
2129       seqs = viewport.getAlignment().getSequencesArray();
2130     }
2131
2132     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2133             "Remove Gapped Columns", seqs, start, end,
2134             viewport.getAlignment());
2135
2136     addHistoryItem(removeGapCols);
2137
2138     statusBar.setText(MessageManager.formatMessage(
2139             "label.removed_empty_columns", new String[]
2140             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2141
2142     // This is to maintain viewport position on first residue
2143     // of first sequence
2144     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2145     int startRes = seq.findPosition(viewport.startRes);
2146     // ShiftList shifts;
2147     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2148     // edit.alColumnChanges=shifts.getInverse();
2149     // if (viewport.hasHiddenColumns)
2150     // viewport.getColumnSelection().compensateForEdits(shifts);
2151     viewport.setStartRes(seq.findIndex(startRes) - 1);
2152     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153             .getSequences());
2154
2155   }
2156
2157   public void removeAllGapsMenuItem_actionPerformed()
2158   {
2159     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2160
2161     SequenceI[] seqs;
2162     if (viewport.getSelectionGroup() != null)
2163     {
2164       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2165               viewport.getHiddenRepSequences());
2166       start = viewport.getSelectionGroup().getStartRes();
2167       end = viewport.getSelectionGroup().getEndRes();
2168     }
2169     else
2170     {
2171       seqs = viewport.getAlignment().getSequencesArray();
2172     }
2173
2174     // This is to maintain viewport position on first residue
2175     // of first sequence
2176     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2177     int startRes = seq.findPosition(viewport.startRes);
2178
2179     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2180             viewport.getAlignment()));
2181
2182     viewport.setStartRes(seq.findIndex(startRes) - 1);
2183
2184     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2185             .getSequences());
2186
2187   }
2188
2189   public void findMenuItem_actionPerformed()
2190   {
2191     new Finder(alignPanel);
2192   }
2193
2194   /**
2195    * create a new view derived from the current view
2196    *
2197    * @param viewtitle
2198    * @return frame for the new view
2199    */
2200   public AlignFrame newView(String viewtitle)
2201   {
2202     AlignmentI newal;
2203     if (viewport.hasHiddenRows())
2204     {
2205       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2206               .getFullAlignment().getSequencesArray());
2207     }
2208     else
2209     {
2210       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2211     }
2212
2213     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2214     {
2215       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2216       {
2217         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2218         {
2219           newal.addAnnotation(viewport.getAlignment()
2220                   .getAlignmentAnnotation()[i]);
2221         }
2222       }
2223     }
2224
2225     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2226
2227     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2228     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2229     PaintRefresher.Register(newaf.alignPanel,
2230             newaf.alignPanel.av.getSequenceSetId());
2231
2232     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2233             newaf.alignPanel.av.getSequenceSetId());
2234     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2235             newaf.alignPanel.av.getSequenceSetId());
2236
2237     Vector comps = (Vector) PaintRefresher.components.get(viewport
2238             .getSequenceSetId());
2239     int viewSize = -1;
2240     for (int i = 0; i < comps.size(); i++)
2241     {
2242       if (comps.elementAt(i) instanceof AlignmentPanel)
2243       {
2244         viewSize++;
2245       }
2246     }
2247
2248     String title = new String(this.getTitle());
2249     if (viewtitle != null)
2250     {
2251       title = viewtitle + " ( " + title + ")";
2252     }
2253     else
2254     {
2255       if (title.indexOf("(View") > -1)
2256       {
2257         title = title.substring(0, title.indexOf("(View"));
2258       }
2259       title += "(View " + viewSize + ")";
2260     }
2261
2262     newaf.setTitle(title.toString());
2263
2264     newaf.viewport.historyList = viewport.historyList;
2265     newaf.viewport.redoList = viewport.redoList;
2266     return newaf;
2267   }
2268
2269   /**
2270    *
2271    * @return list of feature groups on the view
2272    */
2273   public String[] getFeatureGroups()
2274   {
2275     FeatureRenderer fr = null;
2276     if (alignPanel != null
2277             && (fr = alignPanel.getFeatureRenderer()) != null)
2278     {
2279       List gps = fr.getFeatureGroups();
2280       int p=0;
2281       String[] _gps = new String[gps.size()];
2282       for (Object gp:gps)
2283       {
2284         _gps[p++] = gp.toString();
2285       }
2286       return _gps;
2287     }
2288     return null;
2289   }
2290
2291   /**
2292    * get sequence feature groups that are hidden or shown
2293    *
2294    * @param visible
2295    *          true is visible
2296    * @return list
2297    */
2298   public String[] getFeatureGroupsOfState(boolean visible)
2299   {
2300     FeatureRenderer fr = null;
2301     if (alignPanel != null
2302             && (fr = alignPanel.getFeatureRenderer()) != null)
2303     {
2304       List gps = fr.getGroups(visible);
2305       int p=0;
2306       String[] _gps = new String[gps.size()];
2307       for (Object gp:gps)
2308       {
2309         _gps[p++] = gp.toString();
2310       }
2311       return _gps;
2312     }
2313     return null;
2314   }
2315
2316   /**
2317    * Change the display state for the given feature groups
2318    *
2319    * @param groups
2320    *          list of group strings
2321    * @param state
2322    *          visible or invisible
2323    */
2324   public void setFeatureGroupState(String[] groups, boolean state)
2325   {
2326     FeatureRenderer fr = null;
2327     this.sequenceFeatures.setState(true);
2328     viewport.setShowSequenceFeatures(true);
2329     if (alignPanel != null
2330             && (fr = alignPanel.getFeatureRenderer()) != null)
2331     {
2332
2333       fr.setGroupVisibility(Arrays.asList(groups), state);
2334       alignPanel.seqPanel.seqCanvas.repaint();
2335       if (alignPanel.overviewPanel != null)
2336       {
2337         alignPanel.overviewPanel.updateOverviewImage();
2338       }
2339     }
2340   }
2341
2342   public void seqLimits_itemStateChanged()
2343   {
2344     viewport.setShowJVSuffix(seqLimits.getState());
2345     alignPanel.fontChanged();
2346     alignPanel.paintAlignment(true);
2347   }
2348
2349   protected void colourTextMenuItem_actionPerformed()
2350   {
2351     viewport.setColourText(colourTextMenuItem.getState());
2352     alignPanel.paintAlignment(true);
2353   }
2354
2355   protected void displayNonconservedMenuItem_actionPerformed()
2356   {
2357     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2358     alignPanel.paintAlignment(true);
2359   }
2360
2361   protected void wrapMenuItem_actionPerformed()
2362   {
2363     viewport.setWrapAlignment(wrapMenuItem.getState());
2364     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2365     scaleAbove.setEnabled(wrapMenuItem.getState());
