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.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.TCoffeeScoreFile;
  56 import jalview.schemes.Blosum62ColourScheme;
  57 import jalview.schemes.BuriedColourScheme;
  58 import jalview.schemes.ClustalxColourScheme;
  59 import jalview.schemes.ColourSchemeI;
  60 import jalview.schemes.HelixColourScheme;
  61 import jalview.schemes.HydrophobicColourScheme;
  62 import jalview.schemes.NucleotideColourScheme;
  63 import jalview.schemes.PIDColourScheme;
  64 import jalview.schemes.PurinePyrimidineColourScheme;
  65 import jalview.schemes.RNAHelicesColourChooser;
  66 import jalview.schemes.StrandColourScheme;
  67 import jalview.schemes.TCoffeeColourScheme;
  68 import jalview.schemes.TaylorColourScheme;
  69 import jalview.schemes.TurnColourScheme;
  70 import jalview.schemes.ZappoColourScheme;
  71 import jalview.structure.StructureSelectionManager;
  72 import jalview.structures.models.AAStructureBindingModel;
  73 import jalview.util.MappingUtils;
  74 import jalview.util.MessageManager;
  75 import jalview.viewmodel.AlignmentViewport;
  76
  77 import java.awt.BorderLayout;
  78 import java.awt.Canvas;
  79 import java.awt.CheckboxMenuItem;
  80 import java.awt.Color;
  81 import java.awt.FlowLayout;
  82 import java.awt.Font;
  83 import java.awt.FontMetrics;
  84 import java.awt.Frame;
  85 import java.awt.Graphics;
  86 import java.awt.Label;
  87 import java.awt.Menu;
  88 import java.awt.MenuBar;
  89 import java.awt.MenuItem;
  90 import java.awt.Panel;
  91 import java.awt.event.ActionEvent;
  92 import java.awt.event.ActionListener;
  93 import java.awt.event.FocusEvent;
  94 import java.awt.event.FocusListener;
  95 import java.awt.event.ItemEvent;
  96 import java.awt.event.ItemListener;
  97 import java.awt.event.KeyEvent;
  98 import java.awt.event.KeyListener;
  99 import java.awt.event.WindowAdapter;
 100 import java.awt.event.WindowEvent;
 101 import java.io.IOException;
 102 import java.net.URL;
 103 import java.net.URLEncoder;
 104 import java.util.Arrays;
 105 import java.util.Deque;
 106 import java.util.HashMap;
 107 import java.util.Hashtable;
 108 import java.util.List;
 109 import java.util.Map;
 110 import java.util.StringTokenizer;
 111 import java.util.Vector;
 112
 113 import org.jmol.viewer.Viewer;
 114
 115 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 116         ItemListener, KeyListener, AlignViewControllerGuiI
 117 {
 118   public AlignViewControllerI avc;
 119
 120   public AlignmentPanel alignPanel;
 121
 122   public AlignViewport viewport;
 123
 124   // width and height may be overridden by applet parameters
 125   int frameWidth = 700;
 126
 127   int frameHeight = 500;
 128
 129   String jalviewServletURL;
 130
 131   /*
 132    * Flag for showing autocalculated consensus above or below other consensus
 133    * rows
 134    */
 135   private boolean showAutoCalculatedAbove;
 136
 137   private SequenceAnnotationOrder annotationSortOrder;
 138
 139   /**
 140    * Constructor that creates the frame and adds it to the display.
 141    *
 142    * @param al
 143    * @param applet
 144    * @param title
 145    * @param embedded
 146    */
 147   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 148           boolean embedded)
 149   {
 150     this(al, applet, title, embedded, true);
 151   }
 152
 153   /**
 154    * Constructor that optionally allows the frame to be displayed or only
 155    * created.
 156    *
 157    * @param al
 158    * @param applet
 159    * @param title
 160    * @param embedded
 161    * @param addToDisplay
 162    */
 163   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 164           boolean embedded, boolean addToDisplay)
 165   {
 166     this(al, null, null, applet, title, embedded, addToDisplay);
 167   }
 168
 169   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 170           ColumnSelection columnSelection, JalviewLite applet,
 171           String title, boolean embedded)
 172   {
 173     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 174   }
 175
 176   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 177           ColumnSelection columnSelection, JalviewLite applet,
 178           String title, boolean embedded, boolean addToDisplay)
 179   {
 180     if (applet != null)
 181     {
 182       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 183     }
 184
 185     try
 186     {
 187       jbInit();
 188     } catch (Exception ex)
 189     {
 190       ex.printStackTrace();
 191     }
 192     // need to get window geometry before we calculate alignment layout
 193     if (applet != null)
 194     {
 195       String param;
 196       try
 197       {
 198         param = applet.getParameter("windowWidth");
 199         if (param != null)
 200         {
 201           int width = Integer.parseInt(param);
 202           frameWidth = width;
 203         }
 204         param = applet.getParameter("windowHeight");
 205         if (param != null)
 206         {
 207           int height = Integer.parseInt(param);
 208           frameHeight = height;
 209         }
 210       } catch (Exception ex)
 211       {
 212       }
 213     }
 214     viewport = new AlignViewport(al, applet);
 215
 216     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 217     {
 218       viewport.hideSequence(hiddenSeqs);
 219     }
 220     if (columnSelection != null)
 221     {
 222       viewport.setColumnSelection(columnSelection);
 223     }
 224
 225     alignPanel = new AlignmentPanel(this, viewport);
 226     avc = new jalview.controller.AlignViewController(this, viewport,
 227             alignPanel);
 228     viewport.updateConservation(alignPanel);
 229     viewport.updateConsensus(alignPanel);
 230
 231     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 232     followMouseOverFlag.setState(viewport.isFollowHighlight());
 233     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 234     showGroupConservation.setState(viewport.isShowGroupConservation());
 235     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 236     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 237     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 238     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 239     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 240     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 241     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 242     showAlignmentAnnotations.setState(true);
 243     showSequenceAnnotations.setState(false);
 244
 245     seqLimits.setState(viewport.getShowJVSuffix());
 246
 247     if (applet != null)
 248     {
 249       String param = applet.getParameter("sortBy");
 250       if (param != null)
 251       {
 252         if (param.equalsIgnoreCase("Id"))
 253         {
 254           sortIDMenuItem_actionPerformed();
 255         }
 256         else if (param.equalsIgnoreCase("Pairwise Identity"))
 257         {
 258           sortPairwiseMenuItem_actionPerformed();
 259         }
 260         else if (param.equalsIgnoreCase("Length"))
 261         {
 262           sortLengthMenuItem_actionPerformed();
 263         }
 264       }
 265
 266       param = applet.getParameter("wrap");
 267       if (param != null)
 268       {
 269         if (param.equalsIgnoreCase("true"))
 270         {
 271           wrapMenuItem.setState(true);
 272           wrapMenuItem_actionPerformed();
 273         }
 274       }
 275       param = applet.getParameter("centrecolumnlabels");
 276       if (param != null)
 277       {
 278         centreColumnLabelFlag.setState(true);
 279         centreColumnLabelFlag_stateChanged();
 280       }
 281
 282     }
 283     if (viewport.getAlignment().isNucleotide())
 284     {
 285       viewport.updateStrucConsensus(alignPanel);
 286       if (viewport.getAlignment().hasRNAStructure())
 287       {
 288         RNAHelixColour.setEnabled(true);
 289       }
 290       else
 291       {
 292         RNAHelixColour.setEnabled(false);
 293       }
 294     }
 295     else
 296     {
 297       RNAHelixColour.setEnabled(false);
 298       purinePyrimidineColour.setEnabled(false);
 299     }
 300     // Some JVMS send keyevents to Top frame or lowest panel,
 301     // Havent worked out why yet. So add to both this frame and seqCanvas for
 302     // now
 303     this.addKeyListener(this);
 304     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 305     alignPanel.idPanel.idCanvas.addKeyListener(this);
 306     alignPanel.scalePanel.addKeyListener(this);
 307     alignPanel.annotationPanel.addKeyListener(this);
 308     alignPanel.annotationPanelHolder.addKeyListener(this);
 309     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 310     alignPanel.alabels.addKeyListener(this);
 311
 312     setAnnotationsVisibility();
 313
 314     if (addToDisplay)
 315     {
 316       addToDisplay(embedded);
 317     }
 318   }
 319
 320   /**
 321    * @param embedded
 322    */
 323   public void addToDisplay(boolean embedded)
 324   {
 325     createAlignFrameWindow(embedded);
 326     validate();
 327     alignPanel.adjustAnnotationHeight();
 328     alignPanel.paintAlignment(true);
 329   }
 330
 331   public AlignViewport getAlignViewport()
 332   {
 333     return viewport;
 334   }
 335
 336   public SeqCanvas getSeqcanvas()
 337   {
 338     return alignPanel.seqPanel.seqCanvas;
 339   }
 340
 341   /**
 342    * Load a features file onto the alignment
 343    *
 344    * @param file
 345    *          file URL, content, or other resolvable path
 346    * @param type
 347    *          is protocol for accessing data referred to by file
 348    */
 349
 350   public boolean parseFeaturesFile(String file, DataSourceType type)
 351   {
 352     return parseFeaturesFile(file, type, true);
 353   }
 354
 355   /**
 356    * Load a features file onto the alignment
 357    *
 358    * @param file
 359    *          file URL, content, or other resolvable path
 360    * @param paste
 361    *          is protocol for accessing data referred to by file
 362    * @param autoenabledisplay
 363    *          when true, display features flag will be automatically enabled if
 364    *          features are loaded
 365    * @return true if data parsed as a features file
 366    */
 367   public boolean parseFeaturesFile(String file, DataSourceType paste,
 368           boolean autoenabledisplay)
 369   {
 370     boolean featuresFile = false;
 371     try
 372     {
 373       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 374               .getFeatureRenderer().getFeatureColours();
 375       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 376               "relaxedidmatch", false);
 377       featuresFile = new FeaturesFile(file, paste).parse(
 378               viewport.getAlignment(), colours, true, relaxedIdMatching);
 379     } catch (Exception ex)
 380     {
 381       ex.printStackTrace();
 382     }
 383
 384     if (featuresFile)
 385     {
 386       if (autoenabledisplay)
 387       {
 388         viewport.setShowSequenceFeatures(true);
 389         sequenceFeatures.setState(true);
 390       }
 391       if (alignPanel.seqPanel.seqCanvas.fr != null)
 392       {
 393         // update the min/max ranges where necessary
 394         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 395       }
 396       if (viewport.featureSettings != null)
 397       {
 398         viewport.featureSettings.refreshTable();
 399       }
 400       alignPanel.paintAlignment(true);
 401       statusBar.setText(MessageManager
 402               .getString("label.successfully_added_features_alignment"));
 403     }
 404     return featuresFile;
 405   }
 406
 407   @Override
 408   public void keyPressed(KeyEvent evt)
 409   {
 410     if (viewport.cursorMode
 411             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 412                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 413                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 414             && Character.isDigit(evt.getKeyChar()))
 415     {
 416       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 417     }
 418
 419     switch (evt.getKeyCode())
 420     {
 421     case 27: // escape key
 422       deselectAllSequenceMenuItem_actionPerformed();
 423
 424       alignPanel.alabels.cancelDrag();
 425       break;
 426     case KeyEvent.VK_X:
 427       if (evt.isControlDown() || evt.isMetaDown())
 428       {
 429         cut_actionPerformed();
 430       }
 431       break;
 432     case KeyEvent.VK_C:
 433       if (viewport.cursorMode && !evt.isControlDown())
 434       {
 435         alignPanel.seqPanel.setCursorColumn();
 436       }
 437       if (evt.isControlDown() || evt.isMetaDown())
 438       {
 439         copy_actionPerformed();
 440       }
 441       break;
 442     case KeyEvent.VK_V:
 443       if (evt.isControlDown())
 444       {
 445         paste(evt.isShiftDown());
 446       }
 447       break;
 448     case KeyEvent.VK_A:
 449       if (evt.isControlDown() || evt.isMetaDown())
 450       {
 451         selectAllSequenceMenuItem_actionPerformed();
 452       }
 453       break;
 454     case KeyEvent.VK_DOWN:
 455       if (viewport.cursorMode)
 456       {
 457         alignPanel.seqPanel.moveCursor(0, 1);
 458       }
 459       else
 460       {
 461         moveSelectedSequences(false);
 462       }
 463       break;
 464
 465     case KeyEvent.VK_UP:
 466       if (viewport.cursorMode)
 467       {
 468         alignPanel.seqPanel.moveCursor(0, -1);
 469       }
 470       else
 471       {
 472         moveSelectedSequences(true);
 473       }
 474       break;
 475
 476     case KeyEvent.VK_LEFT:
 477       if (evt.isAltDown() || !viewport.cursorMode)
 478       {
 479         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 480       }
 481       else
 482       {
 483         alignPanel.seqPanel.moveCursor(-1, 0);
 484       }
 485       break;
 486
 487     case KeyEvent.VK_RIGHT:
 488       if (evt.isAltDown() || !viewport.cursorMode)
 489       {
 490         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 491       }
 492       else
 493       {
 494         alignPanel.seqPanel.moveCursor(1, 0);
 495       }
 496       break;
 497
 498     case KeyEvent.VK_SPACE:
 499       if (viewport.cursorMode)
 500       {
 501         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 502                 || evt.isShiftDown() || evt.isAltDown());
 503       }
 504       break;
 505
 506     case KeyEvent.VK_DELETE:
 507     case KeyEvent.VK_BACK_SPACE:
 508       if (viewport.cursorMode)
 509       {
 510         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 511                 || evt.isShiftDown() || evt.isAltDown());
 512       }
 513       else
 514       {
 515         cut_actionPerformed();
 516         alignPanel.seqPanel.seqCanvas.repaint();
 517       }
 518       break;
 519
 520     case KeyEvent.VK_S:
 521       if (viewport.cursorMode)
 522       {
 523         alignPanel.seqPanel.setCursorRow();
 524       }
 525       break;
 526     case KeyEvent.VK_P:
 527       if (viewport.cursorMode)
 528       {
 529         alignPanel.seqPanel.setCursorPosition();
 530       }
 531       break;
 532
 533     case KeyEvent.VK_ENTER:
 534     case KeyEvent.VK_COMMA:
 535       if (viewport.cursorMode)
 536       {
 537         alignPanel.seqPanel.setCursorRowAndColumn();
 538       }
 539       break;
 540
 541     case KeyEvent.VK_Q:
 542       if (viewport.cursorMode)
 543       {
 544         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 545       }
 546       break;
 547     case KeyEvent.VK_M:
 548       if (viewport.cursorMode)
 549       {
 550         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 551       }
 552       break;
 553
 554     case KeyEvent.VK_F2:
 555       viewport.cursorMode = !viewport.cursorMode;
 556       statusBar.setText(MessageManager.formatMessage(
 557               "label.keyboard_editing_mode",
 558               new String[] { (viewport.cursorMode ? "on" : "off") }));
 559       if (viewport.cursorMode)
 560       {
 561         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 562         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 563       }
 564       break;
 565
 566     case KeyEvent.VK_F:
 567       if (evt.isControlDown())
 568       {
 569         findMenuItem_actionPerformed();
 570       }
 571       break;
 572
 573     case KeyEvent.VK_H:
 574     {
 575       boolean toggleSeqs = !evt.isControlDown();
 576       boolean toggleCols = !evt.isShiftDown();
 577       toggleHiddenRegions(toggleSeqs, toggleCols);
 578       break;
 579     }
 580
 581     case KeyEvent.VK_PAGE_UP:
 582       if (viewport.getWrapAlignment())
 583       {
 584         alignPanel.scrollUp(true);
 585       }
 586       else
 587       {
 588         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 589                 - viewport.endSeq + viewport.startSeq);
 590       }
 591       break;
 592
 593     case KeyEvent.VK_PAGE_DOWN:
 594       if (viewport.getWrapAlignment())
 595       {
 596         alignPanel.scrollUp(false);
 597       }
 598       else
 599       {
 600         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 601                 + viewport.endSeq - viewport.startSeq);
 602       }
 603       break;
 604
 605     case KeyEvent.VK_Z:
 606       if (evt.isControlDown())
 607       {
 608         undoMenuItem_actionPerformed();
 609       }
 610       break;
 611
 612     case KeyEvent.VK_Y:
 613       if (evt.isControlDown())
 614       {
 615         redoMenuItem_actionPerformed();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_L:
 620       if (evt.isControlDown())
 621       {
 622         trimAlignment(true);
 623       }
 624       break;
 625
 626     case KeyEvent.VK_R:
 627       if (evt.isControlDown())
 628       {
 629         trimAlignment(false);
 630       }
 631       break;
 632
 633     case KeyEvent.VK_E:
 634       if (evt.isControlDown())
 635       {
 636         if (evt.isShiftDown())
 637         {
 638           this.removeAllGapsMenuItem_actionPerformed();
 639         }
 640         else
 641         {
 642           removeGappedColumnMenuItem_actionPerformed();
 643         }
 644       }
 645       break;
 646     case KeyEvent.VK_I:
 647       if (evt.isControlDown())
 648       {
 649         if (evt.isAltDown())
 650         {
 651           invertColSel_actionPerformed();
 652         }
 653         else
 654         {
 655           invertSequenceMenuItem_actionPerformed();
 656         }
 657       }
 658       break;
 659
 660     case KeyEvent.VK_G:
 661       if (evt.isControlDown())
 662       {
 663         if (evt.isShiftDown())
 664         {
 665           this.unGroup_actionPerformed();
 666         }
 667         else
 668         {
 669           this.createGroup_actionPerformed();
 670         }
 671       }
 672       break;
 673
 674     case KeyEvent.VK_U:
 675       if (evt.isControlDown())
 676       {
 677         this.deleteGroups_actionPerformed();
 678       }
 679       break;
 680
 681     case KeyEvent.VK_T:
 682       if (evt.isControlDown())
 683       {
 684         newView(null);
 685       }
 686       break;
 687
 688     }
 689     alignPanel.paintAlignment(true);
 690   }
 691
 692   /**
 693    * called by key handler and the hide all/show all menu items
 694    *
 695    * @param toggleSeqs
 696    * @param toggleCols
 697    */
 698   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 699   {
 700     boolean hide = false;
 701     SequenceGroup sg = viewport.getSelectionGroup();
 702     if (!toggleSeqs && !toggleCols)
 703     {
 704       // Hide everything by the current selection - this is a hack - we do the
 705       // invert and then hide
 706       // first check that there will be visible columns after the invert.
