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.Rectangle;
  99 import java.awt.event.ActionEvent;
 100 import java.awt.event.ActionListener;
 101 import java.awt.event.FocusEvent;
 102 import java.awt.event.FocusListener;
 103 import java.awt.event.ItemEvent;
 104 import java.awt.event.ItemListener;
 105 import java.awt.event.KeyEvent;
 106 import java.awt.event.KeyListener;
 107 import java.awt.event.WindowAdapter;
 108 import java.awt.event.WindowEvent;
 109 import java.io.IOException;
 110 import java.io.UnsupportedEncodingException;
 111 import java.net.URL;
 112 import java.net.URLEncoder;
 113 import java.util.Arrays;
 114 import java.util.Deque;
 115 import java.util.HashMap;
 116 import java.util.List;
 117 import java.util.Map;
 118 import java.util.StringTokenizer;
 119 import java.util.Vector;
 120
 121 import org.jmol.viewer.Viewer;
 122
 123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 124         ItemListener, KeyListener, AlignViewControllerGuiI
 125 {
 126   public AlignViewControllerI avc;
 127
 128   public AlignmentPanel alignPanel;
 129
 130   public AlignViewport viewport;
 131
 132   // width and height may be overridden by applet parameters
 133   int frameWidth = 700;
 134
 135   int frameHeight = 500;
 136
 137   String jalviewServletURL;
 138
 139   /*
 140    * Flag for showing autocalculated consensus above or below other consensus
 141    * rows
 142    */
 143   private boolean showAutoCalculatedAbove;
 144
 145   private SequenceAnnotationOrder annotationSortOrder;
 146
 147   /**
 148    * Constructor that creates the frame and adds it to the display.
 149    *
 150    * @param al
 151    * @param applet
 152    * @param title
 153    * @param embedded
 154    */
 155   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 156           boolean embedded)
 157   {
 158     this(al, applet, title, embedded, true);
 159   }
 160
 161   /**
 162    * Constructor that optionally allows the frame to be displayed or only
 163    * created.
 164    *
 165    * @param al
 166    * @param applet
 167    * @param title
 168    * @param embedded
 169    * @param addToDisplay
 170    */
 171   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 172           boolean embedded, boolean addToDisplay)
 173   {
 174     this(al, null, null, applet, title, embedded, addToDisplay);
 175   }
 176
 177   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 178           HiddenColumns hidden, JalviewLite applet, String title,
 179           boolean embedded)
 180   {
 181     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 182   }
 183
 184   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 185           HiddenColumns hidden, JalviewLite applet, String title,
 186           boolean embedded, boolean addToDisplay)
 187   {
 188     if (applet != null)
 189     {
 190       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 191     }
 192
 193     try
 194     {
 195       jbInit();
 196     } catch (Exception ex)
 197     {
 198       ex.printStackTrace();
 199     }
 200     // need to get window geometry before we calculate alignment layout
 201     if (applet != null)
 202     {
 203       String param;
 204       try
 205       {
 206         param = applet.getParameter("windowWidth");
 207         if (param != null)
 208         {
 209           int width = Integer.parseInt(param);
 210           frameWidth = width;
 211         }
 212         param = applet.getParameter("windowHeight");
 213         if (param != null)
 214         {
 215           int height = Integer.parseInt(param);
 216           frameHeight = height;
 217         }
 218       } catch (Exception ex)
 219       {
 220       }
 221     }
 222     viewport = new AlignViewport(al, applet);
 223
 224     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 225     {
 226       viewport.hideSequence(hiddenSeqs);
 227     }
 228     if (hidden != null)
 229     {
 230       viewport.getAlignment().setHiddenColumns(hidden);
 231     }
 232     viewport.setScaleAboveWrapped(scaleAbove.getState());
 233
 234     alignPanel = new AlignmentPanel(this, viewport);
 235     avc = new jalview.controller.AlignViewController(this, viewport,
 236             alignPanel);
 237     viewport.updateConservation(alignPanel);
 238     viewport.updateConsensus(alignPanel);
 239
 240     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 241     followMouseOverFlag.setState(viewport.isFollowHighlight());
 242     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 243     showGroupConservation.setState(viewport.isShowGroupConservation());
