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.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet,
 177           String title, boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet,
 184           String title, boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 394               "relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true);
 419       statusBar.setText(MessageManager
 420               .getString("label.successfully_added_features_alignment"));
 421     }
 422     return featuresFile;
 423   }
 424
 425   @Override
 426   public void keyPressed(KeyEvent evt)
 427   {
 428     ViewportRanges ranges = viewport.getRanges();
 429
 430     if (viewport.cursorMode
 431             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 432                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 433                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 434             && Character.isDigit(evt.getKeyChar()))
 435     {
 436       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 437     }
 438
 439     switch (evt.getKeyCode())
 440     {
 441     case 27: // escape key
 442       deselectAllSequenceMenuItem_actionPerformed();
 443
 444       alignPanel.alabels.cancelDrag();
 445       break;
 446     case KeyEvent.VK_X:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         cut_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_C:
 453       if (viewport.cursorMode && !evt.isControlDown())
 454       {
 455         alignPanel.seqPanel.setCursorColumn();
 456       }
 457       if (evt.isControlDown() || evt.isMetaDown())
 458       {
 459         copy_actionPerformed();
 460       }
 461       break;
 462     case KeyEvent.VK_V:
 463       if (evt.isControlDown())
 464       {
 465         paste(evt.isShiftDown());
 466       }
 467       break;
 468     case KeyEvent.VK_A:
 469       if (evt.isControlDown() || evt.isMetaDown())
 470       {
 471         selectAllSequenceMenuItem_actionPerformed();
 472       }
 473       break;
 474     case KeyEvent.VK_DOWN:
 475       if (viewport.cursorMode)
 476       {
 477         alignPanel.seqPanel.moveCursor(0, 1);
 478       }
 479       else
 480       {
 481         moveSelectedSequences(false);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_UP:
 486       if (viewport.cursorMode)
 487       {
 488         alignPanel.seqPanel.moveCursor(0, -1);
 489       }
 490       else
 491       {
 492         moveSelectedSequences(true);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_LEFT:
 497       if (evt.isAltDown() || !viewport.cursorMode)
 498       {
 499         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 500       }
 501       else
 502       {
 503         alignPanel.seqPanel.moveCursor(-1, 0);
 504       }
 505       break;
 506
 507     case KeyEvent.VK_RIGHT:
 508       if (evt.isAltDown() || !viewport.cursorMode)
 509       {
 510         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 511       }
 512       else
 513       {
 514         alignPanel.seqPanel.moveCursor(1, 0);
 515       }
 516       break;
 517
 518     case KeyEvent.VK_SPACE:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 522                 || evt.isShiftDown() || evt.isAltDown());
 523       }
 524       break;
 525
 526     case KeyEvent.VK_DELETE:
 527     case KeyEvent.VK_BACK_SPACE:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 531                 || evt.isShiftDown() || evt.isAltDown());
 532       }
 533       else
 534       {
 535         cut_actionPerformed();
 536         alignPanel.seqPanel.seqCanvas.repaint();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_S:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setCursorRow();
 544       }
 545       break;
 546     case KeyEvent.VK_P:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setCursorPosition();
 550       }
 551       break;
 552
 553     case KeyEvent.VK_ENTER:
 554     case KeyEvent.VK_COMMA:
 555       if (viewport.cursorMode)
 556       {
 557         alignPanel.seqPanel.setCursorRowAndColumn();
 558       }
 559       break;
 560
 561     case KeyEvent.VK_Q:
 562       if (viewport.cursorMode)
 563       {
 564         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 565       }
 566       break;
 567     case KeyEvent.VK_M:
 568       if (viewport.cursorMode)
 569       {
 570         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 571       }
 572       break;
 573
 574     case KeyEvent.VK_F2:
 575       viewport.cursorMode = !viewport.cursorMode;
 576       statusBar.setText(MessageManager.formatMessage(
 577               "label.keyboard_editing_mode",
 578               new String[] { (viewport.cursorMode ? "on" : "off") }));
 579       if (viewport.cursorMode)
 580       {
 581         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 582         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 583       }
 584       break;
 585
 586     case KeyEvent.VK_F:
 587       if (evt.isControlDown())
 588       {
 589         findMenuItem_actionPerformed();
 590       }
 591       break;
 592
 593     case KeyEvent.VK_H:
 594     {
 595       boolean toggleSeqs = !evt.isControlDown();
 596       boolean toggleCols = !evt.isShiftDown();
 597       toggleHiddenRegions(toggleSeqs, toggleCols);
 598       break;
 599     }
 600
 601     case KeyEvent.VK_PAGE_UP:
 602       ranges.pageUp();
 603       break;
 604
 605     case KeyEvent.VK_PAGE_DOWN:
 606       ranges.pageDown();
 607       break;
 608
 609     case KeyEvent.VK_Z:
 610       if (evt.isControlDown())
 611       {
 612         undoMenuItem_actionPerformed();
 613       }
 614       break;
 615
 616     case KeyEvent.VK_Y:
 617       if (evt.isControlDown())
 618       {
 619         redoMenuItem_actionPerformed();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_L:
 624       if (evt.isControlDown())
 625       {
 626         trimAlignment(true);
 627       }
 628       break;
 629
 630     case KeyEvent.VK_R:
 631       if (evt.isControlDown())
 632       {
 633         trimAlignment(false);
 634       }
 635       break;
 636
 637     case KeyEvent.VK_E:
 638       if (evt.isControlDown())
 639       {
 640         if (evt.isShiftDown())
 641         {
 642           this.removeAllGapsMenuItem_actionPerformed();
 643         }
 644         else
 645         {
 646           removeGappedColumnMenuItem_actionPerformed();
 647         }
 648       }
 649       break;
 650     case KeyEvent.VK_I:
 651       if (evt.isControlDown())
 652       {
 653         if (evt.isAltDown())
 654         {
 655           invertColSel_actionPerformed();
 656         }
 657         else
 658         {
 659           invertSequenceMenuItem_actionPerformed();
 660         }
 661       }
 662       break;
 663
 664     case KeyEvent.VK_G:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isShiftDown())
 668         {
 669           this.unGroup_actionPerformed();
 670         }
 671         else
 672         {
 673           this.createGroup_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_U:
 679       if (evt.isControlDown())
 680       {
 681         this.deleteGroups_actionPerformed();
 682       }
 683       break;
 684
 685     case KeyEvent.VK_T:
 686       if (evt.isControlDown())
 687       {
 688         newView(null);
 689       }
 690       break;
 691
 692     }
 693     alignPanel.paintAlignment(true);
 694   }
 695
 696   /**
 697    * called by key handler and the hide all/show all menu items
 698    *
 699    * @param toggleSeqs
 700    * @param toggleCols
 701    */
 702   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 703   {
 704     boolean hide = false;
 705     SequenceGroup sg = viewport.getSelectionGroup();
 706     if (!toggleSeqs && !toggleCols)
 707     {
 708       // Hide everything by the current selection - this is a hack - we do the
 709       // invert and then hide
 710       // first check that there will be visible columns after the invert.
 711       if (viewport.hasSelectedColumns()
 712               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 713                       .getEndRes()))
 714       {
 715         // now invert the sequence set, if required - empty selection implies
 716         // that no hiding is required.
 717         if (sg != null)
 718         {
 719           invertSequenceMenuItem_actionPerformed();
 720           sg = viewport.getSelectionGroup();
 721           toggleSeqs = true;
 722
 723         }
 724         viewport.expandColSelection(sg, true);
 725         // finally invert the column selection and get the new sequence
 726         // selection and indicate it should be hidden.
 727         invertColSel_actionPerformed();
 728         toggleCols = true;
 729       }
 730     }
 731
 732     if (toggleSeqs)
 733     {
 734       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 735       {
 736         hide = true;
 737         viewport.hideAllSelectedSeqs();
 738       }
 739       else if (!(toggleCols && viewport.hasSelectedColumns()))
 740       {
 741         viewport.showAllHiddenSeqs();
 742       }
 743     }
 744
 745     if (toggleCols)
 746     {
 747       if (viewport.hasSelectedColumns())
 748       {
 749         viewport.hideSelectedColumns();
 750         if (!toggleSeqs)
 751         {
 752           viewport.setSelectionGroup(sg);
 753         }
 754       }
 755       else if (!hide)
 756       {
 757         viewport.showAllHiddenColumns();
 758       }
 759       viewport.sendSelection();
 760     }
 761   }
 762
 763   @Override
 764   public void keyReleased(KeyEvent evt)
 765   {
 766   }
 767
 768   @Override
 769   public void keyTyped(KeyEvent evt)
 770   {
 771   }
 772
 773   @Override
 774   public void itemStateChanged(ItemEvent evt)
 775   {
 776     final Object source = evt.getSource();
 777     if (source == displayNonconservedMenuItem)
 778     {
 779       displayNonconservedMenuItem_actionPerformed();
 780     }
 781     else if (source == colourTextMenuItem)
 782     {
 783       colourTextMenuItem_actionPerformed();
 784     }
 785     else if (source == wrapMenuItem)
 786     {
 787       wrapMenuItem_actionPerformed();
 788     }
 789     else if (source == scaleAbove)
 790     {
 791       viewport.setScaleAboveWrapped(scaleAbove.getState());
 792     }
 793     else if (source == scaleLeft)
 794     {
 795       viewport.setScaleLeftWrapped(scaleLeft.getState());
 796     }
 797     else if (source == scaleRight)
 798     {
 799       viewport.setScaleRightWrapped(scaleRight.getState());
 800     }
 801     else if (source == seqLimits)
 802     {
 803       seqLimits_itemStateChanged();
 804     }
 805     else if (source == viewBoxesMenuItem)
 806     {
 807       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 808     }
 809     else if (source == viewTextMenuItem)
 810     {
 811       viewport.setShowText(viewTextMenuItem.getState());
 812     }
 813     else if (source == renderGapsMenuItem)
 814     {
 815       viewport.setRenderGaps(renderGapsMenuItem.getState());
 816     }
 817     else if (source == annotationPanelMenuItem)
 818     {
 819       boolean showAnnotations = annotationPanelMenuItem.getState();
 820       showAlignmentAnnotations.setEnabled(showAnnotations);
 821       showSequenceAnnotations.setEnabled(showAnnotations);
 822       viewport.setShowAnnotation(showAnnotations);
 823       alignPanel.setAnnotationVisible(showAnnotations);
 824     }
 825     else if (source == sequenceFeatures)
 826     {
 827       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 828       alignPanel.seqPanel.seqCanvas.repaint();
 829     }
 830     else if (source == showAlignmentAnnotations)
 831     {
 832       setAnnotationsVisibility();
 833     }
 834     else if (source == showSequenceAnnotations)
 835     {
 836       setAnnotationsVisibility();
 837     }
 838     else if (source == sortAnnBySequence)
 839     {
 840       boolean newState = sortAnnBySequence.getState();
 841       sortAnnByLabel.setState(false);
 842       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 843               : SequenceAnnotationOrder.NONE);
 844       setViewportAnnotationOrder();
 845     }
 846     else if (source == sortAnnByLabel)
 847     {
 848       boolean newState = sortAnnByLabel.getState();
 849       sortAnnBySequence.setState(false);
 850       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 851               : SequenceAnnotationOrder.NONE);
 852       setViewportAnnotationOrder();
 853     }
 854     else if (source == showAutoFirst)
 855     {
 856       showAutoLast.setState(!showAutoFirst.getState());
 857       setShowAutoCalculatedAbove(showAutoFirst.getState());
 858       setViewportAnnotationOrder();
 859     }
 860     else if (source == showAutoLast)
 861     {
 862       showAutoFirst.setState(!showAutoLast.getState());
 863       setShowAutoCalculatedAbove(showAutoFirst.getState());
 864       setViewportAnnotationOrder();
 865     }
 866     else if (source == conservationMenuItem)
 867     {
 868       conservationMenuItem_actionPerformed();
 869     }
 870     else if (source == abovePIDThreshold)
 871     {
 872       abovePIDThreshold_actionPerformed();
 873     }
 874     else if (source == applyToAllGroups)
 875     {
 876       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 877     }
 878     else if (source == autoCalculate)
 879     {
 880       viewport.autoCalculateConsensus = autoCalculate.getState();
 881     }
 882     else if (source == sortByTree)
 883     {
 884       viewport.sortByTree = sortByTree.getState();
 885     }
 886     else if (source == this.centreColumnLabelFlag)
 887     {
 888       centreColumnLabelFlag_stateChanged();
 889     }
 890     else if (source == this.followMouseOverFlag)
 891     {
 892       mouseOverFlag_stateChanged();
 893     }
 894     else if (source == showGroupConsensus)
 895     {
 896       showGroupConsensus_actionPerformed();
 897     }
 898     else if (source == showGroupConservation)
 899     {
 900       showGroupConservation_actionPerformed();
 901     }
 902     else if (source == showSequenceLogo)
 903     {
 904       showSequenceLogo_actionPerformed();
 905     }
 906     else if (source == normSequenceLogo)
 907     {
 908       normSequenceLogo_actionPerformed();
 909     }
 910     else if (source == showConsensusHistogram)
 911     {
 912       showConsensusHistogram_actionPerformed();
 913     }
 914     else if (source == applyAutoAnnotationSettings)
 915     {
 916       applyAutoAnnotationSettings_actionPerformed();
 917     }
 918     alignPanel.paintAlignment(true);
 919   }
 920
 921   /**
 922    * Set the visibility state of sequence-related and/or alignment-related
 923    * annotations depending on checkbox selections, and repaint.
 924    *
 925    * @param visible
 926    */
 927   private void setAnnotationsVisibility()
 928   {
 929     boolean showForAlignment = showAlignmentAnnotations.getState();
 930     boolean showForSequences = showSequenceAnnotations.getState();
 931     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 932     {
 933       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 934               .getAlignmentAnnotation())
 935       {
 936         boolean visible = (aa.sequenceRef == null ? showForAlignment
 937                 : showForSequences);
 938         aa.visible = visible;
 939       }
 940     }
 941     alignPanel.validateAnnotationDimensions(true);
 942     validate();
 943     repaint();
 944   }
 945
 946   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 947   {
 948     this.annotationSortOrder = order;
 949   }
 950
 951   /**
 952    * Set flags on the viewport that control annotation ordering
 953    */
 954   private void setViewportAnnotationOrder()
 955   {
 956     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 957     this.alignPanel.av
 958             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 959   }
 960
 961   private void setShowAutoCalculatedAbove(boolean showAbove)
 962   {
 963     this.showAutoCalculatedAbove = showAbove;
 964   }
 965
 966   private void mouseOverFlag_stateChanged()
 967   {
 968     viewport.setFollowHighlight(followMouseOverFlag.getState());
 969     // TODO: could kick the scrollTo mechanism to reset view for current
 970     // searchresults.