 707       if ((viewport.getColumnSelection() != null
 708               && viewport.getColumnSelection().getSelected() != null && viewport
 709               .getColumnSelection().getSelected().size() > 0)
 710               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 711                       .getEndRes()))
 712       {
 713         // now invert the sequence set, if required - empty selection implies
 714         // that no hiding is required.
 715         if (sg != null)
 716         {
 717           invertSequenceMenuItem_actionPerformed();
 718           sg = viewport.getSelectionGroup();
 719           toggleSeqs = true;
 720
 721         }
 722         viewport.expandColSelection(sg, true);
 723         // finally invert the column selection and get the new sequence
 724         // selection and indicate it should be hidden.
 725         invertColSel_actionPerformed();
 726         toggleCols = true;
 727       }
 728     }
 729
 730     if (toggleSeqs)
 731     {
 732       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 733       {
 734         hide = true;
 735         viewport.hideAllSelectedSeqs();
 736       }
 737       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 738               .size() > 0))
 739       {
 740         viewport.showAllHiddenSeqs();
 741       }
 742     }
 743
 744     if (toggleCols)
 745     {
 746       if (viewport.getColumnSelection().getSelected().size() > 0)
 747       {
 748         viewport.hideSelectedColumns();
 749         if (!toggleSeqs)
 750         {
 751           viewport.setSelectionGroup(sg);
 752         }
 753       }
 754       else if (!hide)
 755       {
 756         viewport.showAllHiddenColumns();
 757       }
 758       viewport.sendSelection();
 759     }
 760   }
 761
 762   @Override
 763   public void keyReleased(KeyEvent evt)
 764   {
 765   }
 766
 767   @Override
 768   public void keyTyped(KeyEvent evt)
 769   {
 770   }
 771
 772   @Override
 773   public void itemStateChanged(ItemEvent evt)
 774   {
 775     final Object source = evt.getSource();
 776     if (source == displayNonconservedMenuItem)
 777     {
 778       displayNonconservedMenuItem_actionPerformed();
 779     }
 780     else if (source == colourTextMenuItem)
 781     {
 782       colourTextMenuItem_actionPerformed();
 783     }
 784     else if (source == wrapMenuItem)
 785     {
 786       wrapMenuItem_actionPerformed();
 787     }
 788     else if (source == scaleAbove)
 789     {
 790       viewport.setScaleAboveWrapped(scaleAbove.getState());
 791     }
 792     else if (source == scaleLeft)
 793     {
 794       viewport.setScaleLeftWrapped(scaleLeft.getState());
 795     }
 796     else if (source == scaleRight)
 797     {
 798       viewport.setScaleRightWrapped(scaleRight.getState());
 799     }
 800     else if (source == seqLimits)
 801     {
 802       seqLimits_itemStateChanged();
 803     }
 804     else if (source == viewBoxesMenuItem)
 805     {
 806       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 807     }
 808     else if (source == viewTextMenuItem)
 809     {
 810       viewport.setShowText(viewTextMenuItem.getState());
 811     }
 812     else if (source == renderGapsMenuItem)
 813     {
 814       viewport.setRenderGaps(renderGapsMenuItem.getState());
 815     }
 816     else if (source == annotationPanelMenuItem)
 817     {
 818       boolean showAnnotations = annotationPanelMenuItem.getState();
 819       showAlignmentAnnotations.setEnabled(showAnnotations);
 820       showSequenceAnnotations.setEnabled(showAnnotations);
 821       viewport.setShowAnnotation(showAnnotations);
 822       alignPanel.setAnnotationVisible(showAnnotations);
 823     }
 824     else if (source == sequenceFeatures)
 825     {
 826       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 827       alignPanel.seqPanel.seqCanvas.repaint();
 828     }
 829     else if (source == showAlignmentAnnotations)
 830     {
 831       setAnnotationsVisibility();
 832     }
 833     else if (source == showSequenceAnnotations)
 834     {
 835       setAnnotationsVisibility();
 836     }
 837     else if (source == sortAnnBySequence)
 838     {
 839       boolean newState = sortAnnBySequence.getState();
 840       sortAnnByLabel.setState(false);
 841       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 842               : SequenceAnnotationOrder.NONE);
 843       setViewportAnnotationOrder();
 844     }
 845     else if (source == sortAnnByLabel)
 846     {
 847       boolean newState = sortAnnByLabel.getState();
 848       sortAnnBySequence.setState(false);
 849       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 850               : SequenceAnnotationOrder.NONE);
 851       setViewportAnnotationOrder();
 852     }
 853     else if (source == showAutoFirst)
 854     {
 855       showAutoLast.setState(!showAutoFirst.getState());
 856       setShowAutoCalculatedAbove(showAutoFirst.getState());
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == showAutoLast)
 860     {
 861       showAutoFirst.setState(!showAutoLast.getState());
 862       setShowAutoCalculatedAbove(showAutoFirst.getState());
 863       setViewportAnnotationOrder();
 864     }
 865     else if (source == conservationMenuItem)
 866     {
 867       conservationMenuItem_actionPerformed();
 868     }
 869     else if (source == abovePIDThreshold)
 870     {
 871       abovePIDThreshold_actionPerformed();
 872     }
 873     else if (source == applyToAllGroups)
 874     {
 875       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 876     }
 877     else if (source == autoCalculate)
 878     {
 879       viewport.autoCalculateConsensus = autoCalculate.getState();
 880     }
 881     else if (source == sortByTree)
 882     {
 883       viewport.sortByTree = sortByTree.getState();
 884     }
 885     else if (source == this.centreColumnLabelFlag)
 886     {
 887       centreColumnLabelFlag_stateChanged();
 888     }
 889     else if (source == this.followMouseOverFlag)
 890     {
 891       mouseOverFlag_stateChanged();
 892     }
 893     else if (source == showGroupConsensus)
 894     {
 895       showGroupConsensus_actionPerformed();
 896     }
 897     else if (source == showGroupConservation)
 898     {
 899       showGroupConservation_actionPerformed();
 900     }
 901     else if (source == showSequenceLogo)
 902     {
 903       showSequenceLogo_actionPerformed();
 904     }
 905     else if (source == normSequenceLogo)
 906     {
 907       normSequenceLogo_actionPerformed();
 908     }
 909     else if (source == showConsensusHistogram)
 910     {
 911       showConsensusHistogram_actionPerformed();
 912     }
 913     else if (source == applyAutoAnnotationSettings)
 914     {
 915       applyAutoAnnotationSettings_actionPerformed();
 916     }
 917     alignPanel.paintAlignment(true);
 918   }
 919
 920   /**
 921    * Set the visibility state of sequence-related and/or alignment-related
 922    * annotations depending on checkbox selections, and repaint.
 923    *
 924    * @param visible
 925    */
 926   private void setAnnotationsVisibility()
 927   {
 928     boolean showForAlignment = showAlignmentAnnotations.getState();
 929     boolean showForSequences = showSequenceAnnotations.getState();
 930     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 931     {
 932       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 933             .getAlignmentAnnotation())
 934     {
 935       boolean visible = (aa.sequenceRef == null ? showForAlignment
 936               : showForSequences);
 937       aa.visible = visible;
 938       }
 939     }
 940     alignPanel.validateAnnotationDimensions(true);
 941     validate();
 942     repaint();
 943   }
 944
 945   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 946   {
 947     this.annotationSortOrder = order;
 948   }
 949
 950   /**
 951    * Set flags on the viewport that control annotation ordering
 952    */
 953   private void setViewportAnnotationOrder()
 954   {
 955     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 956     this.alignPanel.av
 957             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 958   }
 959
 960   private void setShowAutoCalculatedAbove(boolean showAbove)
 961   {
 962     this.showAutoCalculatedAbove = showAbove;
 963   }
 964
 965   private void mouseOverFlag_stateChanged()
 966   {
 967     viewport.setFollowHighlight(followMouseOverFlag.getState());
 968     // TODO: could kick the scrollTo mechanism to reset view for current
 969     // searchresults.
 970   }
 971
 972   private void centreColumnLabelFlag_stateChanged()
 973   {
 974     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 975     this.alignPanel.annotationPanel.repaint();
 976   }
 977
 978   @Override
 979   public void actionPerformed(ActionEvent evt)
 980   {
 981     viewport.applet.currentAlignFrame = this;
 982
 983     Object source = evt.getSource();
 984
 985     if (source == inputText)
 986     {
 987       inputText_actionPerformed();
 988     }
 989     else if (source == loadTree)
 990     {
 991       loadTree_actionPerformed();
 992     }
 993     else if (source == loadApplication)
 994     {
 995       launchFullApplication();
 996     }
 997     else if (source == loadAnnotations)
 998     {
 999       loadAnnotations();
1000     }
1001     else if (source == outputAnnotations)
1002     {
1003       outputAnnotations(true);
1004     }
1005     else if (source == outputFeatures)
1006     {
1007       outputFeatures(true, "Jalview");
1008     }
1009     else if (source == closeMenuItem)
1010     {
1011       closeMenuItem_actionPerformed();
1012     }
1013     else if (source == copy)
1014     {
1015       copy_actionPerformed();
1016     }
1017     else if (source == undoMenuItem)
1018     {
1019       undoMenuItem_actionPerformed();
1020     }
1021     else if (source == redoMenuItem)
1022     {
1023       redoMenuItem_actionPerformed();
1024     }
1025     else if (source == inputText)
1026     {
1027       inputText_actionPerformed();
1028     }
1029     else if (source == closeMenuItem)
1030     {
1031       closeMenuItem_actionPerformed();
1032     }
1033     else if (source == undoMenuItem)
1034     {
1035       undoMenuItem_actionPerformed();
1036     }
1037     else if (source == redoMenuItem)
1038     {
1039       redoMenuItem_actionPerformed();
1040     }
1041     else if (source == copy)
1042     {
1043       copy_actionPerformed();
1044     }
1045     else if (source == pasteNew)
1046     {
1047       pasteNew_actionPerformed();
1048     }
1049     else if (source == pasteThis)
1050     {
1051       pasteThis_actionPerformed();
1052     }
1053     else if (source == cut)
1054     {
1055       cut_actionPerformed();
1056     }
1057     else if (source == delete)
1058     {
1059       delete_actionPerformed();
1060     }
1061     else if (source == grpsFromSelection)
1062     {
1063       makeGrpsFromSelection_actionPerformed();
1064     }
1065     else if (source == deleteGroups)
1066     {
1067       deleteGroups_actionPerformed();
1068     }
1069     else if (source == selectAllSequenceMenuItem)
1070     {
1071       selectAllSequenceMenuItem_actionPerformed();
1072     }
1073     else if (source == deselectAllSequenceMenuItem)
1074     {
1075       deselectAllSequenceMenuItem_actionPerformed();
1076     }
1077     else if (source == invertSequenceMenuItem)
1078     {
1079       invertSequenceMenuItem_actionPerformed();
1080       // uncomment to slave sequence selections in split frame
1081       // viewport.sendSelection();
1082     }
1083     else if (source == invertColSel)
1084     {
1085       viewport.invertColumnSelection();
1086       alignPanel.paintAlignment(true);
1087       viewport.sendSelection();
1088     }
1089     else if (source == remove2LeftMenuItem)
1090     {
1091       trimAlignment(true);
1092     }
1093     else if (source == remove2RightMenuItem)
1094     {
1095       trimAlignment(false);
1096     }
1097     else if (source == removeGappedColumnMenuItem)
1098     {
1099       removeGappedColumnMenuItem_actionPerformed();
1100     }
1101     else if (source == removeAllGapsMenuItem)
1102     {
1103       removeAllGapsMenuItem_actionPerformed();
1104     }
1105     else if (source == findMenuItem)
1106     {
1107       findMenuItem_actionPerformed();
1108     }
1109     else if (source == font)
1110     {
1111       new FontChooser(alignPanel);
1112     }
1113     else if (source == newView)
1114     {
1115       newView(null);
1116     }
1117     else if (source == showColumns)
1118     {
1119       viewport.showAllHiddenColumns();
1120       alignPanel.paintAlignment(true);
1121       viewport.sendSelection();
1122     }
1123     else if (source == showSeqs)
1124     {
1125       viewport.showAllHiddenSeqs();
1126       alignPanel.paintAlignment(true);
1127       // uncomment if we want to slave sequence selections in split frame
1128       // viewport.sendSelection();
1129     }
1130     else if (source == hideColumns)
1131     {
1132       viewport.hideSelectedColumns();
1133       alignPanel.paintAlignment(true);
1134       viewport.sendSelection();
1135     }
1136     else if (source == hideSequences
1137             && viewport.getSelectionGroup() != null)
1138     {
1139       viewport.hideAllSelectedSeqs();
1140       alignPanel.paintAlignment(true);
1141       // uncomment if we want to slave sequence selections in split frame
1142       // viewport.sendSelection();
1143     }
1144     else if (source == hideAllButSelection)
1145     {
1146       toggleHiddenRegions(false, false);
1147       alignPanel.paintAlignment(true);
1148       viewport.sendSelection();
1149     }
1150     else if (source == hideAllSelection)
1151     {
1152       SequenceGroup sg = viewport.getSelectionGroup();
1153       viewport.expandColSelection(sg, false);
1154       viewport.hideAllSelectedSeqs();
1155       viewport.hideSelectedColumns();
1156       alignPanel.paintAlignment(true);
1157       viewport.sendSelection();
1158     }
1159     else if (source == showAllHidden)
1160     {
1161       viewport.showAllHiddenColumns();
1162       viewport.showAllHiddenSeqs();
1163       alignPanel.paintAlignment(true);
1164       viewport.sendSelection();
1165     }
1166     else if (source == showGroupConsensus)
1167     {
1168       showGroupConsensus_actionPerformed();
1169     }
1170     else if (source == showGroupConservation)
1171     {
1172       showGroupConservation_actionPerformed();
1173     }
1174     else if (source == showSequenceLogo)
1175     {
1176       showSequenceLogo_actionPerformed();
1177     }
1178     else if (source == normSequenceLogo)
1179     {
1180       normSequenceLogo_actionPerformed();
1181     }
1182     else if (source == showConsensusHistogram)
1183     {
1184       showConsensusHistogram_actionPerformed();
1185     }
1186     else if (source == applyAutoAnnotationSettings)
1187     {
1188       applyAutoAnnotationSettings_actionPerformed();