 244     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 245     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 246     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 247     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 248     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 249     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 250     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 251     showAlignmentAnnotations.setState(true);
 252     showSequenceAnnotations.setState(false);
 253
 254     seqLimits.setState(viewport.getShowJVSuffix());
 255
 256     if (applet != null)
 257     {
 258       String param = applet.getParameter("sortBy");
 259       if (param != null)
 260       {
 261         if (param.equalsIgnoreCase("Id"))
 262         {
 263           sortIDMenuItem_actionPerformed();
 264         }
 265         else if (param.equalsIgnoreCase("Pairwise Identity"))
 266         {
 267           sortPairwiseMenuItem_actionPerformed();
 268         }
 269         else if (param.equalsIgnoreCase("Length"))
 270         {
 271           sortLengthMenuItem_actionPerformed();
 272         }
 273       }
 274
 275       param = applet.getParameter("wrap");
 276       if (param != null)
 277       {
 278         if (param.equalsIgnoreCase("true"))
 279         {
 280           wrapMenuItem.setState(true);
 281           wrapMenuItem_actionPerformed();
 282         }
 283       }
 284       param = applet.getParameter("centrecolumnlabels");
 285       if (param != null)
 286       {
 287         centreColumnLabelFlag.setState(true);
 288         centreColumnLabelFlag_stateChanged();
 289       }
 290
 291     }
 292     if (viewport.getAlignment().isNucleotide())
 293     {
 294       conservationMenuItem.setEnabled(false);
 295       clustalColour.setEnabled(false);
 296       BLOSUM62Colour.setEnabled(false);
 297       zappoColour.setEnabled(false);
 298       taylorColour.setEnabled(false);
 299       hydrophobicityColour.setEnabled(false);
 300       helixColour.setEnabled(false);
 301       strandColour.setEnabled(false);
 302       turnColour.setEnabled(false);
 303       buriedColour.setEnabled(false);
 304       viewport.updateStrucConsensus(alignPanel);
 305       if (viewport.getAlignment().hasRNAStructure())
 306       {
 307         RNAHelixColour.setEnabled(true);
 308       }
 309       else
 310       {
 311         RNAHelixColour.setEnabled(false);
 312       }
 313     }
 314     else
 315     {
 316       RNAHelixColour.setEnabled(false);
 317       purinePyrimidineColour.setEnabled(false);
 318       nucleotideColour.setEnabled(false);
 319     }
 320     // Some JVMS send keyevents to Top frame or lowest panel,
 321     // Havent worked out why yet. So add to both this frame and seqCanvas for
 322     // now
 323     this.addKeyListener(this);
 324     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 325     alignPanel.idPanel.idCanvas.addKeyListener(this);
 326     alignPanel.scalePanel.addKeyListener(this);
 327     alignPanel.annotationPanel.addKeyListener(this);
 328     alignPanel.annotationPanelHolder.addKeyListener(this);
 329     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 330     alignPanel.alabels.addKeyListener(this);
 331
 332     setAnnotationsVisibility();
 333
 334     if (addToDisplay)
 335     {
 336       addToDisplay(embedded);
 337     }
 338   }
 339
 340   /**
 341    * @param embedded
 342    */
 343   public void addToDisplay(boolean embedded)
 344   {
 345     createAlignFrameWindow(embedded);
 346     validate();
 347     alignPanel.adjustAnnotationHeight();
 348     alignPanel.paintAlignment(true, true);
 349   }
 350
 351   public AlignViewport getAlignViewport()
 352   {
 353     return viewport;
 354   }
 355
 356   public SeqCanvas getSeqcanvas()
 357   {
 358     return alignPanel.seqPanel.seqCanvas;
 359   }
 360
 361   /**
 362    * Load a features file onto the alignment
 363    *
 364    * @param file
 365    *          file URL, content, or other resolvable path
 366    * @param type
 367    *          is protocol for accessing data referred to by file
 368    */
 369
 370   public boolean parseFeaturesFile(String file, DataSourceType type)
 371   {
 372     return parseFeaturesFile(file, type, true);
 373   }
 374
 375   /**
 376    * Load a features file onto the alignment
 377    *
 378    * @param file
 379    *          file URL, content, or other resolvable path
 380    * @param sourceType
 381    *          is protocol for accessing data referred to by file
 382    * @param autoenabledisplay
 383    *          when true, display features flag will be automatically enabled if
 384    *          features are loaded
 385    * @return true if data parsed as a features file