 971   }
 972
 973   private void centreColumnLabelFlag_stateChanged()
 974   {
 975     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 976     this.alignPanel.annotationPanel.repaint();
 977   }
 978
 979   @Override
 980   public void actionPerformed(ActionEvent evt)
 981   {
 982     viewport.applet.currentAlignFrame = this;
 983
 984     Object source = evt.getSource();
 985
 986     if (source == inputText)
 987     {
 988       inputText_actionPerformed();
 989     }
 990     else if (source == loadTree)
 991     {
 992       loadTree_actionPerformed();
 993     }
 994     else if (source == loadApplication)
 995     {
 996       launchFullApplication();
 997     }
 998     else if (source == loadAnnotations)
 999     {
1000       loadAnnotations();
1001     }
1002     else if (source == outputAnnotations)
1003     {
1004       outputAnnotations(true);
1005     }
1006     else if (source == outputFeatures)
1007     {
1008       outputFeatures(true, "Jalview");
1009     }
1010     else if (source == closeMenuItem)
1011     {
1012       closeMenuItem_actionPerformed();
1013     }
1014     else if (source == copy)
1015     {
1016       copy_actionPerformed();
1017     }
1018     else if (source == undoMenuItem)
1019     {
1020       undoMenuItem_actionPerformed();
1021     }
1022     else if (source == redoMenuItem)
1023     {
1024       redoMenuItem_actionPerformed();
1025     }
1026     else if (source == inputText)
1027     {
1028       inputText_actionPerformed();
1029     }
1030     else if (source == closeMenuItem)
1031     {
1032       closeMenuItem_actionPerformed();
1033     }
1034     else if (source == undoMenuItem)
1035     {
1036       undoMenuItem_actionPerformed();
1037     }
1038     else if (source == redoMenuItem)
1039     {
1040       redoMenuItem_actionPerformed();
1041     }
1042     else if (source == copy)
1043     {
1044       copy_actionPerformed();
1045     }
1046     else if (source == pasteNew)
1047     {
1048       pasteNew_actionPerformed();
1049     }
1050     else if (source == pasteThis)
1051     {
1052       pasteThis_actionPerformed();
1053     }
1054     else if (source == cut)
1055     {
1056       cut_actionPerformed();
1057     }
1058     else if (source == delete)
1059     {
1060       delete_actionPerformed();
1061     }
1062     else if (source == createGroup)
1063     {
1064       createGroup_actionPerformed();
1065     }
1066     else if (source == unGroup)
1067     {
1068       unGroup_actionPerformed();
1069     }
1070     else if (source == grpsFromSelection)
1071     {
1072       makeGrpsFromSelection_actionPerformed();
1073     }
1074     else if (source == deleteGroups)
1075     {
1076       deleteGroups_actionPerformed();
1077     }
1078     else if (source == selectAllSequenceMenuItem)
1079     {
1080       selectAllSequenceMenuItem_actionPerformed();
1081     }
1082     else if (source == deselectAllSequenceMenuItem)
1083     {
1084       deselectAllSequenceMenuItem_actionPerformed();
1085     }
1086     else if (source == invertSequenceMenuItem)
1087     {
1088       invertSequenceMenuItem_actionPerformed();
1089       // uncomment to slave sequence selections in split frame
1090       // viewport.sendSelection();
1091     }
1092     else if (source == invertColSel)
1093     {
1094       viewport.invertColumnSelection();
1095       alignPanel.paintAlignment(true);
1096       viewport.sendSelection();
1097     }
1098     else if (source == remove2LeftMenuItem)
1099     {
1100       trimAlignment(true);
1101     }
1102     else if (source == remove2RightMenuItem)
1103     {
1104       trimAlignment(false);
1105     }
1106     else if (source == removeGappedColumnMenuItem)
1107     {
1108       removeGappedColumnMenuItem_actionPerformed();
1109     }
1110     else if (source == removeAllGapsMenuItem)
1111     {
1112       removeAllGapsMenuItem_actionPerformed();
1113     }
1114     else if (source == findMenuItem)
1115     {
1116       findMenuItem_actionPerformed();
1117     }
1118     else if (source == font)
1119     {
1120       new FontChooser(alignPanel);
1121     }
1122     else if (source == newView)
1123     {
1124       newView(null);
1125     }
1126     else if (source == showColumns)
1127     {
1128       viewport.showAllHiddenColumns();
1129       alignPanel.paintAlignment(true);
1130       viewport.sendSelection();
1131     }
1132     else if (source == showSeqs)
1133     {
1134       viewport.showAllHiddenSeqs();
1135       alignPanel.paintAlignment(true);
1136       // uncomment if we want to slave sequence selections in split frame
1137       // viewport.sendSelection();
1138     }
1139     else if (source == hideColumns)
1140     {
1141       viewport.hideSelectedColumns();
1142       alignPanel.paintAlignment(true);
1143       viewport.sendSelection();
1144     }
1145     else if (source == hideSequences
1146             && viewport.getSelectionGroup() != null)
1147     {
1148       viewport.hideAllSelectedSeqs();
1149       alignPanel.paintAlignment(true);
1150       // uncomment if we want to slave sequence selections in split frame
1151       // viewport.sendSelection();
1152     }
1153     else if (source == hideAllButSelection)
1154     {
1155       toggleHiddenRegions(false, false);
1156       alignPanel.paintAlignment(true);
1157       viewport.sendSelection();
1158     }
1159     else if (source == hideAllSelection)
1160     {
1161       SequenceGroup sg = viewport.getSelectionGroup();
1162       viewport.expandColSelection(sg, false);
1163       viewport.hideAllSelectedSeqs();
1164       viewport.hideSelectedColumns();
1165       alignPanel.paintAlignment(true);
1166       viewport.sendSelection();
1167     }
1168     else if (source == showAllHidden)
1169     {
1170       viewport.showAllHiddenColumns();
1171       viewport.showAllHiddenSeqs();
1172       alignPanel.paintAlignment(true);
1173       viewport.sendSelection();
1174     }
1175     else if (source == showGroupConsensus)
1176     {
1177       showGroupConsensus_actionPerformed();
1178     }
1179     else if (source == showGroupConservation)
1180     {
1181       showGroupConservation_actionPerformed();
1182     }
1183     else if (source == showSequenceLogo)
1184     {
1185       showSequenceLogo_actionPerformed();
1186     }
1187     else if (source == normSequenceLogo)
1188     {
1189       normSequenceLogo_actionPerformed();
1190     }
1191     else if (source == showConsensusHistogram)
1192     {
1193       showConsensusHistogram_actionPerformed();
1194     }
1195     else if (source == applyAutoAnnotationSettings)
1196     {
1197       applyAutoAnnotationSettings_actionPerformed();
1198     }
1199     else if (source == featureSettings)
1200     {
1201       new FeatureSettings(alignPanel);
1202     }
1203     else if (source == alProperties)
1204     {
1205       StringBuffer contents = new jalview.io.AlignmentProperties(
1206               viewport.getAlignment()).formatAsString();
1207       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1208       cap.setText(contents.toString());
1209       Frame frame = new Frame();
1210       frame.add(cap);
1211       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1212               "label.alignment_properties", new String[] { getTitle() }),
1213               400, 250);
1214     }
1215     else if (source == overviewMenuItem)
1216     {
1217       overviewMenuItem_actionPerformed();
1218     }
1219     else if (source == noColourmenuItem)
1220     {
1221       changeColour(null);
1222     }
1223     else if (source == clustalColour)
1224     {
1225       abovePIDThreshold.setState(false);
1226       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1227     }
1228     else if (source == zappoColour)
1229     {
1230       changeColour(new ZappoColourScheme());
1231     }
1232     else if (source == taylorColour)
1233     {
1234       changeColour(new TaylorColourScheme());
1235     }
1236     else if (source == hydrophobicityColour)
1237     {
1238       changeColour(new HydrophobicColourScheme());
1239     }
1240     else if (source == helixColour)
1241     {
1242       changeColour(new HelixColourScheme());
1243     }
1244     else if (source == strandColour)
1245     {
1246       changeColour(new StrandColourScheme());
1247     }
1248     else if (source == turnColour)
1249     {
1250       changeColour(new TurnColourScheme());
1251     }
1252     else if (source == buriedColour)
1253     {
1254       changeColour(new BuriedColourScheme());
1255     }
1256     else if (source == nucleotideColour)
1257     {
1258       changeColour(new NucleotideColourScheme());
1259     }
1260     else if (source == purinePyrimidineColour)
1261     {
1262       changeColour(new PurinePyrimidineColourScheme());
1263     }
1264     // else if (source == RNAInteractionColour)
1265     // {
1266     // changeColour(new RNAInteractionColourScheme());
1267     // }
1268     else if (source == RNAHelixColour)
1269     {
1270       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1271       // new RNAHelicesColourChooser(viewport, alignPanel);
1272     }
1273     else if (source == modifyPID)
1274     {
1275       modifyPID_actionPerformed();
1276     }
1277     else if (source == modifyConservation)
1278     {
1279       modifyConservation_actionPerformed();
1280     }
1281     else if (source == userDefinedColour)
1282     {
1283       new UserDefinedColours(alignPanel, null);
1284     }
1285     else if (source == PIDColour)
1286     {
1287       changeColour(new PIDColourScheme());
1288     }
1289     else if (source == BLOSUM62Colour)
1290     {
1291       changeColour(new Blosum62ColourScheme());
1292     }
1293     else if (source == tcoffeeColour)
1294     {
1295       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1296     }
1297     else if (source == annotationColour)
1298     {
1299       new AnnotationColourChooser(viewport, alignPanel);
1300     }
1301     else if (source == annotationColumnSelection)
1302     {
1303       new AnnotationColumnChooser(viewport, alignPanel);
1304     }
1305     else if (source == sortPairwiseMenuItem)
1306     {
1307       sortPairwiseMenuItem_actionPerformed();
1308     }
1309     else if (source == sortIDMenuItem)
1310     {
1311       sortIDMenuItem_actionPerformed();
1312     }
1313     else if (source == sortLengthMenuItem)
1314     {
1315       sortLengthMenuItem_actionPerformed();
1316     }
1317     else if (source == sortGroupMenuItem)
1318     {
1319       sortGroupMenuItem_actionPerformed();
1320     }
1321     else if (source == removeRedundancyMenuItem)
1322     {
1323       removeRedundancyMenuItem_actionPerformed();
1324     }
1325     else if (source == pairwiseAlignmentMenuItem)
1326     {
1327       pairwiseAlignmentMenuItem_actionPerformed();
1328     }
1329     else if (source == PCAMenuItem)
1330     {
1331       PCAMenuItem_actionPerformed();
1332     }
1333     else if (source == averageDistanceTreeMenuItem)
1334     {
1335       averageDistanceTreeMenuItem_actionPerformed();
1336     }
1337     else if (source == neighbourTreeMenuItem)
1338     {
1339       neighbourTreeMenuItem_actionPerformed();
1340     }
1341     else if (source == njTreeBlosumMenuItem)
1342     {
1343       njTreeBlosumMenuItem_actionPerformed();
1344     }
1345     else if (source == avDistanceTreeBlosumMenuItem)
1346     {
1347       avTreeBlosumMenuItem_actionPerformed();
1348     }
1349     else if (source == documentation)
1350     {
1351       documentation_actionPerformed();
1352     }
1353     else if (source == about)
1354     {
1355       about_actionPerformed();
1356     }
1357
1358   }
1359
1360   public void inputText_actionPerformed()
1361   {
1362     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1363     Frame frame = new Frame();
1364     frame.add(cap);
1365     jalview.bin.JalviewLite.addFrame(frame,
1366             MessageManager.getString("label.input_cut_paste"), 500, 500);
1367   }
1368
1369   protected void outputText_actionPerformed(ActionEvent e)
1370   {
1371     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1372     Frame frame = new Frame();
1373     frame.add(cap);
1374     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1375             "label.alignment_output_command",
1376             new Object[] { e.getActionCommand() }), 600, 500);
1377
1378     FileFormatI fileFormat = FileFormats.getInstance().forName(
1379             e.getActionCommand());
1380     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1381             fileFormat, viewport.getAlignment(),
1382             viewport.getShowJVSuffix()));
1383   }
1384
1385   public void loadAnnotations()
1386   {
1387     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388     cap.setText(MessageManager
1389             .getString("label.paste_features_annotations_Tcoffee_here"));
1390     cap.setAnnotationImport();
1391     Frame frame = new Frame();
1392     frame.add(cap);
1393     jalview.bin.JalviewLite.addFrame(frame,
1394             MessageManager.getString("action.paste_annotations"), 400, 300);
1395
1396   }
1397
1398   public String outputAnnotations(boolean displayTextbox)
1399   {
1400     String annotation = new AnnotationFile()
1401             .printAnnotationsForView(viewport);
1402
1403     if (displayTextbox)
1404     {
1405       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1406       Frame frame = new Frame();
1407       frame.add(cap);
1408       jalview.bin.JalviewLite.addFrame(frame,
1409               MessageManager.getString("label.annotations"), 600, 500);
1410       cap.setText(annotation);
1411     }
1412
1413     return annotation;
1414   }
1415
1416   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1417   {
1418     if (alignPanel.getFeatureRenderer() != null
1419             && viewport.getFeaturesDisplayed() != null)
1420     {
1421       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1422
1423     }
1424     return null;
1425   }
1426
1427   public String outputFeatures(boolean displayTextbox, String format)
1428   {
1429     String features;
1430     FeaturesFile formatter = new FeaturesFile();
1431     if (format.equalsIgnoreCase("Jalview"))
1432     {
1433       features = formatter.printJalviewFormat(viewport.getAlignment()
1434               .getSequencesArray(), getDisplayedFeatureCols());
1435     }
1436     else
1437     {
1438       features = formatter.printGffFormat(viewport.getAlignment()
1439               .getSequencesArray(), getDisplayedFeatureCols());
1440     }
1441
1442     if (displayTextbox)
1443     {
1444       boolean frimport = false;
1445       if (features == null || features.equals("No Features Visible"))
1446       {
1447         features = "# No features visible - paste some and import them here.";
1448         frimport = true;
1449       }
1450
1451       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1452       if (frimport)
1453       {
1454         cap.setAnnotationImport();
1455       }
1456       Frame frame = new Frame();
1457       frame.add(cap);
1458       jalview.bin.JalviewLite.addFrame(frame,
1459               MessageManager.getString("label.features"), 600, 500);
1460       cap.setText(features);
1461     }
1462     else
1463     {
1464       if (features == null)
1465       {
1466         features = "";
1467       }
1468     }
1469
1470     return features;
1471   }
1472
1473   void launchFullApplication()
1474   {
1475     StringBuffer url = new StringBuffer(jalviewServletURL);
1476
1477     // allow servlet parameters to be passed in applet parameter
1478     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1479             : "?";
1480     url.append(firstSep);
1481
1482     url.append("open="
1483             + appendProtocol(viewport.applet.getParameter("file")));
1484
1485     if (viewport.applet.getParameter("features") != null)
1486     {
1487       url.append("&features=");
1488       url.append(appendProtocol(viewport.applet.getParameter("features")));
1489     }
1490
1491     if (viewport.applet.getParameter("annotations") != null)
1492     {
1493       url.append("&annotations=");
1494       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1495     }
1496
1497     if (viewport.applet.getParameter("jnetfile") != null
1498             || viewport.applet.getParameter("jpredfile") != null)
1499     {
1500       url.append("&annotations=");
1501       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1502               .getParameter("jnetfile") : viewport.applet
1503               .getParameter("jpredfile")));
1504     }
1505
1506     if (viewport.applet.getParameter("defaultColour") != null)
1507     {
1508       url.append("&colour="
1509               + removeWhiteSpace(viewport.applet
1510                       .getParameter("defaultColour")));
1511     }
1512
1513     if (viewport.applet.getParameter("userDefinedColour") != null)
1514     {
1515       url.append("&colour="
1516               + removeWhiteSpace(viewport.applet
1517                       .getParameter("userDefinedColour")));
1518     }
1519     if (viewport.applet.getParameter("tree") != null)
1520     {
1521       url.append("&tree="
1522               + appendProtocol(viewport.applet.getParameter("tree")));
1523     }
1524     if (viewport.applet.getParameter("treeFile") != null)
1525     {
1526       url.append("&tree="
1527               + appendProtocol(viewport.applet.getParameter("treeFile")));
1528     }
1529
1530     showURL(url.toString(), "FULL_APP");
1531   }
1532
1533   String removeWhiteSpace(String colour)
1534   {
1535     StringBuffer sb = new StringBuffer();
1536     for (int i = 0; i < colour.length(); i++)
1537     {
1538       if (Character.isWhitespace(colour.charAt(i)))
1539       {
1540         sb.append("%20");
1541       }
1542       else
1543       {
1544         sb.append(colour.charAt(i));
1545       }
1546     }
1547
1548     return sb.toString();
1549   }
1550
1551   String appendProtocol(String url)
1552   {
1553     try
1554     {
1555       new URL(url);
1556       url = URLEncoder.encode(url);
1557     }
1558     /*
1559      * When we finally deprecate 1.1 compatibility, we can start to use
1560      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1561      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1562      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1563      * ex.printStackTrace(); }