1189     }
1190     else if (source == featureSettings)
1191     {
1192       new FeatureSettings(alignPanel);
1193     }
1194     else if (source == alProperties)
1195     {
1196       StringBuffer contents = new jalview.io.AlignmentProperties(
1197               viewport.getAlignment()).formatAsString();
1198       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1199       cap.setText(contents.toString());
1200       Frame frame = new Frame();
1201       frame.add(cap);
1202       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1203               "label.alignment_properties", new String[] { getTitle() }),
1204               400, 250);
1205     }
1206     else if (source == overviewMenuItem)
1207     {
1208       overviewMenuItem_actionPerformed();
1209     }
1210     else if (source == noColourmenuItem)
1211     {
1212       changeColour(null);
1213     }
1214     else if (source == clustalColour)
1215     {
1216       abovePIDThreshold.setState(false);
1217       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1218     }
1219     else if (source == zappoColour)
1220     {
1221       changeColour(new ZappoColourScheme());
1222     }
1223     else if (source == taylorColour)
1224     {
1225       changeColour(new TaylorColourScheme());
1226     }
1227     else if (source == hydrophobicityColour)
1228     {
1229       changeColour(new HydrophobicColourScheme());
1230     }
1231     else if (source == helixColour)
1232     {
1233       changeColour(new HelixColourScheme());
1234     }
1235     else if (source == strandColour)
1236     {
1237       changeColour(new StrandColourScheme());
1238     }
1239     else if (source == turnColour)
1240     {
1241       changeColour(new TurnColourScheme());
1242     }
1243     else if (source == buriedColour)
1244     {
1245       changeColour(new BuriedColourScheme());
1246     }
1247     else if (source == nucleotideColour)
1248     {
1249       changeColour(new NucleotideColourScheme());
1250     }
1251     else if (source == purinePyrimidineColour)
1252     {
1253       changeColour(new PurinePyrimidineColourScheme());
1254     }
1255     // else if (source == RNAInteractionColour)
1256     // {
1257     // changeColour(new RNAInteractionColourScheme());
1258     // }
1259     else if (source == RNAHelixColour)
1260     {
1261       new RNAHelicesColourChooser(viewport, alignPanel);
1262     }
1263     else if (source == modifyPID)
1264     {
1265       modifyPID_actionPerformed();
1266     }
1267     else if (source == modifyConservation)
1268     {
1269       modifyConservation_actionPerformed();
1270     }
1271     else if (source == userDefinedColour)
1272     {
1273       new UserDefinedColours(alignPanel, null);
1274     }
1275     else if (source == PIDColour)
1276     {
1277       changeColour(new PIDColourScheme());
1278     }
1279     else if (source == BLOSUM62Colour)
1280     {
1281       changeColour(new Blosum62ColourScheme());
1282     }
1283     else if (source == tcoffeeColour)
1284     {
1285       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1286     }
1287     else if (source == annotationColour)
1288     {
1289       new AnnotationColourChooser(viewport, alignPanel);
1290     }
1291     else if (source == annotationColumnSelection)
1292     {
1293       new AnnotationColumnChooser(viewport, alignPanel);
1294     }
1295     else if (source == sortPairwiseMenuItem)
1296     {
1297       sortPairwiseMenuItem_actionPerformed();
1298     }
1299     else if (source == sortIDMenuItem)
1300     {
1301       sortIDMenuItem_actionPerformed();
1302     }
1303     else if (source == sortLengthMenuItem)
1304     {
1305       sortLengthMenuItem_actionPerformed();
1306     }
1307     else if (source == sortGroupMenuItem)
1308     {
1309       sortGroupMenuItem_actionPerformed();
1310     }
1311     else if (source == removeRedundancyMenuItem)
1312     {
1313       removeRedundancyMenuItem_actionPerformed();
1314     }
1315     else if (source == pairwiseAlignmentMenuItem)
1316     {
1317       pairwiseAlignmentMenuItem_actionPerformed();
1318     }
1319     else if (source == PCAMenuItem)
1320     {
1321       PCAMenuItem_actionPerformed();
1322     }
1323     else if (source == averageDistanceTreeMenuItem)
1324     {
1325       averageDistanceTreeMenuItem_actionPerformed();
1326     }
1327     else if (source == neighbourTreeMenuItem)
1328     {
1329       neighbourTreeMenuItem_actionPerformed();
1330     }
1331     else if (source == njTreeBlosumMenuItem)
1332     {
1333       njTreeBlosumMenuItem_actionPerformed();
1334     }
1335     else if (source == avDistanceTreeBlosumMenuItem)
1336     {
1337       avTreeBlosumMenuItem_actionPerformed();
1338     }
1339     else if (source == documentation)
1340     {
1341       documentation_actionPerformed();
1342     }
1343     else if (source == about)
1344     {
1345       about_actionPerformed();
1346     }
1347
1348   }
1349
1350   public void inputText_actionPerformed()
1351   {
1352     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353     Frame frame = new Frame();
1354     frame.add(cap);
1355     jalview.bin.JalviewLite.addFrame(frame,
1356             MessageManager.getString("label.input_cut_paste"), 500, 500);
1357   }
1358
1359   protected void outputText_actionPerformed(ActionEvent e)
1360   {
1361     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1362     Frame frame = new Frame();
1363     frame.add(cap);
1364     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1365             "label.alignment_output_command",
1366             new Object[] { e.getActionCommand() }), 600, 500);
1367
1368     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1369     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1370             e.getActionCommand(), viewport.getAlignment(),
1371             viewport.getShowJVSuffix()));
1372   }
1373
1374   public void loadAnnotations()
1375   {
1376     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377     cap.setText(MessageManager
1378             .getString("label.paste_features_annotations_Tcoffee_here"));
1379     cap.setAnnotationImport();
1380     Frame frame = new Frame();
1381     frame.add(cap);
1382     jalview.bin.JalviewLite.addFrame(frame,
1383             MessageManager.getString("action.paste_annotations"), 400, 300);
1384
1385   }
1386
1387   public String outputAnnotations(boolean displayTextbox)
1388   {
1389     String annotation = new AnnotationFile()
1390             .printAnnotationsForView(viewport);
1391
1392     if (displayTextbox)
1393     {
1394       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1395       Frame frame = new Frame();
1396       frame.add(cap);
1397       jalview.bin.JalviewLite.addFrame(frame,
1398               MessageManager.getString("label.annotations"), 600, 500);
1399       cap.setText(annotation);
1400     }
1401
1402     return annotation;
1403   }
1404
1405   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1406   {
1407     if (alignPanel.getFeatureRenderer() != null
1408             && viewport.getFeaturesDisplayed() != null)
1409     {
1410       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1411
1412     }
1413     return null;
1414   }
1415
1416   public String outputFeatures(boolean displayTextbox, String format)
1417   {
1418     String features;
1419     FeaturesFile formatter = new FeaturesFile();
1420     if (format.equalsIgnoreCase("Jalview"))
1421     {
1422       features = formatter.printJalviewFormat(viewport
1423               .getAlignment().getSequencesArray(),
1424               getDisplayedFeatureCols());
1425     }
1426     else
1427     {
1428       features = formatter.printGffFormat(viewport.getAlignment()
1429               .getSequencesArray(), getDisplayedFeatureCols());
1430     }
1431
1432     if (displayTextbox)
1433     {
1434       boolean frimport = false;
1435       if (features == null || features.equals("No Features Visible"))
1436       {
1437         features = "# No features visible - paste some and import them here.";
1438         frimport = true;
1439       }
1440
1441       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1442       if (frimport)
1443       {
1444         cap.setAnnotationImport();
1445       }
1446       Frame frame = new Frame();
1447       frame.add(cap);
1448       jalview.bin.JalviewLite.addFrame(frame,
1449               MessageManager.getString("label.features"), 600, 500);
1450       cap.setText(features);
1451     }
1452     else
1453     {
1454       if (features == null)
1455       {
1456         features = "";
1457       }
1458     }
1459
1460     return features;
1461   }
1462
1463   void launchFullApplication()
1464   {
1465     StringBuffer url = new StringBuffer(jalviewServletURL);
1466
1467     // allow servlet parameters to be passed in applet parameter
1468     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1469             : "?";
1470     url.append(firstSep);
1471
1472     url.append("open="
1473             + appendProtocol(viewport.applet.getParameter("file")));
1474
1475     if (viewport.applet.getParameter("features") != null)
1476     {
1477       url.append("&features=");
1478       url.append(appendProtocol(viewport.applet.getParameter("features")));
1479     }
1480
1481     if (viewport.applet.getParameter("annotations") != null)
1482     {
1483       url.append("&annotations=");
1484       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1485     }
1486
1487     if (viewport.applet.getParameter("jnetfile") != null)
1488     {
1489       url.append("&annotations=");
1490       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1491     }
1492
1493     if (viewport.applet.getParameter("defaultColour") != null)
1494     {
1495       url.append("&colour="
1496               + removeWhiteSpace(viewport.applet
1497                       .getParameter("defaultColour")));
1498     }
1499
1500     if (viewport.applet.getParameter("userDefinedColour") != null)
1501     {
1502       url.append("&colour="
1503               + removeWhiteSpace(viewport.applet
1504                       .getParameter("userDefinedColour")));
1505     }
1506     if (viewport.applet.getParameter("tree") != null)
1507     {
1508       url.append("&tree="
1509               + appendProtocol(viewport.applet.getParameter("tree")));
1510     }
1511     if (viewport.applet.getParameter("treeFile") != null)
1512     {
1513       url.append("&tree="
1514               + appendProtocol(viewport.applet.getParameter("treeFile")));
1515     }
1516
1517     showURL(url.toString(), "FULL_APP");
1518   }
1519
1520   String removeWhiteSpace(String colour)
1521   {
1522     StringBuffer sb = new StringBuffer();
1523     for (int i = 0; i < colour.length(); i++)
1524     {
1525       if (Character.isWhitespace(colour.charAt(i)))
1526       {
1527         sb.append("%20");
1528       }
1529       else
1530       {
1531         sb.append(colour.charAt(i));
1532       }
1533     }
1534
1535     return sb.toString();
1536   }
1537
1538   String appendProtocol(String url)
1539   {
1540     try
1541     {
1542       new URL(url);
1543       url = URLEncoder.encode(url);
1544     }
1545     /*
1546      * When we finally deprecate 1.1 compatibility, we can start to use
1547      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1548      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1549      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1550      * ex.printStackTrace(); }
1551      */
1552     catch (java.net.MalformedURLException ex)
1553     {
1554       url = viewport.applet.getCodeBase() + url;
1555     }
1556     return url;
1557   }
1558
1559   public void closeMenuItem_actionPerformed()
1560   {
1561     PaintRefresher.RemoveComponent(alignPanel);
1562     if (alignPanel.seqPanel != null
1563             && alignPanel.seqPanel.seqCanvas != null)
1564     {
1565       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1566     }
1567     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1568     {
1569       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1570     }
1571
1572     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1573     {
1574       System.exit(0);
1575     }
1576     else
1577     {
1578     }
1579     viewport = null;
1580     alignPanel = null;
1581     this.dispose();
1582   }
1583
1584   /**
1585    * TODO: JAL-1104
1586    */
1587   void updateEditMenuBar()
1588   {
1589
1590     if (viewport.getHistoryList().size() > 0)
1591     {
1592       undoMenuItem.setEnabled(true);
1593       CommandI command = viewport.getHistoryList().peek();
1594       undoMenuItem.setLabel(MessageManager.formatMessage(
1595               "label.undo_command",
1596               new Object[] { command.getDescription() }));
1597     }
1598     else
1599     {
1600       undoMenuItem.setEnabled(false);
1601       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1602     }
1603
1604     if (viewport.getRedoList().size() > 0)
1605     {
1606       redoMenuItem.setEnabled(true);
1607
1608       CommandI command = viewport.getRedoList().peek();
1609       redoMenuItem.setLabel(MessageManager.formatMessage(
1610               "label.redo_command",
1611               new Object[] { command.getDescription() }));
1612     }
1613     else
1614     {
1615       redoMenuItem.setEnabled(false);
1616       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1617     }
1618   }
1619
1620   /**
1621    * TODO: JAL-1104
1622    */
1623   @Override
1624   public void addHistoryItem(CommandI command)
1625   {
1626     if (command.getSize() > 0)
1627     {
1628       viewport.addToHistoryList(command);
1629       viewport.clearRedoList();
1630       updateEditMenuBar();
1631       viewport.updateHiddenColumns();
1632     }
1633   }
1634
1635   /**
1636    * TODO: JAL-1104 DOCUMENT ME!
1637    *
1638    * @param e
1639    *          DOCUMENT ME!
1640    */
1641   protected void undoMenuItem_actionPerformed()
1642   {
1643     if (viewport.getHistoryList().isEmpty())
1644     {
1645       return;
1646     }
1647
1648     CommandI command = viewport.getHistoryList().pop();
1649     viewport.addToRedoList(command);
1650     command.undoCommand(null);
1651
1652     AlignmentViewport originalSource = getOriginatingSource(command);
1653     // JBPNote Test
1654     if (originalSource != viewport)
1655     {
1656       System.err
1657               .println("Warning: Viewport object mismatch whilst undoing");
1658     }
1659     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1660                                           // viewport.getColumnSelection().getHiddenColumns()
1661                                           // != null;
1662     updateEditMenuBar();
1663     originalSource.firePropertyChange("alignment", null, originalSource
1664             .getAlignment().getSequences());
1665   }
1666
1667   /**
1668    * TODO: JAL-1104 DOCUMENT ME!
1669    *
1670    * @param e
1671    *          DOCUMENT ME!
