src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.AlignViewportI;
  28 import jalview.api.FeatureColourI;
  29 import jalview.api.FeatureRenderer;
  30 import jalview.api.FeatureSettingsControllerI;
  31 import jalview.api.SequenceStructureBinding;
  32 import jalview.bin.JalviewLite;
  33 import jalview.commands.CommandI;
  34 import jalview.commands.EditCommand;
  35 import jalview.commands.EditCommand.Action;
  36 import jalview.commands.OrderCommand;
  37 import jalview.commands.RemoveGapColCommand;
  38 import jalview.commands.RemoveGapsCommand;
  39 import jalview.commands.SlideSequencesCommand;
  40 import jalview.commands.TrimRegionCommand;
  41 import jalview.datamodel.Alignment;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.AlignmentOrder;
  45 import jalview.datamodel.ColumnSelection;
  46 import jalview.datamodel.PDBEntry;
  47 import jalview.datamodel.Sequence;
  48 import jalview.datamodel.SequenceGroup;
  49 import jalview.datamodel.SequenceI;
  50 import jalview.io.AnnotationFile;
  51 import jalview.io.AppletFormatAdapter;
  52 import jalview.io.DataSourceType;
  53 import jalview.io.FeaturesFile;
  54 import jalview.io.FileFormat;
  55 import jalview.io.FileFormatI;
  56 import jalview.io.FileFormats;
  57 import jalview.io.TCoffeeScoreFile;
  58 import jalview.schemes.Blosum62ColourScheme;
  59 import jalview.schemes.BuriedColourScheme;
  60 import jalview.schemes.ClustalxColourScheme;
  61 import jalview.schemes.ColourSchemeI;
  62 import jalview.schemes.HelixColourScheme;
  63 import jalview.schemes.HydrophobicColourScheme;
  64 import jalview.schemes.NucleotideColourScheme;
  65 import jalview.schemes.PIDColourScheme;
  66 import jalview.schemes.PurinePyrimidineColourScheme;
  67 import jalview.schemes.RNAHelicesColour;
  68 import jalview.schemes.StrandColourScheme;
  69 import jalview.schemes.TCoffeeColourScheme;
  70 import jalview.schemes.TaylorColourScheme;
  71 import jalview.schemes.TurnColourScheme;
  72 import jalview.schemes.ZappoColourScheme;
  73 import jalview.structure.StructureSelectionManager;
  74 import jalview.structures.models.AAStructureBindingModel;
  75 import jalview.util.MappingUtils;
  76 import jalview.util.MessageManager;
  77 import jalview.viewmodel.AlignmentViewport;
  78 import jalview.viewmodel.ViewportRanges;
  79
  80 import java.awt.BorderLayout;
  81 import java.awt.Canvas;
  82 import java.awt.CheckboxMenuItem;
  83 import java.awt.Color;
  84 import java.awt.FlowLayout;
  85 import java.awt.Font;
  86 import java.awt.FontMetrics;
  87 import java.awt.Frame;
  88 import java.awt.Graphics;
  89 import java.awt.Label;
  90 import java.awt.Menu;
  91 import java.awt.MenuBar;
  92 import java.awt.MenuItem;
  93 import java.awt.Panel;
  94 import java.awt.event.ActionEvent;
  95 import java.awt.event.ActionListener;
  96 import java.awt.event.FocusEvent;
  97 import java.awt.event.FocusListener;
  98 import java.awt.event.ItemEvent;
  99 import java.awt.event.ItemListener;
 100 import java.awt.event.KeyEvent;
 101 import java.awt.event.KeyListener;
 102 import java.awt.event.WindowAdapter;
 103 import java.awt.event.WindowEvent;
 104 import java.io.IOException;
 105 import java.net.URL;
 106 import java.net.URLEncoder;
 107 import java.util.Arrays;
 108 import java.util.Deque;
 109 import java.util.HashMap;
 110 import java.util.List;
 111 import java.util.Map;
 112 import java.util.StringTokenizer;
 113 import java.util.Vector;
 114
 115 import org.jmol.viewer.Viewer;
 116
 117 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 118         ItemListener, KeyListener, AlignViewControllerGuiI
 119 {
 120   public AlignViewControllerI avc;
 121
 122   public AlignmentPanel alignPanel;
 123
 124   public AlignViewport viewport;
 125
 126   // width and height may be overridden by applet parameters
 127   int frameWidth = 700;
 128
 129   int frameHeight = 500;
 130
 131   String jalviewServletURL;
 132
 133   /*
 134    * Flag for showing autocalculated consensus above or below other consensus
 135    * rows
 136    */
 137   private boolean showAutoCalculatedAbove;
 138
 139   private SequenceAnnotationOrder annotationSortOrder;
 140
 141   /**
 142    * Constructor that creates the frame and adds it to the display.
 143    *
 144    * @param al
 145    * @param applet
 146    * @param title
 147    * @param embedded
 148    */
 149   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 150           boolean embedded)
 151   {
 152     this(al, applet, title, embedded, true);
 153   }
 154
 155   /**
 156    * Constructor that optionally allows the frame to be displayed or only
 157    * created.
 158    *
 159    * @param al
 160    * @param applet
 161    * @param title
 162    * @param embedded
 163    * @param addToDisplay
 164    */
 165   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 166           boolean embedded, boolean addToDisplay)
 167   {
 168     this(al, null, null, applet, title, embedded, addToDisplay);
 169   }
 170
 171   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 172           ColumnSelection columnSelection, JalviewLite applet,
 173           String title, boolean embedded)
 174   {
 175     this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
 176   }
 177
 178   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 179           ColumnSelection columnSelection, JalviewLite applet,
 180           String title, boolean embedded, boolean addToDisplay)
 181   {
 182     if (applet != null)
 183     {
 184       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 185     }
 186
 187     try
 188     {
 189       jbInit();
 190     } catch (Exception ex)
 191     {
 192       ex.printStackTrace();
 193     }
 194     // need to get window geometry before we calculate alignment layout
 195     if (applet != null)
 196     {
 197       String param;
 198       try
 199       {
 200         param = applet.getParameter("windowWidth");
 201         if (param != null)
 202         {
 203           int width = Integer.parseInt(param);
 204           frameWidth = width;
 205         }
 206         param = applet.getParameter("windowHeight");
 207         if (param != null)
 208         {
 209           int height = Integer.parseInt(param);
 210           frameHeight = height;
 211         }
 212       } catch (Exception ex)
 213       {
 214       }
 215     }
 216     viewport = new AlignViewport(al, applet);
 217
 218     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 219     {
 220       viewport.hideSequence(hiddenSeqs);
 221     }
 222     if (columnSelection != null)
 223     {
 224       viewport.setColumnSelection(columnSelection);
 225     }
 226     viewport.setScaleAboveWrapped(scaleAbove.getState());
 227
 228     alignPanel = new AlignmentPanel(this, viewport);
 229     avc = new jalview.controller.AlignViewController(this, viewport,
 230             alignPanel);
 231     viewport.updateConservation(alignPanel);
 232     viewport.updateConsensus(alignPanel);
 233
 234     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 235     followMouseOverFlag.setState(viewport.isFollowHighlight());
 236     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 237     showGroupConservation.setState(viewport.isShowGroupConservation());
 238     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 239     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 240     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 241     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 242     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 243     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 244     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 245     showAlignmentAnnotations.setState(true);
 246     showSequenceAnnotations.setState(false);
 247
 248     seqLimits.setState(viewport.getShowJVSuffix());
 249
 250     if (applet != null)
 251     {
 252       String param = applet.getParameter("sortBy");
 253       if (param != null)
 254       {
 255         if (param.equalsIgnoreCase("Id"))
 256         {
 257           sortIDMenuItem_actionPerformed();
 258         }
 259         else if (param.equalsIgnoreCase("Pairwise Identity"))
 260         {
 261           sortPairwiseMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Length"))
 264         {
 265           sortLengthMenuItem_actionPerformed();
 266         }
 267       }
 268
 269       param = applet.getParameter("wrap");
 270       if (param != null)
 271       {
 272         if (param.equalsIgnoreCase("true"))
 273         {
 274           wrapMenuItem.setState(true);
 275           wrapMenuItem_actionPerformed();
 276         }
 277       }
 278       param = applet.getParameter("centrecolumnlabels");
 279       if (param != null)
 280       {
 281         centreColumnLabelFlag.setState(true);
 282         centreColumnLabelFlag_stateChanged();
 283       }
 284
 285     }
 286     if (viewport.getAlignment().isNucleotide())
 287     {
 288       conservationMenuItem.setEnabled(false);
 289       clustalColour.setEnabled(false);
 290       BLOSUM62Colour.setEnabled(false);
 291       zappoColour.setEnabled(false);
 292       taylorColour.setEnabled(false);
 293       hydrophobicityColour.setEnabled(false);
 294       helixColour.setEnabled(false);
 295       strandColour.setEnabled(false);
 296       turnColour.setEnabled(false);
 297       buriedColour.setEnabled(false);
 298       viewport.updateStrucConsensus(alignPanel);
 299       if (viewport.getAlignment().hasRNAStructure())
 300       {
 301         RNAHelixColour.setEnabled(true);
 302       }
 303       else
 304       {
 305         RNAHelixColour.setEnabled(false);
 306       }
 307     }
 308     else
 309     {
 310       RNAHelixColour.setEnabled(false);
 311       purinePyrimidineColour.setEnabled(false);
 312       nucleotideColour.setEnabled(false);
 313     }
 314     // Some JVMS send keyevents to Top frame or lowest panel,
 315     // Havent worked out why yet. So add to both this frame and seqCanvas for
 316     // now
 317     this.addKeyListener(this);
 318     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 319     alignPanel.idPanel.idCanvas.addKeyListener(this);
 320     alignPanel.scalePanel.addKeyListener(this);
 321     alignPanel.annotationPanel.addKeyListener(this);
 322     alignPanel.annotationPanelHolder.addKeyListener(this);
 323     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 324     alignPanel.alabels.addKeyListener(this);
 325
 326     setAnnotationsVisibility();
 327
 328     if (addToDisplay)
 329     {
 330       addToDisplay(embedded);
 331     }
 332   }
 333
 334   /**
 335    * @param embedded
 336    */
 337   public void addToDisplay(boolean embedded)
 338   {
 339     createAlignFrameWindow(embedded);
 340     validate();
 341     alignPanel.adjustAnnotationHeight();
 342     alignPanel.paintAlignment(true);
 343   }
 344
 345   public AlignViewport getAlignViewport()
 346   {
 347     return viewport;
 348   }
 349
 350   public SeqCanvas getSeqcanvas()
 351   {
 352     return alignPanel.seqPanel.seqCanvas;
 353   }
 354
 355   /**
 356    * Load a features file onto the alignment
 357    *
 358    * @param file
 359    *          file URL, content, or other resolvable path
 360    * @param type
 361    *          is protocol for accessing data referred to by file
 362    */
 363
 364   public boolean parseFeaturesFile(String file, DataSourceType type)
 365   {
 366     return parseFeaturesFile(file, type, true);
 367   }
 368
 369   /**
 370    * Load a features file onto the alignment
 371    *
 372    * @param file
 373    *          file URL, content, or other resolvable path
 374    * @param sourceType
 375    *          is protocol for accessing data referred to by file
 376    * @param autoenabledisplay
 377    *          when true, display features flag will be automatically enabled if
 378    *          features are loaded
 379    * @return true if data parsed as a features file
 380    */
 381   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 382           boolean autoenabledisplay)
 383   {
 384     boolean featuresFile = false;
 385     try
 386     {
 387       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 388               .getFeatureRenderer().getFeatureColours();
 389       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 390               "relaxedidmatch", false);
 391       featuresFile = new FeaturesFile(file, sourceType).parse(
 392               viewport.getAlignment(), colours, true, relaxedIdMatching);
 393     } catch (Exception ex)
 394     {
 395       ex.printStackTrace();
 396     }
 397
 398     if (featuresFile)
 399     {
 400       if (autoenabledisplay)
 401       {
 402         viewport.setShowSequenceFeatures(true);
 403         sequenceFeatures.setState(true);
 404       }
 405       if (alignPanel.seqPanel.seqCanvas.fr != null)
 406       {
 407         // update the min/max ranges where necessary
 408         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 409       }
 410       if (viewport.featureSettings != null)
 411       {
 412         viewport.featureSettings.refreshTable();
 413       }
 414       alignPanel.paintAlignment(true);
 415       statusBar.setText(MessageManager
 416               .getString("label.successfully_added_features_alignment"));
 417     }
 418     return featuresFile;
 419   }
 420
 421   @Override
 422   public void keyPressed(KeyEvent evt)
 423   {
 424     ViewportRanges ranges = viewport.getRanges();
 425
 426     if (viewport.cursorMode
 427             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 428                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 429                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 430             && Character.isDigit(evt.getKeyChar()))
 431     {
 432       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 433     }
 434
 435     switch (evt.getKeyCode())
 436     {
 437     case 27: // escape key
 438       deselectAllSequenceMenuItem_actionPerformed();
 439
 440       alignPanel.alabels.cancelDrag();
 441       break;
 442     case KeyEvent.VK_X:
 443       if (evt.isControlDown() || evt.isMetaDown())
 444       {
 445         cut_actionPerformed();
 446       }
 447       break;
 448     case KeyEvent.VK_C:
 449       if (viewport.cursorMode && !evt.isControlDown())
 450       {
 451         alignPanel.seqPanel.setCursorColumn();
 452       }
 453       if (evt.isControlDown() || evt.isMetaDown())
 454       {
 455         copy_actionPerformed();
 456       }
 457       break;
 458     case KeyEvent.VK_V:
 459       if (evt.isControlDown())
 460       {
 461         paste(evt.isShiftDown());
 462       }
 463       break;
 464     case KeyEvent.VK_A:
 465       if (evt.isControlDown() || evt.isMetaDown())
 466       {
 467         selectAllSequenceMenuItem_actionPerformed();
 468       }
 469       break;
 470     case KeyEvent.VK_DOWN:
 471       if (viewport.cursorMode)
 472       {
 473         alignPanel.seqPanel.moveCursor(0, 1);
 474       }
 475       else
 476       {
 477         moveSelectedSequences(false);
 478       }
 479       break;
 480
 481     case KeyEvent.VK_UP:
 482       if (viewport.cursorMode)
 483       {
 484         alignPanel.seqPanel.moveCursor(0, -1);
 485       }
 486       else
 487       {
 488         moveSelectedSequences(true);
 489       }
 490       break;
 491
 492     case KeyEvent.VK_LEFT:
 493       if (evt.isAltDown() || !viewport.cursorMode)
 494       {
 495         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 496       }
 497       else
 498       {
 499         alignPanel.seqPanel.moveCursor(-1, 0);
 500       }
 501       break;
 502
 503     case KeyEvent.VK_RIGHT:
 504       if (evt.isAltDown() || !viewport.cursorMode)
 505       {
 506         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 507       }
 508       else
 509       {
 510         alignPanel.seqPanel.moveCursor(1, 0);
 511       }
 512       break;
 513
 514     case KeyEvent.VK_SPACE:
 515       if (viewport.cursorMode)
 516       {
 517         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 518                 || evt.isShiftDown() || evt.isAltDown());
 519       }
 520       break;
 521
 522     case KeyEvent.VK_DELETE:
 523     case KeyEvent.VK_BACK_SPACE:
 524       if (viewport.cursorMode)
 525       {
 526         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 527                 || evt.isShiftDown() || evt.isAltDown());
 528       }
 529       else
 530       {
 531         cut_actionPerformed();
 532         alignPanel.seqPanel.seqCanvas.repaint();
 533       }
 534       break;
 535
 536     case KeyEvent.VK_S:
 537       if (viewport.cursorMode)
 538       {
 539         alignPanel.seqPanel.setCursorRow();
 540       }
 541       break;
 542     case KeyEvent.VK_P:
 543       if (viewport.cursorMode)
 544       {
 545         alignPanel.seqPanel.setCursorPosition();
 546       }
 547       break;
 548
 549     case KeyEvent.VK_ENTER:
 550     case KeyEvent.VK_COMMA:
 551       if (viewport.cursorMode)
 552       {
 553         alignPanel.seqPanel.setCursorRowAndColumn();
 554       }
 555       break;
 556
 557     case KeyEvent.VK_Q:
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 561       }
 562       break;
 563     case KeyEvent.VK_M:
 564       if (viewport.cursorMode)
 565       {
 566         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 567       }
 568       break;
 569
 570     case KeyEvent.VK_F2:
 571       viewport.cursorMode = !viewport.cursorMode;
 572       statusBar.setText(MessageManager.formatMessage(
 573               "label.keyboard_editing_mode",
 574               new String[] { (viewport.cursorMode ? "on" : "off") }));
 575       if (viewport.cursorMode)
 576       {
 577         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 578         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 579       }
 580       break;
 581
 582     case KeyEvent.VK_F:
 583       if (evt.isControlDown())
 584       {
 585         findMenuItem_actionPerformed();
 586       }
 587       break;
 588
 589     case KeyEvent.VK_H:
 590     {
 591       boolean toggleSeqs = !evt.isControlDown();
 592       boolean toggleCols = !evt.isShiftDown();
 593       toggleHiddenRegions(toggleSeqs, toggleCols);
 594       break;
 595     }
 596
 597     case KeyEvent.VK_PAGE_UP:
 598       if (viewport.getWrapAlignment())
 599       {
 600         ranges.scrollUp(true);
 601       }
 602       else
 603       {
 604         ranges.pageUp();
 605       }
 606       break;
 607
 608     case KeyEvent.VK_PAGE_DOWN:
 609       if (viewport.getWrapAlignment())
 610       {
 611         ranges.scrollUp(false);
 612       }
 613       else
 614       {
 615         ranges.pageDown();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_Z:
 620       if (evt.isControlDown())
 621       {
 622         undoMenuItem_actionPerformed();
 623       }
 624       break;
 625
 626     case KeyEvent.VK_Y:
 627       if (evt.isControlDown())
 628       {
 629         redoMenuItem_actionPerformed();
 630       }
 631       break;
 632
 633     case KeyEvent.VK_L:
 634       if (evt.isControlDown())
 635       {
 636         trimAlignment(true);
 637       }
 638       break;
 639
 640     case KeyEvent.VK_R:
 641       if (evt.isControlDown())
 642       {
 643         trimAlignment(false);
 644       }
 645       break;
 646
 647     case KeyEvent.VK_E:
 648       if (evt.isControlDown())
 649       {
 650         if (evt.isShiftDown())
 651         {
 652           this.removeAllGapsMenuItem_actionPerformed();
 653         }
 654         else
 655         {
 656           removeGappedColumnMenuItem_actionPerformed();
 657         }
 658       }
 659       break;
 660     case KeyEvent.VK_I:
 661       if (evt.isControlDown())
 662       {
 663         if (evt.isAltDown())
 664         {
 665           invertColSel_actionPerformed();
 666         }
 667         else
 668         {
 669           invertSequenceMenuItem_actionPerformed();
 670         }
 671       }
 672       break;
 673
 674     case KeyEvent.VK_G:
 675       if (evt.isControlDown())
 676       {
 677         if (evt.isShiftDown())
 678         {
 679           this.unGroup_actionPerformed();
 680         }
 681         else
 682         {
 683           this.createGroup_actionPerformed();
 684         }
 685       }
 686       break;
 687
 688     case KeyEvent.VK_U:
 689       if (evt.isControlDown())
 690       {
 691         this.deleteGroups_actionPerformed();
 692       }
 693       break;
 694
 695     case KeyEvent.VK_T:
 696       if (evt.isControlDown())
 697       {
 698         newView(null);
 699       }
 700       break;
 701
 702     }
 703     alignPanel.paintAlignment(true);
 704   }
 705
 706   /**
 707    * called by key handler and the hide all/show all menu items
 708    *
 709    * @param toggleSeqs
 710    * @param toggleCols
 711    */
 712   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 713   {
 714     boolean hide = false;
 715     SequenceGroup sg = viewport.getSelectionGroup();
 716     if (!toggleSeqs && !toggleCols)
 717     {
 718       // Hide everything by the current selection - this is a hack - we do the
 719       // invert and then hide
 720       // first check that there will be visible columns after the invert.