1564      */
1565     catch (java.net.MalformedURLException ex)
1566     {
1567       url = viewport.applet.getCodeBase() + url;
1568     }
1569     return url;
1570   }
1571
1572   public void closeMenuItem_actionPerformed()
1573   {
1574     PaintRefresher.RemoveComponent(alignPanel);
1575     if (alignPanel.seqPanel != null
1576             && alignPanel.seqPanel.seqCanvas != null)
1577     {
1578       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1579     }
1580     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1581     {
1582       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1583     }
1584
1585     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1586     {
1587       System.exit(0);
1588     }
1589     else
1590     {
1591     }
1592     viewport = null;
1593     alignPanel = null;
1594     this.dispose();
1595   }
1596
1597   /**
1598    * TODO: JAL-1104
1599    */
1600   void updateEditMenuBar()
1601   {
1602
1603     if (viewport.getHistoryList().size() > 0)
1604     {
1605       undoMenuItem.setEnabled(true);
1606       CommandI command = viewport.getHistoryList().peek();
1607       undoMenuItem.setLabel(MessageManager.formatMessage(
1608               "label.undo_command",
1609               new Object[] { command.getDescription() }));
1610     }
1611     else
1612     {
1613       undoMenuItem.setEnabled(false);
1614       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1615     }
1616
1617     if (viewport.getRedoList().size() > 0)
1618     {
1619       redoMenuItem.setEnabled(true);
1620
1621       CommandI command = viewport.getRedoList().peek();
1622       redoMenuItem.setLabel(MessageManager.formatMessage(
1623               "label.redo_command",
1624               new Object[] { command.getDescription() }));
1625     }
1626     else
1627     {
1628       redoMenuItem.setEnabled(false);
1629       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1630     }
1631   }
1632
1633   /**
1634    * TODO: JAL-1104
1635    */
1636   @Override
1637   public void addHistoryItem(CommandI command)
1638   {
1639     if (command.getSize() > 0)
1640     {
1641       viewport.addToHistoryList(command);
1642       viewport.clearRedoList();
1643       updateEditMenuBar();
1644       viewport.updateHiddenColumns();
1645     }
1646   }
1647
1648   /**
1649    * TODO: JAL-1104 DOCUMENT ME!
1650    *
1651    * @param e
1652    *          DOCUMENT ME!
1653    */
1654   protected void undoMenuItem_actionPerformed()
1655   {
1656     if (viewport.getHistoryList().isEmpty())
1657     {
1658       return;
1659     }
1660
1661     CommandI command = viewport.getHistoryList().pop();
1662     viewport.addToRedoList(command);
1663     command.undoCommand(null);
1664
1665     AlignmentViewport originalSource = getOriginatingSource(command);
1666     // JBPNote Test
1667     if (originalSource != viewport)
1668     {
1669       System.err
1670               .println("Warning: Viewport object mismatch whilst undoing");
1671     }
1672     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1673                                           // viewport.getColumnSelection().getHiddenColumns()
1674                                           // != null;
1675     updateEditMenuBar();
1676     originalSource.firePropertyChange("alignment", null, originalSource
1677             .getAlignment().getSequences());
1678   }
1679
1680   /**
1681    * TODO: JAL-1104 DOCUMENT ME!
1682    *
1683    * @param e
1684    *          DOCUMENT ME!
1685    */
1686   protected void redoMenuItem_actionPerformed()
1687   {
1688     if (viewport.getRedoList().isEmpty())
1689     {
1690       return;
1691     }
1692
1693     CommandI command = viewport.getRedoList().pop();
1694     viewport.addToHistoryList(command);
1695     command.doCommand(null);
1696
1697     AlignmentViewport originalSource = getOriginatingSource(command);
1698     // JBPNote Test
1699     if (originalSource != viewport)
1700     {
1701       System.err
1702               .println("Warning: Viewport object mismatch whilst re-doing");
1703     }
1704     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1705                                           // viewport.getColumnSelection().getHiddenColumns()
1706                                           // != null;
1707
1708     updateEditMenuBar();
1709     originalSource.firePropertyChange("alignment", null, originalSource
1710             .getAlignment().getSequences());
1711   }
1712
1713   AlignmentViewport getOriginatingSource(CommandI command)
1714   {
1715     AlignmentViewport originalSource = null;
1716     // For sequence removal and addition, we need to fire
1717     // the property change event FROM the viewport where the
1718     // original alignment was altered
1719     AlignmentI al = null;
1720     if (command instanceof EditCommand)
1721     {
1722       EditCommand editCommand = (EditCommand) command;
1723       al = editCommand.getAlignment();
1724       Vector comps = (Vector) PaintRefresher.components.get(viewport
1725               .getSequenceSetId());
1726       for (int i = 0; i < comps.size(); i++)
1727       {
1728         if (comps.elementAt(i) instanceof AlignmentPanel)
1729         {
1730           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1731           {
1732             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1733             break;
1734           }
1735         }
1736       }
1737     }
1738
1739     if (originalSource == null)
1740     {
1741       // The original view is closed, we must validate
1742       // the current view against the closed view first
1743       if (al != null)
1744       {
1745         PaintRefresher.validateSequences(al, viewport.getAlignment());
1746       }
1747
1748       originalSource = viewport;
1749     }
1750
1751     return originalSource;
1752   }
1753
1754   /**
1755    * Move the currently selected sequences up or down one position in the
1756    * alignment
1757    *
1758    * @param up
1759    */
1760   public void moveSelectedSequences(boolean up)
1761   {
1762     SequenceGroup sg = viewport.getSelectionGroup();
1763     if (sg == null)
1764     {
1765       return;
1766     }
1767     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1768             up ? null : viewport.getHiddenRepSequences(), up);
1769     alignPanel.paintAlignment(true);
1770
1771     /*
1772      * Also move cDNA/protein complement sequences
1773      */
1774     AlignViewportI complement = viewport.getCodingComplement();
1775     if (complement != null)
1776     {
1777       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1778               viewport, complement);
1779       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1780               up ? null : complement.getHiddenRepSequences(), up);
1781       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1782     }
1783   }
1784
1785   synchronized void slideSequences(boolean right, int size)
1786   {
1787     List<SequenceI> sg = new Vector<>();
1788     if (viewport.cursorMode)
1789     {
1790       sg.add(viewport.getAlignment().getSequenceAt(
1791               alignPanel.seqPanel.seqCanvas.cursorY));
1792     }
1793     else if (viewport.getSelectionGroup() != null
1794             && viewport.getSelectionGroup().getSize() != viewport
1795                     .getAlignment().getHeight())
1796     {
1797       sg = viewport.getSelectionGroup().getSequences(
1798               viewport.getHiddenRepSequences());
1799     }
1800
1801     if (sg.size() < 1)
1802     {
1803       return;
1804     }
1805
1806     Vector<SequenceI> invertGroup = new Vector();
1807
1808     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1809     {
1810       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1811       {
1812         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1813       }
1814     }
1815
1816     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1817
1818     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1819             .size()]);
1820     for (int i = 0; i < invertGroup.size(); i++)
1821     {
1822       seqs2[i] = invertGroup.elementAt(i);
1823     }
1824
1825     SlideSequencesCommand ssc;
1826     if (right)
1827     {
1828       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1829               size, viewport.getGapCharacter());
1830     }
1831     else
1832     {
1833       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1834               size, viewport.getGapCharacter());
1835     }
1836
1837     int groupAdjustment = 0;
1838     if (ssc.getGapsInsertedBegin() && right)
1839     {
1840       if (viewport.cursorMode)
1841       {
1842         alignPanel.seqPanel.moveCursor(size, 0);
1843       }
1844       else
1845       {
1846         groupAdjustment = size;
1847       }
1848     }
1849     else if (!ssc.getGapsInsertedBegin() && !right)
1850     {
1851       if (viewport.cursorMode)
1852       {
1853         alignPanel.seqPanel.moveCursor(-size, 0);
1854       }
1855       else
1856       {
1857         groupAdjustment = -size;
1858       }
1859     }
1860
1861     if (groupAdjustment != 0)
1862     {
1863       viewport.getSelectionGroup().setStartRes(
1864               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1865       viewport.getSelectionGroup().setEndRes(
1866               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1867     }
1868
1869     boolean appendHistoryItem = false;
1870     Deque<CommandI> historyList = viewport.getHistoryList();
1871     if (historyList != null && historyList.size() > 0
1872             && historyList.peek() instanceof SlideSequencesCommand)
1873     {
1874       appendHistoryItem = ssc
1875               .appendSlideCommand((SlideSequencesCommand) historyList
1876                       .peek());
1877     }
1878
1879     if (!appendHistoryItem)
1880     {
1881       addHistoryItem(ssc);
1882     }
1883
1884     repaint();
1885   }
1886
1887   static StringBuffer copiedSequences;
1888
1889   static Vector<int[]> copiedHiddenColumns;
1890
1891   protected void copy_actionPerformed()
1892   {
1893     if (viewport.getSelectionGroup() == null)
1894     {
1895       return;
1896     }
1897
1898     SequenceGroup sg = viewport.getSelectionGroup();
1899     copiedSequences = new StringBuffer();
1900     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1901     for (int i = 0; i < sg.getSize(); i++)
1902     {
1903       SequenceI seq = sg.getSequenceAt(i);
1904       int index = viewport.getAlignment().findIndex(seq);
1905       orderedSeqs.put(index, seq);
1906     }
1907
1908     int index = 0, startRes, endRes;
1909     char ch;
1910
1911     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1912     {
1913       copiedHiddenColumns = new Vector<>(viewport.getAlignment()
1914               .getHiddenColumns().getHiddenColumnsCopy());
1915       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1916       for (int[] region : copiedHiddenColumns)
1917       {
1918         region[0] = region[0] - hiddenOffset;
1919         region[1] = region[1] - hiddenOffset;
1920       }
1921     }
1922     else
1923     {
1924       copiedHiddenColumns = null;
1925     }
1926
1927     for (int i = 0; i < sg.getSize(); i++)
1928     {
1929       SequenceI seq = null;
1930
1931       while (seq == null)
1932       {
1933         if (orderedSeqs.containsKey(index))
1934         {
1935           seq = orderedSeqs.get(index);
1936           index++;
1937           break;
1938         }
1939         else
1940         {
1941           index++;
1942         }
1943       }
1944
1945       // FIND START RES
1946       // Returns residue following index if gap
1947       startRes = seq.findPosition(sg.getStartRes());
1948
1949       // FIND END RES
1950       // Need to find the residue preceeding index if gap
1951       endRes = 0;
1952
1953       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1954       {
1955         ch = seq.getCharAt(j);
1956         if (!jalview.util.Comparison.isGap((ch)))
1957         {
1958           endRes++;
1959         }
1960       }
1961
1962       if (endRes > 0)
1963       {
1964         endRes += seq.getStart() - 1;
1965       }
1966
1967       copiedSequences.append(seq.getName()
1968               + "\t"
1969               + startRes
1970               + "\t"
1971               + endRes
1972               + "\t"
1973               + seq.getSequenceAsString(sg.getStartRes(),
1974                       sg.getEndRes() + 1) + "\n");
1975     }
1976
1977   }
1978
1979   protected void pasteNew_actionPerformed()
1980   {
1981     paste(true);
1982   }
1983
1984   protected void pasteThis_actionPerformed()
1985   {
1986     paste(false);
1987   }
1988
1989   void paste(boolean newAlignment)
1990   {
1991     try
1992     {
1993
1994       if (copiedSequences == null)
1995       {
1996         return;
1997       }
1998
1999       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2000       Vector seqs = new Vector();
2001       while (st.hasMoreElements())
2002       {
2003         String name = st.nextToken();
2004         int start = Integer.parseInt(st.nextToken());
2005         int end = Integer.parseInt(st.nextToken());
2006         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2007       }
2008       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2009       for (int i = 0; i < seqs.size(); i++)
2010       {
2011         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2012       }
2013
2014       if (newAlignment)
2015       {
2016         String newtitle = MessageManager
2017                 .getString("label.copied_sequences");
2018         if (getTitle().startsWith(
2019                 MessageManager.getString("label.copied_sequences")))
2020         {
2021           newtitle = getTitle();
2022         }
2023         else
2024         {
2025           newtitle = newtitle.concat(MessageManager.formatMessage(
2026                   "label.from_msname", new String[] { getTitle() }));
2027         }
2028         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2029                 viewport.applet, newtitle, false);
2030         if (copiedHiddenColumns != null)
2031         {
2032           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2033           {
2034             int[] region = copiedHiddenColumns.elementAt(i);
2035             af.viewport.hideColumns(region[0], region[1]);
2036           }
2037         }
2038
2039         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2040                 frameHeight);
2041       }
2042       else
2043       {
2044         addSequences(newSeqs);
2045       }
2046
2047     } catch (Exception ex)
2048     {
2049     } // could be anything being pasted in here
2050
2051   }
2052
2053   void addSequences(SequenceI[] seqs)
2054   {
2055     for (int i = 0; i < seqs.length; i++)
2056     {
2057       viewport.getAlignment().addSequence(seqs[i]);
2058     }
2059
2060     // !newAlignment
2061     addHistoryItem(new EditCommand(
2062             MessageManager.getString("label.add_sequences"), Action.PASTE,
2063             seqs, 0, viewport.getAlignment().getWidth(),
2064             viewport.getAlignment()));
2065
2066     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2067     viewport.getAlignment().getWidth();
2068     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2069             .getSequences());
2070
2071   }
2072
2073   protected void cut_actionPerformed()
2074   {
2075     copy_actionPerformed();
2076     delete_actionPerformed();
2077   }
2078
2079   protected void delete_actionPerformed()
2080   {
2081
2082     SequenceGroup sg = viewport.getSelectionGroup();
2083     if (sg == null)
2084     {
2085       return;
2086     }
2087
2088     Vector seqs = new Vector();
2089     SequenceI seq;
2090     for (int i = 0; i < sg.getSize(); i++)
2091     {
2092       seq = sg.getSequenceAt(i);
2093       seqs.addElement(seq);
2094     }
2095
2096     /*
2097      * If the cut affects all sequences, warn, remove highlighted columns
2098      */
2099     if (sg.getSize() == viewport.getAlignment().getHeight())
2100     {
2101       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2102               .getAlignment().getWidth()) ? true : false;
2103       if (isEntireAlignWidth)
2104       {
2105         String title = MessageManager.getString("label.delete_all");
2106         Panel infoPanel = new Panel();
2107         infoPanel.setLayout(new FlowLayout());
2108         infoPanel
2109                 .add(new Label(MessageManager.getString("warn.delete_all")));
2110
2111         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2112         dialog.setMainPanel(infoPanel);
2113         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2114         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2115         dialog.setVisible(true);
2116
2117         if (!dialog.accept)
2118         {
2119           return;
2120         }
2121       }
2122       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2123               sg.getEndRes() + 1);
2124     }
2125
2126     SequenceI[] cut = new SequenceI[seqs.size()];
2127     for (int i = 0; i < seqs.size(); i++)
2128     {
2129       cut[i] = (SequenceI) seqs.elementAt(i);
2130     }
2131
2132     /*
2133      * //ADD HISTORY ITEM
2134      */
2135     addHistoryItem(new EditCommand(
2136             MessageManager.getString("label.cut_sequences"), Action.CUT,
2137             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2138             viewport.getAlignment()));
2139
2140     viewport.setSelectionGroup(null);
2141     viewport.getAlignment().deleteGroup(sg);
2142
2143     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2144             .getSequences());
2145
2146     if (viewport.getAlignment().getHeight() < 1)
2147     {
2148       this.setVisible(false);
2149     }
2150     viewport.sendSelection();
2151   }
2152
2153   /**
2154    * group consensus toggled
2155    *
2156    */
2157   protected void showGroupConsensus_actionPerformed()
2158   {
2159     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2160     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161
2162   }
2163
2164   /**
2165    * group conservation toggled.