1672    */
1673   protected void redoMenuItem_actionPerformed()
1674   {
1675     if (viewport.getRedoList().isEmpty())
1676     {
1677       return;
1678     }
1679
1680     CommandI command = viewport.getRedoList().pop();
1681     viewport.addToHistoryList(command);
1682     command.doCommand(null);
1683
1684     AlignmentViewport originalSource = getOriginatingSource(command);
1685     // JBPNote Test
1686     if (originalSource != viewport)
1687     {
1688       System.err
1689               .println("Warning: Viewport object mismatch whilst re-doing");
1690     }
1691     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1692                                           // viewport.getColumnSelection().getHiddenColumns()
1693                                           // != null;
1694
1695     updateEditMenuBar();
1696     originalSource.firePropertyChange("alignment", null, originalSource
1697             .getAlignment().getSequences());
1698   }
1699
1700   AlignmentViewport getOriginatingSource(CommandI command)
1701   {
1702     AlignmentViewport originalSource = null;
1703     // For sequence removal and addition, we need to fire
1704     // the property change event FROM the viewport where the
1705     // original alignment was altered
1706     AlignmentI al = null;
1707     if (command instanceof EditCommand)
1708     {
1709       EditCommand editCommand = (EditCommand) command;
1710       al = editCommand.getAlignment();
1711       Vector comps = (Vector) PaintRefresher.components.get(viewport
1712               .getSequenceSetId());
1713       for (int i = 0; i < comps.size(); i++)
1714       {
1715         if (comps.elementAt(i) instanceof AlignmentPanel)
1716         {
1717           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1718           {
1719             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1720             break;
1721           }
1722         }
1723       }
1724     }
1725
1726     if (originalSource == null)
1727     {
1728       // The original view is closed, we must validate
1729       // the current view against the closed view first
1730       if (al != null)
1731       {
1732         PaintRefresher.validateSequences(al, viewport.getAlignment());
1733       }
1734
1735       originalSource = viewport;
1736     }
1737
1738     return originalSource;
1739   }
1740
1741   /**
1742    * Move the currently selected sequences up or down one position in the
1743    * alignment
1744    *
1745    * @param up
1746    */
1747   public void moveSelectedSequences(boolean up)
1748   {
1749     SequenceGroup sg = viewport.getSelectionGroup();
1750     if (sg == null)
1751     {
1752       return;
1753     }
1754     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1755             up ? null : viewport.getHiddenRepSequences(), up);
1756     alignPanel.paintAlignment(true);
1757
1758     /*
1759      * Also move cDNA/protein complement sequences
1760      */
1761     AlignViewportI complement = viewport.getCodingComplement();
1762     if (complement != null)
1763     {
1764       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1765               viewport, complement);
1766       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1767               up ? null : complement.getHiddenRepSequences(), up);
1768       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1769     }
1770   }
1771
1772   synchronized void slideSequences(boolean right, int size)
1773   {
1774     List<SequenceI> sg = new Vector<SequenceI>();
1775     if (viewport.cursorMode)
1776     {
1777       sg.add(viewport.getAlignment().getSequenceAt(
1778               alignPanel.seqPanel.seqCanvas.cursorY));
1779     }
1780     else if (viewport.getSelectionGroup() != null
1781             && viewport.getSelectionGroup().getSize() != viewport
1782                     .getAlignment().getHeight())
1783     {
1784       sg = viewport.getSelectionGroup().getSequences(
1785               viewport.getHiddenRepSequences());
1786     }
1787
1788     if (sg.size() < 1)
1789     {
1790       return;
1791     }
1792
1793     Vector<SequenceI> invertGroup = new Vector();
1794
1795     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1796     {
1797       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1798       {
1799         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1800       }
1801     }
1802
1803     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1804
1805     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1806             .size()]);
1807     for (int i = 0; i < invertGroup.size(); i++)
1808     {
1809       seqs2[i] = invertGroup.elementAt(i);
1810     }
1811
1812     SlideSequencesCommand ssc;
1813     if (right)
1814     {
1815       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1816               size, viewport.getGapCharacter());
1817     }
1818     else
1819     {
1820       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1821               size, viewport.getGapCharacter());
1822     }
1823
1824     int groupAdjustment = 0;
1825     if (ssc.getGapsInsertedBegin() && right)
1826     {
1827       if (viewport.cursorMode)
1828       {
1829         alignPanel.seqPanel.moveCursor(size, 0);
1830       }
1831       else
1832       {
1833         groupAdjustment = size;
1834       }
1835     }
1836     else if (!ssc.getGapsInsertedBegin() && !right)
1837     {
1838       if (viewport.cursorMode)
1839       {
1840         alignPanel.seqPanel.moveCursor(-size, 0);
1841       }
1842       else
1843       {
1844         groupAdjustment = -size;
1845       }
1846     }
1847
1848     if (groupAdjustment != 0)
1849     {
1850       viewport.getSelectionGroup().setStartRes(
1851               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1852       viewport.getSelectionGroup().setEndRes(
1853               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1854     }
1855
1856     boolean appendHistoryItem = false;
1857     Deque<CommandI> historyList = viewport.getHistoryList();
1858     if (historyList != null && historyList.size() > 0
1859             && historyList.peek() instanceof SlideSequencesCommand)
1860     {
1861       appendHistoryItem = ssc
1862               .appendSlideCommand((SlideSequencesCommand) historyList
1863                       .peek());
1864     }
1865
1866     if (!appendHistoryItem)
1867     {
1868       addHistoryItem(ssc);
1869     }
1870
1871     repaint();
1872   }
1873
1874   static StringBuffer copiedSequences;
1875
1876   static Vector copiedHiddenColumns;
1877
1878   protected void copy_actionPerformed()
1879   {
1880     if (viewport.getSelectionGroup() == null)
1881     {
1882       return;
1883     }
1884
1885     SequenceGroup sg = viewport.getSelectionGroup();
1886     copiedSequences = new StringBuffer();
1887     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1888     for (int i = 0; i < sg.getSize(); i++)
1889     {
1890       SequenceI seq = sg.getSequenceAt(i);
1891       int index = viewport.getAlignment().findIndex(seq);
1892       orderedSeqs.put(index, seq);
1893     }
1894
1895     int index = 0, startRes, endRes;
1896     char ch;
1897
1898     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1899     {
1900       copiedHiddenColumns = new Vector();
1901       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1902       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1903       {
1904         copiedHiddenColumns.addElement(new int[] {
1905             region[0] - hiddenOffset, region[1] - hiddenOffset });
1906       }
1907     }
1908     else
1909     {
1910       copiedHiddenColumns = null;
1911     }
1912
1913     for (int i = 0; i < sg.getSize(); i++)
1914     {
1915       SequenceI seq = null;
1916
1917       while (seq == null)
1918       {
1919         if (orderedSeqs.containsKey(index))
1920         {
1921           seq = orderedSeqs.get(index);
1922           index++;
1923           break;
1924         }
1925         else
1926         {
1927           index++;
1928         }
1929       }
1930
1931       // FIND START RES
1932       // Returns residue following index if gap
1933       startRes = seq.findPosition(sg.getStartRes());
1934
1935       // FIND END RES
1936       // Need to find the residue preceeding index if gap
1937       endRes = 0;
1938
1939       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1940       {
1941         ch = seq.getCharAt(j);
1942         if (!jalview.util.Comparison.isGap((ch)))
1943         {
1944           endRes++;
1945         }
1946       }
1947
1948       if (endRes > 0)
1949       {
1950         endRes += seq.getStart() - 1;
1951       }
1952
1953       copiedSequences.append(seq.getName()
1954               + "\t"
1955               + startRes
1956               + "\t"
1957               + endRes
1958               + "\t"
1959               + seq.getSequenceAsString(sg.getStartRes(),
1960                       sg.getEndRes() + 1) + "\n");
1961     }
1962
1963   }
1964
1965   protected void pasteNew_actionPerformed()
1966   {
1967     paste(true);
1968   }
1969
1970   protected void pasteThis_actionPerformed()
1971   {
1972     paste(false);
1973   }
1974
1975   void paste(boolean newAlignment)
1976   {
1977     try
1978     {
1979
1980       if (copiedSequences == null)
1981       {
1982         return;
1983       }
1984
1985       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1986       Vector seqs = new Vector();
1987       while (st.hasMoreElements())
1988       {
1989         String name = st.nextToken();
1990         int start = Integer.parseInt(st.nextToken());
1991         int end = Integer.parseInt(st.nextToken());
1992         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1993       }
1994       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1995       for (int i = 0; i < seqs.size(); i++)
1996       {
1997         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1998       }
1999
2000       if (newAlignment)
2001       {
2002         String newtitle = MessageManager
2003                 .getString("label.copied_sequences");
2004         if (getTitle().startsWith(
2005                 MessageManager.getString("label.copied_sequences")))
2006         {
2007           newtitle = getTitle();
2008         }
2009         else
2010         {
2011           newtitle = newtitle.concat(MessageManager.formatMessage(
2012                   "label.from_msname", new String[] { getTitle() }));
2013         }
2014         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2015                 viewport.applet, newtitle, false);
2016         if (copiedHiddenColumns != null)
2017         {
2018           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2019           {
2020             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2021             af.viewport.hideColumns(region[0], region[1]);
2022           }
2023         }
2024
2025         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2026                 frameHeight);
2027       }
2028       else
2029       {
2030         addSequences(newSeqs);
2031       }
2032
2033     } catch (Exception ex)
2034     {
2035     } // could be anything being pasted in here
2036
2037   }
2038
2039   void addSequences(SequenceI[] seqs)
2040   {
2041     for (int i = 0; i < seqs.length; i++)
2042     {
2043       viewport.getAlignment().addSequence(seqs[i]);
2044     }
2045
2046     // !newAlignment
2047     addHistoryItem(new EditCommand(
2048             MessageManager.getString("label.add_sequences"), Action.PASTE,
2049             seqs, 0, viewport.getAlignment().getWidth(),
2050             viewport.getAlignment()));
2051
2052     viewport.setEndSeq(viewport.getAlignment().getHeight());
2053     viewport.getAlignment().getWidth();
2054     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2055             .getSequences());
2056
2057   }
2058
2059   protected void cut_actionPerformed()
2060   {
2061     copy_actionPerformed();
2062     delete_actionPerformed();
2063   }
2064
2065   protected void delete_actionPerformed()
2066   {
2067
2068     SequenceGroup sg = viewport.getSelectionGroup();
2069     if (sg == null)
2070     {
2071       return;
2072     }
2073
2074     Vector seqs = new Vector();
2075     SequenceI seq;
2076     for (int i = 0; i < sg.getSize(); i++)
2077     {
2078       seq = sg.getSequenceAt(i);
2079       seqs.addElement(seq);
2080     }
2081
2082     /*
2083      * If the cut affects all sequences, warn, remove highlighted columns
2084      */
2085     if (sg.getSize() == viewport.getAlignment().getHeight())
2086     {
2087       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2088               .getAlignment().getWidth()) ? true : false;
2089       if (isEntireAlignWidth)
2090       {
2091         String title = MessageManager.getString("label.delete_all");
2092         Panel infoPanel = new Panel();
2093         infoPanel.setLayout(new FlowLayout());
2094         infoPanel
2095                 .add(new Label(MessageManager.getString("warn.delete_all")));
2096
2097         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2098         dialog.setMainPanel(infoPanel);
2099         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2100         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2101         dialog.setVisible(true);
2102
2103         if (!dialog.accept)
2104         {
2105           return;
2106         }
2107       }
2108       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2109               sg.getEndRes() + 1);
2110     }
2111
2112     SequenceI[] cut = new SequenceI[seqs.size()];
2113     for (int i = 0; i < seqs.size(); i++)
2114     {
2115       cut[i] = (SequenceI) seqs.elementAt(i);
2116     }
2117
2118     /*
2119      * //ADD HISTORY ITEM
2120      */
2121     addHistoryItem(new EditCommand(
2122             MessageManager.getString("label.cut_sequences"), Action.CUT,
2123             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2124             viewport.getAlignment()));
2125
2126     viewport.setSelectionGroup(null);
2127     viewport.getAlignment().deleteGroup(sg);
2128
2129     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2130             .getSequences());
2131
2132     if (viewport.getAlignment().getHeight() < 1)
2133     {
2134       this.setVisible(false);
2135     }
2136     viewport.sendSelection();
2137   }
2138
2139   /**
2140    * group consensus toggled
2141    *
2142    */
2143   protected void showGroupConsensus_actionPerformed()
2144   {
2145     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2146     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2147
2148   }
2149
2150   /**
2151    * group conservation toggled.