 386    */
 387   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 388           boolean autoenabledisplay)
 389   {
 390     boolean featuresFile = false;
 391     try
 392     {
 393       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 394               .getFeatureRenderer().getFeatureColours();
 395       boolean relaxedIdMatching = viewport.applet
 396               .getDefaultParameter("relaxedidmatch", false);
 397       featuresFile = new FeaturesFile(file, sourceType).parse(
 398               viewport.getAlignment(), colours, true, relaxedIdMatching);
 399     } catch (Exception ex)
 400     {
 401       ex.printStackTrace();
 402     }
 403
 404     if (featuresFile)
 405     {
 406       if (autoenabledisplay)
 407       {
 408         viewport.setShowSequenceFeatures(true);
 409         sequenceFeatures.setState(true);
 410       }
 411       if (alignPanel.seqPanel.seqCanvas.fr != null)
 412       {
 413         // update the min/max ranges where necessary
 414         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 415       }
 416       if (viewport.featureSettings != null)
 417       {
 418         viewport.featureSettings.refreshTable();
 419       }
 420       alignPanel.paintAlignment(true, true);
 421       setStatus(MessageManager
 422               .getString("label.successfully_added_features_alignment"));
 423     }
 424     return featuresFile;
 425   }
 426
 427   @Override
 428   public void keyPressed(KeyEvent evt)
 429   {
 430     ViewportRanges ranges = viewport.getRanges();
 431
 432     if (viewport.cursorMode
 433             && ((evt.getKeyCode() >= KeyEvent.VK_0
 434                     && evt.getKeyCode() <= KeyEvent.VK_9)
 435                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 436                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 437             && Character.isDigit(evt.getKeyChar()))
 438     {
 439       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 440     }
 441
 442     switch (evt.getKeyCode())
 443     {
 444     case 27: // escape key
 445       deselectAllSequenceMenuItem_actionPerformed();
 446
 447       alignPanel.alabels.cancelDrag();
 448       break;
 449     case KeyEvent.VK_X:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         cut_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_C:
 456       if (viewport.cursorMode && !evt.isControlDown())
 457       {
 458         alignPanel.seqPanel.setCursorColumn();
 459       }
 460       if (evt.isControlDown() || evt.isMetaDown())
 461       {
 462         copy_actionPerformed();
 463       }
 464       break;
 465     case KeyEvent.VK_V:
 466       if (evt.isControlDown())
 467       {
 468         paste(evt.isShiftDown());
 469       }
 470       break;
 471     case KeyEvent.VK_A:
 472       if (evt.isControlDown() || evt.isMetaDown())
 473       {
 474         selectAllSequenceMenuItem_actionPerformed();
 475       }
 476       break;
 477     case KeyEvent.VK_DOWN:
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.moveCursor(0, 1);
 481       }
 482       else
 483       {
 484         moveSelectedSequences(false);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_UP:
 489       if (viewport.cursorMode)
 490       {
 491         alignPanel.seqPanel.moveCursor(0, -1);
 492       }
 493       else
 494       {
 495         moveSelectedSequences(true);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_LEFT:
 500       if (evt.isAltDown() || !viewport.cursorMode)
 501       {
 502         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 503       }
 504       else
 505       {
 506         alignPanel.seqPanel.moveCursor(-1, 0);
 507       }
 508       break;
 509
 510     case KeyEvent.VK_RIGHT:
 511       if (evt.isAltDown() || !viewport.cursorMode)
 512       {
 513         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 514       }
 515       else
 516       {
 517         alignPanel.seqPanel.moveCursor(1, 0);
 518       }
 519       break;
 520
 521     case KeyEvent.VK_SPACE:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 525                 || evt.isShiftDown() || evt.isAltDown());
 526       }
 527       break;
 528
 529     case KeyEvent.VK_DELETE:
 530     case KeyEvent.VK_BACK_SPACE:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 534                 || evt.isShiftDown() || evt.isAltDown());
 535       }
 536       else
 537       {
 538         cut_actionPerformed();
 539         alignPanel.seqPanel.seqCanvas.repaint();
 540       }
 541       break;
 542
 543     case KeyEvent.VK_S:
 544       if (viewport.cursorMode)
 545       {
 546         alignPanel.seqPanel.setCursorRow();