2166    */
2167   protected void showGroupConservation_actionPerformed()
2168   {
2169     viewport.setShowGroupConservation(showGroupConservation.getState());
2170     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2171   }
2172
2173   /*
2174    * (non-Javadoc)
2175    *
2176    * @see
2177    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2178    * .event.ActionEvent)
2179    */
2180   protected void showConsensusHistogram_actionPerformed()
2181   {
2182     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   /*
2187    * (non-Javadoc)
2188    *
2189    * @see
2190    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2191    * .event.ActionEvent)
2192    */
2193   protected void showSequenceLogo_actionPerformed()
2194   {
2195     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   protected void normSequenceLogo_actionPerformed()
2200   {
2201     showSequenceLogo.setState(true);
2202     viewport.setShowSequenceLogo(true);
2203     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2204     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2205   }
2206
2207   protected void applyAutoAnnotationSettings_actionPerformed()
2208   {
2209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210   }
2211
2212   protected void makeGrpsFromSelection_actionPerformed()
2213   {
2214     if (avc.makeGroupsFromSelection())
2215     {
2216       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2217       alignPanel.updateAnnotation();
2218       alignPanel.paintAlignment(true);
2219     }
2220   }
2221
2222   protected void createGroup_actionPerformed()
2223   {
2224     avc.createGroup();
2225   }
2226
2227   protected void unGroup_actionPerformed()
2228   {
2229     if (avc.unGroup())
2230     {
2231       alignPanel.alignmentChanged();
2232     }
2233   }
2234
2235   protected void deleteGroups_actionPerformed()
2236   {
2237     if (avc.deleteGroups())
2238     {
2239       alignPanel.alignmentChanged();
2240     }
2241   }
2242
2243   public void selectAllSequenceMenuItem_actionPerformed()
2244   {
2245     SequenceGroup sg = new SequenceGroup();
2246     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2247     {
2248       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2249     }
2250     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2251     viewport.setSelectionGroup(sg);
2252     // JAL-2034 - should delegate to
2253     // alignPanel to decide if overview needs
2254     // updating.
2255     alignPanel.paintAlignment(false);
2256     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257     viewport.sendSelection();
2258   }
2259
2260   public void deselectAllSequenceMenuItem_actionPerformed()
2261   {
2262     if (viewport.cursorMode)
2263     {
2264       alignPanel.seqPanel.keyboardNo1 = null;
2265       alignPanel.seqPanel.keyboardNo2 = null;
2266     }
2267     viewport.setSelectionGroup(null);
2268     viewport.getColumnSelection().clear();
2269     viewport.setSelectionGroup(null);
2270     alignPanel.idPanel.idCanvas.searchResults = null;
2271     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2272     // JAL-2034 - should delegate to
2273     // alignPanel to decide if overview needs
2274     // updating.
2275     alignPanel.paintAlignment(false);
2276     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277     viewport.sendSelection();
2278   }
2279
2280   public void invertSequenceMenuItem_actionPerformed()
2281   {
2282     SequenceGroup sg = viewport.getSelectionGroup();
2283     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2284     {
2285       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2286     }
2287
2288     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289     viewport.sendSelection();
2290   }
2291
2292   public void invertColSel_actionPerformed()
2293   {
2294     viewport.invertColumnSelection();
2295     alignPanel.paintAlignment(true);
2296     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297     viewport.sendSelection();
2298   }
2299
2300   void trimAlignment(boolean trimLeft)
2301   {
2302     AlignmentI al = viewport.getAlignment();
2303     ViewportRanges ranges = viewport.getRanges();
2304     ColumnSelection colSel = viewport.getColumnSelection();
2305     int column;
2306
2307     if (!colSel.isEmpty())
2308     {
2309       if (trimLeft)
2310       {
2311         column = colSel.getMin();
2312       }
2313       else
2314       {
2315         column = colSel.getMax();
2316       }
2317
2318       SequenceI[] seqs;
2319       if (viewport.getSelectionGroup() != null)
2320       {
2321         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2322                 viewport.getHiddenRepSequences());
2323       }
2324       else
2325       {
2326         seqs = al.getSequencesArray();
2327       }
2328
2329       TrimRegionCommand trimRegion;
2330       if (trimLeft)
2331       {
2332         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2333                 column, al);
2334         ranges.setStartRes(0);
2335       }
2336       else
2337       {
2338         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2339                 column, al);
2340       }
2341
2342       statusBar.setText(MessageManager.formatMessage(
2343               "label.removed_columns",
2344               new String[] { Integer.valueOf(trimRegion.getSize())
2345                       .toString() }));
2346       addHistoryItem(trimRegion);
2347
2348       for (SequenceGroup sg : al.getGroups())
2349       {
2350         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2351                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2352         {
2353           al.deleteGroup(sg);
2354         }
2355       }
2356
2357       viewport.firePropertyChange("alignment", null, al.getSequences());
2358     }
2359   }
2360
2361   public void removeGappedColumnMenuItem_actionPerformed()
2362   {
2363     AlignmentI al = viewport.getAlignment();
2364     ViewportRanges ranges = viewport.getRanges();
2365     int start = 0;
2366     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2367
2368     SequenceI[] seqs;
2369     if (viewport.getSelectionGroup() != null)
2370     {
2371       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2372               viewport.getHiddenRepSequences());
2373       start = viewport.getSelectionGroup().getStartRes();
2374       end = viewport.getSelectionGroup().getEndRes();
2375     }
2376     else
2377     {
2378       seqs = viewport.getAlignment().getSequencesArray();
2379     }
2380
2381     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2382             "Remove Gapped Columns", seqs, start, end,
2383             viewport.getAlignment());
2384
2385     addHistoryItem(removeGapCols);
2386
2387     statusBar.setText(MessageManager.formatMessage(
2388             "label.removed_empty_columns",
2389             new String[] { Integer.valueOf(removeGapCols.getSize())
2390                     .toString() }));
2391
2392     // This is to maintain viewport position on first residue
2393     // of first sequence
2394     SequenceI seq = al.getSequenceAt(0);
2395     int startRes = seq.findPosition(ranges.getStartRes());
2396     // ShiftList shifts;
2397     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2398     // edit.alColumnChanges=shifts.getInverse();
2399     // if (viewport.hasHiddenColumns)
2400     // viewport.getColumnSelection().compensateForEdits(shifts);
2401     ranges.setStartRes(seq.findIndex(startRes) - 1);
2402     viewport.firePropertyChange("alignment", null, al.getSequences());
2403
2404   }
2405
2406   public void removeAllGapsMenuItem_actionPerformed()
2407   {
2408     AlignmentI al = viewport.getAlignment();
2409     ViewportRanges ranges = viewport.getRanges();
2410     int start = 0;
2411     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2412
2413     SequenceI[] seqs;
2414     if (viewport.getSelectionGroup() != null)
2415     {
2416       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2417               viewport.getHiddenRepSequences());
2418       start = viewport.getSelectionGroup().getStartRes();
2419       end = viewport.getSelectionGroup().getEndRes();
2420     }
2421     else
2422     {
2423       seqs = viewport.getAlignment().getSequencesArray();
2424     }
2425
2426     // This is to maintain viewport position on first residue
2427     // of first sequence
2428     SequenceI seq = al.getSequenceAt(0);
2429     int startRes = seq.findPosition(ranges.getStartRes());
2430
2431     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2432             al));
2433
2434     ranges.setStartRes(seq.findIndex(startRes) - 1);
2435
2436     viewport.firePropertyChange("alignment", null, al.getSequences());
2437
2438   }
2439
2440   public void findMenuItem_actionPerformed()
2441   {
2442     new Finder(alignPanel);
2443   }
2444
2445   /**
2446    * create a new view derived from the current view
2447    *
2448    * @param viewtitle
2449    * @return frame for the new view
2450    */
2451   public AlignFrame newView(String viewtitle)
2452   {
2453     AlignmentI newal;
2454     if (viewport.hasHiddenRows())
2455     {
2456       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2457               .getFullAlignment().getSequencesArray());
2458     }
2459     else
2460     {
2461       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2462     }
2463
2464     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2465     {
2466       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2467       {
2468         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2469         {
2470           newal.addAnnotation(viewport.getAlignment()
2471                   .getAlignmentAnnotation()[i]);
2472         }
2473       }
2474     }
2475
2476     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2477
2478     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2479     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2480     PaintRefresher.Register(newaf.alignPanel,
2481             newaf.alignPanel.av.getSequenceSetId());
2482
2483     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2484             newaf.alignPanel.av.getSequenceSetId());
2485     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2486             newaf.alignPanel.av.getSequenceSetId());
2487
2488     Vector comps = (Vector) PaintRefresher.components.get(viewport
2489             .getSequenceSetId());
2490     int viewSize = -1;
2491     for (int i = 0; i < comps.size(); i++)
2492     {
2493       if (comps.elementAt(i) instanceof AlignmentPanel)
2494       {
2495         viewSize++;
2496       }
2497     }
2498
2499     String title = new String(this.getTitle());
2500     if (viewtitle != null)
2501     {
2502       title = viewtitle + " ( " + title + ")";
2503     }
2504     else
2505     {
2506       if (title.indexOf("(View") > -1)
2507       {
2508         title = title.substring(0, title.indexOf("(View"));
2509       }
2510       title += "(View " + viewSize + ")";
2511     }
2512
2513     newaf.setTitle(title.toString());
2514
2515     newaf.viewport.setHistoryList(viewport.getHistoryList());
2516     newaf.viewport.setRedoList(viewport.getRedoList());
2517     return newaf;
2518   }
2519
2520   /**
2521    *
2522    * @return list of feature groups on the view
2523    */
2524   public String[] getFeatureGroups()
2525   {
2526     FeatureRenderer fr = null;
2527     if (alignPanel != null
2528             && (fr = alignPanel.getFeatureRenderer()) != null)
2529     {
2530       List<String> gps = fr.getFeatureGroups();
2531       String[] _gps = gps.toArray(new String[gps.size()]);
2532       return _gps;
2533     }
2534     return null;
2535   }
2536
2537   /**
2538    * get sequence feature groups that are hidden or shown
2539    *
2540    * @param visible
2541    *          true is visible
2542    * @return list
2543    */
2544   public String[] getFeatureGroupsOfState(boolean visible)
2545   {
2546     FeatureRenderer fr = null;
2547     if (alignPanel != null
2548             && (fr = alignPanel.getFeatureRenderer()) != null)
2549     {
2550       List<String> gps = fr.getGroups(visible);
2551       String[] _gps = gps.toArray(new String[gps.size()]);
2552       return _gps;
2553     }
2554     return null;
2555   }
2556
2557   /**
2558    * Change the display state for the given feature groups
2559    *
2560    * @param groups
2561    *          list of group strings
2562    * @param state
2563    *          visible or invisible
2564    */
2565   public void setFeatureGroupState(String[] groups, boolean state)
2566   {
2567     FeatureRenderer fr = null;
2568     this.sequenceFeatures.setState(true);
2569     viewport.setShowSequenceFeatures(true);
2570     if (alignPanel != null
2571             && (fr = alignPanel.getFeatureRenderer()) != null)
2572     {
2573
2574       fr.setGroupVisibility(Arrays.asList(groups), state);
2575       alignPanel.seqPanel.seqCanvas.repaint();
2576       if (alignPanel.overviewPanel != null)
2577       {
2578         alignPanel.overviewPanel.updateOverviewImage();
2579       }
2580     }
2581   }
2582
2583   public void seqLimits_itemStateChanged()
2584   {
2585     viewport.setShowJVSuffix(seqLimits.getState());
2586     alignPanel.fontChanged();
2587     alignPanel.paintAlignment(true);
2588   }
2589
2590   protected void colourTextMenuItem_actionPerformed()
2591   {
2592     viewport.setColourText(colourTextMenuItem.getState());
2593     alignPanel.paintAlignment(true);
2594   }
2595
2596   protected void displayNonconservedMenuItem_actionPerformed()
2597   {
2598     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2599     alignPanel.paintAlignment(true);
2600   }
2601
2602   protected void wrapMenuItem_actionPerformed()
2603   {
2604     viewport.setWrapAlignment(wrapMenuItem.getState());
2605     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2606     scaleAbove.setEnabled(wrapMenuItem.getState());
2607     scaleLeft.setEnabled(wrapMenuItem.getState());
2608     scaleRight.setEnabled(wrapMenuItem.getState());
2609     alignPanel.paintAlignment(true);
2610   }
2611
2612   public void overviewMenuItem_actionPerformed()
2613   {
2614     if (alignPanel.overviewPanel != null)
2615     {
2616       return;
2617     }
2618
2619     Frame frame = new Frame();
2620     OverviewPanel overview = new OverviewPanel(alignPanel);
2621     frame.add(overview);
2622     // +50 must allow for applet frame window
2623     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2624             "label.overview_params", new String[] { this.getTitle() }),
2625             overview.getPreferredSize().width,
2626             overview.getPreferredSize().height + 50);
2627
2628     frame.pack();
2629     final AlignmentPanel ap = alignPanel;
2630     frame.addWindowListener(new WindowAdapter()
2631     {
2632       @Override
2633       public void windowClosing(WindowEvent e)
2634       {
2635         if (ap != null)
2636         {
2637           ap.setOverviewPanel(null);
2638         }
2639       };
2640     });
2641
2642     alignPanel.setOverviewPanel(overview);
2643
2644   }
2645
2646   @Override
2647   public void changeColour(ColourSchemeI cs)
2648   {
2649     viewport.setGlobalColourScheme(cs);
2650
2651     alignPanel.paintAlignment(true);
2652   }
2653
2654   protected void modifyPID_actionPerformed()