 721       if (viewport.hasSelectedColumns()
 722               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 723                       .getEndRes()))
 724       {
 725         // now invert the sequence set, if required - empty selection implies
 726         // that no hiding is required.
 727         if (sg != null)
 728         {
 729           invertSequenceMenuItem_actionPerformed();
 730           sg = viewport.getSelectionGroup();
 731           toggleSeqs = true;
 732
 733         }
 734         viewport.expandColSelection(sg, true);
 735         // finally invert the column selection and get the new sequence
 736         // selection and indicate it should be hidden.
 737         invertColSel_actionPerformed();
 738         toggleCols = true;
 739       }
 740     }
 741
 742     if (toggleSeqs)
 743     {
 744       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 745       {
 746         hide = true;
 747         viewport.hideAllSelectedSeqs();
 748       }
 749       else if (!(toggleCols && viewport.hasSelectedColumns()))
 750       {
 751         viewport.showAllHiddenSeqs();
 752       }
 753     }
 754
 755     if (toggleCols)
 756     {
 757       if (viewport.hasSelectedColumns())
 758       {
 759         viewport.hideSelectedColumns();
 760         if (!toggleSeqs)
 761         {
 762           viewport.setSelectionGroup(sg);
 763         }
 764       }
 765       else if (!hide)
 766       {
 767         viewport.showAllHiddenColumns();
 768       }
 769       viewport.sendSelection();
 770     }
 771   }
 772
 773   @Override
 774   public void keyReleased(KeyEvent evt)
 775   {
 776   }
 777
 778   @Override
 779   public void keyTyped(KeyEvent evt)
 780   {
 781   }
 782
 783   @Override
 784   public void itemStateChanged(ItemEvent evt)
 785   {
 786     final Object source = evt.getSource();
 787     if (source == displayNonconservedMenuItem)
 788     {
 789       displayNonconservedMenuItem_actionPerformed();
 790     }
 791     else if (source == colourTextMenuItem)
 792     {
 793       colourTextMenuItem_actionPerformed();
 794     }
 795     else if (source == wrapMenuItem)
 796     {
 797       wrapMenuItem_actionPerformed();
 798     }
 799     else if (source == scaleAbove)
 800     {
 801       viewport.setScaleAboveWrapped(scaleAbove.getState());
 802     }
 803     else if (source == scaleLeft)
 804     {
 805       viewport.setScaleLeftWrapped(scaleLeft.getState());
 806     }
 807     else if (source == scaleRight)
 808     {
 809       viewport.setScaleRightWrapped(scaleRight.getState());
 810     }
 811     else if (source == seqLimits)
 812     {
 813       seqLimits_itemStateChanged();
 814     }
 815     else if (source == viewBoxesMenuItem)
 816     {
 817       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 818     }
 819     else if (source == viewTextMenuItem)
 820     {
 821       viewport.setShowText(viewTextMenuItem.getState());
 822     }
 823     else if (source == renderGapsMenuItem)
 824     {
 825       viewport.setRenderGaps(renderGapsMenuItem.getState());
 826     }
 827     else if (source == annotationPanelMenuItem)
 828     {
 829       boolean showAnnotations = annotationPanelMenuItem.getState();
 830       showAlignmentAnnotations.setEnabled(showAnnotations);
 831       showSequenceAnnotations.setEnabled(showAnnotations);
 832       viewport.setShowAnnotation(showAnnotations);
 833       alignPanel.setAnnotationVisible(showAnnotations);
 834     }
 835     else if (source == sequenceFeatures)
 836     {
 837       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 838       alignPanel.seqPanel.seqCanvas.repaint();
 839     }
 840     else if (source == showAlignmentAnnotations)
 841     {
 842       setAnnotationsVisibility();
 843     }
 844     else if (source == showSequenceAnnotations)
 845     {
 846       setAnnotationsVisibility();
 847     }
 848     else if (source == sortAnnBySequence)
 849     {
 850       boolean newState = sortAnnBySequence.getState();
 851       sortAnnByLabel.setState(false);
 852       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 853               : SequenceAnnotationOrder.NONE);
 854       setViewportAnnotationOrder();
 855     }
 856     else if (source == sortAnnByLabel)
 857     {
 858       boolean newState = sortAnnByLabel.getState();
 859       sortAnnBySequence.setState(false);
 860       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 861               : SequenceAnnotationOrder.NONE);
 862       setViewportAnnotationOrder();
 863     }
 864     else if (source == showAutoFirst)
 865     {
 866       showAutoLast.setState(!showAutoFirst.getState());
 867       setShowAutoCalculatedAbove(showAutoFirst.getState());
 868       setViewportAnnotationOrder();
 869     }
 870     else if (source == showAutoLast)
 871     {
 872       showAutoFirst.setState(!showAutoLast.getState());
 873       setShowAutoCalculatedAbove(showAutoFirst.getState());
 874       setViewportAnnotationOrder();
 875     }
 876     else if (source == conservationMenuItem)
 877     {
 878       conservationMenuItem_actionPerformed();
 879     }
 880     else if (source == abovePIDThreshold)
 881     {
 882       abovePIDThreshold_actionPerformed();
 883     }
 884     else if (source == applyToAllGroups)
 885     {
 886       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 887     }
 888     else if (source == autoCalculate)
 889     {
 890       viewport.autoCalculateConsensus = autoCalculate.getState();
 891     }
 892     else if (source == sortByTree)
 893     {
 894       viewport.sortByTree = sortByTree.getState();
 895     }
 896     else if (source == this.centreColumnLabelFlag)
 897     {
 898       centreColumnLabelFlag_stateChanged();
 899     }
 900     else if (source == this.followMouseOverFlag)
 901     {
 902       mouseOverFlag_stateChanged();
 903     }
 904     else if (source == showGroupConsensus)
 905     {
 906       showGroupConsensus_actionPerformed();
 907     }
 908     else if (source == showGroupConservation)
 909     {
 910       showGroupConservation_actionPerformed();
 911     }
 912     else if (source == showSequenceLogo)
 913     {
 914       showSequenceLogo_actionPerformed();
 915     }
 916     else if (source == normSequenceLogo)
 917     {
 918       normSequenceLogo_actionPerformed();
 919     }
 920     else if (source == showConsensusHistogram)
 921     {
 922       showConsensusHistogram_actionPerformed();
 923     }
 924     else if (source == applyAutoAnnotationSettings)
 925     {
 926       applyAutoAnnotationSettings_actionPerformed();
 927     }
 928     alignPanel.paintAlignment(true);
 929   }
 930
 931   /**
 932    * Set the visibility state of sequence-related and/or alignment-related
 933    * annotations depending on checkbox selections, and repaint.
 934    *
 935    * @param visible
 936    */
 937   private void setAnnotationsVisibility()
 938   {
 939     boolean showForAlignment = showAlignmentAnnotations.getState();
 940     boolean showForSequences = showSequenceAnnotations.getState();
 941     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 942     {
 943       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 944               .getAlignmentAnnotation())
 945       {
 946         boolean visible = (aa.sequenceRef == null ? showForAlignment
 947                 : showForSequences);
 948         aa.visible = visible;
 949       }
 950     }
 951     alignPanel.validateAnnotationDimensions(true);
 952     validate();
 953     repaint();
 954   }
 955
 956   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 957   {
 958     this.annotationSortOrder = order;
 959   }
 960
 961   /**
 962    * Set flags on the viewport that control annotation ordering
 963    */
 964   private void setViewportAnnotationOrder()
 965   {
 966     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 967     this.alignPanel.av
 968             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 969   }
 970
 971   private void setShowAutoCalculatedAbove(boolean showAbove)
 972   {
 973     this.showAutoCalculatedAbove = showAbove;
 974   }
 975
 976   private void mouseOverFlag_stateChanged()
 977   {
 978     viewport.setFollowHighlight(followMouseOverFlag.getState());
 979     // TODO: could kick the scrollTo mechanism to reset view for current
 980     // searchresults.
