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