2655   {
2656     if (viewport.getAbovePIDThreshold()
2657             && viewport.getGlobalColourScheme() != null)
2658     {
2659       SliderPanel.setPIDSliderSource(alignPanel,
2660               viewport.getResidueShading(), alignPanel.getViewName());
2661       SliderPanel.showPIDSlider();
2662     }
2663   }
2664
2665   protected void modifyConservation_actionPerformed()
2666   {
2667     if (viewport.getConservationSelected()
2668             && viewport.getGlobalColourScheme() != null)
2669     {
2670       SliderPanel.setConservationSlider(alignPanel,
2671               viewport.getResidueShading(), alignPanel.getViewName());
2672       SliderPanel.showConservationSlider();
2673     }
2674   }
2675
2676   protected void conservationMenuItem_actionPerformed()
2677   {
2678     boolean selected = conservationMenuItem.getState();
2679     modifyConservation.setEnabled(selected);
2680     viewport.setConservationSelected(selected);
2681     viewport.getResidueShading().setConservationApplied(selected);
2682
2683     changeColour(viewport.getGlobalColourScheme());
2684
2685     if (selected)
2686     {
2687       modifyConservation_actionPerformed();
2688     }
2689     else
2690     {
2691       SliderPanel.hideConservationSlider();
2692     }
2693   }
2694
2695   public void abovePIDThreshold_actionPerformed()
2696   {
2697     boolean selected = abovePIDThreshold.getState();
2698     modifyPID.setEnabled(selected);
2699     viewport.setAbovePIDThreshold(selected);
2700     if (!selected)
2701     {
2702       viewport.getResidueShading().setThreshold(0,
2703               viewport.isIgnoreGapsConsensus());
2704     }
2705
2706     changeColour(viewport.getGlobalColourScheme());
2707
2708     if (selected)
2709     {
2710       modifyPID_actionPerformed();
2711     }
2712     else
2713     {
2714       SliderPanel.hidePIDSlider();
2715     }
2716   }
2717
2718   public void sortPairwiseMenuItem_actionPerformed()
2719   {
2720     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2721     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2722             .getAlignment().getSequenceAt(0));
2723
2724     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2725             viewport.getAlignment()));
2726     alignPanel.paintAlignment(true);
2727   }
2728
2729   public void sortIDMenuItem_actionPerformed()
2730   {
2731     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732     AlignmentSorter.sortByID(viewport.getAlignment());
2733     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2734             viewport.getAlignment()));
2735     alignPanel.paintAlignment(true);
2736   }
2737
2738   public void sortLengthMenuItem_actionPerformed()
2739   {
2740     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2741     AlignmentSorter.sortByLength(viewport.getAlignment());
2742     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2743             viewport.getAlignment()));
2744     alignPanel.paintAlignment(true);
2745   }
2746
2747   public void sortGroupMenuItem_actionPerformed()
2748   {
2749     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750     AlignmentSorter.sortByGroup(viewport.getAlignment());
2751     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2752             viewport.getAlignment()));
2753     alignPanel.paintAlignment(true);
2754
2755   }
2756
2757   public void removeRedundancyMenuItem_actionPerformed()
2758   {
2759     new RedundancyPanel(alignPanel);
2760   }
2761
2762   public void pairwiseAlignmentMenuItem_actionPerformed()
2763   {
2764     if (viewport.getSelectionGroup() != null
2765             && viewport.getSelectionGroup().getSize() > 1)
2766     {
2767       Frame frame = new Frame();
2768       frame.add(new PairwiseAlignPanel(alignPanel));
2769       jalview.bin.JalviewLite.addFrame(frame,
2770               MessageManager.getString("action.pairwise_alignment"), 600,
2771               500);
2772     }
2773   }
2774
2775   public void PCAMenuItem_actionPerformed()
2776   {
2777     // are the sequences aligned?
2778     if (!viewport.getAlignment().isAligned(false))
2779     {
2780       SequenceI current;
2781       int Width = viewport.getAlignment().getWidth();
2782
2783       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2784       {
2785         current = viewport.getAlignment().getSequenceAt(i);
2786
2787         if (current.getLength() < Width)
2788         {
2789           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2790         }
2791       }
2792       alignPanel.paintAlignment(true);
2793     }
2794
2795     if ((viewport.getSelectionGroup() != null
2796             && viewport.getSelectionGroup().getSize() < 4 && viewport
2797             .getSelectionGroup().getSize() > 0)
2798             || viewport.getAlignment().getHeight() < 4)
2799     {
2800       return;
2801     }
2802
2803     try
2804     {
2805       new PCAPanel(viewport);
2806     } catch (java.lang.OutOfMemoryError ex)
2807     {
2808     }
2809
2810   }
2811
2812   public void averageDistanceTreeMenuItem_actionPerformed()
2813   {
2814     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2815             "Average distance tree using PID");
2816   }
2817
2818   public void neighbourTreeMenuItem_actionPerformed()
2819   {
2820     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2821             "Neighbour joining tree using PID");
2822   }
2823
2824   protected void njTreeBlosumMenuItem_actionPerformed()
2825   {
2826     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2827             .getBlosum62().getName(),
2828             "Neighbour joining tree using BLOSUM62");
2829   }
2830
2831   protected void avTreeBlosumMenuItem_actionPerformed()
2832   {
2833     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2834             .getBlosum62().getName(),
2835             "Average distance tree using BLOSUM62");
2836   }
2837
2838   void newTreePanel(String type, String pwType, String title)
2839   {
2840     // are the sequences aligned?
2841     if (!viewport.getAlignment().isAligned(false))
2842     {
2843       SequenceI current;
2844       int Width = viewport.getAlignment().getWidth();
2845
2846       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2847       {
2848         current = viewport.getAlignment().getSequenceAt(i);
2849
2850         if (current.getLength() < Width)
2851         {
2852           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2853         }
2854       }
2855       alignPanel.paintAlignment(true);
2856
2857     }
2858
2859     if ((viewport.getSelectionGroup() != null && viewport
2860             .getSelectionGroup().getSize() > 1)
2861             || (viewport.getAlignment().getHeight() > 1))
2862     {
2863       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2864
2865       addTreeMenuItem(tp, title);
2866
2867       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2868     }
2869   }
2870
2871   void loadTree_actionPerformed()
2872   {
2873     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2874     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2875     cap.setTreeImport();
2876     Frame frame = new Frame();
2877     frame.add(cap);
2878     jalview.bin.JalviewLite.addFrame(frame,
2879             MessageManager.getString("label.paste_newick_file"), 400, 300);
2880   }
2881
2882   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2883   {
2884     TreePanel tp = new TreePanel(alignPanel, treeFile,
2885             MessageManager.getString("label.load_tree_from_file"), tree);
2886     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2887     addTreeMenuItem(tp, treeFile);
2888   }
2889
2890   /**
2891    * sort the alignment using the given treePanel
2892    *
2893    * @param treePanel
2894    *          tree used to sort view
2895    * @param title
2896    *          string used for undo event name
2897    */
2898   public void sortByTree(TreePanel treePanel, String title)
2899   {
2900     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2901     AlignmentSorter
2902             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2903     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2904     // HistoryItem.SORT));
2905     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2906             "label.order_by_params", new String[] { title }), oldOrder,
2907             viewport.getAlignment()));
2908     alignPanel.paintAlignment(true);
2909   }
2910
2911   /**
2912    * Do any automatic reordering of the alignment and add the necessary bits to
2913    * the menu structure for the new tree
2914    *
2915    * @param treePanel
2916    * @param title
2917    */
2918   protected void addTreeMenuItem(final TreePanel treePanel,
2919           final String title)
2920   {
2921     final MenuItem item = new MenuItem(title);
2922     sortByTreeMenu.add(item);
2923     item.addActionListener(new java.awt.event.ActionListener()
2924     {
2925       @Override
2926       public void actionPerformed(ActionEvent evt)
2927       {
2928         sortByTree(treePanel, title); // treePanel.getTitle());
2929       }
2930     });
2931
2932     treePanel.addWindowListener(new WindowAdapter()
2933     {
2934       @Override
2935       public void windowOpened(WindowEvent e)
2936       {
2937         if (viewport.sortByTree)
2938         {
2939           sortByTree(treePanel, title);
2940         }
2941         super.windowOpened(e);
2942       }
2943
2944       @Override
2945       public void windowClosing(WindowEvent e)
2946       {
2947         sortByTreeMenu.remove(item);
2948       };
2949     });
2950   }
2951
2952   public boolean sortBy(AlignmentOrder alorder, String undoname)
2953   {
2954     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2955     if (viewport.applet.debug)
2956     {
2957       System.err.println("Sorting " + alorder.getOrder().size()
2958               + " in alignment '" + getTitle() + "'");
2959     }
2960     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2961     if (undoname != null)
2962     {
2963       addHistoryItem(new OrderCommand(undoname, oldOrder,
2964               viewport.getAlignment()));
2965     }
2966     alignPanel.paintAlignment(true);
2967     return true;
2968   }
2969
2970   protected void documentation_actionPerformed()
2971   {
2972     alignPanel.av.applet.openJalviewHelpUrl();
2973   }
2974
2975   protected void about_actionPerformed()
2976   {
2977
2978     class AboutPanel extends Canvas
2979     {
2980       String version;
2981
2982       String builddate;
2983
2984       public AboutPanel(String version, String builddate)
2985       {
2986         this.version = version;
2987         this.builddate = builddate;
2988       }
2989
2990       @Override
2991       public void paint(Graphics g)
2992       {
2993         g.setColor(Color.white);
2994         g.fillRect(0, 0, getSize().width, getSize().height);
2995         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2996         FontMetrics fm = g.getFontMetrics();
2997         int fh = fm.getHeight();
2998         int y = 5, x = 7;
2999         g.setColor(Color.black);
3000         // TODO: update this text for each release or centrally store it for
3001         // lite and application
3002         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3003         g.drawString(MessageManager.formatMessage(
3004                 "label.jalviewLite_release", new String[] { version }), x,
3005                 y += fh);
3006         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3007         g.drawString(MessageManager.formatMessage(
3008                 "label.jaview_build_date", new String[] { builddate }), x,
3009                 y += fh);
3010         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3011         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3012                 x, y += fh * 1.5);
3013         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3014                 x + 50, y += fh + 8);
3015         g.drawString(
3016                 MessageManager.getString("label.jalview_dev_managers"), x,
3017                 y += fh);
3018         g.drawString(MessageManager
3019                 .getString("label.jalview_distribution_lists"), x, y += fh);
3020         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3021                 x, y += fh + 8);
3022         g.drawString(
3023                 MessageManager.getString("label.jalview_cite_1_authors"),
3024                 x, y += fh);
3025         g.drawString(
3026                 MessageManager.getString("label.jalview_cite_1_title"), x,
3027                 y += fh);
3028         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3029                 x, y += fh);
3030       }
3031     }
3032
3033     Frame frame = new Frame();
3034     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3035             .getBuildDate()));
3036     jalview.bin.JalviewLite.addFrame(frame,
3037             MessageManager.getString("label.jalview"), 580, 220);
3038
3039   }
3040
3041   public void showURL(String url, String target)
3042   {
3043     if (viewport.applet == null)
3044     {
3045       System.out.println("Not running as applet - no browser available.");
3046     }
3047     else
3048     {
3049       viewport.applet.showURL(url, target);
3050     }
3051   }
3052
3053   // ////////////////////////////////////////////////////////////////////////////////
3054   // JBuilder Graphics here
3055
3056   MenuBar alignFrameMenuBar = new MenuBar();
3057
3058   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3059
3060   MenuItem loadApplication = new MenuItem(
3061           MessageManager.getString("label.view_full_application"));
3062
3063   MenuItem loadTree = new MenuItem(
3064           MessageManager.getString("label.load_associated_tree"));
3065
3066   MenuItem loadAnnotations = new MenuItem(
3067           MessageManager.getString("label.load_features_annotations"));
3068
3069   MenuItem outputFeatures = new MenuItem(
3070           MessageManager.getString("label.export_features"));
3071
3072   MenuItem outputAnnotations = new MenuItem(
3073           MessageManager.getString("label.export_annotations"));
3074
3075   MenuItem closeMenuItem = new MenuItem(
3076           MessageManager.getString("action.close"));
3077
3078   MenuItem selectAllSequenceMenuItem = new MenuItem(
3079           MessageManager.getString("action.select_all"));
3080
3081   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3082           MessageManager.getString("action.deselect_all"));
3083
3084   MenuItem invertSequenceMenuItem = new MenuItem(
3085           MessageManager.getString("action.invert_selection"));
3086
3087   MenuItem remove2LeftMenuItem = new MenuItem();
3088
3089   MenuItem remove2RightMenuItem = new MenuItem();
3090
3091   MenuItem removeGappedColumnMenuItem = new MenuItem();
3092
3093   MenuItem removeAllGapsMenuItem = new MenuItem();
3094
3095   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3096
3097   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3098
3099   MenuItem sortPairwiseMenuItem = new MenuItem();
3100
3101   MenuItem sortIDMenuItem = new MenuItem();
3102
3103   MenuItem sortLengthMenuItem = new MenuItem();
3104
3105   MenuItem sortGroupMenuItem = new MenuItem();
3106
3107   MenuItem removeRedundancyMenuItem = new MenuItem();
3108