 981   }
 982
 983   private void centreColumnLabelFlag_stateChanged()
 984   {
 985     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 986     this.alignPanel.annotationPanel.repaint();
 987   }
 988
 989   @Override
 990   public void actionPerformed(ActionEvent evt)
 991   {
 992     viewport.applet.currentAlignFrame = this;
 993
 994     Object source = evt.getSource();
 995
 996     if (source == inputText)
 997     {
 998       inputText_actionPerformed();
 999     }
1000     else if (source == loadTree)
1001     {
1002       loadTree_actionPerformed();
1003     }
1004     else if (source == loadApplication)
1005     {
1006       launchFullApplication();
1007     }
1008     else if (source == loadAnnotations)
1009     {
1010       loadAnnotations();
1011     }
1012     else if (source == outputAnnotations)
1013     {
1014       outputAnnotations(true);
1015     }
1016     else if (source == outputFeatures)
1017     {
1018       outputFeatures(true, "Jalview");
1019     }
1020     else if (source == closeMenuItem)
1021     {
1022       closeMenuItem_actionPerformed();
1023     }
1024     else if (source == copy)
1025     {
1026       copy_actionPerformed();
1027     }
1028     else if (source == undoMenuItem)
1029     {
1030       undoMenuItem_actionPerformed();
1031     }
1032     else if (source == redoMenuItem)
1033     {
1034       redoMenuItem_actionPerformed();
1035     }
1036     else if (source == inputText)
1037     {
1038       inputText_actionPerformed();
1039     }
1040     else if (source == closeMenuItem)
1041     {
1042       closeMenuItem_actionPerformed();
1043     }
1044     else if (source == undoMenuItem)
1045     {
1046       undoMenuItem_actionPerformed();
1047     }
1048     else if (source == redoMenuItem)
1049     {
1050       redoMenuItem_actionPerformed();
1051     }
1052     else if (source == copy)
1053     {
1054       copy_actionPerformed();
1055     }
1056     else if (source == pasteNew)
1057     {
1058       pasteNew_actionPerformed();
1059     }
1060     else if (source == pasteThis)
1061     {
1062       pasteThis_actionPerformed();
1063     }
1064     else if (source == cut)
1065     {
1066       cut_actionPerformed();
1067     }
1068     else if (source == delete)
1069     {
1070       delete_actionPerformed();
1071     }
1072     else if (source == createGroup)
1073     {
1074       createGroup_actionPerformed();
1075     }
1076     else if (source == unGroup)
1077     {
1078       unGroup_actionPerformed();
1079     }
1080     else if (source == grpsFromSelection)
1081     {
1082       makeGrpsFromSelection_actionPerformed();
1083     }
1084     else if (source == deleteGroups)
1085     {
1086       deleteGroups_actionPerformed();
1087     }
1088     else if (source == selectAllSequenceMenuItem)
1089     {
1090       selectAllSequenceMenuItem_actionPerformed();
1091     }
1092     else if (source == deselectAllSequenceMenuItem)
1093     {
1094       deselectAllSequenceMenuItem_actionPerformed();
1095     }
1096     else if (source == invertSequenceMenuItem)
1097     {
1098       invertSequenceMenuItem_actionPerformed();
1099       // uncomment to slave sequence selections in split frame
1100       // viewport.sendSelection();
1101     }
1102     else if (source == invertColSel)
1103     {
1104       viewport.invertColumnSelection();
1105       alignPanel.paintAlignment(true);
1106       viewport.sendSelection();
1107     }
1108     else if (source == remove2LeftMenuItem)
1109     {
1110       trimAlignment(true);
1111     }
1112     else if (source == remove2RightMenuItem)
1113     {
1114       trimAlignment(false);
1115     }
1116     else if (source == removeGappedColumnMenuItem)
1117     {
1118       removeGappedColumnMenuItem_actionPerformed();
1119     }
1120     else if (source == removeAllGapsMenuItem)
1121     {
1122       removeAllGapsMenuItem_actionPerformed();
1123     }
1124     else if (source == findMenuItem)
1125     {
1126       findMenuItem_actionPerformed();
1127     }
1128     else if (source == font)
1129     {
1130       new FontChooser(alignPanel);
1131     }
1132     else if (source == newView)
1133     {
1134       newView(null);
1135     }
1136     else if (source == showColumns)
1137     {
1138       viewport.showAllHiddenColumns();
1139       alignPanel.paintAlignment(true);
1140       viewport.sendSelection();
1141     }
1142     else if (source == showSeqs)
1143     {
1144       viewport.showAllHiddenSeqs();
1145       alignPanel.paintAlignment(true);
1146       // uncomment if we want to slave sequence selections in split frame
1147       // viewport.sendSelection();
1148     }
1149     else if (source == hideColumns)
1150     {
1151       viewport.hideSelectedColumns();
1152       alignPanel.paintAlignment(true);
1153       viewport.sendSelection();
1154     }
1155     else if (source == hideSequences
1156             && viewport.getSelectionGroup() != null)
1157     {
1158       viewport.hideAllSelectedSeqs();
1159       alignPanel.paintAlignment(true);
1160       // uncomment if we want to slave sequence selections in split frame
1161       // viewport.sendSelection();
1162     }
1163     else if (source == hideAllButSelection)
1164     {
1165       toggleHiddenRegions(false, false);
1166       alignPanel.paintAlignment(true);
1167       viewport.sendSelection();
1168     }
1169     else if (source == hideAllSelection)
1170     {
1171       SequenceGroup sg = viewport.getSelectionGroup();
1172       viewport.expandColSelection(sg, false);
1173       viewport.hideAllSelectedSeqs();
1174       viewport.hideSelectedColumns();
1175       alignPanel.paintAlignment(true);
1176       viewport.sendSelection();
1177     }
1178     else if (source == showAllHidden)
1179     {
1180       viewport.showAllHiddenColumns();
1181       viewport.showAllHiddenSeqs();
1182       alignPanel.paintAlignment(true);
1183       viewport.sendSelection();
1184     }
1185     else if (source == showGroupConsensus)
1186     {
1187       showGroupConsensus_actionPerformed();
1188     }
1189     else if (source == showGroupConservation)
1190     {
1191       showGroupConservation_actionPerformed();
1192     }
1193     else if (source == showSequenceLogo)
1194     {
1195       showSequenceLogo_actionPerformed();
1196     }
1197     else if (source == normSequenceLogo)
1198     {
1199       normSequenceLogo_actionPerformed();
1200     }
1201     else if (source == showConsensusHistogram)
1202     {
1203       showConsensusHistogram_actionPerformed();
1204     }
1205     else if (source == applyAutoAnnotationSettings)
1206     {
1207       applyAutoAnnotationSettings_actionPerformed();
1208     }
1209     else if (source == featureSettings)
1210     {
1211       new FeatureSettings(alignPanel);
1212     }
1213     else if (source == alProperties)
1214     {
1215       StringBuffer contents = new jalview.io.AlignmentProperties(
1216               viewport.getAlignment()).formatAsString();
1217       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1218       cap.setText(contents.toString());
1219       Frame frame = new Frame();
1220       frame.add(cap);
1221       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1222               "label.alignment_properties", new String[] { getTitle() }),
1223               400, 250);
1224     }
1225     else if (source == overviewMenuItem)
1226     {
1227       overviewMenuItem_actionPerformed();
1228     }
1229     else if (source == noColourmenuItem)
1230     {
1231       changeColour(null);
1232     }
1233     else if (source == clustalColour)
1234     {
1235       abovePIDThreshold.setState(false);
1236       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1237     }
1238     else if (source == zappoColour)
1239     {
1240       changeColour(new ZappoColourScheme());
1241     }
1242     else if (source == taylorColour)
1243     {
1244       changeColour(new TaylorColourScheme());
1245     }
1246     else if (source == hydrophobicityColour)
1247     {
1248       changeColour(new HydrophobicColourScheme());
1249     }
1250     else if (source == helixColour)
1251     {
1252       changeColour(new HelixColourScheme());
1253     }
1254     else if (source == strandColour)
1255     {
1256       changeColour(new StrandColourScheme());
1257     }
1258     else if (source == turnColour)
1259     {
1260       changeColour(new TurnColourScheme());
1261     }
1262     else if (source == buriedColour)
1263     {
1264       changeColour(new BuriedColourScheme());
1265     }
1266     else if (source == nucleotideColour)
1267     {
1268       changeColour(new NucleotideColourScheme());
1269     }
1270     else if (source == purinePyrimidineColour)
1271     {
1272       changeColour(new PurinePyrimidineColourScheme());
1273     }
1274     // else if (source == RNAInteractionColour)
1275     // {
1276     // changeColour(new RNAInteractionColourScheme());
1277     // }
1278     else if (source == RNAHelixColour)
1279     {
1280       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1281       // new RNAHelicesColourChooser(viewport, alignPanel);
1282     }
1283     else if (source == modifyPID)
1284     {
1285       modifyPID_actionPerformed();
1286     }
1287     else if (source == modifyConservation)
1288     {
1289       modifyConservation_actionPerformed();
1290     }
1291     else if (source == userDefinedColour)
1292     {
1293       new UserDefinedColours(alignPanel, null);
1294     }
1295     else if (source == PIDColour)
1296     {
1297       changeColour(new PIDColourScheme());
1298     }
1299     else if (source == BLOSUM62Colour)
1300     {
1301       changeColour(new Blosum62ColourScheme());
1302     }
1303     else if (source == tcoffeeColour)
1304     {
1305       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1306     }
1307     else if (source == annotationColour)
1308     {
1309       new AnnotationColourChooser(viewport, alignPanel);
1310     }
1311     else if (source == annotationColumnSelection)
1312     {
1313       new AnnotationColumnChooser(viewport, alignPanel);
1314     }
1315     else if (source == sortPairwiseMenuItem)
1316     {
1317       sortPairwiseMenuItem_actionPerformed();
1318     }
1319     else if (source == sortIDMenuItem)
1320     {
1321       sortIDMenuItem_actionPerformed();
1322     }
1323     else if (source == sortLengthMenuItem)
1324     {
1325       sortLengthMenuItem_actionPerformed();
1326     }
1327     else if (source == sortGroupMenuItem)
1328     {
1329       sortGroupMenuItem_actionPerformed();
1330     }
1331     else if (source == removeRedundancyMenuItem)
1332     {
1333       removeRedundancyMenuItem_actionPerformed();
1334     }
1335     else if (source == pairwiseAlignmentMenuItem)
1336     {
1337       pairwiseAlignmentMenuItem_actionPerformed();
1338     }
1339     else if (source == PCAMenuItem)
1340     {
1341       PCAMenuItem_actionPerformed();
1342     }
1343     else if (source == averageDistanceTreeMenuItem)
1344     {
1345       averageDistanceTreeMenuItem_actionPerformed();
1346     }
1347     else if (source == neighbourTreeMenuItem)
1348     {
1349       neighbourTreeMenuItem_actionPerformed();
1350     }
1351     else if (source == njTreeBlosumMenuItem)
1352     {
1353       njTreeBlosumMenuItem_actionPerformed();
1354     }
1355     else if (source == avDistanceTreeBlosumMenuItem)
1356     {
1357       avTreeBlosumMenuItem_actionPerformed();
1358     }
1359     else if (source == documentation)
1360     {
1361       documentation_actionPerformed();
1362     }
1363     else if (source == about)
1364     {
1365       about_actionPerformed();
1366     }
1367
1368   }
1369
1370   public void inputText_actionPerformed()
1371   {
1372     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373     Frame frame = new Frame();
1374     frame.add(cap);
1375     jalview.bin.JalviewLite.addFrame(frame,
1376             MessageManager.getString("label.input_cut_paste"), 500, 500);
1377   }
1378
1379   protected void outputText_actionPerformed(ActionEvent e)
1380   {
1381     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1382     Frame frame = new Frame();
1383     frame.add(cap);
1384     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1385             "label.alignment_output_command",
1386             new Object[] { e.getActionCommand() }), 600, 500);
1387
1388     FileFormatI fileFormat = FileFormats.getInstance().forName(
1389             e.getActionCommand());
1390     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1391             fileFormat, viewport.getAlignment(),
1392             viewport.getShowJVSuffix()));
1393   }
1394
1395   public void loadAnnotations()
1396   {
1397     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1398     cap.setText(MessageManager
1399             .getString("label.paste_features_annotations_Tcoffee_here"));
1400     cap.setAnnotationImport();
1401     Frame frame = new Frame();
1402     frame.add(cap);
1403     jalview.bin.JalviewLite.addFrame(frame,
1404             MessageManager.getString("action.paste_annotations"), 400, 300);
1405
1406   }
1407
1408   public String outputAnnotations(boolean displayTextbox)
1409   {
1410     String annotation = new AnnotationFile()
1411             .printAnnotationsForView(viewport);
1412
1413     if (displayTextbox)
1414     {
1415       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1416       Frame frame = new Frame();
1417       frame.add(cap);
1418       jalview.bin.JalviewLite.addFrame(frame,
1419               MessageManager.getString("label.annotations"), 600, 500);
1420       cap.setText(annotation);
1421     }
1422
1423     return annotation;
1424   }
1425
1426   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1427   {
1428     if (alignPanel.getFeatureRenderer() != null
1429             && viewport.getFeaturesDisplayed() != null)
1430     {
1431       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1432
1433     }
1434     return null;
1435   }
1436
1437   public String outputFeatures(boolean displayTextbox, String format)
1438   {
1439     String features;
1440     FeaturesFile formatter = new FeaturesFile();
1441     if (format.equalsIgnoreCase("Jalview"))
1442     {
1443       features = formatter.printJalviewFormat(viewport.getAlignment()
1444               .getSequencesArray(), getDisplayedFeatureCols());
1445     }
1446     else
1447     {
1448       features = formatter.printGffFormat(viewport.getAlignment()
1449               .getSequencesArray(), getDisplayedFeatureCols());
1450     }
1451
1452     if (displayTextbox)
1453     {
1454       boolean frimport = false;
1455       if (features == null || features.equals("No Features Visible"))
1456       {
1457         features = "# No features visible - paste some and import them here.";
1458         frimport = true;
1459       }
1460
1461       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1462       if (frimport)
1463       {
1464         cap.setAnnotationImport();
1465       }
1466       Frame frame = new Frame();
1467       frame.add(cap);
1468       jalview.bin.JalviewLite.addFrame(frame,
1469               MessageManager.getString("label.features"), 600, 500);
1470       cap.setText(features);
1471     }
1472     else
1473     {
1474       if (features == null)
1475       {
1476         features = "";
1477       }
1478     }
1479
1480     return features;
1481   }
1482
1483   void launchFullApplication()
1484   {
1485     StringBuffer url = new StringBuffer(jalviewServletURL);
1486
1487     // allow servlet parameters to be passed in applet parameter
1488     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1489             : "?";
1490     url.append(firstSep);
1491
1492     url.append("open="
1493             + appendProtocol(viewport.applet.getParameter("file")));
1494
1495     if (viewport.applet.getParameter("features") != null)
1496     {
1497       url.append("&features=");
1498       url.append(appendProtocol(viewport.applet.getParameter("features")));
1499     }
1500
1501     if (viewport.applet.getParameter("annotations") != null)
1502     {
1503       url.append("&annotations=");
1504       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1505     }
1506
1507     if (viewport.applet.getParameter("jnetfile") != null
1508             || viewport.applet.getParameter("jpredfile") != null)
1509     {
1510       url.append("&annotations=");
1511       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1512               .getParameter("jnetfile") : viewport.applet
1513               .getParameter("jpredfile")));
1514     }
1515
1516     if (viewport.applet.getParameter("defaultColour") != null)
1517     {
1518       url.append("&colour="
1519               + removeWhiteSpace(viewport.applet
1520                       .getParameter("defaultColour")));
1521     }
1522
1523     if (viewport.applet.getParameter("userDefinedColour") != null)
1524     {
1525       url.append("&colour="
1526               + removeWhiteSpace(viewport.applet
1527                       .getParameter("userDefinedColour")));
1528     }
1529     if (viewport.applet.getParameter("tree") != null)
1530     {
1531       url.append("&tree="
1532               + appendProtocol(viewport.applet.getParameter("tree")));
1533     }
1534     if (viewport.applet.getParameter("treeFile") != null)
1535     {
1536       url.append("&tree="
1537               + appendProtocol(viewport.applet.getParameter("treeFile")));
1538     }
1539
1540     showURL(url.toString(), "FULL_APP");
1541   }
1542
1543   String removeWhiteSpace(String colour)
1544   {
1545     StringBuffer sb = new StringBuffer();
1546     for (int i = 0; i < colour.length(); i++)
1547     {
1548       if (Character.isWhitespace(colour.charAt(i)))
1549       {
1550         sb.append("%20");
1551       }
1552       else
1553       {
1554         sb.append(colour.charAt(i));
1555       }
1556     }
1557
1558     return sb.toString();
1559   }
1560
1561   String appendProtocol(String url)
1562   {
1563     try
1564     {
1565       new URL(url);
1566       url = URLEncoder.encode(url);
1567     }
1568     /*
1569      * When we finally deprecate 1.1 compatibility, we can start to use
1570      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1571      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1572      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1573      * ex.printStackTrace(); }
1574      */
1575     catch (java.net.MalformedURLException ex)
1576     {
1577       url = viewport.applet.getCodeBase() + url;
1578     }
1579     return url;
1580   }
1581
1582   public void closeMenuItem_actionPerformed()
1583   {
1584     PaintRefresher.RemoveComponent(alignPanel);
1585     if (alignPanel.seqPanel != null
1586             && alignPanel.seqPanel.seqCanvas != null)
1587     {
1588       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1589     }
1590     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1591     {
1592       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1593     }
1594
1595     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1596     {
1597       System.exit(0);
1598     }
1599     else
1600     {
1601     }
1602     viewport = null;
1603     alignPanel = null;
1604     this.dispose();
1605   }
1606
1607   /**
1608    * TODO: JAL-1104
1609    */
1610   void updateEditMenuBar()
1611   {
1612
1613     if (viewport.getHistoryList().size() > 0)
1614     {
1615       undoMenuItem.setEnabled(true);
1616       CommandI command = viewport.getHistoryList().peek();
1617       undoMenuItem.setLabel(MessageManager.formatMessage(
1618               "label.undo_command",
1619               new Object[] { command.getDescription() }));
1620     }
1621     else
1622     {
1623       undoMenuItem.setEnabled(false);
1624       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1625     }
1626
1627     if (viewport.getRedoList().size() > 0)
1628     {
1629       redoMenuItem.setEnabled(true);
1630
1631       CommandI command = viewport.getRedoList().peek();
1632       redoMenuItem.setLabel(MessageManager.formatMessage(
1633               "label.redo_command",
1634               new Object[] { command.getDescription() }));
1635     }
1636     else
1637     {
1638       redoMenuItem.setEnabled(false);
1639       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1640     }
1641   }
1642
1643   /**
1644    * TODO: JAL-1104
1645    */
1646   @Override
1647   public void addHistoryItem(CommandI command)
1648   {
1649     if (command.getSize() > 0)
1650     {
1651       viewport.addToHistoryList(command);
1652       viewport.clearRedoList();
1653       updateEditMenuBar();
1654       viewport.updateHiddenColumns();
1655     }
1656   }
1657
1658   /**
1659    * TODO: JAL-1104 DOCUMENT ME!
1660    *
1661    * @param e
1662    *          DOCUMENT ME!
1663    */
1664   protected void undoMenuItem_actionPerformed()
1665   {
1666     if (viewport.getHistoryList().isEmpty())
1667     {
1668       return;
1669     }
1670
1671     CommandI command = viewport.getHistoryList().pop();
1672     viewport.addToRedoList(command);
1673     command.undoCommand(null);
1674
1675     AlignmentViewport originalSource = getOriginatingSource(command);
1676     // JBPNote Test
1677     if (originalSource != viewport)
1678     {
1679       System.err
1680               .println("Warning: Viewport object mismatch whilst undoing");
1681     }
1682     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1683                                           // viewport.getColumnSelection().getHiddenColumns()
1684                                           // != null;
1685     updateEditMenuBar();
1686     originalSource.firePropertyChange("alignment", null, originalSource
1687             .getAlignment().getSequences());
1688   }
1689
1690   /**
1691    * TODO: JAL-1104 DOCUMENT ME!
1692    *
1693    * @param e
1694    *          DOCUMENT ME!