2152    */
2153   protected void showGroupConservation_actionPerformed()
2154   {
2155     viewport.setShowGroupConservation(showGroupConservation.getState());
2156     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157   }
2158
2159   /*
2160    * (non-Javadoc)
2161    *
2162    * @see
2163    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2164    * .event.ActionEvent)
2165    */
2166   protected void showConsensusHistogram_actionPerformed()
2167   {
2168     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2169     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170   }
2171
2172   /*
2173    * (non-Javadoc)
2174    *
2175    * @see
2176    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2177    * .event.ActionEvent)
2178    */
2179   protected void showSequenceLogo_actionPerformed()
2180   {
2181     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2182     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183   }
2184
2185   protected void normSequenceLogo_actionPerformed()
2186   {
2187     showSequenceLogo.setState(true);
2188     viewport.setShowSequenceLogo(true);
2189     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2190     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2191   }
2192
2193   protected void applyAutoAnnotationSettings_actionPerformed()
2194   {
2195     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196   }
2197
2198   protected void makeGrpsFromSelection_actionPerformed()
2199   {
2200     if (avc.makeGroupsFromSelection())
2201     {
2202       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2203       alignPanel.updateAnnotation();
2204       alignPanel.paintAlignment(true);
2205     }
2206   }
2207
2208   protected void createGroup_actionPerformed()
2209   {
2210     avc.createGroup();
2211   }
2212
2213   protected void unGroup_actionPerformed()
2214   {
2215     if (avc.unGroup())
2216     {
2217       alignPanel.alignmentChanged();
2218     }
2219   }
2220
2221   protected void deleteGroups_actionPerformed()
2222   {
2223     if (avc.deleteGroups())
2224     {
2225       alignPanel.alignmentChanged();
2226     }
2227   }
2228
2229   public void selectAllSequenceMenuItem_actionPerformed()
2230   {
2231     SequenceGroup sg = new SequenceGroup();
2232     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2233     {
2234       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2235     }
2236     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2237     viewport.setSelectionGroup(sg);
2238     alignPanel.paintAlignment(true);
2239     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2240     viewport.sendSelection();
2241   }
2242
2243   public void deselectAllSequenceMenuItem_actionPerformed()
2244   {
2245     if (viewport.cursorMode)
2246     {
2247       alignPanel.seqPanel.keyboardNo1 = null;
2248       alignPanel.seqPanel.keyboardNo2 = null;
2249     }
2250     viewport.setSelectionGroup(null);
2251     viewport.getColumnSelection().clear();
2252     viewport.setSelectionGroup(null);
2253     alignPanel.idPanel.idCanvas.searchResults = null;
2254     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2255     alignPanel.paintAlignment(true);
2256     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257     viewport.sendSelection();
2258   }
2259
2260   public void invertSequenceMenuItem_actionPerformed()
2261   {
2262     SequenceGroup sg = viewport.getSelectionGroup();
2263     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2264     {
2265       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2266     }
2267
2268     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2269     viewport.sendSelection();
2270   }
2271
2272   public void invertColSel_actionPerformed()
2273   {
2274     viewport.invertColumnSelection();
2275     alignPanel.paintAlignment(true);
2276     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277     viewport.sendSelection();
2278   }
2279
2280   void trimAlignment(boolean trimLeft)
2281   {
2282     ColumnSelection colSel = viewport.getColumnSelection();
2283     int column;
2284
2285     if (!colSel.isEmpty())
2286     {
2287       if (trimLeft)
2288       {
2289         column = colSel.getMin();
2290       }
2291       else
2292       {
2293         column = colSel.getMax();
2294       }
2295
2296       SequenceI[] seqs;
2297       if (viewport.getSelectionGroup() != null)
2298       {
2299         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2300                 viewport.getHiddenRepSequences());
2301       }
2302       else
2303       {
2304         seqs = viewport.getAlignment().getSequencesArray();
2305       }
2306
2307       TrimRegionCommand trimRegion;
2308       if (trimLeft)
2309       {
2310         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2311                 column, viewport.getAlignment());
2312         viewport.setStartRes(0);
2313       }
2314       else
2315       {
2316         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2317                 column, viewport.getAlignment());
2318       }
2319
2320       statusBar.setText(MessageManager.formatMessage(
2321               "label.removed_columns",
2322               new String[] { Integer.valueOf(trimRegion.getSize())
2323                       .toString() }));
2324       addHistoryItem(trimRegion);
2325
2326       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2327       {
2328         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2329                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2330         {
2331           viewport.getAlignment().deleteGroup(sg);
2332         }
2333       }
2334
2335       viewport.firePropertyChange("alignment", null, viewport
2336               .getAlignment().getSequences());
2337     }
2338   }
2339
2340   public void removeGappedColumnMenuItem_actionPerformed()
2341   {
2342     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2343
2344     SequenceI[] seqs;
2345     if (viewport.getSelectionGroup() != null)
2346     {
2347       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2348               viewport.getHiddenRepSequences());
2349       start = viewport.getSelectionGroup().getStartRes();
2350       end = viewport.getSelectionGroup().getEndRes();
2351     }
2352     else
2353     {
2354       seqs = viewport.getAlignment().getSequencesArray();
2355     }
2356
2357     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2358             "Remove Gapped Columns", seqs, start, end,
2359             viewport.getAlignment());
2360
2361     addHistoryItem(removeGapCols);
2362
2363     statusBar.setText(MessageManager.formatMessage(
2364             "label.removed_empty_columns",
2365             new String[] { Integer.valueOf(removeGapCols.getSize())
2366                     .toString() }));
2367
2368     // This is to maintain viewport position on first residue
2369     // of first sequence
2370     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2371     int startRes = seq.findPosition(viewport.startRes);
2372     // ShiftList shifts;
2373     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2374     // edit.alColumnChanges=shifts.getInverse();
2375     // if (viewport.hasHiddenColumns)
2376     // viewport.getColumnSelection().compensateForEdits(shifts);
2377     viewport.setStartRes(seq.findIndex(startRes) - 1);
2378     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2379             .getSequences());
2380
2381   }
2382
2383   public void removeAllGapsMenuItem_actionPerformed()
2384   {
2385     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2386
2387     SequenceI[] seqs;
2388     if (viewport.getSelectionGroup() != null)
2389     {
2390       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2391               viewport.getHiddenRepSequences());
2392       start = viewport.getSelectionGroup().getStartRes();
2393       end = viewport.getSelectionGroup().getEndRes();
2394     }
2395     else
2396     {
2397       seqs = viewport.getAlignment().getSequencesArray();
2398     }
2399
2400     // This is to maintain viewport position on first residue
2401     // of first sequence
2402     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2403     int startRes = seq.findPosition(viewport.startRes);
2404
2405     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2406             viewport.getAlignment()));
2407
2408     viewport.setStartRes(seq.findIndex(startRes) - 1);
2409
2410     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2411             .getSequences());
2412
2413   }
2414
2415   public void findMenuItem_actionPerformed()
2416   {
2417     new Finder(alignPanel);
2418   }
2419
2420   /**
2421    * create a new view derived from the current view
2422    *
2423    * @param viewtitle
2424    * @return frame for the new view
2425    */
2426   public AlignFrame newView(String viewtitle)
2427   {
2428     AlignmentI newal;
2429     if (viewport.hasHiddenRows())
2430     {
2431       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2432               .getFullAlignment().getSequencesArray());
2433     }
2434     else
2435     {
2436       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2437     }
2438
2439     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2440     {
2441       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2442       {
2443         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2444         {
2445           newal.addAnnotation(viewport.getAlignment()
2446                   .getAlignmentAnnotation()[i]);
2447         }
2448       }
2449     }
2450
2451     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2452
2453     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2454     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2455     PaintRefresher.Register(newaf.alignPanel,
2456             newaf.alignPanel.av.getSequenceSetId());
2457
2458     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2459             newaf.alignPanel.av.getSequenceSetId());
2460     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2461             newaf.alignPanel.av.getSequenceSetId());
2462
2463     Vector comps = (Vector) PaintRefresher.components.get(viewport
2464             .getSequenceSetId());
2465     int viewSize = -1;
2466     for (int i = 0; i < comps.size(); i++)
2467     {
2468       if (comps.elementAt(i) instanceof AlignmentPanel)
2469       {
2470         viewSize++;
2471       }
2472     }
2473
2474     String title = new String(this.getTitle());
2475     if (viewtitle != null)
2476     {
2477       title = viewtitle + " ( " + title + ")";
2478     }
2479     else
2480     {
2481       if (title.indexOf("(View") > -1)
2482       {
2483         title = title.substring(0, title.indexOf("(View"));
2484       }
2485       title += "(View " + viewSize + ")";
2486     }
2487
2488     newaf.setTitle(title.toString());
2489
2490     newaf.viewport.setHistoryList(viewport.getHistoryList());
2491     newaf.viewport.setRedoList(viewport.getRedoList());
2492     return newaf;
2493   }
2494
2495   /**
2496    *
2497    * @return list of feature groups on the view
2498    */
2499   public String[] getFeatureGroups()
2500   {
2501     FeatureRenderer fr = null;
2502     if (alignPanel != null
2503             && (fr = alignPanel.getFeatureRenderer()) != null)
2504     {
2505       List<String> gps = fr.getFeatureGroups();
2506       String[] _gps = gps.toArray(new String[gps.size()]);
2507       return _gps;
2508     }
2509     return null;
2510   }
2511
2512   /**
2513    * get sequence feature groups that are hidden or shown
2514    *
2515    * @param visible
2516    *          true is visible
2517    * @return list
2518    */
2519   public String[] getFeatureGroupsOfState(boolean visible)
2520   {
2521     FeatureRenderer fr = null;
2522     if (alignPanel != null
2523             && (fr = alignPanel.getFeatureRenderer()) != null)
2524     {
2525       List<String> gps = fr.getGroups(visible);
2526       String[] _gps = gps.toArray(new String[gps.size()]);
2527       return _gps;
2528     }
2529     return null;
2530   }
2531
2532   /**
2533    * Change the display state for the given feature groups
2534    *
2535    * @param groups
2536    *          list of group strings
2537    * @param state
2538    *          visible or invisible
2539    */
2540   public void setFeatureGroupState(String[] groups, boolean state)
2541   {
2542     FeatureRenderer fr = null;
2543     this.sequenceFeatures.setState(true);
2544     viewport.setShowSequenceFeatures(true);
2545     if (alignPanel != null
2546             && (fr = alignPanel.getFeatureRenderer()) != null)
2547     {
2548
2549       fr.setGroupVisibility(Arrays.asList(groups), state);
2550       alignPanel.seqPanel.seqCanvas.repaint();
2551       if (alignPanel.overviewPanel != null)
2552       {
2553         alignPanel.overviewPanel.updateOverviewImage();
2554       }
2555     }
2556   }
2557
2558   public void seqLimits_itemStateChanged()
2559   {
2560     viewport.setShowJVSuffix(seqLimits.getState());
2561     alignPanel.fontChanged();
2562     alignPanel.paintAlignment(true);
2563   }
2564
2565   protected void colourTextMenuItem_actionPerformed()
2566   {
2567     viewport.setColourText(colourTextMenuItem.getState());
2568     alignPanel.paintAlignment(true);
2569   }
2570
2571   protected void displayNonconservedMenuItem_actionPerformed()
2572   {
2573     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2574     alignPanel.paintAlignment(true);
2575   }
2576
2577   protected void wrapMenuItem_actionPerformed()
2578   {
2579     viewport.setWrapAlignment(wrapMenuItem.getState());
2580     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2581     scaleAbove.setEnabled(wrapMenuItem.getState());
2582     scaleLeft.setEnabled(wrapMenuItem.getState());
2583     scaleRight.setEnabled(wrapMenuItem.getState());
2584     alignPanel.paintAlignment(true);
2585   }
2586
2587   public void overviewMenuItem_actionPerformed()
2588   {
2589     if (alignPanel.overviewPanel != null)
2590     {
2591       return;
2592     }
2593
2594     Frame frame = new Frame();
2595     OverviewPanel overview = new OverviewPanel(alignPanel);
2596     frame.add(overview);
2597     // +50 must allow for applet frame window
2598     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2599             "label.overview_params", new String[] { this.getTitle() }),
2600             overview.getPreferredSize().width,
2601             overview.getPreferredSize().height + 50);
2602
2603     frame.pack();
2604     final AlignmentPanel ap = alignPanel;
2605     frame.addWindowListener(new WindowAdapter()
2606     {
2607       @Override
2608       public void windowClosing(WindowEvent e)
2609       {
2610         if (ap != null)
2611         {
2612           ap.setOverviewPanel(null);
2613         }
2614       };
2615     });
2616
2617     alignPanel.setOverviewPanel(overview);
2618
2619   }
2620
2621   @Override
2622   public void changeColour(ColourSchemeI cs)
2623   {
2624
2625     if (cs != null)
2626     {
2627       if (viewport.getAbovePIDThreshold())
2628       {
2629         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2630                 cs, "Background"));
2631       }
2632
2633       if (viewport.getConservationSelected())
2634       {
2635         cs.setConservationApplied(true);
2636         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2637                 cs, "Background"));
2638       }
2639       else
2640       {
2641         cs.setConservationApplied(false);
2642       }
2643     }
2644     viewport.setGlobalColourScheme(cs);
2645
2646     alignPanel.paintAlignment(true);
2647   }
2648
2649   protected void modifyPID_actionPerformed()
2650   {
2651     if (viewport.getAbovePIDThreshold()
2652             && viewport.getGlobalColourScheme() != null)
2653     {
2654       SliderPanel.setPIDSliderSource(alignPanel,
2655               viewport.getGlobalColourScheme(), "Background");
2656       SliderPanel.showPIDSlider();
2657     }
2658   }
2659
2660   protected void modifyConservation_actionPerformed()
2661   {
2662     if (viewport.getConservationSelected()
2663             && viewport.getGlobalColourScheme() != null)
2664     {
2665       SliderPanel.setConservationSlider(alignPanel,
2666               viewport.getGlobalColourScheme(), "Background");
2667       SliderPanel.showConservationSlider();
2668     }
2669   }
2670
2671   protected void conservationMenuItem_actionPerformed()
2672   {
2673     viewport.setConservationSelected(conservationMenuItem.getState());
2674
2675     viewport.setAbovePIDThreshold(false);
2676     abovePIDThreshold.setState(false);
2677
2678     changeColour(viewport.getGlobalColourScheme());
2679
2680     modifyConservation_actionPerformed();
2681   }
2682
2683   public void abovePIDThreshold_actionPerformed()
2684   {
2685     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2686
2687     conservationMenuItem.setState(false);
2688     viewport.setConservationSelected(false);
2689
2690     changeColour(viewport.getGlobalColourScheme());
2691
2692     modifyPID_actionPerformed();
2693   }
2694
2695   public void sortPairwiseMenuItem_actionPerformed()
2696   {
2697     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2698     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2699             .getAlignment().getSequenceAt(0), null);
2700
2701     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2702             viewport.getAlignment()));
2703     alignPanel.paintAlignment(true);
2704   }
2705
2706   public void sortIDMenuItem_actionPerformed()
2707   {
2708     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2709     AlignmentSorter.sortByID(viewport.getAlignment());
2710     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2711             viewport.getAlignment()));
2712     alignPanel.paintAlignment(true);
2713   }
2714
2715   public void sortLengthMenuItem_actionPerformed()
2716   {
2717     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2718     AlignmentSorter.sortByLength(viewport.getAlignment());
2719     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2720             viewport.getAlignment()));
2721     alignPanel.paintAlignment(true);
2722   }
2723
2724   public void sortGroupMenuItem_actionPerformed()
2725   {
2726     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2727     AlignmentSorter.sortByGroup(viewport.getAlignment());
2728     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2729             viewport.getAlignment()));
2730     alignPanel.paintAlignment(true);
2731
2732   }
2733
2734   public void removeRedundancyMenuItem_actionPerformed()
2735   {
2736     new RedundancyPanel(alignPanel);
2737   }
2738
2739   public void pairwiseAlignmentMenuItem_actionPerformed()
2740   {
2741     if (viewport.getSelectionGroup() != null
2742             && viewport.getSelectionGroup().getSize() > 1)
2743     {
2744       Frame frame = new Frame();
2745       frame.add(new PairwiseAlignPanel(alignPanel));
2746       jalview.bin.JalviewLite.addFrame(frame,
2747               MessageManager.getString("action.pairwise_alignment"), 600,
2748               500);
2749     }
2750   }
2751
2752   public void PCAMenuItem_actionPerformed()
2753   {
2754     // are the sequences aligned?
2755     if (!viewport.getAlignment().isAligned(false))
2756     {
2757       SequenceI current;
2758       int Width = viewport.getAlignment().getWidth();
2759
2760       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2761       {
2762         current = viewport.getAlignment().getSequenceAt(i);
2763
2764         if (current.getLength() < Width)
2765         {
2766           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2767         }
2768       }
2769       alignPanel.paintAlignment(true);
2770     }
2771
2772     if ((viewport.getSelectionGroup() != null
2773             && viewport.getSelectionGroup().getSize() < 4 && viewport
2774             .getSelectionGroup().getSize() > 0)
2775             || viewport.getAlignment().getHeight() < 4)
2776     {
2777       return;
2778     }
2779
2780     try
2781     {
2782       new PCAPanel(viewport);
2783     } catch (java.lang.OutOfMemoryError ex)
2784     {
2785     }
2786
2787   }
2788
2789   public void averageDistanceTreeMenuItem_actionPerformed()
2790   {
2791     NewTreePanel("AV", "PID", "Average distance tree using PID");
2792   }
2793
2794   public void neighbourTreeMenuItem_actionPerformed()
2795   {
2796     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2797   }
2798
2799   protected void njTreeBlosumMenuItem_actionPerformed()
2800   {
2801     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2802   }
2803
2804   protected void avTreeBlosumMenuItem_actionPerformed()
2805   {
2806     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2807   }
2808
2809   void NewTreePanel(String type, String pwType, String title)
2810   {
2811     // are the sequences aligned?