3109   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3110
3111   MenuItem PCAMenuItem = new MenuItem();
3112
3113   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3114
3115   MenuItem neighbourTreeMenuItem = new MenuItem();
3116
3117   BorderLayout borderLayout1 = new BorderLayout();
3118
3119   public Label statusBar = new Label();
3120
3121   MenuItem clustalColour = new MenuItem();
3122
3123   MenuItem zappoColour = new MenuItem();
3124
3125   MenuItem taylorColour = new MenuItem();
3126
3127   MenuItem hydrophobicityColour = new MenuItem();
3128
3129   MenuItem helixColour = new MenuItem();
3130
3131   MenuItem strandColour = new MenuItem();
3132
3133   MenuItem turnColour = new MenuItem();
3134
3135   MenuItem buriedColour = new MenuItem();
3136
3137   MenuItem purinePyrimidineColour = new MenuItem();
3138
3139   // MenuItem RNAInteractionColour = new MenuItem();
3140
3141   MenuItem RNAHelixColour = new MenuItem();
3142
3143   MenuItem userDefinedColour = new MenuItem();
3144
3145   MenuItem PIDColour = new MenuItem();
3146
3147   MenuItem BLOSUM62Colour = new MenuItem();
3148
3149   MenuItem tcoffeeColour = new MenuItem();
3150
3151   MenuItem njTreeBlosumMenuItem = new MenuItem();
3152
3153   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3154
3155   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3156
3157   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3158
3159   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3160
3161   MenuItem alProperties = new MenuItem(
3162           MessageManager.getString("label.alignment_props"));
3163
3164   MenuItem overviewMenuItem = new MenuItem();
3165
3166   MenuItem undoMenuItem = new MenuItem();
3167
3168   MenuItem redoMenuItem = new MenuItem();
3169
3170   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3171
3172   MenuItem noColourmenuItem = new MenuItem();
3173
3174   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3175
3176   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3177
3178   MenuItem findMenuItem = new MenuItem();
3179
3180   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3181
3182   MenuItem nucleotideColour = new MenuItem();
3183
3184   MenuItem deleteGroups = new MenuItem();
3185
3186   MenuItem grpsFromSelection = new MenuItem();
3187
3188   MenuItem createGroup = new MenuItem();
3189
3190   MenuItem unGroup = new MenuItem();
3191
3192   MenuItem delete = new MenuItem();
3193
3194   MenuItem copy = new MenuItem();
3195
3196   MenuItem cut = new MenuItem();
3197
3198   Menu pasteMenu = new Menu();
3199
3200   MenuItem pasteNew = new MenuItem();
3201
3202   MenuItem pasteThis = new MenuItem();
3203
3204   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3205
3206   MenuItem font = new MenuItem();
3207
3208   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3209
3210   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3211
3212   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3213
3214   MenuItem modifyPID = new MenuItem();
3215
3216   MenuItem modifyConservation = new MenuItem();
3217
3218   CheckboxMenuItem autoCalculate = null;
3219
3220   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3221           "Sort Alignment With New Tree", true);
3222
3223   Menu sortByTreeMenu = new Menu();
3224
3225   MenuItem inputText = new MenuItem();
3226
3227   MenuItem documentation = new MenuItem();
3228
3229   MenuItem about = new MenuItem();
3230
3231   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3232
3233   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3234
3235   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3236
3237   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3238
3239   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3240
3241   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3242
3243   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3244
3245   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3246
3247   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3248
3249   /**
3250    * Initialise menus and other items
3251    *
3252    * @throws Exception
3253    */
3254   private void jbInit() throws Exception
3255   {
3256     setMenuBar(alignFrameMenuBar);
3257
3258     /*
3259      * Configure File menu items and actions
3260      */
3261     inputText
3262             .setLabel(MessageManager.getString("label.input_from_textbox"));
3263     inputText.addActionListener(this);
3264     Menu outputTextboxMenu = new Menu(
3265             MessageManager.getString("label.out_to_textbox"));
3266     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3267     {
3268       MenuItem item = new MenuItem(ff);
3269
3270       item.addActionListener(new java.awt.event.ActionListener()
3271       {
3272         @Override
3273         public void actionPerformed(ActionEvent e)
3274         {
3275           outputText_actionPerformed(e);
3276         }
3277       });
3278
3279       outputTextboxMenu.add(item);
3280     }
3281     closeMenuItem.addActionListener(this);
3282     loadApplication.addActionListener(this);
3283     loadTree.addActionListener(this);
3284     loadAnnotations.addActionListener(this);
3285     outputFeatures.addActionListener(this);
3286     outputAnnotations.addActionListener(this);
3287
3288     /*
3289      * Configure Edit menu items and actions
3290      */
3291     undoMenuItem.setEnabled(false);
3292     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3293     undoMenuItem.addActionListener(this);
3294     redoMenuItem.setEnabled(false);
3295     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3296     redoMenuItem.addActionListener(this);
3297     copy.setLabel(MessageManager.getString("action.copy"));
3298     copy.addActionListener(this);
3299     cut.setLabel(MessageManager.getString("action.cut"));
3300     cut.addActionListener(this);
3301     delete.setLabel(MessageManager.getString("action.delete"));
3302     delete.addActionListener(this);
3303     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3304     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3305     pasteNew.addActionListener(this);
3306     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3307     pasteThis.addActionListener(this);
3308     remove2LeftMenuItem.setLabel(MessageManager
3309             .getString("action.remove_left"));
3310     remove2LeftMenuItem.addActionListener(this);
3311     remove2RightMenuItem.setLabel(MessageManager
3312             .getString("action.remove_right"));
3313     remove2RightMenuItem.addActionListener(this);
3314     removeGappedColumnMenuItem.setLabel(MessageManager
3315             .getString("action.remove_empty_columns"));
3316     removeGappedColumnMenuItem.addActionListener(this);
3317     removeAllGapsMenuItem.setLabel(MessageManager
3318             .getString("action.remove_all_gaps"));
3319     removeAllGapsMenuItem.addActionListener(this);
3320     removeRedundancyMenuItem.setLabel(MessageManager
3321             .getString("action.remove_redundancy"));
3322     removeRedundancyMenuItem.addActionListener(this);
3323
3324     /*
3325      * Configure Select menu items and actions
3326      */
3327     findMenuItem.setLabel(MessageManager.getString("action.find"));
3328     findMenuItem.addActionListener(this);
3329     selectAllSequenceMenuItem.addActionListener(this);
3330     deselectAllSequenceMenuItem.addActionListener(this);
3331     invertSequenceMenuItem.setLabel(MessageManager
3332             .getString("action.invert_sequence_selection"));
3333     invertSequenceMenuItem.addActionListener(this);
3334     invertColSel.setLabel(MessageManager
3335             .getString("action.invert_column_selection"));
3336     invertColSel.addActionListener(this);
3337     deleteGroups.setLabel(MessageManager
3338             .getString("action.undefine_groups"));
3339     deleteGroups.addActionListener(this);
3340     grpsFromSelection.setLabel(MessageManager
3341             .getString("action.make_groups_selection"));
3342     grpsFromSelection.addActionListener(this);
3343     createGroup.setLabel(MessageManager.getString("action.create_group"));
3344     createGroup.addActionListener(this);
3345     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3346     unGroup.addActionListener(this);
3347
3348     annotationColumnSelection.setLabel(MessageManager
3349             .getString("action.select_by_annotation"));
3350     annotationColumnSelection.addActionListener(this);
3351
3352     /*
3353      * Configure View menu items and actions
3354      */
3355     newView.setLabel(MessageManager.getString("action.new_view"));
3356     newView.addActionListener(this);
3357     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3358     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3359     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3360     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3361     hideColumns
3362             .setLabel(MessageManager.getString("label.selected_columns"));
3363     hideSequences.setLabel(MessageManager
3364             .getString("label.selected_sequences"));
3365     hideAllButSelection.setLabel(MessageManager
3366             .getString("label.all_but_selected_region"));
3367     hideAllSelection.setLabel(MessageManager
3368             .getString("label.selected_region"));
3369     showAllHidden.setLabel(MessageManager
3370             .getString("label.all_sequences_columns"));
3371     showColumns.addActionListener(this);
3372     showSeqs.addActionListener(this);
3373     hideColumns.addActionListener(this);
3374     hideSequences.addActionListener(this);
3375     hideAllButSelection.addActionListener(this);
3376     hideAllSelection.addActionListener(this);
3377     showAllHidden.addActionListener(this);
3378     featureSettings.setLabel(MessageManager
3379             .getString("action.feature_settings"));
3380     featureSettings.addActionListener(this);
3381     sequenceFeatures.setLabel(MessageManager
3382             .getString("label.show_sequence_features"));
3383     sequenceFeatures.addItemListener(this);
3384     sequenceFeatures.setState(false);
3385     followMouseOverFlag.setLabel(MessageManager
3386             .getString("label.automatic_scrolling"));
3387     followMouseOverFlag.addItemListener(this);
3388     alProperties.addActionListener(this);
3389     overviewMenuItem.setLabel(MessageManager
3390             .getString("label.overview_window"));
3391     overviewMenuItem.addActionListener(this);
3392
3393     /*
3394      * Configure Annotations menu items and actions
3395      */
3396     annotationPanelMenuItem.setLabel(MessageManager
3397             .getString("label.show_annotations"));
3398     annotationPanelMenuItem.addItemListener(this);
3399     showGroupConsensus.setLabel(MessageManager
3400             .getString("label.group_consensus"));
3401     showGroupConservation.setLabel(MessageManager
3402             .getString("label.group_conservation"));
3403     showConsensusHistogram.setLabel(MessageManager
3404             .getString("label.show_consensus_histogram"));
3405     showSequenceLogo.setLabel(MessageManager
3406             .getString("label.show_consensus_logo"));
3407     normSequenceLogo.setLabel(MessageManager
3408             .getString("label.norm_consensus_logo"));
3409     applyAutoAnnotationSettings.setLabel(MessageManager
3410             .getString("label.apply_all_groups"));
3411     applyAutoAnnotationSettings.setState(true);
3412     Menu autoAnnMenu = new Menu(
3413             MessageManager.getString("label.autocalculated_annotation"));
3414     showGroupConsensus.addItemListener(this);
3415     showGroupConservation.addItemListener(this);
3416     showConsensusHistogram.addItemListener(this);
3417     showSequenceLogo.addItemListener(this);
3418     normSequenceLogo.addItemListener(this);
3419     applyAutoAnnotationSettings.addItemListener(this);
3420     showAlignmentAnnotations = new CheckboxMenuItem(
3421             MessageManager.getString("label.show_all_al_annotations"));
3422     showSequenceAnnotations = new CheckboxMenuItem(
3423             MessageManager.getString("label.show_all_seq_annotations"));
3424     sortAnnBySequence = new CheckboxMenuItem(
3425             MessageManager.getString("label.sort_annotations_by_sequence"));
3426     sortAnnByLabel = new CheckboxMenuItem(
3427             MessageManager.getString("label.sort_annotations_by_label"));
3428     showAutoFirst = new CheckboxMenuItem(
3429             MessageManager.getString("label.show_first"));
3430     showAutoFirst.setState(false); // pending applet parameter
3431     setShowAutoCalculatedAbove(showAutoFirst.getState());
3432     showAutoLast = new CheckboxMenuItem(
3433             MessageManager.getString("label.show_last"));
3434     showAutoLast.setState(!showAutoFirst.getState());
3435     showAlignmentAnnotations.addItemListener(this);
3436     showSequenceAnnotations.addItemListener(this);
3437     sortAnnBySequence.addItemListener(this);
3438     sortAnnByLabel.addItemListener(this);
3439     showAutoFirst.addItemListener(this);
3440     showAutoLast.addItemListener(this);
3441
3442     /*
3443      * Configure Format menu items and actions
3444      */
3445     font.setLabel(MessageManager.getString("action.font"));
3446     font.addActionListener(this);
3447     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3448     scaleAbove.setState(true);
3449     scaleAbove.setEnabled(false);
3450     scaleAbove.addItemListener(this);
3451     scaleLeft.setEnabled(false);
3452     scaleLeft.setState(true);
3453     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3454     scaleLeft.addItemListener(this);
3455     scaleRight.setEnabled(false);
3456     scaleRight.setState(true);
3457     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3458     scaleRight.addItemListener(this);
3459     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3460     viewBoxesMenuItem.setState(true);
3461     viewBoxesMenuItem.addItemListener(this);
3462     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3463     viewTextMenuItem.setState(true);
3464     viewTextMenuItem.addItemListener(this);
3465     colourTextMenuItem.setLabel(MessageManager
3466             .getString("label.colour_text"));
3467     colourTextMenuItem.addItemListener(this);
3468     displayNonconservedMenuItem.setLabel(MessageManager
3469             .getString("label.show_non_conserved"));
3470     displayNonconservedMenuItem.addItemListener(this);
3471     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3472     wrapMenuItem.addItemListener(this);
3473     renderGapsMenuItem.setLabel(MessageManager
3474             .getString("action.show_gaps"));
3475     renderGapsMenuItem.setState(true);
3476     renderGapsMenuItem.addItemListener(this);
3477     centreColumnLabelFlag.setLabel(MessageManager
3478             .getString("label.centre_column_labels"));
3479     centreColumnLabelFlag.addItemListener(this);
3480     seqLimits.setState(true);
3481     seqLimits.setLabel(MessageManager
3482             .getString("label.show_sequence_limits"));
3483     seqLimits.addItemListener(this);
3484
3485     /*
3486      * Configure Colour menu items and actions
3487      */
3488     applyToAllGroups.setLabel(MessageManager
3489             .getString("label.apply_colour_to_all_groups"));