1695    */
1696   protected void redoMenuItem_actionPerformed()
1697   {
1698     if (viewport.getRedoList().isEmpty())
1699     {
1700       return;
1701     }
1702
1703     CommandI command = viewport.getRedoList().pop();
1704     viewport.addToHistoryList(command);
1705     command.doCommand(null);
1706
1707     AlignmentViewport originalSource = getOriginatingSource(command);
1708     // JBPNote Test
1709     if (originalSource != viewport)
1710     {
1711       System.err
1712               .println("Warning: Viewport object mismatch whilst re-doing");
1713     }
1714     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1715                                           // viewport.getColumnSelection().getHiddenColumns()
1716                                           // != null;
1717
1718     updateEditMenuBar();
1719     originalSource.firePropertyChange("alignment", null, originalSource
1720             .getAlignment().getSequences());
1721   }
1722
1723   AlignmentViewport getOriginatingSource(CommandI command)
1724   {
1725     AlignmentViewport originalSource = null;
1726     // For sequence removal and addition, we need to fire
1727     // the property change event FROM the viewport where the
1728     // original alignment was altered
1729     AlignmentI al = null;
1730     if (command instanceof EditCommand)
1731     {
1732       EditCommand editCommand = (EditCommand) command;
1733       al = editCommand.getAlignment();
1734       Vector comps = (Vector) PaintRefresher.components.get(viewport
1735               .getSequenceSetId());
1736       for (int i = 0; i < comps.size(); i++)
1737       {
1738         if (comps.elementAt(i) instanceof AlignmentPanel)
1739         {
1740           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1741           {
1742             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1743             break;
1744           }
1745         }
1746       }
1747     }
1748
1749     if (originalSource == null)
1750     {
1751       // The original view is closed, we must validate
1752       // the current view against the closed view first
1753       if (al != null)
1754       {
1755         PaintRefresher.validateSequences(al, viewport.getAlignment());
1756       }
1757
1758       originalSource = viewport;
1759     }
1760
1761     return originalSource;
1762   }
1763
1764   /**
1765    * Move the currently selected sequences up or down one position in the
1766    * alignment
1767    *
1768    * @param up
1769    */
1770   public void moveSelectedSequences(boolean up)
1771   {
1772     SequenceGroup sg = viewport.getSelectionGroup();
1773     if (sg == null)
1774     {
1775       return;
1776     }
1777     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1778             up ? null : viewport.getHiddenRepSequences(), up);
1779     alignPanel.paintAlignment(true);
1780
1781     /*
1782      * Also move cDNA/protein complement sequences
1783      */
1784     AlignViewportI complement = viewport.getCodingComplement();
1785     if (complement != null)
1786     {
1787       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1788               viewport, complement);
1789       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1790               up ? null : complement.getHiddenRepSequences(), up);
1791       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1792     }
1793   }
1794
1795   synchronized void slideSequences(boolean right, int size)
1796   {
1797     List<SequenceI> sg = new Vector<SequenceI>();
1798     if (viewport.cursorMode)
1799     {
1800       sg.add(viewport.getAlignment().getSequenceAt(
1801               alignPanel.seqPanel.seqCanvas.cursorY));
1802     }
1803     else if (viewport.getSelectionGroup() != null
1804             && viewport.getSelectionGroup().getSize() != viewport
1805                     .getAlignment().getHeight())
1806     {
1807       sg = viewport.getSelectionGroup().getSequences(
1808               viewport.getHiddenRepSequences());
1809     }
1810
1811     if (sg.size() < 1)
1812     {
1813       return;
1814     }
1815
1816     Vector<SequenceI> invertGroup = new Vector();
1817
1818     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1819     {
1820       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1821       {
1822         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1823       }
1824     }
1825
1826     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1827
1828     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1829             .size()]);
1830     for (int i = 0; i < invertGroup.size(); i++)
1831     {
1832       seqs2[i] = invertGroup.elementAt(i);
1833     }
1834
1835     SlideSequencesCommand ssc;
1836     if (right)
1837     {
1838       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1839               size, viewport.getGapCharacter());
1840     }
1841     else
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1844               size, viewport.getGapCharacter());
1845     }
1846
1847     int groupAdjustment = 0;
1848     if (ssc.getGapsInsertedBegin() && right)
1849     {
1850       if (viewport.cursorMode)
1851       {
1852         alignPanel.seqPanel.moveCursor(size, 0);
1853       }
1854       else
1855       {
1856         groupAdjustment = size;
1857       }
1858     }
1859     else if (!ssc.getGapsInsertedBegin() && !right)
1860     {
1861       if (viewport.cursorMode)
1862       {
1863         alignPanel.seqPanel.moveCursor(-size, 0);
1864       }
1865       else
1866       {
1867         groupAdjustment = -size;
1868       }
1869     }
1870
1871     if (groupAdjustment != 0)
1872     {
1873       viewport.getSelectionGroup().setStartRes(
1874               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1875       viewport.getSelectionGroup().setEndRes(
1876               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1877     }
1878
1879     boolean appendHistoryItem = false;
1880     Deque<CommandI> historyList = viewport.getHistoryList();
1881     if (historyList != null && historyList.size() > 0
1882             && historyList.peek() instanceof SlideSequencesCommand)
1883     {
1884       appendHistoryItem = ssc
1885               .appendSlideCommand((SlideSequencesCommand) historyList
1886                       .peek());
1887     }
1888
1889     if (!appendHistoryItem)
1890     {
1891       addHistoryItem(ssc);
1892     }
1893
1894     repaint();
1895   }
1896
1897   static StringBuffer copiedSequences;
1898
1899   static Vector copiedHiddenColumns;
1900
1901   protected void copy_actionPerformed()
1902   {
1903     if (viewport.getSelectionGroup() == null)
1904     {
1905       return;
1906     }
1907
1908     SequenceGroup sg = viewport.getSelectionGroup();
1909     copiedSequences = new StringBuffer();
1910     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1911     for (int i = 0; i < sg.getSize(); i++)
1912     {
1913       SequenceI seq = sg.getSequenceAt(i);
1914       int index = viewport.getAlignment().findIndex(seq);
1915       orderedSeqs.put(index, seq);
1916     }
1917
1918     int index = 0, startRes, endRes;
1919     char ch;
1920
1921     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1922     {
1923       copiedHiddenColumns = new Vector();
1924       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1925       for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1926       {
1927         copiedHiddenColumns.addElement(new int[] {
1928             region[0] - hiddenOffset, region[1] - hiddenOffset });
1929       }
1930     }
1931     else
1932     {
1933       copiedHiddenColumns = null;
1934     }
1935
1936     for (int i = 0; i < sg.getSize(); i++)
1937     {
1938       SequenceI seq = null;
1939
1940       while (seq == null)
1941       {
1942         if (orderedSeqs.containsKey(index))
1943         {
1944           seq = orderedSeqs.get(index);
1945           index++;
1946           break;
1947         }
1948         else
1949         {
1950           index++;
1951         }
1952       }
1953
1954       // FIND START RES
1955       // Returns residue following index if gap
1956       startRes = seq.findPosition(sg.getStartRes());
1957
1958       // FIND END RES
1959       // Need to find the residue preceeding index if gap
1960       endRes = 0;
1961
1962       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1963       {
1964         ch = seq.getCharAt(j);
1965         if (!jalview.util.Comparison.isGap((ch)))
1966         {
1967           endRes++;
1968         }
1969       }
1970
1971       if (endRes > 0)
1972       {
1973         endRes += seq.getStart() - 1;
1974       }
1975
1976       copiedSequences.append(seq.getName()
1977               + "\t"
1978               + startRes
1979               + "\t"
1980               + endRes
1981               + "\t"
1982               + seq.getSequenceAsString(sg.getStartRes(),
1983                       sg.getEndRes() + 1) + "\n");
1984     }
1985
1986   }
1987
1988   protected void pasteNew_actionPerformed()
1989   {
1990     paste(true);
1991   }
1992
1993   protected void pasteThis_actionPerformed()
1994   {
1995     paste(false);
1996   }
1997
1998   void paste(boolean newAlignment)
1999   {
2000     try
2001     {
2002
2003       if (copiedSequences == null)
2004       {
2005         return;
2006       }
2007
2008       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2009       Vector seqs = new Vector();
2010       while (st.hasMoreElements())
2011       {
2012         String name = st.nextToken();
2013         int start = Integer.parseInt(st.nextToken());
2014         int end = Integer.parseInt(st.nextToken());
2015         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2016       }
2017       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2018       for (int i = 0; i < seqs.size(); i++)
2019       {
2020         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2021       }
2022
2023       if (newAlignment)
2024       {
2025         String newtitle = MessageManager
2026                 .getString("label.copied_sequences");
2027         if (getTitle().startsWith(
2028                 MessageManager.getString("label.copied_sequences")))
2029         {
2030           newtitle = getTitle();
2031         }
2032         else
2033         {
2034           newtitle = newtitle.concat(MessageManager.formatMessage(
2035                   "label.from_msname", new String[] { getTitle() }));
2036         }
2037         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2038                 viewport.applet, newtitle, false);
2039         if (copiedHiddenColumns != null)
2040         {
2041           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2042           {
2043             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2044             af.viewport.hideColumns(region[0], region[1]);
2045           }
2046         }
2047
2048         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2049                 frameHeight);
2050       }
2051       else
2052       {
2053         addSequences(newSeqs);
2054       }
2055
2056     } catch (Exception ex)
2057     {
2058     } // could be anything being pasted in here
2059
2060   }
2061
2062   void addSequences(SequenceI[] seqs)
2063   {
2064     for (int i = 0; i < seqs.length; i++)
2065     {
2066       viewport.getAlignment().addSequence(seqs[i]);
2067     }
2068
2069     // !newAlignment
2070     addHistoryItem(new EditCommand(
2071             MessageManager.getString("label.add_sequences"), Action.PASTE,
2072             seqs, 0, viewport.getAlignment().getWidth(),
2073             viewport.getAlignment()));
2074
2075     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2076     viewport.getAlignment().getWidth();
2077     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2078             .getSequences());
2079
2080   }
2081
2082   protected void cut_actionPerformed()
2083   {
2084     copy_actionPerformed();
2085     delete_actionPerformed();
2086   }
2087
2088   protected void delete_actionPerformed()
2089   {
2090
2091     SequenceGroup sg = viewport.getSelectionGroup();
2092     if (sg == null)
2093     {
2094       return;
2095     }
2096
2097     Vector seqs = new Vector();
2098     SequenceI seq;
2099     for (int i = 0; i < sg.getSize(); i++)
2100     {
2101       seq = sg.getSequenceAt(i);
2102       seqs.addElement(seq);
2103     }
2104
2105     /*
2106      * If the cut affects all sequences, warn, remove highlighted columns
2107      */
2108     if (sg.getSize() == viewport.getAlignment().getHeight())
2109     {
2110       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2111               .getAlignment().getWidth()) ? true : false;
2112       if (isEntireAlignWidth)
2113       {
2114         String title = MessageManager.getString("label.delete_all");
2115         Panel infoPanel = new Panel();
2116         infoPanel.setLayout(new FlowLayout());
2117         infoPanel
2118                 .add(new Label(MessageManager.getString("warn.delete_all")));
2119
2120         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2121         dialog.setMainPanel(infoPanel);
2122         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2123         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2124         dialog.setVisible(true);
2125
2126         if (!dialog.accept)
2127         {
2128           return;
2129         }
2130       }
2131       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2132               sg.getEndRes() + 1);
2133     }
2134
2135     SequenceI[] cut = new SequenceI[seqs.size()];
2136     for (int i = 0; i < seqs.size(); i++)
2137     {
2138       cut[i] = (SequenceI) seqs.elementAt(i);
2139     }
2140
2141     /*
2142      * //ADD HISTORY ITEM
2143      */
2144     addHistoryItem(new EditCommand(
2145             MessageManager.getString("label.cut_sequences"), Action.CUT,
2146             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2147             viewport.getAlignment()));
2148
2149     viewport.setSelectionGroup(null);
2150     viewport.getAlignment().deleteGroup(sg);
2151
2152     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153             .getSequences());
2154
2155     if (viewport.getAlignment().getHeight() < 1)
2156     {
2157       this.setVisible(false);
2158     }
2159     viewport.sendSelection();
2160   }
2161
2162   /**
2163    * group consensus toggled
2164    *
2165    */
2166   protected void showGroupConsensus_actionPerformed()
2167   {
2168     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2169     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170
2171   }
2172
2173   /**
2174    * group conservation toggled.
2175    */
2176   protected void showGroupConservation_actionPerformed()
2177   {
2178     viewport.setShowGroupConservation(showGroupConservation.getState());
2179     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180   }
2181
2182   /*
2183    * (non-Javadoc)
2184    *
2185    * @see
2186    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2187    * .event.ActionEvent)
2188    */
2189   protected void showConsensusHistogram_actionPerformed()
2190   {
2191     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2192     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193   }
2194
2195   /*
2196    * (non-Javadoc)
2197    *
2198    * @see
2199    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2200    * .event.ActionEvent)
2201    */
2202   protected void showSequenceLogo_actionPerformed()
2203   {
2204     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2205     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2206   }
2207
2208   protected void normSequenceLogo_actionPerformed()
2209   {
2210     showSequenceLogo.setState(true);
2211     viewport.setShowSequenceLogo(true);
2212     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2213     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2214   }
2215
2216   protected void applyAutoAnnotationSettings_actionPerformed()
2217   {
2218     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2219   }
2220
2221   protected void makeGrpsFromSelection_actionPerformed()
2222   {
2223     if (avc.makeGroupsFromSelection())
2224     {
2225       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2226       alignPanel.updateAnnotation();
2227       alignPanel.paintAlignment(true);
2228     }
2229   }
2230
2231   protected void createGroup_actionPerformed()
2232   {
2233     avc.createGroup();
2234   }
2235
2236   protected void unGroup_actionPerformed()
2237   {
2238     if (avc.unGroup())
2239     {
2240       alignPanel.alignmentChanged();
2241     }
2242   }
2243
2244   protected void deleteGroups_actionPerformed()
2245   {
2246     if (avc.deleteGroups())
2247     {
2248       alignPanel.alignmentChanged();
2249     }
2250   }
2251
2252   public void selectAllSequenceMenuItem_actionPerformed()
2253   {
2254     SequenceGroup sg = new SequenceGroup();
2255     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2256     {
2257       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2258     }
2259     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2260     viewport.setSelectionGroup(sg);
2261     // JAL-2034 - should delegate to
2262     // alignPanel to decide if overview needs
2263     // updating.
2264     alignPanel.paintAlignment(false);
2265     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2266     viewport.sendSelection();
2267   }
2268
2269   public void deselectAllSequenceMenuItem_actionPerformed()
2270   {
2271     if (viewport.cursorMode)
2272     {
2273       alignPanel.seqPanel.keyboardNo1 = null;
2274       alignPanel.seqPanel.keyboardNo2 = null;
2275     }
2276     viewport.setSelectionGroup(null);
2277     viewport.getColumnSelection().clear();
2278     viewport.setSelectionGroup(null);
2279     alignPanel.idPanel.idCanvas.searchResults = null;
2280     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2281     // JAL-2034 - should delegate to
2282     // alignPanel to decide if overview needs
2283     // updating.