2812     if (!viewport.getAlignment().isAligned(false))
2813     {
2814       SequenceI current;
2815       int Width = viewport.getAlignment().getWidth();
2816
2817       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2818       {
2819         current = viewport.getAlignment().getSequenceAt(i);
2820
2821         if (current.getLength() < Width)
2822         {
2823           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2824         }
2825       }
2826       alignPanel.paintAlignment(true);
2827
2828     }
2829
2830     if ((viewport.getSelectionGroup() != null && viewport
2831             .getSelectionGroup().getSize() > 1)
2832             || (viewport.getAlignment().getHeight() > 1))
2833     {
2834       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2835
2836       addTreeMenuItem(tp, title);
2837
2838       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2839     }
2840   }
2841
2842   void loadTree_actionPerformed()
2843   {
2844     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2845     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2846     cap.setTreeImport();
2847     Frame frame = new Frame();
2848     frame.add(cap);
2849     jalview.bin.JalviewLite.addFrame(frame,
2850             MessageManager.getString("label.paste_newick_file"), 400, 300);
2851   }
2852
2853   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2854   {
2855     TreePanel tp = new TreePanel(alignPanel, treeFile,
2856             MessageManager.getString("label.load_tree_from_file"), tree);
2857     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2858     addTreeMenuItem(tp, treeFile);
2859   }
2860
2861   /**
2862    * sort the alignment using the given treePanel
2863    *
2864    * @param treePanel
2865    *          tree used to sort view
2866    * @param title
2867    *          string used for undo event name
2868    */
2869   public void sortByTree(TreePanel treePanel, String title)
2870   {
2871     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2872     AlignmentSorter
2873             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2874     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2875     // HistoryItem.SORT));
2876     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2877             "label.order_by_params", new String[] { title }), oldOrder,
2878             viewport.getAlignment()));
2879     alignPanel.paintAlignment(true);
2880   }
2881
2882   /**
2883    * Do any automatic reordering of the alignment and add the necessary bits to
2884    * the menu structure for the new tree
2885    *
2886    * @param treePanel
2887    * @param title
2888    */
2889   protected void addTreeMenuItem(final TreePanel treePanel,
2890           final String title)
2891   {
2892     final MenuItem item = new MenuItem(title);
2893     sortByTreeMenu.add(item);
2894     item.addActionListener(new java.awt.event.ActionListener()
2895     {
2896       @Override
2897       public void actionPerformed(ActionEvent evt)
2898       {
2899         sortByTree(treePanel, title); // treePanel.getTitle());
2900       }
2901     });
2902
2903     treePanel.addWindowListener(new WindowAdapter()
2904     {
2905       @Override
2906       public void windowOpened(WindowEvent e)
2907       {
2908         if (viewport.sortByTree)
2909         {
2910           sortByTree(treePanel, title);
2911         }
2912         super.windowOpened(e);
2913       }
2914
2915       @Override
2916       public void windowClosing(WindowEvent e)
2917       {
2918         sortByTreeMenu.remove(item);
2919       };
2920     });
2921   }
2922
2923   public boolean sortBy(AlignmentOrder alorder, String undoname)
2924   {
2925     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2926     if (viewport.applet.debug)
2927     {
2928       System.err.println("Sorting " + alorder.getOrder().size()
2929               + " in alignment '" + getTitle() + "'");
2930     }
2931     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2932     if (undoname != null)
2933     {
2934       addHistoryItem(new OrderCommand(undoname, oldOrder,
2935               viewport.getAlignment()));
2936     }
2937     alignPanel.paintAlignment(true);
2938     return true;
2939   }
2940
2941   protected void documentation_actionPerformed()
2942   {
2943     alignPanel.av.applet.openJalviewHelpUrl();
2944   }
2945
2946   protected void about_actionPerformed()
2947   {
2948
2949     class AboutPanel extends Canvas
2950     {
2951       String version;
2952
2953       String builddate;
2954
2955       public AboutPanel(String version, String builddate)
2956       {
2957         this.version = version;
2958         this.builddate = builddate;
2959       }
2960
2961       @Override
2962       public void paint(Graphics g)
2963       {
2964         g.setColor(Color.white);
2965         g.fillRect(0, 0, getSize().width, getSize().height);
2966         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2967         FontMetrics fm = g.getFontMetrics();
2968         int fh = fm.getHeight();
2969         int y = 5, x = 7;
2970         g.setColor(Color.black);
2971         // TODO: update this text for each release or centrally store it for
2972         // lite and application
2973         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2974         g.drawString(MessageManager.formatMessage(
2975                 "label.jalviewLite_release", new String[] { version }), x,
2976                 y += fh);
2977         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2978         g.drawString(MessageManager.formatMessage(
2979                 "label.jaview_build_date", new String[] { builddate }), x,
2980                 y += fh);
2981         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2982         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2983                 x, y += fh * 1.5);
2984         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2985                 x + 50, y += fh + 8);
2986         g.drawString(
2987                 MessageManager.getString("label.jalview_dev_managers"), x,
2988                 y += fh);
2989         g.drawString(MessageManager
2990                 .getString("label.jalview_distribution_lists"), x, y += fh);
2991         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2992                 x, y += fh + 8);
2993         g.drawString(
2994                 MessageManager.getString("label.jalview_cite_1_authors"),
2995                 x, y += fh);
2996         g.drawString(
2997                 MessageManager.getString("label.jalview_cite_1_title"), x,
2998                 y += fh);
2999         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3000                 x, y += fh);
3001       }
3002     }
3003
3004     Frame frame = new Frame();
3005     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3006             .getBuildDate()));
3007     jalview.bin.JalviewLite.addFrame(frame,
3008             MessageManager.getString("label.jalview"), 580, 220);
3009
3010   }
3011
3012   public void showURL(String url, String target)
3013   {
3014     if (viewport.applet == null)
3015     {
3016       System.out.println("Not running as applet - no browser available.");
3017     }
3018     else
3019     {
3020       viewport.applet.showURL(url, target);
3021     }
3022   }
3023
3024   // ////////////////////////////////////////////////////////////////////////////////
3025   // JBuilder Graphics here
3026
3027   MenuBar alignFrameMenuBar = new MenuBar();
3028
3029   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3030
3031   MenuItem loadApplication = new MenuItem(
3032           MessageManager.getString("label.view_full_application"));
3033
3034   MenuItem loadTree = new MenuItem(
3035           MessageManager.getString("label.load_associated_tree"));
3036
3037   MenuItem loadAnnotations = new MenuItem(
3038           MessageManager.getString("label.load_features_annotations"));
3039
3040   MenuItem outputFeatures = new MenuItem(
3041           MessageManager.getString("label.export_features"));
3042
3043   MenuItem outputAnnotations = new MenuItem(
3044           MessageManager.getString("label.export_annotations"));
3045
3046   MenuItem closeMenuItem = new MenuItem(
3047           MessageManager.getString("action.close"));
3048
3049   MenuItem selectAllSequenceMenuItem = new MenuItem(
3050           MessageManager.getString("action.select_all"));
3051
3052   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3053           MessageManager.getString("action.deselect_all"));
3054
3055   MenuItem invertSequenceMenuItem = new MenuItem(
3056           MessageManager.getString("action.invert_selection"));
3057
3058   MenuItem remove2LeftMenuItem = new MenuItem();
3059
3060   MenuItem remove2RightMenuItem = new MenuItem();
3061
3062   MenuItem removeGappedColumnMenuItem = new MenuItem();
3063
3064   MenuItem removeAllGapsMenuItem = new MenuItem();
3065
3066   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3067
3068   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3069
3070   MenuItem sortPairwiseMenuItem = new MenuItem();
3071
3072   MenuItem sortIDMenuItem = new MenuItem();
3073
3074   MenuItem sortLengthMenuItem = new MenuItem();
3075
3076   MenuItem sortGroupMenuItem = new MenuItem();
3077
3078   MenuItem removeRedundancyMenuItem = new MenuItem();
3079
3080   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3081
3082   MenuItem PCAMenuItem = new MenuItem();
3083
3084   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3085
3086   MenuItem neighbourTreeMenuItem = new MenuItem();
3087
3088   BorderLayout borderLayout1 = new BorderLayout();
3089
3090   public Label statusBar = new Label();
3091
3092   MenuItem clustalColour = new MenuItem();
3093
3094   MenuItem zappoColour = new MenuItem();
3095
3096   MenuItem taylorColour = new MenuItem();
3097
3098   MenuItem hydrophobicityColour = new MenuItem();
3099
3100   MenuItem helixColour = new MenuItem();
3101
3102   MenuItem strandColour = new MenuItem();
3103
3104   MenuItem turnColour = new MenuItem();
3105
3106   MenuItem buriedColour = new MenuItem();
3107
3108   MenuItem purinePyrimidineColour = new MenuItem();
3109
3110   // MenuItem RNAInteractionColour = new MenuItem();
3111
3112   MenuItem RNAHelixColour = new MenuItem();
3113
3114   MenuItem userDefinedColour = new MenuItem();
3115
3116   MenuItem PIDColour = new MenuItem();
3117
3118   MenuItem BLOSUM62Colour = new MenuItem();
3119
3120   MenuItem tcoffeeColour = new MenuItem();
3121
3122   MenuItem njTreeBlosumMenuItem = new MenuItem();
3123
3124   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3125
3126   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3127
3128   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3129
3130   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3131
3132   MenuItem alProperties = new MenuItem(
3133           MessageManager.getString("label.alignment_props"));
3134
3135   MenuItem overviewMenuItem = new MenuItem();
3136
3137   MenuItem undoMenuItem = new MenuItem();
3138
3139   MenuItem redoMenuItem = new MenuItem();
3140
3141   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3142
3143   MenuItem noColourmenuItem = new MenuItem();
3144
3145   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3146
3147   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3148
3149   MenuItem findMenuItem = new MenuItem();
3150
3151   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3152
3153   MenuItem nucleotideColour = new MenuItem();
3154
3155   MenuItem deleteGroups = new MenuItem();
3156
3157   MenuItem grpsFromSelection = new MenuItem();
3158
3159   MenuItem createGroup = new MenuItem();
3160
3161   MenuItem unGroup = new MenuItem();
3162
3163   MenuItem delete = new MenuItem();
3164
3165   MenuItem copy = new MenuItem();
3166
3167   MenuItem cut = new MenuItem();
3168
3169   Menu pasteMenu = new Menu();
3170
3171   MenuItem pasteNew = new MenuItem();
3172
3173   MenuItem pasteThis = new MenuItem();
3174
3175   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3176
3177   MenuItem font = new MenuItem();
3178
3179   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3180
3181   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3182
3183   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3184
3185   MenuItem modifyPID = new MenuItem();
3186
3187   MenuItem modifyConservation = new MenuItem();
3188
3189   CheckboxMenuItem autoCalculate = null;
3190
3191   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3192           "Sort Alignment With New Tree", true);
3193
3194   Menu sortByTreeMenu = new Menu();
3195
3196   MenuItem inputText = new MenuItem();
3197
3198   MenuItem documentation = new MenuItem();
3199
3200   MenuItem about = new MenuItem();
3201
3202   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3203
3204   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3205
3206   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3207
3208   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3213
3214   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3215
3216   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3217
3218   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3219
3220   /**
3221    * Initialise menus and other items
3222    *
3223    * @throws Exception
3224    */
3225   private void jbInit() throws Exception
3226   {
3227     setMenuBar(alignFrameMenuBar);
3228
3229     /*
3230      * Configure File menu items and actions
3231      */
3232     inputText
3233             .setLabel(MessageManager.getString("label.input_from_textbox"));
3234     inputText.addActionListener(this);
3235     Menu outputTextboxMenu = new Menu(
3236             MessageManager.getString("label.out_to_textbox"));
3237     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3238     {
3239
3240       MenuItem item = new MenuItem(
3241               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3242
3243       item.addActionListener(new java.awt.event.ActionListener()
3244       {
3245         @Override
3246         public void actionPerformed(ActionEvent e)
3247         {
3248           outputText_actionPerformed(e);
3249         }
3250       });
3251
3252       outputTextboxMenu.add(item);
3253     }
3254     closeMenuItem.addActionListener(this);
3255     loadApplication.addActionListener(this);
3256     loadTree.addActionListener(this);
3257     loadAnnotations.addActionListener(this);
3258     outputFeatures.addActionListener(this);
3259     outputAnnotations.addActionListener(this);
3260
3261     /*
3262      * Configure Edit menu items and actions
3263      */
3264     undoMenuItem.setEnabled(false);
3265     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3266     undoMenuItem.addActionListener(this);
3267     redoMenuItem.setEnabled(false);
3268     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3269     redoMenuItem.addActionListener(this);
3270     copy.setLabel(MessageManager.getString("action.copy"));
3271     copy.addActionListener(this);
3272     cut.setLabel(MessageManager.getString("action.cut"));
3273     cut.addActionListener(this);
3274     delete.setLabel(MessageManager.getString("action.delete"));
3275     delete.addActionListener(this);
3276     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3277     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3278     pasteNew.addActionListener(this);
3279     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3280     pasteThis.addActionListener(this);
3281     remove2LeftMenuItem.setLabel(MessageManager
3282             .getString("action.remove_left"));
3283     remove2LeftMenuItem.addActionListener(this);
3284     remove2RightMenuItem.setLabel(MessageManager
3285             .getString("action.remove_right"));
3286     remove2RightMenuItem.addActionListener(this);
3287     removeGappedColumnMenuItem.setLabel(MessageManager
3288             .getString("action.remove_empty_columns"));
3289     removeGappedColumnMenuItem.addActionListener(this);
3290     removeAllGapsMenuItem.setLabel(MessageManager
3291             .getString("action.remove_all_gaps"));
3292     removeAllGapsMenuItem.addActionListener(this);
3293     removeRedundancyMenuItem.setLabel(MessageManager
3294             .getString("action.remove_redundancy"));
3295     removeRedundancyMenuItem.addActionListener(this);
3296
3297     /*
3298      * Configure Select menu items and actions
3299      */
3300     findMenuItem.setLabel(MessageManager.getString("action.find"));
3301     findMenuItem.addActionListener(this);
3302     selectAllSequenceMenuItem.addActionListener(this);
3303     deselectAllSequenceMenuItem.addActionListener(this);
3304     invertSequenceMenuItem.setLabel(MessageManager
3305             .getString("action.invert_sequence_selection"));
3306     invertSequenceMenuItem.addActionListener(this);
3307     invertColSel.setLabel(MessageManager
3308             .getString("action.invert_column_selection"));
3309     invertColSel.addActionListener(this);
3310     deleteGroups.setLabel(MessageManager
3311             .getString("action.undefine_groups"));
3312     deleteGroups.addActionListener(this);
3313     grpsFromSelection.setLabel(MessageManager
3314             .getString("action.make_groups_selection"));
3315     grpsFromSelection.addActionListener(this);
3316     createGroup.setLabel(MessageManager.getString("action.create_group"));
3317     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3318     annotationColumnSelection.setLabel(MessageManager
3319             .getString("action.select_by_annotation"));
3320     annotationColumnSelection.addActionListener(this);
3321
3322     /*
3323      * Configure View menu items and actions
3324      */
3325     newView.setLabel(MessageManager.getString("action.new_view"));
3326     newView.addActionListener(this);
3327     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3328     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3329     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3330     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3331     hideColumns
3332             .setLabel(MessageManager.getString("label.selected_columns"));
3333     hideSequences.setLabel(MessageManager
3334             .getString("label.selected_sequences"));
3335     hideAllButSelection.setLabel(MessageManager
3336             .getString("label.all_but_selected_region"));
3337     hideAllSelection.setLabel(MessageManager
3338             .getString("label.selected_region"));
3339     showAllHidden.setLabel(MessageManager
3340             .getString("label.all_sequences_columns"));
3341     showColumns.addActionListener(this);
3342     showSeqs.addActionListener(this);
3343     hideColumns.addActionListener(this);
3344     hideSequences.addActionListener(this);
3345     hideAllButSelection.addActionListener(this);
3346     hideAllSelection.addActionListener(this);
3347     showAllHidden.addActionListener(this);
3348     featureSettings.setLabel(MessageManager
3349             .getString("action.feature_settings"));
3350     featureSettings.addActionListener(this);
3351     sequenceFeatures.setLabel(MessageManager
3352             .getString("label.show_sequence_features"));
3353     sequenceFeatures.addItemListener(this);
3354     sequenceFeatures.setState(false);
3355     followMouseOverFlag.setLabel(MessageManager
3356             .getString("label.automatic_scrolling"));
3357     followMouseOverFlag.addItemListener(this);
3358     alProperties.addActionListener(this);
3359     overviewMenuItem.setLabel(MessageManager
3360             .getString("label.overview_window"));
3361     overviewMenuItem.addActionListener(this);
3362
3363     /*