 547       }
 548       break;
 549     case KeyEvent.VK_P:
 550       if (viewport.cursorMode)
 551       {
 552         alignPanel.seqPanel.setCursorPosition();
 553       }
 554       break;
 555
 556     case KeyEvent.VK_ENTER:
 557     case KeyEvent.VK_COMMA:
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.setCursorRowAndColumn();
 561       }
 562       break;
 563
 564     case KeyEvent.VK_Q:
 565       if (viewport.cursorMode)
 566       {
 567         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 568       }
 569       break;
 570     case KeyEvent.VK_M:
 571       if (viewport.cursorMode)
 572       {
 573         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 574       }
 575       break;
 576
 577     case KeyEvent.VK_F2:
 578       viewport.cursorMode = !viewport.cursorMode;
 579       setStatus(MessageManager.formatMessage("label.keyboard_editing_mode",
 580               new String[]
 581               { (viewport.cursorMode ? "on" : "off") }));
 582       if (viewport.cursorMode)
 583       {
 584         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 585         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 586       }
 587       break;
 588
 589     case KeyEvent.VK_F:
 590       if (evt.isControlDown())
 591       {
 592         findMenuItem_actionPerformed();
 593       }
 594       break;
 595
 596     case KeyEvent.VK_H:
 597     {
 598       boolean toggleSeqs = !evt.isControlDown();
 599       boolean toggleCols = !evt.isShiftDown();
 600       toggleHiddenRegions(toggleSeqs, toggleCols);
 601       break;
 602     }
 603
 604     case KeyEvent.VK_PAGE_UP:
 605       ranges.pageUp();
 606       break;
 607
 608     case KeyEvent.VK_PAGE_DOWN:
 609       ranges.pageDown();
 610       break;
 611
 612     case KeyEvent.VK_Z:
 613       if (evt.isControlDown())
 614       {
 615         undoMenuItem_actionPerformed();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_Y:
 620       if (evt.isControlDown())
 621       {
 622         redoMenuItem_actionPerformed();
 623       }
 624       break;
 625
 626     case KeyEvent.VK_L:
 627       if (evt.isControlDown())
 628       {
 629         trimAlignment(true);
 630       }
 631       break;
 632
 633     case KeyEvent.VK_R:
 634       if (evt.isControlDown())
 635       {
 636         trimAlignment(false);
 637       }
 638       break;
 639
 640     case KeyEvent.VK_E:
 641       if (evt.isControlDown())
 642       {
 643         if (evt.isShiftDown())
 644         {
 645           this.removeAllGapsMenuItem_actionPerformed();
 646         }
 647         else
 648         {
 649           removeGappedColumnMenuItem_actionPerformed();
 650         }
 651       }
 652       break;
 653     case KeyEvent.VK_I:
 654       if (evt.isControlDown())
 655       {
 656         if (evt.isAltDown())
 657         {
 658           invertColSel_actionPerformed();
 659         }
 660         else
 661         {
 662           invertSequenceMenuItem_actionPerformed();
 663         }
 664       }
 665       break;
 666
 667     case KeyEvent.VK_G:
 668       if (evt.isControlDown())
 669       {
 670         if (evt.isShiftDown())
 671         {
 672           this.unGroup_actionPerformed();
 673         }
 674         else
 675         {
 676           this.createGroup_actionPerformed();
 677         }
 678       }
 679       break;
 680
 681     case KeyEvent.VK_U:
 682       if (evt.isControlDown())
 683       {
 684         this.deleteGroups_actionPerformed();
 685       }
 686       break;
 687
 688     case KeyEvent.VK_T:
 689       if (evt.isControlDown())
 690       {
 691         newView(null);
 692       }
 693       break;
 694
 695     }
 696     // TODO: repaint flags set only if the keystroke warrants it
 697     alignPanel.paintAlignment(true, true);
 698   }
 699
 700   /**
 701    * called by key handler and the hide all/show all menu items
 702    *
 703    * @param toggleSeqs
 704    * @param toggleCols
 705    */
 706   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 707   {
 708     boolean hide = false;
 709     SequenceGroup sg = viewport.getSelectionGroup();
 710     if (!toggleSeqs && !toggleCols)
 711     {
 712       // Hide everything by the current selection - this is a hack - we do the
 713       // invert and then hide
 714       // first check that there will be visible columns after the invert.
 715       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 716               && sg.getStartRes() <= sg.getEndRes()))
 717       {
 718         // now invert the sequence set, if required - empty selection implies
 719         // that no hiding is required.