2284     alignPanel.paintAlignment(false);
2285     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2286     viewport.sendSelection();
2287   }
2288
2289   public void invertSequenceMenuItem_actionPerformed()
2290   {
2291     SequenceGroup sg = viewport.getSelectionGroup();
2292     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2293     {
2294       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2295     }
2296
2297     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2298     viewport.sendSelection();
2299   }
2300
2301   public void invertColSel_actionPerformed()
2302   {
2303     viewport.invertColumnSelection();
2304     alignPanel.paintAlignment(true);
2305     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2306     viewport.sendSelection();
2307   }
2308
2309   void trimAlignment(boolean trimLeft)
2310   {
2311     AlignmentI al = viewport.getAlignment();
2312     ViewportRanges ranges = viewport.getRanges();
2313     ColumnSelection colSel = viewport.getColumnSelection();
2314     int column;
2315
2316     if (!colSel.isEmpty())
2317     {
2318       if (trimLeft)
2319       {
2320         column = colSel.getMin();
2321       }
2322       else
2323       {
2324         column = colSel.getMax();
2325       }
2326
2327       SequenceI[] seqs;
2328       if (viewport.getSelectionGroup() != null)
2329       {
2330         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2331                 viewport.getHiddenRepSequences());
2332       }
2333       else
2334       {
2335         seqs = al.getSequencesArray();
2336       }
2337
2338       TrimRegionCommand trimRegion;
2339       if (trimLeft)
2340       {
2341         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2342                 column, al);
2343         ranges.setStartRes(0);
2344       }
2345       else
2346       {
2347         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2348                 column, al);
2349       }
2350
2351       statusBar.setText(MessageManager.formatMessage(
2352               "label.removed_columns",
2353               new String[] { Integer.valueOf(trimRegion.getSize())
2354                       .toString() }));
2355       addHistoryItem(trimRegion);
2356
2357       for (SequenceGroup sg : al.getGroups())
2358       {
2359         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2360                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2361         {
2362           al.deleteGroup(sg);
2363         }
2364       }
2365
2366       viewport.firePropertyChange("alignment", null, al.getSequences());
2367     }
2368   }
2369
2370   public void removeGappedColumnMenuItem_actionPerformed()
2371   {
2372     AlignmentI al = viewport.getAlignment();
2373     ViewportRanges ranges = viewport.getRanges();
2374     int start = 0;
2375     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2376
2377     SequenceI[] seqs;
2378     if (viewport.getSelectionGroup() != null)
2379     {
2380       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2381               viewport.getHiddenRepSequences());
2382       start = viewport.getSelectionGroup().getStartRes();
2383       end = viewport.getSelectionGroup().getEndRes();
2384     }
2385     else
2386     {
2387       seqs = viewport.getAlignment().getSequencesArray();
2388     }
2389
2390     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2391             "Remove Gapped Columns", seqs, start, end,
2392             viewport.getAlignment());
2393
2394     addHistoryItem(removeGapCols);
2395
2396     statusBar.setText(MessageManager.formatMessage(
2397             "label.removed_empty_columns",
2398             new String[] { Integer.valueOf(removeGapCols.getSize())
2399                     .toString() }));
2400
2401     // This is to maintain viewport position on first residue
2402     // of first sequence
2403     SequenceI seq = al.getSequenceAt(0);
2404     int startRes = seq.findPosition(ranges.getStartRes());
2405     // ShiftList shifts;
2406     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2407     // edit.alColumnChanges=shifts.getInverse();
2408     // if (viewport.hasHiddenColumns)
2409     // viewport.getColumnSelection().compensateForEdits(shifts);
2410     ranges.setStartRes(seq.findIndex(startRes) - 1);
2411     viewport.firePropertyChange("alignment", null, al.getSequences());
2412
2413   }
2414
2415   public void removeAllGapsMenuItem_actionPerformed()
2416   {
2417     AlignmentI al = viewport.getAlignment();
2418     ViewportRanges ranges = viewport.getRanges();
2419     int start = 0;
2420     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2421
2422     SequenceI[] seqs;
2423     if (viewport.getSelectionGroup() != null)
2424     {
2425       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2426               viewport.getHiddenRepSequences());
2427       start = viewport.getSelectionGroup().getStartRes();
2428       end = viewport.getSelectionGroup().getEndRes();
2429     }
2430     else
2431     {
2432       seqs = viewport.getAlignment().getSequencesArray();
2433     }
2434
2435     // This is to maintain viewport position on first residue
2436     // of first sequence
2437     SequenceI seq = al.getSequenceAt(0);
2438     int startRes = seq.findPosition(ranges.getStartRes());
2439
2440     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2441             al));
2442
2443     ranges.setStartRes(seq.findIndex(startRes) - 1);
2444
2445     viewport.firePropertyChange("alignment", null, al.getSequences());
2446
2447   }
2448
2449   public void findMenuItem_actionPerformed()
2450   {
2451     new Finder(alignPanel);
2452   }
2453
2454   /**
2455    * create a new view derived from the current view
2456    *
2457    * @param viewtitle
2458    * @return frame for the new view
2459    */
2460   public AlignFrame newView(String viewtitle)
2461   {
2462     AlignmentI newal;
2463     if (viewport.hasHiddenRows())
2464     {
2465       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2466               .getFullAlignment().getSequencesArray());
2467     }
2468     else
2469     {
2470       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2471     }
2472
2473     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2474     {
2475       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2476       {
2477         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2478         {
2479           newal.addAnnotation(viewport.getAlignment()
2480                   .getAlignmentAnnotation()[i]);
2481         }
2482       }
2483     }
2484
2485     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2486
2487     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2488     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2489     PaintRefresher.Register(newaf.alignPanel,
2490             newaf.alignPanel.av.getSequenceSetId());
2491
2492     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2493             newaf.alignPanel.av.getSequenceSetId());
2494     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2495             newaf.alignPanel.av.getSequenceSetId());
2496
2497     Vector comps = (Vector) PaintRefresher.components.get(viewport
2498             .getSequenceSetId());
2499     int viewSize = -1;
2500     for (int i = 0; i < comps.size(); i++)
2501     {
2502       if (comps.elementAt(i) instanceof AlignmentPanel)
2503       {
2504         viewSize++;
2505       }
2506     }
2507
2508     String title = new String(this.getTitle());
2509     if (viewtitle != null)
2510     {
2511       title = viewtitle + " ( " + title + ")";
2512     }
2513     else
2514     {
2515       if (title.indexOf("(View") > -1)
2516       {
2517         title = title.substring(0, title.indexOf("(View"));
2518       }
2519       title += "(View " + viewSize + ")";
2520     }
2521
2522     newaf.setTitle(title.toString());
2523
2524     newaf.viewport.setHistoryList(viewport.getHistoryList());
2525     newaf.viewport.setRedoList(viewport.getRedoList());
2526     return newaf;
2527   }
2528
2529   /**
2530    *
2531    * @return list of feature groups on the view
2532    */
2533   public String[] getFeatureGroups()
2534   {
2535     FeatureRenderer fr = null;
2536     if (alignPanel != null
2537             && (fr = alignPanel.getFeatureRenderer()) != null)
2538     {
2539       List<String> gps = fr.getFeatureGroups();
2540       String[] _gps = gps.toArray(new String[gps.size()]);
2541       return _gps;
2542     }
2543     return null;
2544   }
2545
2546   /**
2547    * get sequence feature groups that are hidden or shown
2548    *
2549    * @param visible
2550    *          true is visible
2551    * @return list
2552    */
2553   public String[] getFeatureGroupsOfState(boolean visible)
2554   {
2555     FeatureRenderer fr = null;
2556     if (alignPanel != null
2557             && (fr = alignPanel.getFeatureRenderer()) != null)
2558     {
2559       List<String> gps = fr.getGroups(visible);
2560       String[] _gps = gps.toArray(new String[gps.size()]);
2561       return _gps;
2562     }
2563     return null;
2564   }
2565
2566   /**
2567    * Change the display state for the given feature groups
2568    *
2569    * @param groups
2570    *          list of group strings
2571    * @param state
2572    *          visible or invisible
2573    */
2574   public void setFeatureGroupState(String[] groups, boolean state)
2575   {
2576     FeatureRenderer fr = null;
2577     this.sequenceFeatures.setState(true);
2578     viewport.setShowSequenceFeatures(true);
2579     if (alignPanel != null
2580             && (fr = alignPanel.getFeatureRenderer()) != null)
2581     {
2582
2583       fr.setGroupVisibility(Arrays.asList(groups), state);
2584       alignPanel.seqPanel.seqCanvas.repaint();
2585       if (alignPanel.overviewPanel != null)
2586       {
2587         alignPanel.overviewPanel.updateOverviewImage();
2588       }
2589     }
2590   }
2591
2592   public void seqLimits_itemStateChanged()
2593   {
2594     viewport.setShowJVSuffix(seqLimits.getState());
2595     alignPanel.fontChanged();
2596     alignPanel.paintAlignment(true);
2597   }
2598
2599   protected void colourTextMenuItem_actionPerformed()
2600   {
2601     viewport.setColourText(colourTextMenuItem.getState());
2602     alignPanel.paintAlignment(true);
2603   }
2604
2605   protected void displayNonconservedMenuItem_actionPerformed()
2606   {
2607     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2608     alignPanel.paintAlignment(true);
2609   }
2610
2611   protected void wrapMenuItem_actionPerformed()
2612   {
2613     viewport.setWrapAlignment(wrapMenuItem.getState());
2614     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2615     scaleAbove.setEnabled(wrapMenuItem.getState());
2616     scaleLeft.setEnabled(wrapMenuItem.getState());
2617     scaleRight.setEnabled(wrapMenuItem.getState());
2618     alignPanel.paintAlignment(true);
2619   }
2620
2621   public void overviewMenuItem_actionPerformed()
2622   {
2623     if (alignPanel.overviewPanel != null)
2624     {
2625       return;
2626     }
2627
2628     Frame frame = new Frame();
2629     OverviewPanel overview = new OverviewPanel(alignPanel);
2630     frame.add(overview);
2631     // +50 must allow for applet frame window
2632     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2633             "label.overview_params", new String[] { this.getTitle() }),
2634             overview.getPreferredSize().width,
2635             overview.getPreferredSize().height + 50);
2636
2637     frame.pack();
2638     final AlignmentPanel ap = alignPanel;
2639     frame.addWindowListener(new WindowAdapter()
2640     {
2641       @Override
2642       public void windowClosing(WindowEvent e)
2643       {
2644         if (ap != null)
2645         {
2646           ap.setOverviewPanel(null);
2647         }
2648       };
2649     });
2650
2651     alignPanel.setOverviewPanel(overview);
2652
2653   }
2654
2655   @Override
2656   public void changeColour(ColourSchemeI cs)
2657   {
2658     viewport.setGlobalColourScheme(cs);
2659
2660     alignPanel.paintAlignment(true);
2661   }
2662
2663   protected void modifyPID_actionPerformed()
2664   {
2665     if (viewport.getAbovePIDThreshold()
2666             && viewport.getGlobalColourScheme() != null)
2667     {
2668       SliderPanel.setPIDSliderSource(alignPanel,
2669               viewport.getResidueShading(), alignPanel.getViewName());
2670       SliderPanel.showPIDSlider();
2671     }
2672   }
2673
2674   protected void modifyConservation_actionPerformed()
2675   {
2676     if (viewport.getConservationSelected()
2677             && viewport.getGlobalColourScheme() != null)
2678     {
2679       SliderPanel.setConservationSlider(alignPanel,
2680               viewport.getResidueShading(), alignPanel.getViewName());
2681       SliderPanel.showConservationSlider();
2682     }
2683   }
2684
2685   protected void conservationMenuItem_actionPerformed()
2686   {
2687     boolean selected = conservationMenuItem.getState();
2688     modifyConservation.setEnabled(selected);
2689     viewport.setConservationSelected(selected);
2690     viewport.getResidueShading().setConservationApplied(selected);
2691
2692     changeColour(viewport.getGlobalColourScheme());
2693
2694     if (selected)
2695     {
2696       modifyConservation_actionPerformed();
2697     }
2698     else
2699     {
2700       SliderPanel.hideConservationSlider();
2701     }
2702   }
2703
2704   public void abovePIDThreshold_actionPerformed()
2705   {
2706     boolean selected = abovePIDThreshold.getState();
2707     modifyPID.setEnabled(selected);
2708     viewport.setAbovePIDThreshold(selected);
2709     if (!selected)
2710     {
2711       viewport.getResidueShading().setThreshold(0,
2712               viewport.isIgnoreGapsConsensus());
2713     }
2714
2715     changeColour(viewport.getGlobalColourScheme());
2716
2717     if (selected)
2718     {
2719       modifyPID_actionPerformed();
2720     }
2721     else
2722     {
2723       SliderPanel.hidePIDSlider();
2724     }
2725   }
2726
2727   public void sortPairwiseMenuItem_actionPerformed()
2728   {
2729     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2730     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2731             .getAlignment().getSequenceAt(0), null);
2732
2733     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true);
2736   }
2737
2738   public void sortIDMenuItem_actionPerformed()
2739   {
2740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741     AlignmentSorter.sortByID(viewport.getAlignment());
2742     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2743             viewport.getAlignment()));
2744     alignPanel.paintAlignment(true);
2745   }
2746
2747   public void sortLengthMenuItem_actionPerformed()
2748   {
2749     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750     AlignmentSorter.sortByLength(viewport.getAlignment());
2751     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2752             viewport.getAlignment()));
2753     alignPanel.paintAlignment(true);
2754   }
2755
2756   public void sortGroupMenuItem_actionPerformed()
2757   {
2758     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2759     AlignmentSorter.sortByGroup(viewport.getAlignment());
2760     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2761             viewport.getAlignment()));
2762     alignPanel.paintAlignment(true);
2763
2764   }
2765
2766   public void removeRedundancyMenuItem_actionPerformed()
2767   {
2768     new RedundancyPanel(alignPanel);
2769   }
2770
2771   public void pairwiseAlignmentMenuItem_actionPerformed()
2772   {
2773     if (viewport.getSelectionGroup() != null
2774             && viewport.getSelectionGroup().getSize() > 1)
2775     {
2776       Frame frame = new Frame();
2777       frame.add(new PairwiseAlignPanel(alignPanel));
2778       jalview.bin.JalviewLite.addFrame(frame,
2779               MessageManager.getString("action.pairwise_alignment"), 600,
2780               500);
2781     }
2782   }
2783
2784   public void PCAMenuItem_actionPerformed()
2785   {
2786     // are the sequences aligned?
2787     if (!viewport.getAlignment().isAligned(false))
2788     {
2789       SequenceI current;
2790       int Width = viewport.getAlignment().getWidth();
2791
2792       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2793       {
2794         current = viewport.getAlignment().getSequenceAt(i);
2795
2796         if (current.getLength() < Width)
2797         {
2798           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2799         }
2800       }
2801       alignPanel.paintAlignment(true);
2802     }
2803
2804     if ((viewport.getSelectionGroup() != null
2805             && viewport.getSelectionGroup().getSize() < 4 && viewport
2806             .getSelectionGroup().getSize() > 0)
2807             || viewport.getAlignment().getHeight() < 4)
2808     {
2809       return;
2810     }
2811
2812     try
2813     {
2814       new PCAPanel(viewport);
2815     } catch (java.lang.OutOfMemoryError ex)
2816     {
2817     }
2818
2819   }
2820
2821   public void averageDistanceTreeMenuItem_actionPerformed()
2822   {
2823     NewTreePanel("AV", "PID", "Average distance tree using PID");
2824   }
2825
2826   public void neighbourTreeMenuItem_actionPerformed()
2827   {
2828     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2829   }
2830
2831   protected void njTreeBlosumMenuItem_actionPerformed()
2832   {
2833     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2834   }
2835
2836   protected void avTreeBlosumMenuItem_actionPerformed()
2837   {
2838     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2839   }
2840
2841   void NewTreePanel(String type, String pwType, String title)
2842   {
2843     // are the sequences aligned?