2366     scaleLeft.setEnabled(wrapMenuItem.getState());
2367     scaleRight.setEnabled(wrapMenuItem.getState());
2368     alignPanel.paintAlignment(true);
2369   }
2370
2371   public void overviewMenuItem_actionPerformed()
2372   {
2373     if (alignPanel.overviewPanel != null)
2374     {
2375       return;
2376     }
2377
2378     Frame frame = new Frame();
2379     OverviewPanel overview = new OverviewPanel(alignPanel);
2380     frame.add(overview);
2381     // +50 must allow for applet frame window
2382     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2383             "label.overview_params", new String[]
2384             { this.getTitle() }), overview.getPreferredSize().width,
2385             overview.getPreferredSize().height + 50);
2386
2387     frame.pack();
2388     final AlignmentPanel ap = alignPanel;
2389     frame.addWindowListener(new WindowAdapter()
2390     {
2391       @Override
2392       public void windowClosing(WindowEvent e)
2393       {
2394         if (ap != null)
2395         {
2396           ap.setOverviewPanel(null);
2397         }
2398       };
2399     });
2400
2401     alignPanel.setOverviewPanel(overview);
2402
2403   }
2404
2405   void changeColour(ColourSchemeI cs)
2406   {
2407     int threshold = 0;
2408
2409     if (cs != null)
2410     {
2411       if (viewport.getAbovePIDThreshold())
2412       {
2413         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2414                 cs, "Background"));
2415       }
2416
2417       if (viewport.getConservationSelected())
2418       {
2419         cs.setConservationApplied(true);
2420         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2421                 cs, "Background"));
2422       }
2423       else
2424       {
2425         cs.setConservationApplied(false);
2426       }
2427     }
2428     viewport.setGlobalColourScheme(cs);
2429
2430     if (alignPanel.getOverviewPanel() != null)
2431     {
2432       alignPanel.getOverviewPanel().updateOverviewImage();
2433     }
2434
2435     jalview.structure.StructureSelectionManager
2436             .getStructureSelectionManager(viewport.applet)
2437             .sequenceColoursChanged(alignPanel);
2438
2439     alignPanel.paintAlignment(true);
2440   }
2441
2442   protected void modifyPID_actionPerformed()
2443   {
2444     if (viewport.getAbovePIDThreshold()
2445             && viewport.getGlobalColourScheme() != null)
2446     {
2447       SliderPanel.setPIDSliderSource(alignPanel,
2448               viewport.getGlobalColourScheme(), "Background");
2449       SliderPanel.showPIDSlider();
2450     }
2451   }
2452
2453   protected void modifyConservation_actionPerformed()
2454   {
2455     if (viewport.getConservationSelected()
2456             && viewport.getGlobalColourScheme() != null)
2457     {
2458       SliderPanel.setConservationSlider(alignPanel,
2459               viewport.getGlobalColourScheme(), "Background");
2460       SliderPanel.showConservationSlider();
2461     }
2462   }
2463
2464   protected void conservationMenuItem_actionPerformed()
2465   {
2466     viewport.setConservationSelected(conservationMenuItem.getState());
2467
2468     viewport.setAbovePIDThreshold(false);
2469     abovePIDThreshold.setState(false);
2470
2471     changeColour(viewport.getGlobalColourScheme());
2472
2473     modifyConservation_actionPerformed();
2474   }
2475
2476   public void abovePIDThreshold_actionPerformed()
2477   {
2478     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2479
2480     conservationMenuItem.setState(false);
2481     viewport.setConservationSelected(false);
2482
2483     changeColour(viewport.getGlobalColourScheme());
2484
2485     modifyPID_actionPerformed();
2486   }
2487
2488   public void sortPairwiseMenuItem_actionPerformed()
2489   {
2490     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2491     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2492             .getAlignment().getSequenceAt(0), null);
2493
2494     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2495             viewport.getAlignment()));
2496     alignPanel.paintAlignment(true);
2497   }
2498
2499   public void sortIDMenuItem_actionPerformed()
2500   {
2501     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2502     AlignmentSorter.sortByID(viewport.getAlignment());
2503     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2504             viewport.getAlignment()));
2505     alignPanel.paintAlignment(true);
2506   }
2507
2508   public void sortLengthMenuItem_actionPerformed()
2509   {
2510     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2511     AlignmentSorter.sortByLength(viewport.getAlignment());
2512     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2513             viewport.getAlignment()));
2514     alignPanel.paintAlignment(true);
2515   }
2516
2517   public void sortGroupMenuItem_actionPerformed()
2518   {
2519     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2520     AlignmentSorter.sortByGroup(viewport.getAlignment());
2521     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2522             viewport.getAlignment()));
2523     alignPanel.paintAlignment(true);
2524
2525   }
2526
2527   public void removeRedundancyMenuItem_actionPerformed()
2528   {
2529     new RedundancyPanel(alignPanel);
2530   }
2531
2532   public void pairwiseAlignmentMenuItem_actionPerformed()
2533   {
2534     if (viewport.getSelectionGroup() != null
2535             && viewport.getSelectionGroup().getSize() > 1)
2536     {
2537       Frame frame = new Frame();
2538       frame.add(new PairwiseAlignPanel(alignPanel));
2539       jalview.bin.JalviewLite.addFrame(frame,
2540               MessageManager.getString("action.pairwise_alignment"), 600,
2541               500);
2542     }
2543   }
2544
2545   public void PCAMenuItem_actionPerformed()
2546   {
2547     // are the sequences aligned?
2548     if (!viewport.getAlignment().isAligned(false))
2549     {
2550       SequenceI current;
2551       int Width = viewport.getAlignment().getWidth();
2552
2553       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2554       {
2555         current = viewport.getAlignment().getSequenceAt(i);
2556
2557         if (current.getLength() < Width)
2558         {
2559           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2560         }
2561       }
2562       alignPanel.paintAlignment(true);
2563     }
2564
2565     if ((viewport.getSelectionGroup() != null
2566             && viewport.getSelectionGroup().getSize() < 4 && viewport
2567             .getSelectionGroup().getSize() > 0)
2568             || viewport.getAlignment().getHeight() < 4)
2569     {
2570       return;
2571     }
2572
2573     try
2574     {
2575       new PCAPanel(viewport);
2576     } catch (java.lang.OutOfMemoryError ex)
2577     {
2578     }
2579
2580   }
2581
2582   public void averageDistanceTreeMenuItem_actionPerformed()
2583   {
2584     NewTreePanel("AV", "PID", "Average distance tree using PID");
2585   }
2586
2587   public void neighbourTreeMenuItem_actionPerformed()
2588   {
2589     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2590   }
2591
2592   protected void njTreeBlosumMenuItem_actionPerformed()
2593   {
2594     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2595   }
2596
2597   protected void avTreeBlosumMenuItem_actionPerformed()
2598   {
2599     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2600   }
2601
2602   void NewTreePanel(String type, String pwType, String title)
2603   {
2604     // are the sequences aligned?