3490     applyToAllGroups.setState(true);
3491     applyToAllGroups.addItemListener(this);
3492     clustalColour.setLabel(MessageManager
3493             .getString("label.colourScheme_clustal"));
3494     clustalColour.addActionListener(this);
3495     zappoColour.setLabel(MessageManager
3496             .getString("label.colourScheme_zappo"));
3497     zappoColour.addActionListener(this);
3498     taylorColour.setLabel(MessageManager
3499             .getString("label.colourScheme_taylor"));
3500     taylorColour.addActionListener(this);
3501     hydrophobicityColour.setLabel(MessageManager
3502             .getString("label.colourScheme_hydrophobic"));
3503     hydrophobicityColour.addActionListener(this);
3504     helixColour.setLabel(MessageManager
3505             .getString("label.colourScheme_helix_propensity"));
3506     helixColour.addActionListener(this);
3507     strandColour.setLabel(MessageManager
3508             .getString("label.colourScheme_strand_propensity"));
3509     strandColour.addActionListener(this);
3510     turnColour.setLabel(MessageManager
3511             .getString("label.colourScheme_turn_propensity"));
3512     turnColour.addActionListener(this);
3513     buriedColour.setLabel(MessageManager
3514             .getString("label.colourScheme_buried_index"));
3515     buriedColour.addActionListener(this);
3516     purinePyrimidineColour.setLabel(MessageManager
3517             .getString("label.colourScheme_purine/pyrimidine"));
3518     purinePyrimidineColour.addActionListener(this);
3519     // RNAInteractionColour.setLabel(MessageManager
3520     // .getString("label.rna_interaction"));
3521     // RNAInteractionColour.addActionListener(this);
3522     RNAHelixColour.setLabel(MessageManager
3523             .getString("label.colourScheme_rna_helices"));
3524     RNAHelixColour.addActionListener(this);
3525     userDefinedColour.setLabel(MessageManager
3526             .getString("action.user_defined"));
3527     userDefinedColour.addActionListener(this);
3528     PIDColour.setLabel(MessageManager
3529             .getString("label.colourScheme_%_identity"));
3530     PIDColour.addActionListener(this);
3531     BLOSUM62Colour.setLabel(MessageManager
3532             .getString("label.colourScheme_blosum62"));
3533     BLOSUM62Colour.addActionListener(this);
3534     tcoffeeColour.setLabel(MessageManager
3535             .getString("label.colourScheme_t-coffee_scores"));
3536     // it will be enabled only if a score file is provided
3537     tcoffeeColour.setEnabled(false);
3538     tcoffeeColour.addActionListener(this);
3539     conservationMenuItem.setLabel(MessageManager
3540             .getString("action.by_conservation"));
3541     conservationMenuItem.addItemListener(this);
3542     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3543     noColourmenuItem.addActionListener(this);
3544     abovePIDThreshold.setLabel(MessageManager
3545             .getString("label.above_identity_threshold"));
3546     abovePIDThreshold.addItemListener(this);
3547     nucleotideColour.setLabel(MessageManager
3548             .getString("label.colourScheme_nucleotide"));
3549     nucleotideColour.addActionListener(this);
3550     modifyPID.setLabel(MessageManager
3551             .getString("label.modify_identity_threshold"));
3552     modifyPID.setEnabled(abovePIDThreshold.getState());
3553     modifyPID.addActionListener(this);
3554     modifyConservation.setLabel(MessageManager
3555             .getString("label.modify_conservation_threshold"));
3556     modifyConservation.setEnabled(conservationMenuItem.getState());
3557     modifyConservation.addActionListener(this);
3558     annotationColour.setLabel(MessageManager
3559             .getString("action.by_annotation"));
3560     annotationColour.addActionListener(this);
3561
3562     /*
3563      * Configure Calculate menu items and actions
3564      */
3565     sortPairwiseMenuItem.setLabel(MessageManager
3566             .getString("action.by_pairwise_id"));
3567     sortPairwiseMenuItem.addActionListener(this);
3568     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3569     sortIDMenuItem.addActionListener(this);
3570     sortLengthMenuItem.setLabel(MessageManager
3571             .getString("action.by_length"));
3572     sortLengthMenuItem.addActionListener(this);
3573     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3574     sortGroupMenuItem.addActionListener(this);
3575     pairwiseAlignmentMenuItem.setLabel(MessageManager
3576             .getString("action.pairwise_alignment"));
3577     pairwiseAlignmentMenuItem.addActionListener(this);
3578     PCAMenuItem.setLabel(MessageManager
3579             .getString("label.principal_component_analysis"));
3580     PCAMenuItem.addActionListener(this);
3581     autoCalculate = new CheckboxMenuItem(
3582             MessageManager.getString("label.autocalculate_consensus"), true);
3583     averageDistanceTreeMenuItem.setLabel(MessageManager
3584             .getString("label.average_distance_identity"));
3585     averageDistanceTreeMenuItem.addActionListener(this);
3586     neighbourTreeMenuItem.setLabel(MessageManager
3587             .getString("label.neighbour_joining_identity"));
3588     neighbourTreeMenuItem.addActionListener(this);
3589     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3590             .getString("label.average_distance_blosum62"));
3591     avDistanceTreeBlosumMenuItem.addActionListener(this);
3592     njTreeBlosumMenuItem.setLabel(MessageManager
3593             .getString("label.neighbour_blosum62"));
3594     njTreeBlosumMenuItem.addActionListener(this);
3595     sortByTreeMenu.setLabel(MessageManager
3596             .getString("action.by_tree_order"));
3597     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3598     Menu calculateTreeMenu = new Menu(
3599             MessageManager.getString("action.calculate_tree"));
3600     autoCalculate.addItemListener(this);
3601     sortByTree.addItemListener(this);
3602
3603     /*
3604      * Configure Help menu items and actions
3605      */
3606     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3607     documentation.setLabel(MessageManager.getString("label.documentation"));
3608     documentation.addActionListener(this);
3609     about.setLabel(MessageManager.getString("label.about"));
3610     about.addActionListener(this);
3611
3612     /*
3613      * Add top level menus to frame
3614      */
3615     alignFrameMenuBar.add(fileMenu);
3616     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3617     alignFrameMenuBar.add(editMenu);
3618     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3619     alignFrameMenuBar.add(selectMenu);
3620     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3621     alignFrameMenuBar.add(viewMenu);
3622     Menu annotationsMenu = new Menu(
3623             MessageManager.getString("action.annotations"));
3624     alignFrameMenuBar.add(annotationsMenu);
3625     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3626     alignFrameMenuBar.add(formatMenu);
3627     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3628     alignFrameMenuBar.add(colourMenu);
3629     Menu calculateMenu = new Menu(
3630             MessageManager.getString("action.calculate"));
3631     alignFrameMenuBar.add(calculateMenu);
3632     alignFrameMenuBar.add(helpMenu);
3633
3634     /*
3635      * File menu
3636      */
3637     fileMenu.add(inputText);
3638     fileMenu.add(loadTree);
3639     fileMenu.add(loadAnnotations);
3640     fileMenu.addSeparator();
3641     fileMenu.add(outputTextboxMenu);
3642     fileMenu.add(outputFeatures);
3643     fileMenu.add(outputAnnotations);
3644     if (jalviewServletURL != null)
3645     {
3646       fileMenu.add(loadApplication);
3647     }
3648     fileMenu.addSeparator();
3649     fileMenu.add(closeMenuItem);
3650
3651     /*
3652      * Edit menu
3653      */
3654     editMenu.add(undoMenuItem);
3655     editMenu.add(redoMenuItem);
3656     editMenu.add(cut);
3657     editMenu.add(copy);
3658     pasteMenu.add(pasteNew);
3659     pasteMenu.add(pasteThis);
3660     editMenu.add(pasteMenu);
3661     editMenu.add(delete);
3662     editMenu.addSeparator();
3663     editMenu.add(remove2LeftMenuItem);
3664     editMenu.add(remove2RightMenuItem);
3665     editMenu.add(removeGappedColumnMenuItem);
3666     editMenu.add(removeAllGapsMenuItem);
3667     editMenu.add(removeRedundancyMenuItem);
3668
3669     /*
3670      * Select menu
3671      */
3672     selectMenu.add(findMenuItem);
3673     selectMenu.addSeparator();
3674     selectMenu.add(selectAllSequenceMenuItem);
3675     selectMenu.add(deselectAllSequenceMenuItem);
3676     selectMenu.add(invertSequenceMenuItem);
3677     selectMenu.add(invertColSel);
3678     selectMenu.add(createGroup);
3679     selectMenu.add(unGroup);
3680     selectMenu.add(grpsFromSelection);
3681     selectMenu.add(deleteGroups);
3682     selectMenu.add(annotationColumnSelection);
3683
3684     /*
3685      * View menu
3686      */
3687     viewMenu.add(newView);
3688     viewMenu.addSeparator();
3689     showMenu.add(showColumns);
3690     showMenu.add(showSeqs);
3691     showMenu.add(showAllHidden);
3692     viewMenu.add(showMenu);
3693     hideMenu.add(hideColumns);
3694     hideMenu.add(hideSequences);
3695     hideMenu.add(hideAllSelection);
3696     hideMenu.add(hideAllButSelection);
3697     viewMenu.add(hideMenu);
3698     viewMenu.addSeparator();
3699     viewMenu.add(followMouseOverFlag);
3700     viewMenu.addSeparator();
3701     viewMenu.add(sequenceFeatures);
3702     viewMenu.add(featureSettings);
3703     viewMenu.addSeparator();
3704     viewMenu.add(alProperties);
3705     viewMenu.addSeparator();
3706     viewMenu.add(overviewMenuItem);
3707
3708     /*
3709      * Annotations menu
3710      */
3711     annotationsMenu.add(annotationPanelMenuItem);
3712     annotationsMenu.addSeparator();
3713     annotationsMenu.add(showAlignmentAnnotations);
3714     annotationsMenu.add(showSequenceAnnotations);
3715     annotationsMenu.add(sortAnnBySequence);
3716     annotationsMenu.add(sortAnnByLabel);
3717     annotationsMenu.addSeparator();
3718     autoAnnMenu.add(showAutoFirst);
3719     autoAnnMenu.add(showAutoLast);
3720     autoAnnMenu.addSeparator();
3721     autoAnnMenu.add(applyAutoAnnotationSettings);
3722     autoAnnMenu.add(showConsensusHistogram);
3723     autoAnnMenu.add(showSequenceLogo);
3724     autoAnnMenu.add(normSequenceLogo);
3725     autoAnnMenu.addSeparator();
3726     autoAnnMenu.add(showGroupConservation);
3727     autoAnnMenu.add(showGroupConsensus);
3728     annotationsMenu.add(autoAnnMenu);
3729
3730     /*
3731      * Format menu
3732      */
3733     formatMenu.add(font);
3734     formatMenu.add(seqLimits);
3735     formatMenu.add(wrapMenuItem);
3736     formatMenu.add(scaleAbove);
3737     formatMenu.add(scaleLeft);
3738     formatMenu.add(scaleRight);
3739     formatMenu.add(viewBoxesMenuItem);
3740     formatMenu.add(viewTextMenuItem);
3741     formatMenu.add(colourTextMenuItem);
3742     formatMenu.add(displayNonconservedMenuItem);
3743     formatMenu.add(renderGapsMenuItem);
3744     formatMenu.add(centreColumnLabelFlag);
3745
3746     /*
3747      * Colour menu
3748      */
3749     colourMenu.add(applyToAllGroups);
3750     colourMenu.addSeparator();
3751     colourMenu.add(noColourmenuItem);
3752     colourMenu.add(clustalColour);
3753     colourMenu.add(BLOSUM62Colour);
3754     colourMenu.add(PIDColour);
3755     colourMenu.add(zappoColour);
3756     colourMenu.add(taylorColour);
3757     colourMenu.add(hydrophobicityColour);
3758     colourMenu.add(helixColour);
3759     colourMenu.add(strandColour);
3760     colourMenu.add(turnColour);
3761     colourMenu.add(buriedColour);
3762     colourMenu.add(nucleotideColour);
3763     colourMenu.add(purinePyrimidineColour);
3764     // colourMenu.add(RNAInteractionColour);
3765     colourMenu.add(tcoffeeColour);
3766     colourMenu.add(userDefinedColour);
3767     colourMenu.addSeparator();
3768     colourMenu.add(conservationMenuItem);
3769     colourMenu.add(modifyConservation);
3770     colourMenu.add(abovePIDThreshold);
3771     colourMenu.add(modifyPID);
3772     colourMenu.add(annotationColour);
3773     colourMenu.add(RNAHelixColour);
3774
3775     /*
3776      * Calculate menu
3777      */
3778     sortMenu.add(sortIDMenuItem);
3779     sortMenu.add(sortLengthMenuItem);
3780     sortMenu.add(sortByTreeMenu);
3781     sortMenu.add(sortGroupMenuItem);
3782     sortMenu.add(sortPairwiseMenuItem);
3783     calculateMenu.add(sortMenu);
3784     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3785     calculateTreeMenu.add(neighbourTreeMenuItem);
3786     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3787     calculateTreeMenu.add(njTreeBlosumMenuItem);
3788     calculateMenu.add(calculateTreeMenu);
3789     calculateMenu.addSeparator();
3790     calculateMenu.add(pairwiseAlignmentMenuItem);
3791     calculateMenu.add(PCAMenuItem);
3792     calculateMenu.add(autoCalculate);
3793     calculateMenu.add(sortByTree);
3794
3795     /*
3796      * Help menu
3797      */
3798     helpMenu.add(documentation);
3799     helpMenu.add(about);
3800
3801     /*
3802      * Status bar
3803      */
3804     statusBar.setBackground(Color.white);
3805     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3806     statusBar.setText(MessageManager.getString("label.status_bar"));
3807     this.add(statusBar, BorderLayout.SOUTH);
3808   }
3809
3810   @Override
3811   public void setStatus(String string)
3812   {
3813     statusBar.setText(string);
3814   };
3815
3816   MenuItem featureSettings = new MenuItem();
3817
3818   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3819
3820   MenuItem annotationColour = new MenuItem();
3821
3822   MenuItem annotationColumnSelection = new MenuItem();
3823
3824   MenuItem invertColSel = new MenuItem();
3825
3826   MenuItem showColumns = new MenuItem();
3827
3828   MenuItem showSeqs = new MenuItem();
3829
3830   MenuItem hideColumns = new MenuItem();
3831
3832   MenuItem hideSequences = new MenuItem();
3833
3834   MenuItem hideAllButSelection = new MenuItem();
3835
3836   MenuItem hideAllSelection = new MenuItem();
3837
3838   MenuItem showAllHidden = new MenuItem();
3839
3840   MenuItem newView = new MenuItem();
3841
3842   private CheckboxMenuItem showAlignmentAnnotations;
3843
3844   private CheckboxMenuItem showSequenceAnnotations;
3845
3846   private CheckboxMenuItem sortAnnBySequence;
3847
3848   private CheckboxMenuItem sortAnnByLabel;
3849
3850   private CheckboxMenuItem showAutoFirst;
3851
3852   private CheckboxMenuItem showAutoLast;
3853
3854   private SplitFrame splitFrame;
3855
3856   /**
3857    * Attach the alignFrame panels after embedding menus, if necessary. This used
3858    * to be called setEmbedded, but is now creates the dropdown menus in a
3859    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3860    *
3861    * @param reallyEmbedded
3862    *          true to attach the view to the applet area on the page rather than
3863    *          in a new window
3864    */
3865   public void createAlignFrameWindow(boolean reallyEmbedded)
3866   {
3867     if (reallyEmbedded)
3868     {
3869       embedAlignFrameInApplet(viewport.applet);
3870     }
3871     else
3872     {
3873       // //////
3874       // test and embed menu bar if necessary.