2844     if (!viewport.getAlignment().isAligned(false))
2845     {
2846       SequenceI current;
2847       int Width = viewport.getAlignment().getWidth();
2848
2849       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2850       {
2851         current = viewport.getAlignment().getSequenceAt(i);
2852
2853         if (current.getLength() < Width)
2854         {
2855           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2856         }
2857       }
2858       alignPanel.paintAlignment(true);
2859
2860     }
2861
2862     if ((viewport.getSelectionGroup() != null && viewport
2863             .getSelectionGroup().getSize() > 1)
2864             || (viewport.getAlignment().getHeight() > 1))
2865     {
2866       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2867
2868       addTreeMenuItem(tp, title);
2869
2870       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2871     }
2872   }
2873
2874   void loadTree_actionPerformed()
2875   {
2876     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2877     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2878     cap.setTreeImport();
2879     Frame frame = new Frame();
2880     frame.add(cap);
2881     jalview.bin.JalviewLite.addFrame(frame,
2882             MessageManager.getString("label.paste_newick_file"), 400, 300);
2883   }
2884
2885   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2886   {
2887     TreePanel tp = new TreePanel(alignPanel, treeFile,
2888             MessageManager.getString("label.load_tree_from_file"), tree);
2889     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2890     addTreeMenuItem(tp, treeFile);
2891   }
2892
2893   /**
2894    * sort the alignment using the given treePanel
2895    *
2896    * @param treePanel
2897    *          tree used to sort view
2898    * @param title
2899    *          string used for undo event name
2900    */
2901   public void sortByTree(TreePanel treePanel, String title)
2902   {
2903     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2904     AlignmentSorter
2905             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2906     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2907     // HistoryItem.SORT));
2908     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2909             "label.order_by_params", new String[] { title }), oldOrder,
2910             viewport.getAlignment()));
2911     alignPanel.paintAlignment(true);
2912   }
2913
2914   /**
2915    * Do any automatic reordering of the alignment and add the necessary bits to
2916    * the menu structure for the new tree
2917    *
2918    * @param treePanel
2919    * @param title
2920    */
2921   protected void addTreeMenuItem(final TreePanel treePanel,
2922           final String title)
2923   {
2924     final MenuItem item = new MenuItem(title);
2925     sortByTreeMenu.add(item);
2926     item.addActionListener(new java.awt.event.ActionListener()
2927     {
2928       @Override
2929       public void actionPerformed(ActionEvent evt)
2930       {
2931         sortByTree(treePanel, title); // treePanel.getTitle());
2932       }
2933     });
2934
2935     treePanel.addWindowListener(new WindowAdapter()
2936     {
2937       @Override
2938       public void windowOpened(WindowEvent e)
2939       {
2940         if (viewport.sortByTree)
2941         {
2942           sortByTree(treePanel, title);
2943         }
2944         super.windowOpened(e);
2945       }
2946
2947       @Override
2948       public void windowClosing(WindowEvent e)
2949       {
2950         sortByTreeMenu.remove(item);
2951       };
2952     });
2953   }
2954
2955   public boolean sortBy(AlignmentOrder alorder, String undoname)
2956   {
2957     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2958     if (viewport.applet.debug)
2959     {
2960       System.err.println("Sorting " + alorder.getOrder().size()
2961               + " in alignment '" + getTitle() + "'");
2962     }
2963     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2964     if (undoname != null)
2965     {
2966       addHistoryItem(new OrderCommand(undoname, oldOrder,
2967               viewport.getAlignment()));
2968     }
2969     alignPanel.paintAlignment(true);
2970     return true;
2971   }
2972
2973   protected void documentation_actionPerformed()
2974   {
2975     alignPanel.av.applet.openJalviewHelpUrl();
2976   }
2977
2978   protected void about_actionPerformed()
2979   {
2980
2981     class AboutPanel extends Canvas
2982     {
2983       String version;
2984
2985       String builddate;
2986
2987       public AboutPanel(String version, String builddate)
2988       {
2989         this.version = version;
2990         this.builddate = builddate;
2991       }
2992
2993       @Override
2994       public void paint(Graphics g)
2995       {
2996         g.setColor(Color.white);
2997         g.fillRect(0, 0, getSize().width, getSize().height);
2998         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2999         FontMetrics fm = g.getFontMetrics();
3000         int fh = fm.getHeight();
3001         int y = 5, x = 7;
3002         g.setColor(Color.black);
3003         // TODO: update this text for each release or centrally store it for
3004         // lite and application
3005         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3006         g.drawString(MessageManager.formatMessage(
3007                 "label.jalviewLite_release", new String[] { version }), x,
3008                 y += fh);
3009         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3010         g.drawString(MessageManager.formatMessage(
3011                 "label.jaview_build_date", new String[] { builddate }), x,
3012                 y += fh);
3013         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3015                 x, y += fh * 1.5);
3016         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3017                 x + 50, y += fh + 8);
3018         g.drawString(
3019                 MessageManager.getString("label.jalview_dev_managers"), x,
3020                 y += fh);
3021         g.drawString(MessageManager
3022                 .getString("label.jalview_distribution_lists"), x, y += fh);
3023         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3024                 x, y += fh + 8);
3025         g.drawString(
3026                 MessageManager.getString("label.jalview_cite_1_authors"),
3027                 x, y += fh);
3028         g.drawString(
3029                 MessageManager.getString("label.jalview_cite_1_title"), x,
3030                 y += fh);
3031         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3032                 x, y += fh);
3033       }
3034     }
3035
3036     Frame frame = new Frame();
3037     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3038             .getBuildDate()));
3039     jalview.bin.JalviewLite.addFrame(frame,
3040             MessageManager.getString("label.jalview"), 580, 220);
3041
3042   }
3043
3044   public void showURL(String url, String target)
3045   {
3046     if (viewport.applet == null)
3047     {
3048       System.out.println("Not running as applet - no browser available.");
3049     }
3050     else
3051     {
3052       viewport.applet.showURL(url, target);
3053     }
3054   }
3055
3056   // ////////////////////////////////////////////////////////////////////////////////
3057   // JBuilder Graphics here
3058
3059   MenuBar alignFrameMenuBar = new MenuBar();
3060
3061   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3062
3063   MenuItem loadApplication = new MenuItem(
3064           MessageManager.getString("label.view_full_application"));
3065
3066   MenuItem loadTree = new MenuItem(
3067           MessageManager.getString("label.load_associated_tree"));
3068
3069   MenuItem loadAnnotations = new MenuItem(
3070           MessageManager.getString("label.load_features_annotations"));
3071
3072   MenuItem outputFeatures = new MenuItem(
3073           MessageManager.getString("label.export_features"));
3074
3075   MenuItem outputAnnotations = new MenuItem(
3076           MessageManager.getString("label.export_annotations"));
3077
3078   MenuItem closeMenuItem = new MenuItem(
3079           MessageManager.getString("action.close"));
3080
3081   MenuItem selectAllSequenceMenuItem = new MenuItem(
3082           MessageManager.getString("action.select_all"));
3083
3084   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3085           MessageManager.getString("action.deselect_all"));
3086
3087   MenuItem invertSequenceMenuItem = new MenuItem(
3088           MessageManager.getString("action.invert_selection"));
3089
3090   MenuItem remove2LeftMenuItem = new MenuItem();
3091
3092   MenuItem remove2RightMenuItem = new MenuItem();
3093
3094   MenuItem removeGappedColumnMenuItem = new MenuItem();
3095
3096   MenuItem removeAllGapsMenuItem = new MenuItem();
3097
3098   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3099
3100   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3101
3102   MenuItem sortPairwiseMenuItem = new MenuItem();
3103
3104   MenuItem sortIDMenuItem = new MenuItem();
3105
3106   MenuItem sortLengthMenuItem = new MenuItem();
3107
3108   MenuItem sortGroupMenuItem = new MenuItem();
3109
3110   MenuItem removeRedundancyMenuItem = new MenuItem();
3111
3112   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3113
3114   MenuItem PCAMenuItem = new MenuItem();
3115
3116   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3117
3118   MenuItem neighbourTreeMenuItem = new MenuItem();
3119
3120   BorderLayout borderLayout1 = new BorderLayout();
3121
3122   public Label statusBar = new Label();
3123
3124   MenuItem clustalColour = new MenuItem();
3125
3126   MenuItem zappoColour = new MenuItem();
3127
3128   MenuItem taylorColour = new MenuItem();
3129
3130   MenuItem hydrophobicityColour = new MenuItem();
3131
3132   MenuItem helixColour = new MenuItem();
3133
3134   MenuItem strandColour = new MenuItem();
3135
3136   MenuItem turnColour = new MenuItem();
3137
3138   MenuItem buriedColour = new MenuItem();
3139
3140   MenuItem purinePyrimidineColour = new MenuItem();
3141
3142   // MenuItem RNAInteractionColour = new MenuItem();
3143
3144   MenuItem RNAHelixColour = new MenuItem();
3145
3146   MenuItem userDefinedColour = new MenuItem();
3147
3148   MenuItem PIDColour = new MenuItem();
3149
3150   MenuItem BLOSUM62Colour = new MenuItem();
3151
3152   MenuItem tcoffeeColour = new MenuItem();
3153
3154   MenuItem njTreeBlosumMenuItem = new MenuItem();
3155
3156   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3157
3158   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3159
3160   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3161
3162   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3163
3164   MenuItem alProperties = new MenuItem(
3165           MessageManager.getString("label.alignment_props"));
3166
3167   MenuItem overviewMenuItem = new MenuItem();
3168
3169   MenuItem undoMenuItem = new MenuItem();
3170
3171   MenuItem redoMenuItem = new MenuItem();
3172
3173   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3174
3175   MenuItem noColourmenuItem = new MenuItem();
3176
3177   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3178
3179   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3180
3181   MenuItem findMenuItem = new MenuItem();
3182
3183   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3184
3185   MenuItem nucleotideColour = new MenuItem();
3186
3187   MenuItem deleteGroups = new MenuItem();
3188
3189   MenuItem grpsFromSelection = new MenuItem();
3190
3191   MenuItem createGroup = new MenuItem();
3192
3193   MenuItem unGroup = new MenuItem();
3194
3195   MenuItem delete = new MenuItem();
3196
3197   MenuItem copy = new MenuItem();
3198
3199   MenuItem cut = new MenuItem();
3200
3201   Menu pasteMenu = new Menu();
3202
3203   MenuItem pasteNew = new MenuItem();
3204
3205   MenuItem pasteThis = new MenuItem();
3206
3207   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3208
3209   MenuItem font = new MenuItem();
3210
3211   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3212
3213   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3214
3215   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3216
3217   MenuItem modifyPID = new MenuItem();
3218
3219   MenuItem modifyConservation = new MenuItem();
3220
3221   CheckboxMenuItem autoCalculate = null;
3222
3223   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3224           "Sort Alignment With New Tree", true);
3225
3226   Menu sortByTreeMenu = new Menu();
3227
3228   MenuItem inputText = new MenuItem();
3229
3230   MenuItem documentation = new MenuItem();
3231
3232   MenuItem about = new MenuItem();
3233
3234   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3235
3236   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3237
3238   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3239
3240   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3241
3242   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3243
3244   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3251
3252   /**
3253    * Initialise menus and other items
3254    *
3255    * @throws Exception
3256    */
3257   private void jbInit() throws Exception
3258   {
3259     setMenuBar(alignFrameMenuBar);
3260
3261     /*
3262      * Configure File menu items and actions
3263      */
3264     inputText
3265             .setLabel(MessageManager.getString("label.input_from_textbox"));
3266     inputText.addActionListener(this);
3267     Menu outputTextboxMenu = new Menu(
3268             MessageManager.getString("label.out_to_textbox"));
3269     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3270     {
3271       MenuItem item = new MenuItem(ff);
3272
3273       item.addActionListener(new java.awt.event.ActionListener()
3274       {
3275         @Override
3276         public void actionPerformed(ActionEvent e)
3277         {
3278           outputText_actionPerformed(e);
3279         }
3280       });
3281
3282       outputTextboxMenu.add(item);
3283     }
3284     closeMenuItem.addActionListener(this);
3285     loadApplication.addActionListener(this);
3286     loadTree.addActionListener(this);
3287     loadAnnotations.addActionListener(this);
3288     outputFeatures.addActionListener(this);
3289     outputAnnotations.addActionListener(this);
3290
3291     /*
3292      * Configure Edit menu items and actions
3293      */
3294     undoMenuItem.setEnabled(false);
3295     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3296     undoMenuItem.addActionListener(this);
3297     redoMenuItem.setEnabled(false);
3298     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3299     redoMenuItem.addActionListener(this);
3300     copy.setLabel(MessageManager.getString("action.copy"));
3301     copy.addActionListener(this);
3302     cut.setLabel(MessageManager.getString("action.cut"));
3303     cut.addActionListener(this);
3304     delete.setLabel(MessageManager.getString("action.delete"));
3305     delete.addActionListener(this);
3306     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3307     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3308     pasteNew.addActionListener(this);
3309     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3310     pasteThis.addActionListener(this);
3311     remove2LeftMenuItem.setLabel(MessageManager
3312             .getString("action.remove_left"));
3313     remove2LeftMenuItem.addActionListener(this);
3314     remove2RightMenuItem.setLabel(MessageManager
3315             .getString("action.remove_right"));
3316     remove2RightMenuItem.addActionListener(this);
3317     removeGappedColumnMenuItem.setLabel(MessageManager
3318             .getString("action.remove_empty_columns"));
3319     removeGappedColumnMenuItem.addActionListener(this);
3320     removeAllGapsMenuItem.setLabel(MessageManager
3321             .getString("action.remove_all_gaps"));
3322     removeAllGapsMenuItem.addActionListener(this);
3323     removeRedundancyMenuItem.setLabel(MessageManager
3324             .getString("action.remove_redundancy"));
3325     removeRedundancyMenuItem.addActionListener(this);
3326
3327     /*
3328      * Configure Select menu items and actions
3329      */
3330     findMenuItem.setLabel(MessageManager.getString("action.find"));
3331     findMenuItem.addActionListener(this);
3332     selectAllSequenceMenuItem.addActionListener(this);
3333     deselectAllSequenceMenuItem.addActionListener(this);
3334     invertSequenceMenuItem.setLabel(MessageManager
3335             .getString("action.invert_sequence_selection"));
3336     invertSequenceMenuItem.addActionListener(this);
3337     invertColSel.setLabel(MessageManager
3338             .getString("action.invert_column_selection"));
3339     invertColSel.addActionListener(this);
3340     deleteGroups.setLabel(MessageManager
3341             .getString("action.undefine_groups"));
3342     deleteGroups.addActionListener(this);
3343     grpsFromSelection.setLabel(MessageManager
3344             .getString("action.make_groups_selection"));
3345     grpsFromSelection.addActionListener(this);
3346     createGroup.setLabel(MessageManager.getString("action.create_group"));
3347     createGroup.addActionListener(this);
3348     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3349     unGroup.addActionListener(this);
3350
3351     annotationColumnSelection.setLabel(MessageManager
3352             .getString("action.select_by_annotation"));
3353     annotationColumnSelection.addActionListener(this);
3354
3355     /*
3356      * Configure View menu items and actions
3357      */
3358     newView.setLabel(MessageManager.getString("action.new_view"));
3359     newView.addActionListener(this);
3360     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3361     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3362     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3363     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3364     hideColumns
3365             .setLabel(MessageManager.getString("label.selected_columns"));
3366     hideSequences.setLabel(MessageManager
3367             .getString("label.selected_sequences"));
3368     hideAllButSelection.setLabel(MessageManager
3369             .getString("label.all_but_selected_region"));
3370     hideAllSelection.setLabel(MessageManager
3371             .getString("label.selected_region"));
3372     showAllHidden.setLabel(MessageManager
3373             .getString("label.all_sequences_columns"));
3374     showColumns.addActionListener(this);
3375     showSeqs.addActionListener(this);
3376     hideColumns.addActionListener(this);
3377     hideSequences.addActionListener(this);
3378     hideAllButSelection.addActionListener(this);
3379     hideAllSelection.addActionListener(this);
3380     showAllHidden.addActionListener(this);
3381     featureSettings.setLabel(MessageManager
3382             .getString("action.feature_settings"));
3383     featureSettings.addActionListener(this);
3384     sequenceFeatures.setLabel(MessageManager
3385             .getString("label.show_sequence_features"));
3386     sequenceFeatures.addItemListener(this);
3387     sequenceFeatures.setState(false);
3388     followMouseOverFlag.setLabel(MessageManager
3389             .getString("label.automatic_scrolling"));
3390     followMouseOverFlag.addItemListener(this);
3391     alProperties.addActionListener(this);
3392     overviewMenuItem.setLabel(MessageManager
3393             .getString("label.overview_window"));
3394     overviewMenuItem.addActionListener(this);
3395
3396     /*
3397      * Configure Annotations menu items and actions
3398      */
3399     annotationPanelMenuItem.setLabel(MessageManager
3400             .getString("label.show_annotations"));
3401     annotationPanelMenuItem.addItemListener(this);
3402     showGroupConsensus.setLabel(MessageManager