2605     if (!viewport.getAlignment().isAligned(false))
2606     {
2607       SequenceI current;
2608       int Width = viewport.getAlignment().getWidth();
2609
2610       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2611       {
2612         current = viewport.getAlignment().getSequenceAt(i);
2613
2614         if (current.getLength() < Width)
2615         {
2616           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2617         }
2618       }
2619       alignPanel.paintAlignment(true);
2620
2621     }
2622
2623     if ((viewport.getSelectionGroup() != null && viewport
2624             .getSelectionGroup().getSize() > 1)
2625             || (viewport.getAlignment().getHeight() > 1))
2626     {
2627       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2628
2629       addTreeMenuItem(tp, title);
2630
2631       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2632     }
2633   }
2634
2635   void loadTree_actionPerformed()
2636   {
2637     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2638     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2639     cap.setTreeImport();
2640     Frame frame = new Frame();
2641     frame.add(cap);
2642     jalview.bin.JalviewLite.addFrame(frame,
2643             MessageManager.getString("label.paste_newick_file"), 400, 300);
2644   }
2645
2646   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2647   {
2648     TreePanel tp = new TreePanel(alignPanel, treeFile,
2649             MessageManager.getString("label.load_tree_from_file"), tree);
2650     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2651     addTreeMenuItem(tp, treeFile);
2652   }
2653
2654   /**
2655    * sort the alignment using the given treePanel
2656    *
2657    * @param treePanel
2658    *          tree used to sort view
2659    * @param title
2660    *          string used for undo event name
2661    */
2662   public void sortByTree(TreePanel treePanel, String title)
2663   {
2664     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2665     AlignmentSorter
2666             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2667     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2668     // HistoryItem.SORT));
2669     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2670             "label.order_by_params", new String[]
2671             { title }), oldOrder, viewport.getAlignment()));
2672     alignPanel.paintAlignment(true);
2673   }
2674
2675   /**
2676    * Do any automatic reordering of the alignment and add the necessary bits to
2677    * the menu structure for the new tree
2678    *
2679    * @param treePanel
2680    * @param title
2681    */
2682   protected void addTreeMenuItem(final TreePanel treePanel,
2683           final String title)
2684   {
2685     final MenuItem item = new MenuItem(title);
2686     sortByTreeMenu.add(item);
2687     item.addActionListener(new java.awt.event.ActionListener()
2688     {
2689       @Override
2690       public void actionPerformed(ActionEvent evt)
2691       {
2692         sortByTree(treePanel, title); // treePanel.getTitle());
2693       }
2694     });
2695
2696     treePanel.addWindowListener(new WindowAdapter()
2697     {
2698       @Override
2699       public void windowOpened(WindowEvent e)
2700       {
2701         if (viewport.sortByTree)
2702         {
2703           sortByTree(treePanel, title);
2704         }
2705         super.windowOpened(e);
2706       }
2707
2708       @Override
2709       public void windowClosing(WindowEvent e)
2710       {
2711         sortByTreeMenu.remove(item);
2712       };
2713     });
2714   }
2715
2716   public boolean sortBy(AlignmentOrder alorder, String undoname)
2717   {
2718     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2719     if (viewport.applet.debug)
2720     {
2721       System.err.println("Sorting " + alorder.getOrder().size()
2722               + " in alignment '" + getTitle() + "'");
2723     }
2724     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2725     if (undoname != null)
2726     {
2727       addHistoryItem(new OrderCommand(undoname, oldOrder,
2728               viewport.getAlignment()));
2729     }
2730     alignPanel.paintAlignment(true);
2731     return true;
2732   }
2733
2734   protected void documentation_actionPerformed()
2735   {
2736     alignPanel.av.applet.openJalviewHelpUrl();
2737   }
2738
2739   protected void about_actionPerformed()
2740   {
2741
2742     class AboutPanel extends Canvas
2743     {
2744       String version;
2745
2746       String builddate;
2747
2748       public AboutPanel(String version, String builddate)
2749       {
2750         this.version = version;
2751         this.builddate = builddate;
2752       }
2753
2754       @Override
2755       public void paint(Graphics g)
2756       {
2757         g.setColor(Color.white);
2758         g.fillRect(0, 0, getSize().width, getSize().height);
2759         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2760         FontMetrics fm = g.getFontMetrics();
2761         int fh = fm.getHeight();
2762         int y = 5, x = 7;
2763         g.setColor(Color.black);
2764         // TODO: update this text for each release or centrally store it for
2765         // lite and application
2766         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2767         g.drawString(MessageManager.formatMessage(
2768                 "label.jalviewLite_release", new String[]
2769                 { version }), x, y += fh);
2770         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2771         g.drawString(MessageManager.formatMessage(
2772                 "label.jaview_build_date", new String[]
2773                 { builddate }), x, y += fh);
2774         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2775         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2776                 x, y += fh * 1.5);
2777         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2778                 x + 50, y += fh + 8);
2779         g.drawString(
2780                 MessageManager.getString("label.jalview_dev_managers"), x,
2781                 y += fh);
2782         g.drawString(MessageManager
2783                 .getString("label.jalview_distribution_lists"), x, y += fh);
2784         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2785                 x, y += fh + 8);
2786         g.drawString(
2787                 MessageManager.getString("label.jalview_cite_1_authors"),
2788                 x, y += fh);
2789         g.drawString(
2790                 MessageManager.getString("label.jalview_cite_1_title"), x,
2791                 y += fh);
2792         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2793                 x, y += fh);
2794       }
2795     }
2796
2797     Frame frame = new Frame();
2798     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2799             .getBuildDate()));
2800     jalview.bin.JalviewLite.addFrame(frame,
2801             MessageManager.getString("label.jalview"), 580, 220);
2802
2803   }
2804
2805   public void showURL(String url, String target)
2806   {
2807     if (viewport.applet == null)
2808     {
2809       System.out.println("Not running as applet - no browser available.");
2810     }
2811     else
2812     {
2813       viewport.applet.showURL(url, target);
2814     }
2815   }
2816
2817   // ////////////////////////////////////////////////////////////////////////////////
2818   // JBuilder Graphics here
2819
2820   MenuBar alignFrameMenuBar = new MenuBar();
2821
2822   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2823
2824   MenuItem loadApplication = new MenuItem(
2825           MessageManager.getString("label.view_full_application"));
2826
2827   MenuItem loadTree = new MenuItem(
2828           MessageManager.getString("label.load_associated_tree"));
2829
2830   MenuItem loadAnnotations = new MenuItem(
2831           MessageManager.getString("label.load_features_annotations"));
2832
2833   MenuItem outputFeatures = new MenuItem(
2834           MessageManager.getString("label.export_features").concat("..."));
2835
2836   MenuItem outputAnnotations = new MenuItem(
2837           MessageManager.getString("label.export_annotations").concat("..."));