3364      * Configure Annotations menu items and actions
3365      */
3366     annotationPanelMenuItem.setLabel(MessageManager
3367             .getString("label.show_annotations"));
3368     annotationPanelMenuItem.addItemListener(this);
3369     showGroupConsensus.setLabel(MessageManager
3370             .getString("label.group_consensus"));
3371     showGroupConservation.setLabel(MessageManager
3372             .getString("label.group_conservation"));
3373     showConsensusHistogram.setLabel(MessageManager
3374             .getString("label.show_consensus_histogram"));
3375     showSequenceLogo.setLabel(MessageManager
3376             .getString("label.show_consensus_logo"));
3377     normSequenceLogo.setLabel(MessageManager
3378             .getString("label.norm_consensus_logo"));
3379     applyAutoAnnotationSettings.setLabel(MessageManager
3380             .getString("label.apply_all_groups"));
3381     applyAutoAnnotationSettings.setState(true);
3382     Menu autoAnnMenu = new Menu(
3383             MessageManager.getString("label.autocalculated_annotation"));
3384     showGroupConsensus.addItemListener(this);
3385     showGroupConservation.addItemListener(this);
3386     showConsensusHistogram.addItemListener(this);
3387     showSequenceLogo.addItemListener(this);
3388     normSequenceLogo.addItemListener(this);
3389     applyAutoAnnotationSettings.addItemListener(this);
3390     showAlignmentAnnotations = new CheckboxMenuItem(
3391             MessageManager.getString("label.show_all_al_annotations"));
3392     showSequenceAnnotations = new CheckboxMenuItem(
3393             MessageManager.getString("label.show_all_seq_annotations"));
3394     sortAnnBySequence = new CheckboxMenuItem(
3395             MessageManager.getString("label.sort_annotations_by_sequence"));
3396     sortAnnByLabel = new CheckboxMenuItem(
3397             MessageManager.getString("label.sort_annotations_by_label"));
3398     showAutoFirst = new CheckboxMenuItem(
3399             MessageManager.getString("label.show_first"));
3400     showAutoFirst.setState(false); // pending applet parameter
3401     setShowAutoCalculatedAbove(showAutoFirst.getState());
3402     showAutoLast = new CheckboxMenuItem(
3403             MessageManager.getString("label.show_last"));
3404     showAutoLast.setState(!showAutoFirst.getState());
3405     showAlignmentAnnotations.addItemListener(this);
3406     showSequenceAnnotations.addItemListener(this);
3407     sortAnnBySequence.addItemListener(this);
3408     sortAnnByLabel.addItemListener(this);
3409     showAutoFirst.addItemListener(this);
3410     showAutoLast.addItemListener(this);
3411
3412     /*
3413      * Configure Format menu items and actions
3414      */
3415     font.setLabel(MessageManager.getString("action.font"));
3416     font.addActionListener(this);
3417     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3418     scaleAbove.setState(true);
3419     scaleAbove.setEnabled(false);
3420     scaleAbove.addItemListener(this);
3421     scaleLeft.setEnabled(false);
3422     scaleLeft.setState(true);
3423     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3424     scaleLeft.addItemListener(this);
3425     scaleRight.setEnabled(false);
3426     scaleRight.setState(true);
3427     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3428     scaleRight.addItemListener(this);
3429     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3430     viewBoxesMenuItem.setState(true);
3431     viewBoxesMenuItem.addItemListener(this);
3432     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3433     viewTextMenuItem.setState(true);
3434     viewTextMenuItem.addItemListener(this);
3435     colourTextMenuItem.setLabel(MessageManager
3436             .getString("label.colour_text"));
3437     colourTextMenuItem.addItemListener(this);
3438     displayNonconservedMenuItem.setLabel(MessageManager
3439             .getString("label.show_non_conversed"));
3440     displayNonconservedMenuItem.addItemListener(this);
3441     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3442     wrapMenuItem.addItemListener(this);
3443     renderGapsMenuItem.setLabel(MessageManager
3444             .getString("action.show_gaps"));
3445     renderGapsMenuItem.setState(true);
3446     renderGapsMenuItem.addItemListener(this);
3447     centreColumnLabelFlag.setLabel(MessageManager
3448             .getString("label.centre_column_labels"));
3449     centreColumnLabelFlag.addItemListener(this);
3450     seqLimits.setState(true);
3451     seqLimits.setLabel(MessageManager
3452             .getString("label.show_sequence_limits"));
3453     seqLimits.addItemListener(this);
3454
3455     /*
3456      * Configure Colour menu items and actions
3457      */
3458     applyToAllGroups.setLabel(MessageManager
3459             .getString("label.apply_colour_to_all_groups"));
3460     applyToAllGroups.setState(true);
3461     applyToAllGroups.addItemListener(this);
3462     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3463     clustalColour.addActionListener(this);
3464     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3465     zappoColour.addActionListener(this);
3466     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3467     taylorColour.addActionListener(this);
3468     hydrophobicityColour.setLabel(MessageManager
3469             .getString("label.hydrophobicity"));
3470     hydrophobicityColour.addActionListener(this);
3471     helixColour
3472             .setLabel(MessageManager.getString("label.helix_propensity"));
3473     helixColour.addActionListener(this);
3474     strandColour.setLabel(MessageManager
3475             .getString("label.strand_propensity"));
3476     strandColour.addActionListener(this);
3477     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3478     turnColour.addActionListener(this);
3479     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3480     buriedColour.addActionListener(this);
3481     purinePyrimidineColour.setLabel(MessageManager
3482             .getString("label.purine_pyrimidine"));
3483     purinePyrimidineColour.addActionListener(this);
3484     // RNAInteractionColour.setLabel(MessageManager
3485     // .getString("label.rna_interaction"));
3486     // RNAInteractionColour.addActionListener(this);
3487     RNAHelixColour.setLabel(MessageManager
3488             .getString("action.by_rna_helixes"));
3489     RNAHelixColour.addActionListener(this);
3490     userDefinedColour.setLabel(MessageManager
3491             .getString("action.user_defined"));
3492     userDefinedColour.addActionListener(this);
3493     PIDColour.setLabel(MessageManager
3494             .getString("label.percentage_identity"));
3495     PIDColour.addActionListener(this);
3496     BLOSUM62Colour.setLabel(MessageManager
3497             .getString("label.blosum62_score"));
3498     BLOSUM62Colour.addActionListener(this);
3499     tcoffeeColour
3500             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3501     // it will be enabled only if a score file is provided
3502     tcoffeeColour.setEnabled(false);
3503     tcoffeeColour.addActionListener(this);
3504     conservationMenuItem.setLabel(MessageManager
3505             .getString("action.by_conservation"));
3506     conservationMenuItem.addItemListener(this);
3507     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3508     noColourmenuItem.addActionListener(this);
3509     abovePIDThreshold.setLabel(MessageManager
3510             .getString("label.above_identity_threshold"));
3511     abovePIDThreshold.addItemListener(this);
3512     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3513     nucleotideColour.addActionListener(this);
3514     modifyPID.setLabel(MessageManager
3515             .getString("label.modify_identity_thereshold"));
3516     modifyPID.addActionListener(this);
3517     modifyConservation.setLabel(MessageManager
3518             .getString("label.modify_conservation_thereshold"));
3519     modifyConservation.addActionListener(this);
3520     annotationColour.setLabel(MessageManager
3521             .getString("action.by_annotation"));
3522     annotationColour.addActionListener(this);
3523
3524     /*
3525      * Configure Calculate menu items and actions
3526      */
3527     sortPairwiseMenuItem.setLabel(MessageManager
3528             .getString("action.by_pairwise_id"));
3529     sortPairwiseMenuItem.addActionListener(this);
3530     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3531     sortIDMenuItem.addActionListener(this);
3532     sortLengthMenuItem.setLabel(MessageManager
3533             .getString("action.by_length"));
3534     sortLengthMenuItem.addActionListener(this);
3535     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3536     sortGroupMenuItem.addActionListener(this);
3537     pairwiseAlignmentMenuItem.setLabel(MessageManager
3538             .getString("action.pairwise_alignment"));
3539     pairwiseAlignmentMenuItem.addActionListener(this);
3540     PCAMenuItem.setLabel(MessageManager
3541             .getString("label.principal_component_analysis"));
3542     PCAMenuItem.addActionListener(this);
3543     autoCalculate = new CheckboxMenuItem(
3544             MessageManager.getString("label.autocalculate_consensus"), true);
3545     averageDistanceTreeMenuItem.setLabel(MessageManager
3546             .getString("label.average_distance_identity"));
3547     averageDistanceTreeMenuItem.addActionListener(this);
3548     neighbourTreeMenuItem.setLabel(MessageManager
3549             .getString("label.neighbour_joining_identity"));
3550     neighbourTreeMenuItem.addActionListener(this);
3551     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3552             .getString("label.average_distance_bloslum62"));
3553     avDistanceTreeBlosumMenuItem.addActionListener(this);
3554     njTreeBlosumMenuItem.setLabel(MessageManager
3555             .getString("label.neighbour_blosum62"));
3556     njTreeBlosumMenuItem.addActionListener(this);
3557     sortByTreeMenu.setLabel(MessageManager
3558             .getString("action.by_tree_order"));
3559     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3560     Menu calculateTreeMenu = new Menu(
3561             MessageManager.getString("action.calculate_tree"));
3562     autoCalculate.addItemListener(this);
3563     sortByTree.addItemListener(this);
3564
3565     /*
3566      * Configure Help menu items and actions
3567      */
3568     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3569     documentation.setLabel(MessageManager.getString("label.documentation"));
3570     documentation.addActionListener(this);
3571     about.setLabel(MessageManager.getString("label.about"));
3572     about.addActionListener(this);
3573
3574     /*
3575      * Add top level menus to frame
3576      */
3577     alignFrameMenuBar.add(fileMenu);
3578     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3579     alignFrameMenuBar.add(editMenu);
3580     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3581     alignFrameMenuBar.add(selectMenu);
3582     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3583     alignFrameMenuBar.add(viewMenu);
3584     Menu annotationsMenu = new Menu(
3585             MessageManager.getString("action.annotations"));
3586     alignFrameMenuBar.add(annotationsMenu);
3587     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3588     alignFrameMenuBar.add(formatMenu);
3589     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3590     alignFrameMenuBar.add(colourMenu);
3591     Menu calculateMenu = new Menu(
3592             MessageManager.getString("action.calculate"));
3593     alignFrameMenuBar.add(calculateMenu);
3594     alignFrameMenuBar.add(helpMenu);
3595
3596     /*
3597      * File menu
3598      */
3599     fileMenu.add(inputText);
3600     fileMenu.add(loadTree);
3601     fileMenu.add(loadAnnotations);
3602     fileMenu.addSeparator();
3603     fileMenu.add(outputTextboxMenu);
3604     fileMenu.add(outputFeatures);
3605     fileMenu.add(outputAnnotations);
3606     if (jalviewServletURL != null)
3607     {
3608       fileMenu.add(loadApplication);
3609     }
3610     fileMenu.addSeparator();
3611     fileMenu.add(closeMenuItem);
3612
3613     /*
3614      * Edit menu
3615      */
3616     editMenu.add(undoMenuItem);
3617     editMenu.add(redoMenuItem);
3618     editMenu.add(cut);
3619     editMenu.add(copy);
3620     pasteMenu.add(pasteNew);
3621     pasteMenu.add(pasteThis);
3622     editMenu.add(pasteMenu);
3623     editMenu.add(delete);
3624     editMenu.addSeparator();
3625     editMenu.add(remove2LeftMenuItem);
3626     editMenu.add(remove2RightMenuItem);
3627     editMenu.add(removeGappedColumnMenuItem);
3628     editMenu.add(removeAllGapsMenuItem);
3629     editMenu.add(removeRedundancyMenuItem);
3630
3631     /*
3632      * Select menu
3633      */
3634     selectMenu.add(findMenuItem);
3635     selectMenu.addSeparator();
3636     selectMenu.add(selectAllSequenceMenuItem);
3637     selectMenu.add(deselectAllSequenceMenuItem);
3638     selectMenu.add(invertSequenceMenuItem);
3639     selectMenu.add(invertColSel);
3640     selectMenu.add(createGroup);
3641     selectMenu.add(unGroup);
3642     selectMenu.add(grpsFromSelection);
3643     selectMenu.add(deleteGroups);
3644     selectMenu.add(annotationColumnSelection);
3645
3646     /*
3647      * View menu
3648      */
3649     viewMenu.add(newView);
3650     viewMenu.addSeparator();
3651     showMenu.add(showColumns);
3652     showMenu.add(showSeqs);
3653     showMenu.add(showAllHidden);
3654     viewMenu.add(showMenu);
3655     hideMenu.add(hideColumns);
3656     hideMenu.add(hideSequences);
3657     hideMenu.add(hideAllSelection);
3658     hideMenu.add(hideAllButSelection);
3659     viewMenu.add(hideMenu);
3660     viewMenu.addSeparator();
3661     viewMenu.add(followMouseOverFlag);
3662     viewMenu.addSeparator();
3663     viewMenu.add(sequenceFeatures);
3664     viewMenu.add(featureSettings);
3665     viewMenu.addSeparator();
3666     viewMenu.add(alProperties);
3667     viewMenu.addSeparator();
3668     viewMenu.add(overviewMenuItem);
3669
3670     /*
3671      * Annotations menu
3672      */
3673     annotationsMenu.add(annotationPanelMenuItem);
3674     annotationsMenu.addSeparator();
3675     annotationsMenu.add(showAlignmentAnnotations);
3676     annotationsMenu.add(showSequenceAnnotations);
3677     annotationsMenu.add(sortAnnBySequence);
3678     annotationsMenu.add(sortAnnByLabel);
3679     annotationsMenu.addSeparator();
3680     autoAnnMenu.add(showAutoFirst);
3681     autoAnnMenu.add(showAutoLast);
3682     autoAnnMenu.addSeparator();
3683     autoAnnMenu.add(applyAutoAnnotationSettings);
3684     autoAnnMenu.add(showConsensusHistogram);
3685     autoAnnMenu.add(showSequenceLogo);
3686     autoAnnMenu.add(normSequenceLogo);
3687     autoAnnMenu.addSeparator();
3688     autoAnnMenu.add(showGroupConservation);
3689     autoAnnMenu.add(showGroupConsensus);
3690     annotationsMenu.add(autoAnnMenu);
3691
3692     /*
3693      * Format menu
3694      */
3695     formatMenu.add(font);
3696     formatMenu.add(seqLimits);
3697     formatMenu.add(wrapMenuItem);
3698     formatMenu.add(scaleAbove);
3699     formatMenu.add(scaleLeft);
3700     formatMenu.add(scaleRight);
3701     formatMenu.add(viewBoxesMenuItem);
3702     formatMenu.add(viewTextMenuItem);
3703     formatMenu.add(colourTextMenuItem);
3704     formatMenu.add(displayNonconservedMenuItem);
3705     formatMenu.add(renderGapsMenuItem);
3706     formatMenu.add(centreColumnLabelFlag);
3707
3708     /*
3709      * Colour menu
3710      */
3711     colourMenu.add(applyToAllGroups);
3712     colourMenu.addSeparator();
3713     colourMenu.add(noColourmenuItem);
3714     colourMenu.add(clustalColour);
3715     colourMenu.add(BLOSUM62Colour);
3716     colourMenu.add(PIDColour);
3717     colourMenu.add(zappoColour);
3718     colourMenu.add(taylorColour);
3719     colourMenu.add(hydrophobicityColour);
3720     colourMenu.add(helixColour);
3721     colourMenu.add(strandColour);
3722     colourMenu.add(turnColour);
3723     colourMenu.add(buriedColour);
3724     colourMenu.add(nucleotideColour);
3725     colourMenu.add(purinePyrimidineColour);
3726     // colourMenu.add(RNAInteractionColour);
3727     colourMenu.add(tcoffeeColour);
3728     colourMenu.add(userDefinedColour);
3729     colourMenu.addSeparator();
3730     colourMenu.add(conservationMenuItem);
3731     colourMenu.add(modifyConservation);
3732     colourMenu.add(abovePIDThreshold);
3733     colourMenu.add(modifyPID);
3734     colourMenu.add(annotationColour);
3735     colourMenu.add(RNAHelixColour);
3736
3737     /*
3738      * Calculate menu
3739      */
3740     sortMenu.add(sortIDMenuItem);
3741     sortMenu.add(sortLengthMenuItem);
3742     sortMenu.add(sortByTreeMenu);
3743     sortMenu.add(sortGroupMenuItem);
3744     sortMenu.add(sortPairwiseMenuItem);
3745     calculateMenu.add(sortMenu);
3746     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3747     calculateTreeMenu.add(neighbourTreeMenuItem);
3748     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3749     calculateTreeMenu.add(njTreeBlosumMenuItem);
3750     calculateMenu.add(calculateTreeMenu);
3751     calculateMenu.addSeparator();
3752     calculateMenu.add(pairwiseAlignmentMenuItem);
3753     calculateMenu.add(PCAMenuItem);
3754     calculateMenu.add(autoCalculate);
3755     calculateMenu.add(sortByTree);
3756
3757     /*
3758      * Help menu
3759      */
3760     helpMenu.add(documentation);
3761     helpMenu.add(about);
3762
3763     /*
3764      * Status bar
3765      */
3766     statusBar.setBackground(Color.white);
3767     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3768     statusBar.setText(MessageManager.getString("label.status_bar"));
3769     this.add(statusBar, BorderLayout.SOUTH);
3770   }
3771
3772   @Override
3773   public void setStatus(String string)
3774   {
3775     statusBar.setText(string);
3776   };
3777
3778   MenuItem featureSettings = new MenuItem();
3779
3780   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3781
3782   MenuItem annotationColour = new MenuItem();
3783
3784   MenuItem annotationColumnSelection = new MenuItem();
3785
3786   MenuItem invertColSel = new MenuItem();
3787
3788   MenuItem showColumns = new MenuItem();
3789
3790   MenuItem showSeqs = new MenuItem();
3791
3792   MenuItem hideColumns = new MenuItem();
3793
3794   MenuItem hideSequences = new MenuItem();
3795
3796   MenuItem hideAllButSelection = new MenuItem();
3797
3798   MenuItem hideAllSelection = new MenuItem();
3799
3800   MenuItem showAllHidden = new MenuItem();
3801
3802   MenuItem newView = new MenuItem();
3803
3804   private CheckboxMenuItem showAlignmentAnnotations;
3805
3806   private CheckboxMenuItem showSequenceAnnotations;
3807
3808   private CheckboxMenuItem sortAnnBySequence;
3809
3810   private CheckboxMenuItem sortAnnByLabel;
3811
3812   private CheckboxMenuItem showAutoFirst;
3813
3814   private CheckboxMenuItem showAutoLast;
3815
3816   private SplitFrame splitFrame;
3817
3818   /**
3819    * Attach the alignFrame panels after embedding menus, if necessary. This used
3820    * to be called setEmbedded, but is now creates the dropdown menus in a
3821    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3822    *
3823    * @param reallyEmbedded
3824    *          true to attach the view to the applet area on the page rather than
3825    *          in a new window
3826    */
3827   public void createAlignFrameWindow(boolean reallyEmbedded)
3828   {
3829     if (reallyEmbedded)
3830     {
3831       embedAlignFrameInApplet(viewport.applet);
3832     }
3833     else
3834     {
3835       // //////
3836       // test and embed menu bar if necessary.