3403             .getString("label.group_consensus"));
3404     showGroupConservation.setLabel(MessageManager
3405             .getString("label.group_conservation"));
3406     showConsensusHistogram.setLabel(MessageManager
3407             .getString("label.show_consensus_histogram"));
3408     showSequenceLogo.setLabel(MessageManager
3409             .getString("label.show_consensus_logo"));
3410     normSequenceLogo.setLabel(MessageManager
3411             .getString("label.norm_consensus_logo"));
3412     applyAutoAnnotationSettings.setLabel(MessageManager
3413             .getString("label.apply_all_groups"));
3414     applyAutoAnnotationSettings.setState(true);
3415     Menu autoAnnMenu = new Menu(
3416             MessageManager.getString("label.autocalculated_annotation"));
3417     showGroupConsensus.addItemListener(this);
3418     showGroupConservation.addItemListener(this);
3419     showConsensusHistogram.addItemListener(this);
3420     showSequenceLogo.addItemListener(this);
3421     normSequenceLogo.addItemListener(this);
3422     applyAutoAnnotationSettings.addItemListener(this);
3423     showAlignmentAnnotations = new CheckboxMenuItem(
3424             MessageManager.getString("label.show_all_al_annotations"));
3425     showSequenceAnnotations = new CheckboxMenuItem(
3426             MessageManager.getString("label.show_all_seq_annotations"));
3427     sortAnnBySequence = new CheckboxMenuItem(
3428             MessageManager.getString("label.sort_annotations_by_sequence"));
3429     sortAnnByLabel = new CheckboxMenuItem(
3430             MessageManager.getString("label.sort_annotations_by_label"));
3431     showAutoFirst = new CheckboxMenuItem(
3432             MessageManager.getString("label.show_first"));
3433     showAutoFirst.setState(false); // pending applet parameter
3434     setShowAutoCalculatedAbove(showAutoFirst.getState());
3435     showAutoLast = new CheckboxMenuItem(
3436             MessageManager.getString("label.show_last"));
3437     showAutoLast.setState(!showAutoFirst.getState());
3438     showAlignmentAnnotations.addItemListener(this);
3439     showSequenceAnnotations.addItemListener(this);
3440     sortAnnBySequence.addItemListener(this);
3441     sortAnnByLabel.addItemListener(this);
3442     showAutoFirst.addItemListener(this);
3443     showAutoLast.addItemListener(this);
3444
3445     /*
3446      * Configure Format menu items and actions
3447      */
3448     font.setLabel(MessageManager.getString("action.font"));
3449     font.addActionListener(this);
3450     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3451     scaleAbove.setState(true);
3452     scaleAbove.setEnabled(false);
3453     scaleAbove.addItemListener(this);
3454     scaleLeft.setEnabled(false);
3455     scaleLeft.setState(true);
3456     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3457     scaleLeft.addItemListener(this);
3458     scaleRight.setEnabled(false);
3459     scaleRight.setState(true);
3460     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3461     scaleRight.addItemListener(this);
3462     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3463     viewBoxesMenuItem.setState(true);
3464     viewBoxesMenuItem.addItemListener(this);
3465     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3466     viewTextMenuItem.setState(true);
3467     viewTextMenuItem.addItemListener(this);
3468     colourTextMenuItem.setLabel(MessageManager
3469             .getString("label.colour_text"));
3470     colourTextMenuItem.addItemListener(this);
3471     displayNonconservedMenuItem.setLabel(MessageManager
3472             .getString("label.show_non_conserved"));
3473     displayNonconservedMenuItem.addItemListener(this);
3474     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3475     wrapMenuItem.addItemListener(this);
3476     renderGapsMenuItem.setLabel(MessageManager
3477             .getString("action.show_gaps"));
3478     renderGapsMenuItem.setState(true);
3479     renderGapsMenuItem.addItemListener(this);
3480     centreColumnLabelFlag.setLabel(MessageManager
3481             .getString("label.centre_column_labels"));
3482     centreColumnLabelFlag.addItemListener(this);
3483     seqLimits.setState(true);
3484     seqLimits.setLabel(MessageManager
3485             .getString("label.show_sequence_limits"));
3486     seqLimits.addItemListener(this);
3487
3488     /*
3489      * Configure Colour menu items and actions
3490      */
3491     applyToAllGroups.setLabel(MessageManager
3492             .getString("label.apply_colour_to_all_groups"));
3493     applyToAllGroups.setState(true);
3494     applyToAllGroups.addItemListener(this);
3495     clustalColour.setLabel(MessageManager
3496             .getString("label.colourScheme_clustal"));
3497     clustalColour.addActionListener(this);
3498     zappoColour.setLabel(MessageManager
3499             .getString("label.colourScheme_zappo"));
3500     zappoColour.addActionListener(this);
3501     taylorColour.setLabel(MessageManager
3502             .getString("label.colourScheme_taylor"));
3503     taylorColour.addActionListener(this);
3504     hydrophobicityColour.setLabel(MessageManager
3505             .getString("label.colourScheme_hydrophobic"));
3506     hydrophobicityColour.addActionListener(this);
3507     helixColour.setLabel(MessageManager
3508             .getString("label.colourScheme_helix_propensity"));
3509     helixColour.addActionListener(this);
3510     strandColour.setLabel(MessageManager
3511             .getString("label.colourScheme_strand_propensity"));
3512     strandColour.addActionListener(this);
3513     turnColour.setLabel(MessageManager
3514             .getString("label.colourScheme_turn_propensity"));
3515     turnColour.addActionListener(this);
3516     buriedColour.setLabel(MessageManager
3517             .getString("label.colourScheme_buried_index"));
3518     buriedColour.addActionListener(this);
3519     purinePyrimidineColour.setLabel(MessageManager
3520             .getString("label.colourScheme_purine/pyrimidine"));
3521     purinePyrimidineColour.addActionListener(this);
3522     // RNAInteractionColour.setLabel(MessageManager
3523     // .getString("label.rna_interaction"));
3524     // RNAInteractionColour.addActionListener(this);
3525     RNAHelixColour.setLabel(MessageManager
3526             .getString("label.colourScheme_rna_helices"));
3527     RNAHelixColour.addActionListener(this);
3528     userDefinedColour.setLabel(MessageManager
3529             .getString("action.user_defined"));
3530     userDefinedColour.addActionListener(this);
3531     PIDColour.setLabel(MessageManager
3532             .getString("label.colourScheme_%_identity"));
3533     PIDColour.addActionListener(this);
3534     BLOSUM62Colour.setLabel(MessageManager
3535             .getString("label.colourScheme_blosum62"));
3536     BLOSUM62Colour.addActionListener(this);
3537     tcoffeeColour.setLabel(MessageManager
3538             .getString("label.colourScheme_t-coffee_scores"));
3539     // it will be enabled only if a score file is provided
3540     tcoffeeColour.setEnabled(false);
3541     tcoffeeColour.addActionListener(this);
3542     conservationMenuItem.setLabel(MessageManager
3543             .getString("action.by_conservation"));
3544     conservationMenuItem.addItemListener(this);
3545     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3546     noColourmenuItem.addActionListener(this);
3547     abovePIDThreshold.setLabel(MessageManager
3548             .getString("label.above_identity_threshold"));
3549     abovePIDThreshold.addItemListener(this);
3550     nucleotideColour.setLabel(MessageManager
3551             .getString("label.colourScheme_nucleotide"));
3552     nucleotideColour.addActionListener(this);
3553     modifyPID.setLabel(MessageManager
3554             .getString("label.modify_identity_threshold"));
3555     modifyPID.setEnabled(abovePIDThreshold.getState());
3556     modifyPID.addActionListener(this);
3557     modifyConservation.setLabel(MessageManager
3558             .getString("label.modify_conservation_threshold"));
3559     modifyConservation.setEnabled(conservationMenuItem.getState());
3560     modifyConservation.addActionListener(this);
3561     annotationColour.setLabel(MessageManager
3562             .getString("action.by_annotation"));
3563     annotationColour.addActionListener(this);
3564
3565     /*
3566      * Configure Calculate menu items and actions
3567      */
3568     sortPairwiseMenuItem.setLabel(MessageManager
3569             .getString("action.by_pairwise_id"));
3570     sortPairwiseMenuItem.addActionListener(this);
3571     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3572     sortIDMenuItem.addActionListener(this);
3573     sortLengthMenuItem.setLabel(MessageManager
3574             .getString("action.by_length"));
3575     sortLengthMenuItem.addActionListener(this);
3576     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3577     sortGroupMenuItem.addActionListener(this);
3578     pairwiseAlignmentMenuItem.setLabel(MessageManager
3579             .getString("action.pairwise_alignment"));
3580     pairwiseAlignmentMenuItem.addActionListener(this);
3581     PCAMenuItem.setLabel(MessageManager
3582             .getString("label.principal_component_analysis"));
3583     PCAMenuItem.addActionListener(this);
3584     autoCalculate = new CheckboxMenuItem(
3585             MessageManager.getString("label.autocalculate_consensus"), true);
3586     averageDistanceTreeMenuItem.setLabel(MessageManager
3587             .getString("label.average_distance_identity"));
3588     averageDistanceTreeMenuItem.addActionListener(this);
3589     neighbourTreeMenuItem.setLabel(MessageManager
3590             .getString("label.neighbour_joining_identity"));
3591     neighbourTreeMenuItem.addActionListener(this);
3592     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3593             .getString("label.average_distance_blosum62"));
3594     avDistanceTreeBlosumMenuItem.addActionListener(this);
3595     njTreeBlosumMenuItem.setLabel(MessageManager
3596             .getString("label.neighbour_blosum62"));
3597     njTreeBlosumMenuItem.addActionListener(this);
3598     sortByTreeMenu.setLabel(MessageManager
3599             .getString("action.by_tree_order"));
3600     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3601     Menu calculateTreeMenu = new Menu(
3602             MessageManager.getString("action.calculate_tree"));
3603     autoCalculate.addItemListener(this);
3604     sortByTree.addItemListener(this);
3605
3606     /*
3607      * Configure Help menu items and actions
3608      */
3609     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3610     documentation.setLabel(MessageManager.getString("label.documentation"));
3611     documentation.addActionListener(this);
3612     about.setLabel(MessageManager.getString("label.about"));
3613     about.addActionListener(this);
3614
3615     /*
3616      * Add top level menus to frame
3617      */
3618     alignFrameMenuBar.add(fileMenu);
3619     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3620     alignFrameMenuBar.add(editMenu);
3621     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3622     alignFrameMenuBar.add(selectMenu);
3623     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3624     alignFrameMenuBar.add(viewMenu);
3625     Menu annotationsMenu = new Menu(
3626             MessageManager.getString("action.annotations"));
3627     alignFrameMenuBar.add(annotationsMenu);
3628     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3629     alignFrameMenuBar.add(formatMenu);
3630     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3631     alignFrameMenuBar.add(colourMenu);
3632     Menu calculateMenu = new Menu(
3633             MessageManager.getString("action.calculate"));
3634     alignFrameMenuBar.add(calculateMenu);
3635     alignFrameMenuBar.add(helpMenu);
3636
3637     /*
3638      * File menu
3639      */
3640     fileMenu.add(inputText);
3641     fileMenu.add(loadTree);
3642     fileMenu.add(loadAnnotations);
3643     fileMenu.addSeparator();
3644     fileMenu.add(outputTextboxMenu);
3645     fileMenu.add(outputFeatures);
3646     fileMenu.add(outputAnnotations);
3647     if (jalviewServletURL != null)
3648     {
3649       fileMenu.add(loadApplication);
3650     }
3651     fileMenu.addSeparator();
3652     fileMenu.add(closeMenuItem);
3653
3654     /*
3655      * Edit menu
3656      */
3657     editMenu.add(undoMenuItem);
3658     editMenu.add(redoMenuItem);
3659     editMenu.add(cut);
3660     editMenu.add(copy);
3661     pasteMenu.add(pasteNew);
3662     pasteMenu.add(pasteThis);
3663     editMenu.add(pasteMenu);
3664     editMenu.add(delete);
3665     editMenu.addSeparator();
3666     editMenu.add(remove2LeftMenuItem);
3667     editMenu.add(remove2RightMenuItem);
3668     editMenu.add(removeGappedColumnMenuItem);
3669     editMenu.add(removeAllGapsMenuItem);
3670     editMenu.add(removeRedundancyMenuItem);
3671
3672     /*
3673      * Select menu
3674      */
3675     selectMenu.add(findMenuItem);
3676     selectMenu.addSeparator();
3677     selectMenu.add(selectAllSequenceMenuItem);
3678     selectMenu.add(deselectAllSequenceMenuItem);
3679     selectMenu.add(invertSequenceMenuItem);
3680     selectMenu.add(invertColSel);
3681     selectMenu.add(createGroup);
3682     selectMenu.add(unGroup);
3683     selectMenu.add(grpsFromSelection);
3684     selectMenu.add(deleteGroups);
3685     selectMenu.add(annotationColumnSelection);
3686
3687     /*
3688      * View menu
3689      */
3690     viewMenu.add(newView);
3691     viewMenu.addSeparator();
3692     showMenu.add(showColumns);
3693     showMenu.add(showSeqs);
3694     showMenu.add(showAllHidden);
3695     viewMenu.add(showMenu);
3696     hideMenu.add(hideColumns);
3697     hideMenu.add(hideSequences);
3698     hideMenu.add(hideAllSelection);
3699     hideMenu.add(hideAllButSelection);
3700     viewMenu.add(hideMenu);
3701     viewMenu.addSeparator();
3702     viewMenu.add(followMouseOverFlag);
3703     viewMenu.addSeparator();
3704     viewMenu.add(sequenceFeatures);
3705     viewMenu.add(featureSettings);
3706     viewMenu.addSeparator();
3707     viewMenu.add(alProperties);
3708     viewMenu.addSeparator();
3709     viewMenu.add(overviewMenuItem);
3710
3711     /*
3712      * Annotations menu
3713      */
3714     annotationsMenu.add(annotationPanelMenuItem);
3715     annotationsMenu.addSeparator();
3716     annotationsMenu.add(showAlignmentAnnotations);
3717     annotationsMenu.add(showSequenceAnnotations);
3718     annotationsMenu.add(sortAnnBySequence);
3719     annotationsMenu.add(sortAnnByLabel);
3720     annotationsMenu.addSeparator();
3721     autoAnnMenu.add(showAutoFirst);
3722     autoAnnMenu.add(showAutoLast);
3723     autoAnnMenu.addSeparator();
3724     autoAnnMenu.add(applyAutoAnnotationSettings);
3725     autoAnnMenu.add(showConsensusHistogram);
3726     autoAnnMenu.add(showSequenceLogo);
3727     autoAnnMenu.add(normSequenceLogo);
3728     autoAnnMenu.addSeparator();
3729     autoAnnMenu.add(showGroupConservation);
3730     autoAnnMenu.add(showGroupConsensus);
3731     annotationsMenu.add(autoAnnMenu);
3732
3733     /*
3734      * Format menu
3735      */
3736     formatMenu.add(font);
3737     formatMenu.add(seqLimits);
3738     formatMenu.add(wrapMenuItem);
3739     formatMenu.add(scaleAbove);
3740     formatMenu.add(scaleLeft);
3741     formatMenu.add(scaleRight);
3742     formatMenu.add(viewBoxesMenuItem);
3743     formatMenu.add(viewTextMenuItem);
3744     formatMenu.add(colourTextMenuItem);
3745     formatMenu.add(displayNonconservedMenuItem);
3746     formatMenu.add(renderGapsMenuItem);
3747     formatMenu.add(centreColumnLabelFlag);
3748
3749     /*
3750      * Colour menu
3751      */
3752     colourMenu.add(applyToAllGroups);
3753     colourMenu.addSeparator();
3754     colourMenu.add(noColourmenuItem);
3755     colourMenu.add(clustalColour);
3756     colourMenu.add(BLOSUM62Colour);
3757     colourMenu.add(PIDColour);
3758     colourMenu.add(zappoColour);
3759     colourMenu.add(taylorColour);
3760     colourMenu.add(hydrophobicityColour);
3761     colourMenu.add(helixColour);
3762     colourMenu.add(strandColour);
3763     colourMenu.add(turnColour);
3764     colourMenu.add(buriedColour);
3765     colourMenu.add(nucleotideColour);
3766     colourMenu.add(purinePyrimidineColour);
3767     // colourMenu.add(RNAInteractionColour);
3768     colourMenu.add(tcoffeeColour);
3769     colourMenu.add(userDefinedColour);
3770     colourMenu.addSeparator();
3771     colourMenu.add(conservationMenuItem);
3772     colourMenu.add(modifyConservation);
3773     colourMenu.add(abovePIDThreshold);
3774     colourMenu.add(modifyPID);
3775     colourMenu.add(annotationColour);
3776     colourMenu.add(RNAHelixColour);
3777
3778     /*
3779      * Calculate menu
3780      */
3781     sortMenu.add(sortIDMenuItem);
3782     sortMenu.add(sortLengthMenuItem);
3783     sortMenu.add(sortByTreeMenu);
3784     sortMenu.add(sortGroupMenuItem);
3785     sortMenu.add(sortPairwiseMenuItem);
3786     calculateMenu.add(sortMenu);
3787     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3788     calculateTreeMenu.add(neighbourTreeMenuItem);
3789     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3790     calculateTreeMenu.add(njTreeBlosumMenuItem);
3791     calculateMenu.add(calculateTreeMenu);
3792     calculateMenu.addSeparator();
3793     calculateMenu.add(pairwiseAlignmentMenuItem);
3794     calculateMenu.add(PCAMenuItem);
3795     calculateMenu.add(autoCalculate);
3796     calculateMenu.add(sortByTree);
3797
3798     /*
3799      * Help menu
3800      */
3801     helpMenu.add(documentation);
3802     helpMenu.add(about);
3803
3804     /*
3805      * Status bar
3806      */
3807     statusBar.setBackground(Color.white);
3808     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3809     statusBar.setText(MessageManager.getString("label.status_bar"));
3810     this.add(statusBar, BorderLayout.SOUTH);
3811   }
3812
3813   @Override
3814   public void setStatus(String string)
3815   {
3816     statusBar.setText(string);
3817   };
3818
3819   MenuItem featureSettings = new MenuItem();
3820
3821   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3822
3823   MenuItem annotationColour = new MenuItem();
3824
3825   MenuItem annotationColumnSelection = new MenuItem();
3826
3827   MenuItem invertColSel = new MenuItem();
3828
3829   MenuItem showColumns = new MenuItem();
3830
3831   MenuItem showSeqs = new MenuItem();
3832
3833   MenuItem hideColumns = new MenuItem();
3834
3835   MenuItem hideSequences = new MenuItem();
3836
3837   MenuItem hideAllButSelection = new MenuItem();
3838
3839   MenuItem hideAllSelection = new MenuItem();
3840
3841   MenuItem showAllHidden = new MenuItem();
3842
3843   MenuItem newView = new MenuItem();
3844
3845   private CheckboxMenuItem showAlignmentAnnotations;
3846
3847   private CheckboxMenuItem showSequenceAnnotations;
3848
3849   private CheckboxMenuItem sortAnnBySequence;
3850
3851   private CheckboxMenuItem sortAnnByLabel;
3852
3853   private CheckboxMenuItem showAutoFirst;
3854
3855   private CheckboxMenuItem showAutoLast;
3856
3857   private SplitFrame splitFrame;
3858
3859   /**
3860    * Attach the alignFrame panels after embedding menus, if necessary. This used
3861    * to be called setEmbedded, but is now creates the dropdown menus in a
3862    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3863    *
3864    * @param reallyEmbedded
3865    *          true to attach the view to the applet area on the page rather than
3866    *          in a new window
3867    */
3868   public void createAlignFrameWindow(boolean reallyEmbedded)
3869   {
3870     if (reallyEmbedded)
3871     {
3872       embedAlignFrameInApplet(viewport.applet);
3873     }
3874     else
3875     {
3876       // //////
3877       // test and embed menu bar if necessary.