2838
2839   MenuItem closeMenuItem = new MenuItem(
2840           MessageManager.getString("action.close"));
2841
2842   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2843
2844   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2845
2846   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2847
2848   Menu calculateMenu = new Menu(
2849           MessageManager.getString("action.calculate"));
2850
2851   MenuItem selectAllSequenceMenuItem = new MenuItem(
2852           MessageManager.getString("action.select_all"));
2853
2854   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2855           MessageManager.getString("action.deselect_all"));
2856
2857   MenuItem invertSequenceMenuItem = new MenuItem(
2858           MessageManager.getString("action.invert_selection"));
2859
2860   MenuItem remove2LeftMenuItem = new MenuItem();
2861
2862   MenuItem remove2RightMenuItem = new MenuItem();
2863
2864   MenuItem removeGappedColumnMenuItem = new MenuItem();
2865
2866   MenuItem removeAllGapsMenuItem = new MenuItem();
2867
2868   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2869
2870   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2871
2872   MenuItem sortPairwiseMenuItem = new MenuItem();
2873
2874   MenuItem sortIDMenuItem = new MenuItem();
2875
2876   MenuItem sortLengthMenuItem = new MenuItem();
2877
2878   MenuItem sortGroupMenuItem = new MenuItem();
2879
2880   MenuItem removeRedundancyMenuItem = new MenuItem();
2881
2882   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2883
2884   MenuItem PCAMenuItem = new MenuItem();
2885
2886   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2887
2888   MenuItem neighbourTreeMenuItem = new MenuItem();
2889
2890   BorderLayout borderLayout1 = new BorderLayout();
2891
2892   public Label statusBar = new Label();
2893
2894   Menu outputTextboxMenu = new Menu();
2895
2896   MenuItem clustalColour = new MenuItem();
2897
2898   MenuItem zappoColour = new MenuItem();
2899
2900   MenuItem taylorColour = new MenuItem();
2901
2902   MenuItem hydrophobicityColour = new MenuItem();
2903
2904   MenuItem helixColour = new MenuItem();
2905
2906   MenuItem strandColour = new MenuItem();
2907
2908   MenuItem turnColour = new MenuItem();
2909
2910   MenuItem buriedColour = new MenuItem();
2911
2912   MenuItem purinePyrimidineColour = new MenuItem();
2913
2914   MenuItem RNAInteractionColour = new MenuItem();
2915
2916   MenuItem RNAHelixColour = new MenuItem();
2917
2918   MenuItem userDefinedColour = new MenuItem();
2919
2920   MenuItem PIDColour = new MenuItem();
2921
2922   MenuItem BLOSUM62Colour = new MenuItem();
2923
2924   MenuItem tcoffeeColour = new MenuItem();
2925
2926   MenuItem njTreeBlosumMenuItem = new MenuItem();
2927
2928   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2929
2930   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2931
2932   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2933
2934   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2935
2936   MenuItem alProperties = new MenuItem(
2937           MessageManager.getString("label.alignment_props"));
2938
2939   MenuItem overviewMenuItem = new MenuItem();
2940
2941   MenuItem undoMenuItem = new MenuItem();
2942
2943   MenuItem redoMenuItem = new MenuItem();
2944
2945   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2946
2947   MenuItem noColourmenuItem = new MenuItem();
2948
2949   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2950
2951   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2952
2953   MenuItem findMenuItem = new MenuItem();
2954
2955   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2956
2957   MenuItem nucleotideColour = new MenuItem();
2958
2959   MenuItem deleteGroups = new MenuItem();
2960
2961   MenuItem grpsFromSelection = new MenuItem();
2962
2963   MenuItem createGroup = new MenuItem();
2964
2965   MenuItem unGroup = new MenuItem();
2966
2967   MenuItem delete = new MenuItem();
2968
2969   MenuItem copy = new MenuItem();
2970
2971   MenuItem cut = new MenuItem();
2972
2973   Menu pasteMenu = new Menu();
2974
2975   MenuItem pasteNew = new MenuItem();
2976
2977   MenuItem pasteThis = new MenuItem();
2978
2979   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2980
2981   MenuItem font = new MenuItem();
2982
2983   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2984
2985   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2986
2987   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2988
2989   MenuItem modifyPID = new MenuItem();
2990
2991   MenuItem modifyConservation = new MenuItem();
2992
2993   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2994           "Autocalculate Consensus", true);
2995
2996   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2997           "Sort Alignment With New Tree", true);
2998
2999   Menu sortByTreeMenu = new Menu();
3000
3001   Menu sort = new Menu();
3002
3003   Menu calculate = new Menu();
3004
3005   MenuItem inputText = new MenuItem();
3006
3007   Menu helpMenu = new Menu();
3008
3009   MenuItem documentation = new MenuItem();
3010
3011   MenuItem about = new MenuItem();
3012
3013   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3014
3015   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3016
3017   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3018
3019   Menu autoAnnMenu = new Menu();
3020
3021   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3022
3023   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3024
3025   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3026
3027   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3028
3029   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3030
3031   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3032
3033   private void jbInit() throws Exception
3034   {
3035
3036     setMenuBar(alignFrameMenuBar);
3037
3038     MenuItem item;
3039
3040     // dynamically fill save as menu with available formats
3041     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3042     {
3043
3044       item = new MenuItem(
3045               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3046
3047       item.addActionListener(new java.awt.event.ActionListener()
3048       {
3049         @Override
3050         public void actionPerformed(ActionEvent e)
3051         {
3052           outputText_actionPerformed(e);
3053         }
3054       });
3055
3056       outputTextboxMenu.add(item);
3057     }
3058     closeMenuItem.addActionListener(this);
3059     loadApplication.addActionListener(this);
3060
3061     loadTree.addActionListener(this);
3062     loadAnnotations.addActionListener(this);
3063     outputFeatures.addActionListener(this);
3064     outputAnnotations.addActionListener(this);
3065     selectAllSequenceMenuItem.addActionListener(this);
3066     deselectAllSequenceMenuItem.addActionListener(this);
3067     invertSequenceMenuItem.addActionListener(this);
3068     remove2LeftMenuItem.setLabel(MessageManager
3069             .getString("action.remove_left"));
3070     remove2LeftMenuItem.addActionListener(this);
3071     remove2RightMenuItem.setLabel(MessageManager
3072             .getString("action.remove_right"));
3073     remove2RightMenuItem.addActionListener(this);
3074     removeGappedColumnMenuItem.setLabel(MessageManager
3075             .getString("action.remove_empty_columns"));
3076     removeGappedColumnMenuItem.addActionListener(this);
3077     removeAllGapsMenuItem.setLabel(MessageManager
3078             .getString("action.remove_all_gaps"));
3079     removeAllGapsMenuItem.addActionListener(this);
3080     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3081     viewBoxesMenuItem.setState(true);
3082     viewBoxesMenuItem.addItemListener(this);
3083     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3084     viewTextMenuItem.setState(true);
3085     viewTextMenuItem.addItemListener(this);
3086     sortPairwiseMenuItem.setLabel(MessageManager
3087             .getString("action.by_pairwise_id"));
3088     sortPairwiseMenuItem.addActionListener(this);
3089     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3090     sortIDMenuItem.addActionListener(this);
3091     sortLengthMenuItem.setLabel(MessageManager