3837       //
3838       if (embedMenuIfNeeded(alignPanel))
3839       {
3840         /*
3841          * adjust for status bar height too. ? pointless as overridden by layout
3842          * manager
3843          */
3844         alignPanel.setSize(getSize().width,
3845                 getSize().height - statusBar.getHeight());
3846       }
3847       add(statusBar, BorderLayout.SOUTH);
3848       add(alignPanel, BorderLayout.CENTER);
3849       // and register with the applet so it can pass external API calls to us
3850       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3851               frameHeight);
3852     }
3853   }
3854
3855   /**
3856    * Add the components of this AlignFrame to the applet container.
3857    *
3858    * @param theApplet
3859    */
3860   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3861   {
3862     // ////
3863     // Explicitly build the embedded menu panel for the on-page applet
3864     //
3865     // view cannot be closed if its actually on the page
3866     fileMenu.remove(closeMenuItem);
3867     fileMenu.remove(3); // Remove Separator
3868     // construct embedded menu, using default font
3869     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3870     // and actually add the components to the applet area
3871     theApplet.setLayout(new BorderLayout());
3872     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3873     theApplet.add(statusBar, BorderLayout.SOUTH);
3874     // TODO should size be left to the layout manager?
3875     alignPanel.setSize(theApplet.getSize().width,
3876             theApplet.getSize().height - embeddedMenu.getHeight()
3877                     - statusBar.getHeight());
3878     theApplet.add(alignPanel, BorderLayout.CENTER);
3879     final AlignFrame me = this;
3880     theApplet.addFocusListener(new FocusListener()
3881     {
3882
3883       @Override
3884       public void focusLost(FocusEvent e)
3885       {
3886         if (theApplet.currentAlignFrame == me)
3887         {
3888           theApplet.currentAlignFrame = null;
3889         }
3890       }
3891
3892       @Override
3893       public void focusGained(FocusEvent e)
3894       {
3895         theApplet.currentAlignFrame = me;
3896       }
3897     });
3898     theApplet.validate();
3899   }
3900
3901   /**
3902    * create a new binding between structures in an existing jmol viewer instance
3903    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3904    * this does not open a new Jmol window, or modify the display of the
3905    * structures in the original jmol window. Note This method doesn't work
3906    * without an additional javascript library to exchange messages between the
3907    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3908    *
3909    * @param viewer
3910    *          JmolViewer instance
3911    * @param sequenceIds
3912    *          - sequence Ids to search for associations
3913    */
3914   public SequenceStructureBinding addStructureViewInstance(
3915           Object jmolviewer, String[] sequenceIds)
3916   {
3917     Viewer viewer = null;
3918     try
3919     {
3920       viewer = (Viewer) jmolviewer;
3921     } catch (ClassCastException ex)
3922     {
3923       System.err.println("Unsupported viewer object :"
3924               + jmolviewer.getClass());
3925     }
3926     if (viewer == null)
3927     {
3928       System.err.println("Can't use this object as a structure viewer:"
3929               + jmolviewer.getClass());
3930       return null;
3931     }
3932     SequenceI[] seqs = null;
3933     if (sequenceIds == null || sequenceIds.length == 0)
3934     {
3935       seqs = viewport.getAlignment().getSequencesArray();
3936     }
3937     else
3938     {
3939       Vector sqi = new Vector();
3940       AlignmentI al = viewport.getAlignment();
3941       for (int sid = 0; sid < sequenceIds.length; sid++)
3942       {
3943         SequenceI sq = al.findName(sequenceIds[sid]);
3944         if (sq != null)
3945         {
3946           sqi.addElement(sq);
3947         }
3948       }
3949       if (sqi.size() > 0)
3950       {
3951         seqs = new SequenceI[sqi.size()];
3952         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3953         {
3954           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3955         }
3956       }
3957       else
3958       {
3959         return null;
3960       }
3961     }
3962     AAStructureBindingModel jmv = null;
3963     // TODO: search for a jmv that involves viewer
3964     if (jmv == null)
3965     { // create a new viewer/jalview binding.
3966       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3967     }
3968     return jmv;
3969
3970   }
3971
3972   /**
3973    * bind a pdb file to a sequence in the current view
3974    *
3975    * @param sequenceId
3976    *          - sequenceId within the dataset.
3977    * @param pdbEntryString
3978    *          - the short name for the PDB file
3979    * @param pdbFile
3980    *          - pdb file - either a URL or a valid PDB file.
3981    * @return true if binding was as success TODO: consider making an exception
3982    *         structure for indicating when PDB parsing or sequenceId location
3983    *         fails.
3984    */
3985   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3986           String pdbFile)
3987   {
3988     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3989     boolean needtoadd = false;
3990     if (toaddpdb != null)
3991     {
3992       Vector pdbe = toaddpdb.getAllPDBEntries();
3993       PDBEntry pdbentry = null;
3994       if (pdbe != null && pdbe.size() > 0)
3995       {
3996         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3997         {
3998           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3999           if (!pdbentry.getId().equals(pdbEntryString)
4000                   && !pdbentry.getFile().equals(pdbFile))
4001           {
4002             pdbentry = null;
4003           }
4004           else
4005           {
4006             continue;
4007           }
4008         }
4009       }
4010       if (pdbentry == null)
4011       {
4012         pdbentry = new PDBEntry();
4013         pdbentry.setId(pdbEntryString);
4014         pdbentry.setFile(pdbFile);
4015         needtoadd = true; // add this new entry to sequence.
4016       }
4017       // resolve data source
4018       // TODO: this code should be a refactored to an io package
4019       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4020               pdbFile, FileFormat.PDB);
4021       if (protocol == null)
4022       {
4023         return false;
4024       }
4025       if (needtoadd)
4026       {
4027         // make a note of the access mode and add
4028         if (pdbentry.getProperty() == null)
4029         {
4030           pdbentry.setProperty(new Hashtable<String, String>());
4031         }
4032         pdbentry.getProperty().put("protocol", protocol.toString());
4033         toaddpdb.addPDBId(pdbentry);
4034         alignPanel.getStructureSelectionManager()
4035                 .registerPDBEntry(pdbentry);
4036       }
4037     }
4038     return true;
4039   }
4040
4041   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4042   {
4043     if (seqs != null)
4044     {
4045       Vector sequences = new Vector();
4046       for (int i = 0; i < seqs.length; i++)
4047       {
4048         if (seqs[i] != null)
4049         {
4050           sequences.addElement(new Object[] { seqs[i],
4051               (chains != null) ? chains[i] : null });
4052         }
4053       }
4054       seqs = new SequenceI[sequences.size()];
4055       chains = new String[sequences.size()];
4056       for (int i = 0, isize = sequences.size(); i < isize; i++)
4057       {
4058         Object[] oj = (Object[]) sequences.elementAt(i);
4059
4060         seqs[i] = (SequenceI) oj[0];
4061         chains[i] = (String) oj[1];
4062       }
4063     }
4064     return new Object[] { seqs, chains };
4065
4066   }
4067
4068   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4069           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4070   {
4071     // Scrub any null sequences from the array
4072     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4073     seqs = (SequenceI[]) sqch[0];
4074     chains = (String[]) sqch[1];
4075     if (seqs == null || seqs.length == 0)
4076     {
4077       System.err
4078               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4079     }
4080     if (protocol == null)
4081     {
4082       String sourceType = pdb.getProperty().get("protocol");
4083       try
4084       {
4085         protocol = DataSourceType.valueOf(sourceType);
4086       } catch (IllegalArgumentException e)
4087       {
4088         // ignore
4089       }
4090       if (protocol == null)
4091       {
4092         System.err.println("Couldn't work out protocol to open structure: "
4093                 + pdb.getId());
4094         return;
4095       }
4096     }
4097     if (applet.useXtrnalSviewer)
4098     {
4099       // register the association(s) and quit, don't create any windows.
4100       if (StructureSelectionManager.getStructureSelectionManager(applet)
4101               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4102       {
4103         System.err.println("Failed to map " + pdb.getFile() + " ("
4104                 + protocol + ") to any sequences");
4105       }
4106       return;
4107     }
4108     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4109     {
4110       // can only do alignments with Jmol
4111       // find the last jmol window assigned to this alignment
4112       AppletJmol ajm = null, tajm;
4113       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4114       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4115       {
4116         tajm = (AppletJmol) jmols.elementAt(i);
4117         if (tajm.ap.alignFrame == this)
4118         {
4119           ajm = tajm;
4120           break;
4121         }
4122       }
4123       if (ajm != null)
4124       {
4125         System.err
4126                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4127         // try and add the pdb structure
4128         // ajm.addS
4129         ajm = null;
4130       }
4131     }
4132     // otherwise, create a new window
4133     if (applet.jmolAvailable)
4134     {
4135       new AppletJmol(pdb, seqs, chains, alignPanel,
4136               protocol);
4137       applet.lastFrameX += 40;
4138       applet.lastFrameY += 40;
4139     }
4140     else
4141     {
4142       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4143     }
4144
4145   }
4146
4147   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4148           SequenceI[][] seqs, String[][] chains, String[] protocols)
4149   {
4150     // TODO Auto-generated method stub
4151     System.err.println("Aligned Structure View: Not yet implemented.");
4152   }
4153
4154   /**
4155    * modify the current selection, providing the user has not made a selection
4156    * already.
4157    *
4158    * @param sel
4159    *          - sequences from this alignment
4160    * @param csel
4161    *          - columns to be selected on the alignment
4162    */
4163   public void select(SequenceGroup sel, ColumnSelection csel)
4164   {
4165     alignPanel.seqPanel.selection(sel, csel, null);
4166   }
4167
4168   public void scrollTo(int row, int column)
4169   {
4170     alignPanel.seqPanel.scrollTo(row, column);
4171   }
4172
4173   public void scrollToRow(int row)
4174   {
4175     alignPanel.seqPanel.scrollToRow(row);
4176   }
4177
4178   public void scrollToColumn(int column)
4179   {
4180     alignPanel.seqPanel.scrollToColumn(column);
4181   }
4182
4183   /**
4184    * @return the alignments unique ID.
4185    */
4186   public String getSequenceSetId()
4187   {
4188     return viewport.getSequenceSetId();
4189   }
4190
4191   /**
4192    * Load the (T-Coffee) score file from the specified url
4193    *
4194    * @param source
4195    *          File/URL/T-COFFEE score file contents
4196    * @throws IOException
4197    * @return true if alignment was annotated with data from source
4198    */
4199   public boolean loadScoreFile(String source) throws IOException
4200   {
4201
4202     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4203             AppletFormatAdapter.checkProtocol(source));
4204     if (!file.isValid())
4205     {
4206       // TODO: raise dialog for gui
4207       System.err.println("Problems parsing T-Coffee scores: "
4208               + file.getWarningMessage());
4209       System.err.println("Origin was:\n" + source);
4210       return false;
4211     }
4212
4213     /*
4214      * check that the score matrix matches the alignment dimensions
4215      */
4216     AlignmentI aln;
4217     if ((aln = viewport.getAlignment()) != null
4218             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4219                     .getWidth()))
4220     {
4221       // TODO: raise a dialog box here rather than bomb out.
4222       System.err
4223               .println("The scores matrix does not match the alignment dimensions");
4224
4225     }
4226
4227     // TODO add parameter to indicate if matching should be done
4228     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4229     {
4230       alignPanel.fontChanged();
4231       tcoffeeColour.setEnabled(true);
4232       // switch to this color
4233       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4234       return true;
4235     }
4236     else
4237     {
4238       System.err.println("Problems resolving T-Coffee scores:");
4239       if (file.getWarningMessage() != null)
4240       {
4241         System.err.println(file.getWarningMessage());
4242       }
4243     }
4244     return false;
4245   }
4246
4247   public SplitFrame getSplitFrame()
4248   {
4249     return this.splitFrame;
4250   }
4251
4252   public void setSplitFrame(SplitFrame sf)
4253   {
4254     this.splitFrame = sf;
4255   }
4256
4257   // may not need this
4258   @Override
4259   public void setShowSeqFeatures(boolean b)
4260   {
4261     // showSeqFeatures.setSelected(b);
4262     viewport.setShowSequenceFeatures(b);
4263
4264   }
4265
4266   @Override
4267   public void setMenusForViewport()
4268   {
4269     // setMenusFromViewport(viewport);
4270
4271   }
4272
4273   @Override
4274   public void refreshFeatureUI(boolean enableIfNecessary)
4275   {
4276     if (enableIfNecessary)
4277     {
4278       sequenceFeatures.setState(true);
4279       alignPanel.av.setShowSequenceFeatures(true);
4280     }
4281   }
4282
4283   @Override
4284   public FeatureSettingsControllerI getFeatureSettingsUI()
4285   {
4286     return alignPanel.av.featureSettings;
4287   }
4288
4289 }