3878       //
3879       if (embedMenuIfNeeded(alignPanel))
3880       {
3881         /*
3882          * adjust for status bar height too. ? pointless as overridden by layout
3883          * manager
3884          */
3885         alignPanel.setSize(getSize().width,
3886                 getSize().height - statusBar.getHeight());
3887       }
3888       add(statusBar, BorderLayout.SOUTH);
3889       add(alignPanel, BorderLayout.CENTER);
3890       // and register with the applet so it can pass external API calls to us
3891       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3892               frameHeight);
3893     }
3894   }
3895
3896   /**
3897    * Add the components of this AlignFrame to the applet container.
3898    *
3899    * @param theApplet
3900    */
3901   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3902   {
3903     // ////
3904     // Explicitly build the embedded menu panel for the on-page applet
3905     //
3906     // view cannot be closed if its actually on the page
3907     fileMenu.remove(closeMenuItem);
3908     fileMenu.remove(3); // Remove Separator
3909     // construct embedded menu, using default font
3910     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3911     // and actually add the components to the applet area
3912     theApplet.setLayout(new BorderLayout());
3913     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3914     theApplet.add(statusBar, BorderLayout.SOUTH);
3915     // TODO should size be left to the layout manager?
3916     alignPanel.setSize(theApplet.getSize().width,
3917             theApplet.getSize().height - embeddedMenu.getHeight()
3918                     - statusBar.getHeight());
3919     theApplet.add(alignPanel, BorderLayout.CENTER);
3920     final AlignFrame me = this;
3921     theApplet.addFocusListener(new FocusListener()
3922     {
3923
3924       @Override
3925       public void focusLost(FocusEvent e)
3926       {
3927         if (theApplet.currentAlignFrame == me)
3928         {
3929           theApplet.currentAlignFrame = null;
3930         }
3931       }
3932
3933       @Override
3934       public void focusGained(FocusEvent e)
3935       {
3936         theApplet.currentAlignFrame = me;
3937       }
3938     });
3939     theApplet.validate();
3940   }
3941
3942   /**
3943    * create a new binding between structures in an existing jmol viewer instance
3944    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3945    * this does not open a new Jmol window, or modify the display of the
3946    * structures in the original jmol window. Note This method doesn't work
3947    * without an additional javascript library to exchange messages between the
3948    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3949    *
3950    * @param viewer
3951    *          JmolViewer instance
3952    * @param sequenceIds
3953    *          - sequence Ids to search for associations
3954    */
3955   public SequenceStructureBinding addStructureViewInstance(
3956           Object jmolviewer, String[] sequenceIds)
3957   {
3958     Viewer viewer = null;
3959     try
3960     {
3961       viewer = (Viewer) jmolviewer;
3962     } catch (ClassCastException ex)
3963     {
3964       System.err.println("Unsupported viewer object :"
3965               + jmolviewer.getClass());
3966     }
3967     if (viewer == null)
3968     {
3969       System.err.println("Can't use this object as a structure viewer:"
3970               + jmolviewer.getClass());
3971       return null;
3972     }
3973     SequenceI[] seqs = null;
3974     if (sequenceIds == null || sequenceIds.length == 0)
3975     {
3976       seqs = viewport.getAlignment().getSequencesArray();
3977     }
3978     else
3979     {
3980       Vector sqi = new Vector();
3981       AlignmentI al = viewport.getAlignment();
3982       for (int sid = 0; sid < sequenceIds.length; sid++)
3983       {
3984         SequenceI sq = al.findName(sequenceIds[sid]);
3985         if (sq != null)
3986         {
3987           sqi.addElement(sq);
3988         }
3989       }
3990       if (sqi.size() > 0)
3991       {
3992         seqs = new SequenceI[sqi.size()];
3993         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3994         {
3995           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3996         }
3997       }
3998       else
3999       {
4000         return null;
4001       }
4002     }
4003     AAStructureBindingModel jmv = null;
4004     // TODO: search for a jmv that involves viewer
4005     if (jmv == null)
4006     { // create a new viewer/jalview binding.
4007       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4008     }
4009     return jmv;
4010
4011   }
4012
4013   /**
4014    * bind a pdb file to a sequence in the current view
4015    *
4016    * @param sequenceId
4017    *          - sequenceId within the dataset.
4018    * @param pdbEntryString
4019    *          - the short name for the PDB file
4020    * @param pdbFile
4021    *          - pdb file - either a URL or a valid PDB file.
4022    * @return true if binding was as success TODO: consider making an exception
4023    *         structure for indicating when PDB parsing or sequenceId location
4024    *         fails.
4025    */
4026   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4027           String pdbFile)
4028   {
4029     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4030     boolean needtoadd = false;
4031     if (toaddpdb != null)
4032     {
4033       Vector pdbe = toaddpdb.getAllPDBEntries();
4034       PDBEntry pdbentry = null;
4035       if (pdbe != null && pdbe.size() > 0)
4036       {
4037         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4038         {
4039           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4040           if (!pdbentry.getId().equals(pdbEntryString)
4041                   && !pdbentry.getFile().equals(pdbFile))
4042           {
4043             pdbentry = null;
4044           }
4045           else
4046           {
4047             continue;
4048           }
4049         }
4050       }
4051       if (pdbentry == null)
4052       {
4053         pdbentry = new PDBEntry();
4054         pdbentry.setId(pdbEntryString);
4055         pdbentry.setFile(pdbFile);
4056         needtoadd = true; // add this new entry to sequence.
4057       }
4058       // resolve data source
4059       // TODO: this code should be a refactored to an io package
4060       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4061               pdbFile, FileFormat.PDB);
4062       if (protocol == null)
4063       {
4064         return false;
4065       }
4066       if (needtoadd)
4067       {
4068         pdbentry.setProperty("protocol", protocol);
4069         toaddpdb.addPDBId(pdbentry);
4070         alignPanel.getStructureSelectionManager()
4071                 .registerPDBEntry(pdbentry);
4072       }
4073     }
4074     return true;
4075   }
4076
4077   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4078   {
4079     if (seqs != null)
4080     {
4081       Vector sequences = new Vector();
4082       for (int i = 0; i < seqs.length; i++)
4083       {
4084         if (seqs[i] != null)
4085         {
4086           sequences.addElement(new Object[] { seqs[i],
4087               (chains != null) ? chains[i] : null });
4088         }
4089       }
4090       seqs = new SequenceI[sequences.size()];
4091       chains = new String[sequences.size()];
4092       for (int i = 0, isize = sequences.size(); i < isize; i++)
4093       {
4094         Object[] oj = (Object[]) sequences.elementAt(i);
4095
4096         seqs[i] = (SequenceI) oj[0];
4097         chains[i] = (String) oj[1];
4098       }
4099     }
4100     return new Object[] { seqs, chains };
4101
4102   }
4103
4104   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4105           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4106   {
4107     // Scrub any null sequences from the array
4108     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4109     seqs = (SequenceI[]) sqch[0];
4110     chains = (String[]) sqch[1];
4111     if (seqs == null || seqs.length == 0)
4112     {
4113       System.err
4114               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4115     }
4116     if (protocol == null)
4117     {
4118       String sourceType = (String) pdb.getProperty("protocol");
4119       try
4120       {
4121         protocol = DataSourceType.valueOf(sourceType);
4122       } catch (IllegalArgumentException e)
4123       {
4124         // ignore
4125       }
4126       if (protocol == null)
4127       {
4128         System.err.println("Couldn't work out protocol to open structure: "
4129                 + pdb.getId());
4130         return;
4131       }
4132     }
4133     if (applet.useXtrnalSviewer)
4134     {
4135       // register the association(s) and quit, don't create any windows.
4136       if (StructureSelectionManager.getStructureSelectionManager(applet)
4137               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4138       {
4139         System.err.println("Failed to map " + pdb.getFile() + " ("
4140                 + protocol + ") to any sequences");
4141       }
4142       return;
4143     }
4144     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4145     {
4146       // can only do alignments with Jmol
4147       // find the last jmol window assigned to this alignment
4148       AppletJmol ajm = null, tajm;
4149       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4150       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4151       {
4152         tajm = (AppletJmol) jmols.elementAt(i);
4153         if (tajm.ap.alignFrame == this)
4154         {
4155           ajm = tajm;
4156           break;
4157         }
4158       }
4159       if (ajm != null)
4160       {
4161         System.err
4162                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4163         // try and add the pdb structure
4164         // ajm.addS
4165         ajm = null;
4166       }
4167     }
4168     // otherwise, create a new window
4169     if (applet.jmolAvailable)
4170     {
4171       new AppletJmol(pdb, seqs, chains, alignPanel,
4172               protocol);
4173       applet.lastFrameX += 40;
4174       applet.lastFrameY += 40;
4175     }
4176     else
4177     {
4178       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4179     }
4180
4181   }
4182
4183   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4184           SequenceI[][] seqs, String[][] chains, String[] protocols)
4185   {
4186     // TODO Auto-generated method stub
4187     System.err.println("Aligned Structure View: Not yet implemented.");
4188   }
4189
4190   /**
4191    * modify the current selection, providing the user has not made a selection
4192    * already.
4193    *
4194    * @param sel
4195    *          - sequences from this alignment
4196    * @param csel
4197    *          - columns to be selected on the alignment
4198    */
4199   public void select(SequenceGroup sel, ColumnSelection csel)
4200   {
4201     alignPanel.seqPanel.selection(sel, csel, null);
4202   }
4203
4204   public void scrollTo(int row, int column)
4205   {
4206     alignPanel.seqPanel.scrollTo(row, column);
4207   }
4208
4209   public void scrollToRow(int row)
4210   {
4211     alignPanel.seqPanel.scrollToRow(row);
4212   }
4213
4214   public void scrollToColumn(int column)
4215   {
4216     alignPanel.seqPanel.scrollToColumn(column);
4217   }
4218
4219   /**
4220    * @return the alignments unique ID.
4221    */
4222   public String getSequenceSetId()
4223   {
4224     return viewport.getSequenceSetId();
4225   }
4226
4227   /**
4228    * Load the (T-Coffee) score file from the specified url
4229    *
4230    * @param source
4231    *          File/URL/T-COFFEE score file contents
4232    * @throws IOException
4233    * @return true if alignment was annotated with data from source
4234    */
4235   public boolean loadScoreFile(String source) throws IOException
4236   {
4237
4238     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4239             AppletFormatAdapter.checkProtocol(source));
4240     if (!file.isValid())
4241     {
4242       // TODO: raise dialog for gui
4243       System.err.println("Problems parsing T-Coffee scores: "
4244               + file.getWarningMessage());
4245       System.err.println("Origin was:\n" + source);
4246       return false;
4247     }
4248
4249     /*
4250      * check that the score matrix matches the alignment dimensions
4251      */
4252     AlignmentI aln;
4253     if ((aln = viewport.getAlignment()) != null
4254             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4255                     .getWidth()))
4256     {
4257       // TODO: raise a dialog box here rather than bomb out.
4258       System.err
4259               .println("The scores matrix does not match the alignment dimensions");
4260
4261     }
4262
4263     // TODO add parameter to indicate if matching should be done
4264     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4265     {
4266       alignPanel.fontChanged();
4267       tcoffeeColour.setEnabled(true);
4268       // switch to this color
4269       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4270       return true;
4271     }
4272     else
4273     {
4274       System.err.println("Problems resolving T-Coffee scores:");
4275       if (file.getWarningMessage() != null)
4276       {
4277         System.err.println(file.getWarningMessage());
4278       }
4279     }
4280     return false;
4281   }
4282
4283   public SplitFrame getSplitFrame()
4284   {
4285     return this.splitFrame;
4286   }
4287
4288   public void setSplitFrame(SplitFrame sf)
4289   {
4290     this.splitFrame = sf;
4291   }
4292
4293   // may not need this
4294   @Override
4295   public void setShowSeqFeatures(boolean b)
4296   {
4297     // showSeqFeatures.setSelected(b);
4298     viewport.setShowSequenceFeatures(b);
4299
4300   }
4301
4302   @Override
4303   public void setMenusForViewport()
4304   {
4305     // setMenusFromViewport(viewport);
4306
4307   }
4308
4309   @Override
4310   public void refreshFeatureUI(boolean enableIfNecessary)
4311   {
4312     if (enableIfNecessary)
4313     {
4314       sequenceFeatures.setState(true);
4315       alignPanel.av.setShowSequenceFeatures(true);
4316     }
4317   }
4318
4319   @Override
4320   public FeatureSettingsControllerI getFeatureSettingsUI()
4321   {
4322     return alignPanel.av.featureSettings;
4323   }
4324
4325 }