3092             .getString("action.by_length"));
3093     sortLengthMenuItem.addActionListener(this);
3094     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3095     sortGroupMenuItem.addActionListener(this);
3096     removeRedundancyMenuItem.setLabel(MessageManager
3097             .getString("action.remove_redundancy").concat("..."));
3098     removeRedundancyMenuItem.addActionListener(this);
3099     pairwiseAlignmentMenuItem.setLabel(MessageManager
3100             .getString("action.pairwise_alignment"));
3101     pairwiseAlignmentMenuItem.addActionListener(this);
3102     PCAMenuItem.setLabel(MessageManager
3103             .getString("label.principal_component_analysis"));
3104     PCAMenuItem.addActionListener(this);
3105     averageDistanceTreeMenuItem.setLabel(MessageManager
3106             .getString("label.average_distance_identity"));
3107     averageDistanceTreeMenuItem.addActionListener(this);
3108     neighbourTreeMenuItem.setLabel(MessageManager
3109             .getString("label.neighbour_joining_identity"));
3110     neighbourTreeMenuItem.addActionListener(this);
3111     statusBar.setBackground(Color.white);
3112     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3113     statusBar.setText(MessageManager.getString("label.status_bar"));
3114     outputTextboxMenu.setLabel(MessageManager
3115             .getString("label.out_to_textbox"));
3116     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3117
3118     clustalColour.addActionListener(this);
3119     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3120     zappoColour.addActionListener(this);
3121     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3122     taylorColour.addActionListener(this);
3123     hydrophobicityColour.setLabel(MessageManager
3124             .getString("label.hydrophobicity"));
3125     hydrophobicityColour.addActionListener(this);
3126     helixColour
3127             .setLabel(MessageManager.getString("label.helix_propensity"));
3128     helixColour.addActionListener(this);
3129     strandColour.setLabel(MessageManager
3130             .getString("label.strand_propensity"));
3131     strandColour.addActionListener(this);
3132     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3133     turnColour.addActionListener(this);
3134     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3135     buriedColour.addActionListener(this);
3136     purinePyrimidineColour.setLabel(MessageManager
3137             .getString("label.purine_pyrimidine"));
3138     purinePyrimidineColour.addActionListener(this);
3139     RNAInteractionColour.setLabel(MessageManager
3140             .getString("label.rna_interaction"));
3141     RNAInteractionColour.addActionListener(this);
3142     RNAHelixColour.setLabel(MessageManager
3143             .getString("action.by_rna_helixes"));
3144     RNAHelixColour.addActionListener(this);
3145     userDefinedColour.setLabel(MessageManager
3146             .getString("action.user_defined"));
3147     userDefinedColour.addActionListener(this);
3148     PIDColour.setLabel(MessageManager
3149             .getString("label.percentage_identity"));
3150     PIDColour.addActionListener(this);
3151     BLOSUM62Colour.setLabel(MessageManager
3152             .getString("label.blosum62_score"));
3153     BLOSUM62Colour.addActionListener(this);
3154     tcoffeeColour
3155             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3156     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3157                                      // provided
3158     tcoffeeColour.addActionListener(this);
3159     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3160             .getString("label.average_distance_bloslum62"));
3161     avDistanceTreeBlosumMenuItem.addActionListener(this);
3162     njTreeBlosumMenuItem.setLabel(MessageManager
3163             .getString("label.neighbour_blosum62"));
3164     njTreeBlosumMenuItem.addActionListener(this);
3165     annotationPanelMenuItem.setLabel(MessageManager
3166             .getString("label.show_annotations"));
3167     annotationPanelMenuItem.addItemListener(this);
3168     colourTextMenuItem.setLabel(MessageManager
3169             .getString("label.colour_text"));
3170     colourTextMenuItem.addItemListener(this);
3171     displayNonconservedMenuItem.setLabel(MessageManager
3172             .getString("label.show_non_conversed"));
3173     displayNonconservedMenuItem.addItemListener(this);
3174     alProperties.addActionListener(this);
3175     overviewMenuItem.setLabel(MessageManager
3176             .getString("label.overview_window"));
3177     overviewMenuItem.addActionListener(this);
3178     undoMenuItem.setEnabled(false);
3179     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3180     undoMenuItem.addActionListener(this);
3181     redoMenuItem.setEnabled(false);
3182     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3183     redoMenuItem.addActionListener(this);
3184     conservationMenuItem.setLabel(MessageManager
3185             .getString("action.by_conservation"));
3186     conservationMenuItem.addItemListener(this);
3187     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3188     noColourmenuItem.addActionListener(this);
3189     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3190     wrapMenuItem.addItemListener(this);
3191     renderGapsMenuItem.setLabel(MessageManager
3192             .getString("action.show_gaps"));
3193     renderGapsMenuItem.setState(true);
3194     renderGapsMenuItem.addItemListener(this);
3195     findMenuItem.setLabel(MessageManager.getString("action.find"));
3196     findMenuItem.addActionListener(this);
3197     abovePIDThreshold.setLabel(MessageManager
3198             .getString("label.above_identity_threshold"));
3199     abovePIDThreshold.addItemListener(this);
3200     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3201     nucleotideColour.addActionListener(this);
3202     deleteGroups.setLabel(MessageManager
3203             .getString("action.undefine_groups"));
3204     deleteGroups.addActionListener(this);
3205     grpsFromSelection.setLabel(MessageManager
3206             .getString("action.make_groups_selection"));
3207     grpsFromSelection.addActionListener(this);
3208     createGroup.setLabel(MessageManager.getString("action.create_group"));
3209     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3210     copy.setLabel(MessageManager.getString("action.copy"));
3211     copy.addActionListener(this);
3212     cut.setLabel(MessageManager.getString("action.cut"));
3213     cut.addActionListener(this);
3214     delete.setLabel(MessageManager.getString("action.delete"));
3215     delete.addActionListener(this);
3216     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3217     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3218     pasteNew.addActionListener(this);
3219     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3220     pasteThis.addActionListener(this);
3221     applyToAllGroups.setLabel(MessageManager
3222             .getString("label.apply_colour_to_all_groups"));
3223     applyToAllGroups.setState(true);
3224     applyToAllGroups.addItemListener(this);
3225     font.setLabel(MessageManager.getString("action.font"));
3226     font.addActionListener(this);
3227     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3228     scaleAbove.setState(true);
3229     scaleAbove.setEnabled(false);
3230     scaleAbove.addItemListener(this);
3231     scaleLeft.setEnabled(false);
3232     scaleLeft.setState(true);
3233     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3234     scaleLeft.addItemListener(this);
3235     scaleRight.setEnabled(false);
3236     scaleRight.setState(true);
3237     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3238     scaleRight.addItemListener(this);
3239     modifyPID.setLabel(MessageManager
3240             .getString("label.modify_identity_thereshold"));
3241     modifyPID.addActionListener(this);
3242     modifyConservation.setLabel(MessageManager
3243             .getString("label.modify_conservation_thereshold"));
3244     modifyConservation.addActionListener(this);
3245     sortByTreeMenu.setLabel(MessageManager