3875       //
3876       if (embedMenuIfNeeded(alignPanel))
3877       {
3878         /*
3879          * adjust for status bar height too. ? pointless as overridden by layout
3880          * manager
3881          */
3882         alignPanel.setSize(getSize().width,
3883                 getSize().height - statusBar.getHeight());
3884       }
3885       add(statusBar, BorderLayout.SOUTH);
3886       add(alignPanel, BorderLayout.CENTER);
3887       // and register with the applet so it can pass external API calls to us
3888       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3889               frameHeight);
3890     }
3891   }
3892
3893   /**
3894    * Add the components of this AlignFrame to the applet container.
3895    *
3896    * @param theApplet
3897    */
3898   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3899   {
3900     // ////
3901     // Explicitly build the embedded menu panel for the on-page applet
3902     //
3903     // view cannot be closed if its actually on the page
3904     fileMenu.remove(closeMenuItem);
3905     fileMenu.remove(3); // Remove Separator
3906     // construct embedded menu, using default font
3907     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3908     // and actually add the components to the applet area
3909     theApplet.setLayout(new BorderLayout());
3910     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3911     theApplet.add(statusBar, BorderLayout.SOUTH);
3912     // TODO should size be left to the layout manager?
3913     alignPanel.setSize(theApplet.getSize().width,
3914             theApplet.getSize().height - embeddedMenu.getHeight()
3915                     - statusBar.getHeight());
3916     theApplet.add(alignPanel, BorderLayout.CENTER);
3917     final AlignFrame me = this;
3918     theApplet.addFocusListener(new FocusListener()
3919     {
3920
3921       @Override
3922       public void focusLost(FocusEvent e)
3923       {
3924         if (theApplet.currentAlignFrame == me)
3925         {
3926           theApplet.currentAlignFrame = null;
3927         }
3928       }
3929
3930       @Override
3931       public void focusGained(FocusEvent e)
3932       {
3933         theApplet.currentAlignFrame = me;
3934       }
3935     });
3936     theApplet.validate();
3937   }
3938
3939   /**
3940    * create a new binding between structures in an existing jmol viewer instance
3941    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3942    * this does not open a new Jmol window, or modify the display of the
3943    * structures in the original jmol window. Note This method doesn't work
3944    * without an additional javascript library to exchange messages between the
3945    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3946    *
3947    * @param viewer
3948    *          JmolViewer instance
3949    * @param sequenceIds
3950    *          - sequence Ids to search for associations
3951    */
3952   public SequenceStructureBinding addStructureViewInstance(
3953           Object jmolviewer, String[] sequenceIds)
3954   {
3955     Viewer viewer = null;
3956     try
3957     {
3958       viewer = (Viewer) jmolviewer;
3959     } catch (ClassCastException ex)
3960     {
3961       System.err.println("Unsupported viewer object :"
3962               + jmolviewer.getClass());
3963     }
3964     if (viewer == null)
3965     {
3966       System.err.println("Can't use this object as a structure viewer:"
3967               + jmolviewer.getClass());
3968       return null;
3969     }
3970     SequenceI[] seqs = null;
3971     if (sequenceIds == null || sequenceIds.length == 0)
3972     {
3973       seqs = viewport.getAlignment().getSequencesArray();
3974     }
3975     else
3976     {
3977       Vector sqi = new Vector();
3978       AlignmentI al = viewport.getAlignment();
3979       for (int sid = 0; sid < sequenceIds.length; sid++)
3980       {
3981         SequenceI sq = al.findName(sequenceIds[sid]);
3982         if (sq != null)
3983         {
3984           sqi.addElement(sq);
3985         }
3986       }
3987       if (sqi.size() > 0)
3988       {
3989         seqs = new SequenceI[sqi.size()];
3990         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3991         {
3992           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3993         }
3994       }
3995       else
3996       {
3997         return null;
3998       }
3999     }
4000     AAStructureBindingModel jmv = null;
4001     // TODO: search for a jmv that involves viewer
4002     if (jmv == null)
4003     { // create a new viewer/jalview binding.
4004       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4005     }
4006     return jmv;
4007
4008   }
4009
4010   /**
4011    * bind a pdb file to a sequence in the current view
4012    *
4013    * @param sequenceId
4014    *          - sequenceId within the dataset.
4015    * @param pdbEntryString
4016    *          - the short name for the PDB file
4017    * @param pdbFile
4018    *          - pdb file - either a URL or a valid PDB file.
4019    * @return true if binding was as success TODO: consider making an exception
4020    *         structure for indicating when PDB parsing or sequenceId location
4021    *         fails.
4022    */
4023   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4024           String pdbFile)
4025   {
4026     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4027     boolean needtoadd = false;
4028     if (toaddpdb != null)
4029     {
4030       Vector pdbe = toaddpdb.getAllPDBEntries();
4031       PDBEntry pdbentry = null;
4032       if (pdbe != null && pdbe.size() > 0)
4033       {
4034         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4035         {
4036           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4037           if (!pdbentry.getId().equals(pdbEntryString)
4038                   && !pdbentry.getFile().equals(pdbFile))
4039           {
4040             pdbentry = null;
4041           }
4042           else
4043           {
4044             continue;
4045           }
4046         }
4047       }
4048       if (pdbentry == null)
4049       {
4050         pdbentry = new PDBEntry();
4051         pdbentry.setId(pdbEntryString);
4052         pdbentry.setFile(pdbFile);
4053         needtoadd = true; // add this new entry to sequence.
4054       }
4055       // resolve data source
4056       // TODO: this code should be a refactored to an io package
4057       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4058               pdbFile, FileFormat.PDB);
4059       if (protocol == null)
4060       {
4061         return false;
4062       }
4063       if (needtoadd)
4064       {
4065         pdbentry.setProperty("protocol", protocol);
4066         toaddpdb.addPDBId(pdbentry);
4067         alignPanel.getStructureSelectionManager()
4068                 .registerPDBEntry(pdbentry);
4069       }
4070     }
4071     return true;
4072   }
4073
4074   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4075   {
4076     if (seqs != null)
4077     {
4078       Vector sequences = new Vector();
4079       for (int i = 0; i < seqs.length; i++)
4080       {
4081         if (seqs[i] != null)
4082         {
4083           sequences.addElement(new Object[] { seqs[i],
4084               (chains != null) ? chains[i] : null });
4085         }
4086       }
4087       seqs = new SequenceI[sequences.size()];
4088       chains = new String[sequences.size()];
4089       for (int i = 0, isize = sequences.size(); i < isize; i++)
4090       {
4091         Object[] oj = (Object[]) sequences.elementAt(i);
4092
4093         seqs[i] = (SequenceI) oj[0];
4094         chains[i] = (String) oj[1];
4095       }
4096     }
4097     return new Object[] { seqs, chains };
4098
4099   }
4100
4101   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4102           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4103   {
4104     // Scrub any null sequences from the array
4105     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4106     seqs = (SequenceI[]) sqch[0];
4107     chains = (String[]) sqch[1];
4108     if (seqs == null || seqs.length == 0)
4109     {
4110       System.err
4111               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4112     }
4113     if (protocol == null)
4114     {
4115       String sourceType = (String) pdb.getProperty("protocol");
4116       try
4117       {
4118         protocol = DataSourceType.valueOf(sourceType);
4119       } catch (IllegalArgumentException e)
4120       {
4121         // ignore
4122       }
4123       if (protocol == null)
4124       {
4125         System.err.println("Couldn't work out protocol to open structure: "
4126                 + pdb.getId());
4127         return;
4128       }
4129     }
4130     if (applet.useXtrnalSviewer)
4131     {
4132       // register the association(s) and quit, don't create any windows.
4133       if (StructureSelectionManager.getStructureSelectionManager(applet)
4134               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4135       {
4136         System.err.println("Failed to map " + pdb.getFile() + " ("
4137                 + protocol + ") to any sequences");
4138       }
4139       return;
4140     }
4141     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4142     {
4143       // can only do alignments with Jmol
4144       // find the last jmol window assigned to this alignment
4145       AppletJmol ajm = null, tajm;
4146       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4147       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4148       {
4149         tajm = (AppletJmol) jmols.elementAt(i);
4150         if (tajm.ap.alignFrame == this)
4151         {
4152           ajm = tajm;
4153           break;
4154         }
4155       }
4156       if (ajm != null)
4157       {
4158         System.err
4159                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4160         // try and add the pdb structure
4161         // ajm.addS
4162         ajm = null;
4163       }
4164     }
4165     // otherwise, create a new window
4166     if (applet.jmolAvailable)
4167     {
4168       new AppletJmol(pdb, seqs, chains, alignPanel,
4169               protocol);
4170       applet.lastFrameX += 40;
4171       applet.lastFrameY += 40;
4172     }
4173     else
4174     {
4175       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4176     }
4177
4178   }
4179
4180   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4181           SequenceI[][] seqs, String[][] chains, String[] protocols)
4182   {
4183     // TODO Auto-generated method stub
4184     System.err.println("Aligned Structure View: Not yet implemented.");
4185   }
4186
4187   /**
4188    * modify the current selection, providing the user has not made a selection
4189    * already.
4190    *
4191    * @param sel
4192    *          - sequences from this alignment
4193    * @param csel
4194    *          - columns to be selected on the alignment
4195    */
4196   public void select(SequenceGroup sel, ColumnSelection csel,
4197           HiddenColumns hidden)
4198   {
4199     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4200   }
4201
4202   public void scrollTo(int row, int column)
4203   {
4204     alignPanel.seqPanel.scrollTo(row, column);
4205   }
4206
4207   public void scrollToRow(int row)
4208   {
4209     alignPanel.seqPanel.scrollToRow(row);
4210   }
4211
4212   public void scrollToColumn(int column)
4213   {
4214     alignPanel.seqPanel.scrollToColumn(column);
4215   }
4216
4217   /**
4218    * @return the alignments unique ID.
4219    */
4220   public String getSequenceSetId()
4221   {
4222     return viewport.getSequenceSetId();
4223   }
4224
4225   /**
4226    * Load the (T-Coffee) score file from the specified url
4227    *
4228    * @param source
4229    *          File/URL/T-COFFEE score file contents
4230    * @throws IOException
4231    * @return true if alignment was annotated with data from source
4232    */
4233   public boolean loadScoreFile(String source) throws IOException
4234   {
4235
4236     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4237             AppletFormatAdapter.checkProtocol(source));
4238     if (!file.isValid())
4239     {
4240       // TODO: raise dialog for gui
4241       System.err.println("Problems parsing T-Coffee scores: "
4242               + file.getWarningMessage());
4243       System.err.println("Origin was:\n" + source);
4244       return false;
4245     }
4246
4247     /*
4248      * check that the score matrix matches the alignment dimensions
4249      */
4250     AlignmentI aln;
4251     if ((aln = viewport.getAlignment()) != null
4252             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4253                     .getWidth()))
4254     {
4255       // TODO: raise a dialog box here rather than bomb out.
4256       System.err
4257               .println("The scores matrix does not match the alignment dimensions");
4258
4259     }
4260
4261     // TODO add parameter to indicate if matching should be done
4262     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4263     {
4264       alignPanel.fontChanged();
4265       tcoffeeColour.setEnabled(true);
4266       // switch to this color
4267       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4268       return true;
4269     }
4270     else
4271     {
4272       System.err.println("Problems resolving T-Coffee scores:");
4273       if (file.getWarningMessage() != null)
4274       {
4275         System.err.println(file.getWarningMessage());
4276       }
4277     }
4278     return false;
4279   }
4280
4281   public SplitFrame getSplitFrame()
4282   {
4283     return this.splitFrame;
4284   }
4285
4286   public void setSplitFrame(SplitFrame sf)
4287   {
4288     this.splitFrame = sf;
4289   }
4290
4291   // may not need this
4292   @Override
4293   public void setShowSeqFeatures(boolean b)
4294   {
4295     // showSeqFeatures.setSelected(b);
4296     viewport.setShowSequenceFeatures(b);
4297
4298   }
4299
4300   @Override
4301   public void setMenusForViewport()
4302   {
4303     // setMenusFromViewport(viewport);
4304
4305   }
4306
4307   @Override
4308   public void refreshFeatureUI(boolean enableIfNecessary)
4309   {
4310     if (enableIfNecessary)
4311     {
4312       sequenceFeatures.setState(true);
4313       alignPanel.av.setShowSequenceFeatures(true);
4314     }
4315   }
4316
4317   @Override
4318   public FeatureSettingsControllerI getFeatureSettingsUI()
4319   {
4320     return alignPanel.av.featureSettings;
4321   }
4322
4323 }