3246             .getString("action.by_tree_order"));
3247     sort.setLabel(MessageManager.getString("action.sort"));
3248     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3249     autoCalculate.addItemListener(this);
3250     sortByTree.addItemListener(this);
3251     inputText
3252             .setLabel(MessageManager.getString("label.input_from_textbox"));
3253     inputText.addActionListener(this);
3254     centreColumnLabelFlag.setLabel(MessageManager
3255             .getString("label.centre_column_labels"));
3256     centreColumnLabelFlag.addItemListener(this);
3257     followMouseOverFlag.setLabel(MessageManager
3258             .getString("label.automatic_scrolling"));
3259     followMouseOverFlag.addItemListener(this);
3260     helpMenu.setLabel(MessageManager.getString("action.help"));
3261     documentation.setLabel(MessageManager.getString("label.documentation"));
3262     documentation.addActionListener(this);
3263
3264     about.setLabel(MessageManager.getString("label.about"));
3265     about.addActionListener(this);
3266     seqLimits.setState(true);
3267     seqLimits.setLabel(MessageManager
3268             .getString("label.show_sequence_limits"));
3269     seqLimits.addItemListener(this);
3270     featureSettings.setLabel(MessageManager
3271             .getString("label.feature_settings"));
3272     featureSettings.addActionListener(this);
3273     sequenceFeatures.setLabel(MessageManager
3274             .getString("label.sequence_features"));
3275     sequenceFeatures.addItemListener(this);
3276     sequenceFeatures.setState(false);
3277     annotationColour.setLabel(MessageManager
3278             .getString("action.by_annotation"));
3279     annotationColour.addActionListener(this);
3280
3281     annotationColumnSelection.setLabel("Select by Annotation");
3282     annotationColumnSelection.addActionListener(this);
3283
3284     invertSequenceMenuItem.setLabel(MessageManager
3285             .getString("action.invert_sequence_selection"));
3286     invertColSel.setLabel(MessageManager
3287             .getString("action.invert_column_selection"));
3288     menu1.setLabel(MessageManager.getString("action.show"));
3289     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3290     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3291     menu2.setLabel(MessageManager.getString("action.hide"));
3292     hideColumns
3293             .setLabel(MessageManager.getString("label.selected_columns"));
3294     hideSequences.setLabel(MessageManager
3295             .getString("label.selected_sequences"));
3296     hideAllButSelection.setLabel(MessageManager
3297             .getString("label.all_but_selected_region"));
3298     hideAllSelection.setLabel(MessageManager
3299             .getString("label.selected_region"));
3300     showAllHidden.setLabel(MessageManager
3301             .getString("label.all_sequences_columns"));
3302     showGroupConsensus.setLabel(MessageManager
3303             .getString("label.group_consensus"));
3304     showGroupConservation.setLabel(MessageManager
3305             .getString("label.group_conservation"));
3306     showConsensusHistogram.setLabel(MessageManager
3307             .getString("label.show_consensus_histogram"));
3308     showSequenceLogo.setLabel(MessageManager
3309             .getString("label.show_consensus_logo"));
3310     normSequenceLogo.setLabel(MessageManager
3311             .getString("label.norm_consensus_logo"));
3312     applyAutoAnnotationSettings.setLabel(MessageManager
3313             .getString("label.apply_all_groups"));
3314     applyAutoAnnotationSettings.setState(true);
3315     autoAnnMenu.setLabel(MessageManager
3316             .getString("label.autocalculated_annotation"));
3317
3318     invertColSel.addActionListener(this);
3319     showColumns.addActionListener(this);
3320     showSeqs.addActionListener(this);
3321     hideColumns.addActionListener(this);
3322     hideSequences.addActionListener(this);
3323     hideAllButSelection.addActionListener(this);
3324     hideAllSelection.addActionListener(this);
3325     showAllHidden.addActionListener(this);
3326     showGroupConsensus.addItemListener(this);
3327     showGroupConservation.addItemListener(this);
3328     showConsensusHistogram.addItemListener(this);
3329     showSequenceLogo.addItemListener(this);
3330     normSequenceLogo.addItemListener(this);
3331
3332     applyAutoAnnotationSettings.addItemListener(this);
3333     formatMenu.setLabel(MessageManager.getString("action.format"));
3334     selectMenu.setLabel(MessageManager.getString("action.select"));
3335     newView.setLabel(MessageManager.getString("action.new_view"));
3336     newView.addActionListener(this);
3337     alignFrameMenuBar.add(fileMenu);
3338     alignFrameMenuBar.add(editMenu);
3339     alignFrameMenuBar.add(selectMenu);
3340     alignFrameMenuBar.add(viewMenu);
3341     alignFrameMenuBar.add(formatMenu);
3342     alignFrameMenuBar.add(colourMenu);
3343     alignFrameMenuBar.add(calculateMenu);
3344     alignFrameMenuBar.add(helpMenu);
3345
3346     fileMenu.add(inputText);
3347     fileMenu.add(loadTree);
3348     fileMenu.add(loadAnnotations);
3349
3350     fileMenu.addSeparator();
3351     fileMenu.add(outputTextboxMenu);
3352     fileMenu.add(outputFeatures);
3353     fileMenu.add(outputAnnotations);
3354
3355     if (jalviewServletURL != null)
3356     {
3357       fileMenu.add(loadApplication);
3358     }
3359
3360     fileMenu.addSeparator();
3361     fileMenu.add(closeMenuItem);
3362
3363     editMenu.add(undoMenuItem);
3364     editMenu.add(redoMenuItem);
3365     editMenu.add(cut);
3366     editMenu.add(copy);
3367     editMenu.add(pasteMenu);
3368     editMenu.add(delete);
3369     editMenu.addSeparator();
3370     editMenu.add(remove2LeftMenuItem);
3371     editMenu.add(remove2RightMenuItem);
3372     editMenu.add(removeGappedColumnMenuItem);
3373     editMenu.add(removeAllGapsMenuItem);
3374     editMenu.add(removeRedundancyMenuItem);
3375     viewMenu.add(newView);
3376     viewMenu.addSeparator();
3377     viewMenu.add(menu1);
3378     viewMenu.add(menu2);
3379     viewMenu.addSeparator();
3380     viewMenu.add(followMouseOverFlag);
3381     viewMenu.add(annotationPanelMenuItem);
3382     autoAnnMenu.add(applyAutoAnnotationSettings);
3383     autoAnnMenu.add(showConsensusHistogram);
3384     autoAnnMenu.add(showSequenceLogo);
3385     autoAnnMenu.add(normSequenceLogo);
3386     autoAnnMenu.addSeparator();
3387     autoAnnMenu.add(showGroupConservation);
3388     autoAnnMenu.add(showGroupConsensus);
3389     viewMenu.add(autoAnnMenu);
3390     viewMenu.addSeparator();
3391     viewMenu.add(sequenceFeatures);
3392     viewMenu.add(featureSettings);
3393     viewMenu.addSeparator();
3394     viewMenu.add(alProperties);
3395     viewMenu.addSeparator();
3396     viewMenu.add(overviewMenuItem);
3397     colourMenu.add(applyToAllGroups);
3398     colourMenu.addSeparator();
3399     colourMenu.add(noColourmenuItem);
3400     colourMenu.add(clustalColour);
3401     colourMenu.add(BLOSUM62Colour);
3402     colourMenu.add(PIDColour);
3403     colourMenu.add(zappoColour);
3404     colourMenu.add(taylorColour);
3405     colourMenu.add(hydrophobicityColour);
3406     colourMenu.add(helixColour);
3407     colourMenu.add(strandColour);
3408     colourMenu.add(turnColour);
3409     colourMenu.add(buriedColour);
3410     colourMenu.add(nucleotideColour);
3411     colourMenu.add(purinePyrimidineColour);
3412     // colourMenu.add(RNAInteractionColour);
3413     colourMenu.add(tcoffeeColour);
3414     colourMenu.add(userDefinedColour);
3415     colourMenu.addSeparator();
3416     colourMenu.add(conservationMenuItem);
3417     colourMenu.add(modifyConservation);
3418     colourMenu.add(abovePIDThreshold);
3419     colourMenu.add(modifyPID);
3420     colourMenu.add(annotationColour);
3421     colourMenu.add(RNAHelixColour);
3422     calculateMenu.add(sort);
3423     calculateMenu.add(calculate);
3424     calculateMenu.addSeparator();
3425     calculateMenu.add(pairwiseAlignmentMenuItem);
3426     calculateMenu.add(PCAMenuItem);
3427     calculateMenu.add(autoCalculate);
3428     calculateMenu.add(sortByTree);
3429     this.add(statusBar, BorderLayout.SOUTH);
3430     pasteMenu.add(pasteNew);
3431     pasteMenu.add(pasteThis);
3432     sort.add(sortIDMenuItem);
3433     sort.add(sortLengthMenuItem);
3434     sort.add(sortByTreeMenu);
3435     sort.add(sortGroupMenuItem);
3436     sort.add(sortPairwiseMenuItem);
3437     calculate.add(averageDistanceTreeMenuItem);
3438     calculate.add(neighbourTreeMenuItem);
3439     calculate.add(avDistanceTreeBlosumMenuItem);
3440     calculate.add(njTreeBlosumMenuItem);
3441     helpMenu.add(documentation);
3442     helpMenu.add(about);
3443     menu1.add(showColumns);
3444     menu1.add(showSeqs);
3445     menu1.add(showAllHidden);
3446     menu2.add(hideColumns);
3447     menu2.add(hideSequences);
3448     menu2.add(hideAllSelection);
3449     menu2.add(hideAllButSelection);
3450     formatMenu.add(font);
3451     formatMenu.add(seqLimits);
3452     formatMenu.add(wrapMenuItem);
3453     formatMenu.add(scaleAbove);
3454     formatMenu.add(scaleLeft);
3455     formatMenu.add(scaleRight);
3456     formatMenu.add(viewBoxesMenuItem);
3457     formatMenu.add(viewTextMenuItem);
3458     formatMenu.add(colourTextMenuItem);
3459     formatMenu.add(displayNonconservedMenuItem);
3460     formatMenu.add(renderGapsMenuItem);
3461     formatMenu.add(centreColumnLabelFlag);
3462     selectMenu.add(findMenuItem);
3463     selectMenu.addSeparator();
3464     selectMenu.add(selectAllSequenceMenuItem);
3465     selectMenu.add(deselectAllSequenceMenuItem);
3466     selectMenu.add(invertSequenceMenuItem);
3467     selectMenu.add(invertColSel);
3468     selectMenu.add(createGroup);
3469     selectMenu.add(unGroup);
3470     selectMenu.add(grpsFromSelection);
3471     selectMenu.add(deleteGroups);
3472     selectMenu.add(annotationColumnSelection);
3473
3474   }
3475
3476   public void setStatus(String string)
3477   {
3478     statusBar.setText(string);
3479   };
3480
3481   MenuItem featureSettings = new MenuItem();
3482
3483   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3484
3485   MenuItem annotationColour = new MenuItem();
3486
3487   MenuItem annotationColumnSelection = new MenuItem();
3488
3489   MenuItem invertColSel = new MenuItem();
3490
3491   Menu menu1 = new Menu();
3492
3493   MenuItem showColumns = new MenuItem();
3494
3495   MenuItem showSeqs = new MenuItem();
3496
3497   Menu menu2 = new Menu();
3498
3499   MenuItem hideColumns = new MenuItem();
3500
3501   MenuItem hideSequences = new MenuItem();
3502
3503   MenuItem hideAllButSelection = new MenuItem();
3504
3505   MenuItem hideAllSelection = new MenuItem();
3506
3507   MenuItem showAllHidden = new MenuItem();
3508
3509   Menu formatMenu = new Menu();
3510
3511   Menu selectMenu = new Menu();
3512
3513   MenuItem newView = new MenuItem();
3514
3515   /**
3516    * Attach the alignFrame panels after embedding menus, if necessary. This used
3517    * to be called setEmbedded, but is now creates the dropdown menus in a
3518    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3519    *
3520    * @param reallyEmbedded
3521    *          true to attach the view to the applet area on the page rather than
3522    *          in a new window
3523    */
3524   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3525   {
3526     if (reallyEmbedded)
3527     {
3528       // ////
3529       // Explicly build the embedded menu panel for the on-page applet
3530       //
3531       // view cannot be closed if its actually on the page
3532       fileMenu.remove(closeMenuItem);
3533       fileMenu.remove(3); // Remove Seperator
3534       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3535               Font.PLAIN, 11, false); // use our own fonts.
3536       // and actually add the components to the applet area
3537       viewport.applet.setLayout(new BorderLayout());
3538       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3539       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3540       alignPanel.setSize(viewport.applet.getSize().width,
3541               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3542                       - statusBar.HEIGHT);
3543       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3544       final AlignFrame me = this;
3545       viewport.applet.addFocusListener(new FocusListener()
3546       {
3547
3548         @Override
3549         public void focusLost(FocusEvent e)
3550         {
3551           if (me.viewport.applet.currentAlignFrame == me)
3552           {
3553             me.viewport.applet.currentAlignFrame = null;
3554           }
3555         }
3556
3557         @Override
3558         public void focusGained(FocusEvent e)
3559         {
3560           me.viewport.applet.currentAlignFrame = me;
3561         }
3562       });
3563       viewport.applet.validate();
3564     }
3565     else
3566     {
3567       // //////
3568       // test and embed menu bar if necessary.
3569       //
3570       if (embedMenuIfNeeded(alignPanel))
3571       {
3572         // adjust for status bar height too
3573         alignPanel.setSize(getSize().width, getSize().height
3574                 - statusBar.HEIGHT);
3575       }
3576       add(statusBar, BorderLayout.SOUTH);
3577       add(alignPanel, BorderLayout.CENTER);
3578       // and register with the applet so it can pass external API calls to us
3579       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3580               DEFAULT_HEIGHT);
3581     }
3582   }
3583
3584   /**
3585    * create a new binding between structures in an existing jmol viewer instance
3586    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3587    * this does not open a new Jmol window, or modify the display of the
3588    * structures in the original jmol window. Note This method doesn't work
3589    * without an additional javascript library to exchange messages between the
3590    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3591    *
3592    * @param viewer
3593    *          JmolViewer instance
3594    * @param sequenceIds
3595    *          - sequence Ids to search for associations
3596    */
3597   public SequenceStructureBinding addStructureViewInstance(
3598           Object jmolviewer, String[] sequenceIds)
3599   {
3600     org.jmol.api.JmolViewer viewer = null;
3601     try
3602     {
3603       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3604     } catch (ClassCastException ex)
3605     {
3606       System.err.println("Unsupported viewer object :"
3607               + jmolviewer.getClass());
3608     }
3609     if (viewer == null)
3610     {
3611       System.err.println("Can't use this object as a structure viewer:"
3612               + jmolviewer.getClass());
3613       return null;
3614     }
3615     SequenceI[] seqs = null;
3616     if (sequenceIds == null || sequenceIds.length == 0)
3617     {
3618       seqs = viewport.getAlignment().getSequencesArray();
3619     }
3620     else
3621     {
3622       Vector sqi = new Vector();
3623       AlignmentI al = viewport.getAlignment();
3624       for (int sid = 0; sid < sequenceIds.length; sid++)
3625       {
3626         SequenceI sq = al.findName(sequenceIds[sid]);
3627         if (sq != null)
3628         {
3629           sqi.addElement(sq);
3630         }
3631       }
3632       if (sqi.size() > 0)
3633       {
3634         seqs = new SequenceI[sqi.size()];
3635         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3636         {
3637           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3638         }
3639       }
3640       else
3641       {
3642         return null;
3643       }
3644     }
3645     AAStructureBindingModel jmv = null;
3646     // TODO: search for a jmv that involves viewer
3647     if (jmv == null)
3648     { // create a new viewer/jalview binding.
3649       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3650       { seqs });
3651     }
3652     return jmv;
3653
3654   }
3655
3656   /**
3657    * bind a pdb file to a sequence in the current view
3658    *
3659    * @param sequenceId
3660    *          - sequenceId within the dataset.
3661    * @param pdbEntryString
3662    *          - the short name for the PDB file
3663    * @param pdbFile
3664    *          - pdb file - either a URL or a valid PDB file.
3665    * @return true if binding was as success TODO: consider making an exception
3666    *         structure for indicating when PDB parsing or sequenceId location
3667    *         fails.
3668    */
3669   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3670           String pdbFile)
3671   {
3672     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3673     boolean needtoadd = false;
3674     if (toaddpdb != null)
3675     {
3676       Vector pdbe = toaddpdb.getPDBId();
3677       PDBEntry pdbentry = null;
3678       if (pdbe != null && pdbe.size() > 0)
3679       {
3680         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3681         {
3682           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3683           if (!pdbentry.getId().equals(pdbEntryString)
3684                   && !pdbentry.getFile().equals(pdbFile))
3685           {
3686             pdbentry = null;
3687           }
3688           else
3689           {
3690             continue;
3691           }
3692         }
3693       }
3694       if (pdbentry == null)
3695       {
3696         pdbentry = new PDBEntry();
3697         pdbentry.setId(pdbEntryString);
3698         pdbentry.setFile(pdbFile);
3699         needtoadd = true; // add this new entry to sequence.
3700       }
3701       // resolve data source
3702       // TODO: this code should be a refactored to an io package
3703       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3704       if (protocol == null)
3705       {
3706         return false;
3707       }
3708       if (needtoadd)
3709       {
3710         // make a note of the access mode and add
3711         if (pdbentry.getProperty() == null)
3712         {
3713           pdbentry.setProperty(new Hashtable());
3714         }
3715         pdbentry.getProperty().put("protocol", protocol);
3716         toaddpdb.addPDBId(pdbentry);
3717         alignPanel.getStructureSelectionManager()
3718                 .registerPDBEntry(pdbentry);
3719       }
3720     }
3721     return true;
3722   }
3723
3724   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3725   {
3726     if (seqs != null)
3727     {
3728       Vector sequences = new Vector();
3729       for (int i = 0; i < seqs.length; i++)
3730       {
3731         if (seqs[i] != null)
3732         {
3733           sequences.addElement(new Object[]
3734           { seqs[i], (chains != null) ? chains[i] : null });
3735         }
3736       }
3737       seqs = new SequenceI[sequences.size()];
3738       chains = new String[sequences.size()];
3739       for (int i = 0, isize = sequences.size(); i < isize; i++)
3740       {
3741         Object[] oj = (Object[]) sequences.elementAt(i);
3742
3743         seqs[i] = (SequenceI) oj[0];
3744         chains[i] = (String) oj[1];
3745       }
3746     }
3747     return new Object[]
3748     { seqs, chains };
3749
3750   }
3751
3752   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3753           SequenceI[] seqs, String[] chains, String protocol)
3754   {
3755     // Scrub any null sequences from the array
3756     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3757     seqs = (SequenceI[]) sqch[0];
3758     chains = (String[]) sqch[1];
3759     if (seqs == null || seqs.length == 0)
3760     {
3761       System.err
3762               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3763     }
3764     if (protocol == null || protocol.trim().length() == 0
3765             || protocol.equals("null"))
3766     {
3767       protocol = (String) pdb.getProperty().get("protocol");
3768       if (protocol == null)
3769       {
3770         System.err.println("Couldn't work out protocol to open structure: "
3771                 + pdb.getId());
3772         return;
3773       }
3774     }
3775     if (applet.useXtrnalSviewer)
3776     {
3777       // register the association(s) and quit, don't create any windows.
3778       if (StructureSelectionManager.getStructureSelectionManager(applet)
3779               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3780       {
3781         System.err.println("Failed to map " + pdb.getFile() + " ("
3782                 + protocol + ") to any sequences");
3783       }
3784       return;
3785     }
3786     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3787     {
3788       // can only do alignments with Jmol
3789       // find the last jmol window assigned to this alignment
3790       jalview.appletgui.AppletJmol ajm = null, tajm;
3791       Vector jmols = applet
3792               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3793       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3794       {
3795         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3796         if (tajm.ap.alignFrame == this)
3797         {
3798           ajm = tajm;
3799           break;
3800         }
3801       }
3802       if (ajm != null)
3803       {
3804         System.err
3805                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3806         // try and add the pdb structure
3807         // ajm.addS
3808         ajm = null;
3809       }
3810     }
3811     // otherwise, create a new window
3812     if (applet.jmolAvailable)
3813     {
3814       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3815               protocol);
3816       applet.lastFrameX += 40;
3817       applet.lastFrameY += 40;
3818     }
3819     else
3820     {
3821       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3822     }
3823
3824   }
3825
3826   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3827           SequenceI[][] seqs, String[][] chains, String[] protocols)
3828   {
3829     // TODO Auto-generated method stub
3830     System.err.println("Aligned Structure View: Not yet implemented.");
3831   }
3832
3833   /**
3834    * modify the current selection, providing the user has not made a selection
3835    * already.
3836    *
3837    * @param sel
3838    *          - sequences from this alignment
3839    * @param csel
3840    *          - columns to be selected on the alignment
3841    */
3842   public void select(SequenceGroup sel, ColumnSelection csel)
3843   {
3844     alignPanel.seqPanel.selection(sel, csel, null);
3845   }
3846
3847   public void scrollTo(int row, int column)
3848   {
3849     alignPanel.seqPanel.scrollTo(row, column);
3850   }
3851
3852   public void scrollToRow(int row)
3853   {
3854     alignPanel.seqPanel.scrollToRow(row);
3855   }
3856
3857   public void scrollToColumn(int column)
3858   {
3859     alignPanel.seqPanel.scrollToColumn(column);
3860   }
3861
3862   /**
3863    * @return the alignments unique ID.
3864    */
3865   public String getSequenceSetId()
3866   {
3867     return viewport.getSequenceSetId();
3868   }
3869
3870   /**
3871    * Load the (T-Coffee) score file from the specified url
3872    *
3873    * @param source
3874    *          File/URL/T-COFFEE score file contents
3875    * @throws IOException
3876    * @return true if alignment was annotated with data from source
3877    */
3878   public boolean loadScoreFile(String source) throws IOException
3879   {
3880
3881     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3882             AppletFormatAdapter.checkProtocol(source));
3883     if (!file.isValid())
3884     {
3885       // TODO: raise dialog for gui
3886       System.err.println("Problems parsing T-Coffee scores: "
3887               + file.getWarningMessage());
3888       System.err.println("Origin was:\n" + source);
3889       return false;
3890     }
3891
3892     /*
3893      * check that the score matrix matches the alignment dimensions
3894      */
3895     AlignmentI aln;
3896     if ((aln = viewport.getAlignment()) != null
3897             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3898                     .getWidth()))
3899     {
3900       // TODO: raise a dialog box here rather than bomb out.
3901       System.err
3902               .println("The scores matrix does not match the alignment dimensions");
3903
3904     }
3905
3906     // TODO add parameter to indicate if matching should be done
3907     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3908     {
3909       alignPanel.fontChanged();
3910       tcoffeeColour.setEnabled(true);
3911       // switch to this color
3912       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3913       return true;
3914     }
3915     else
3916     {
3917       System.err.println("Problems resolving T-Coffee scores:");
3918       if (file.getWarningMessage() != null)
3919       {
3920         System.err.println(file.getWarningMessage());
3921       }
3922     }
3923     return false;
3924   }
3925
3926 }