 720         if (sg != null)
 721         {
 722           invertSequenceMenuItem_actionPerformed();
 723           sg = viewport.getSelectionGroup();
 724           toggleSeqs = true;
 725
 726         }
 727         viewport.expandColSelection(sg, true);
 728         // finally invert the column selection and get the new sequence
 729         // selection and indicate it should be hidden.
 730         invertColSel_actionPerformed();
 731         toggleCols = true;
 732       }
 733     }
 734
 735     if (toggleSeqs)
 736     {
 737       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 738       {
 739         hide = true;
 740         viewport.hideAllSelectedSeqs();
 741       }
 742       else if (!(toggleCols && viewport.hasSelectedColumns()))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.hasSelectedColumns())
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762       viewport.sendSelection();
 763     }
 764   }
 765
 766   @Override
 767   public void keyReleased(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void keyTyped(KeyEvent evt)
 773   {
 774   }
 775
 776   @Override
 777   public void itemStateChanged(ItemEvent evt)
 778   {
 779     final Object source = evt.getSource();
 780     if (source == displayNonconservedMenuItem)
 781     {
 782       displayNonconservedMenuItem_actionPerformed();
 783     }
 784     else if (source == colourTextMenuItem)
 785     {
 786       colourTextMenuItem_actionPerformed();
 787     }
 788     else if (source == wrapMenuItem)
 789     {
 790       wrapMenuItem_actionPerformed();
 791     }
 792     else if (source == scaleAbove)
 793     {
 794       viewport.setScaleAboveWrapped(scaleAbove.getState());
 795     }
 796     else if (source == scaleLeft)
 797     {
 798       viewport.setScaleLeftWrapped(scaleLeft.getState());
 799     }
 800     else if (source == scaleRight)
 801     {
 802       viewport.setScaleRightWrapped(scaleRight.getState());
 803     }
 804     else if (source == seqLimits)
 805     {
 806       seqLimits_itemStateChanged();
 807     }
 808     else if (source == viewBoxesMenuItem)
 809     {
 810       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 811     }
 812     else if (source == viewTextMenuItem)
 813     {
 814       viewport.setShowText(viewTextMenuItem.getState());
 815     }
 816     else if (source == renderGapsMenuItem)
 817     {
 818       viewport.setRenderGaps(renderGapsMenuItem.getState());
 819     }
 820     else if (source == annotationPanelMenuItem)
 821     {
 822       boolean showAnnotations = annotationPanelMenuItem.getState();
 823       showAlignmentAnnotations.setEnabled(showAnnotations);
 824       showSequenceAnnotations.setEnabled(showAnnotations);
 825       viewport.setShowAnnotation(showAnnotations);
 826       alignPanel.setAnnotationVisible(showAnnotations);
 827     }
 828     else if (source == sequenceFeatures)
 829     {
 830       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 831       alignPanel.seqPanel.seqCanvas.repaint();
 832     }
 833     else if (source == showAlignmentAnnotations)
 834     {
 835       setAnnotationsVisibility();
 836     }
 837     else if (source == showSequenceAnnotations)
 838     {
 839       setAnnotationsVisibility();
 840     }
 841     else if (source == sortAnnBySequence)
 842     {
 843       boolean newState = sortAnnBySequence.getState();
 844       sortAnnByLabel.setState(false);
 845       setAnnotationSortOrder(
 846               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 847                       : SequenceAnnotationOrder.NONE);
 848       setViewportAnnotationOrder();
 849     }
 850     else if (source == sortAnnByLabel)
 851     {
 852       boolean newState = sortAnnByLabel.getState();
 853       sortAnnBySequence.setState(false);
 854       setAnnotationSortOrder(
 855               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 856                       : SequenceAnnotationOrder.NONE);
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == showAutoFirst)
 860     {
 861       showAutoLast.setState(!showAutoFirst.getState());
 862       setShowAutoCalculatedAbove(showAutoFirst.getState());
 863       setViewportAnnotationOrder();
 864     }
 865     else if (source == showAutoLast)
 866     {
 867       showAutoFirst.setState(!showAutoLast.getState());
 868       setShowAutoCalculatedAbove(showAutoFirst.getState());
 869       setViewportAnnotationOrder();
 870     }
 871     else if (source == conservationMenuItem)
 872     {
 873       conservationMenuItem_actionPerformed();
 874     }
 875     else if (source == abovePIDThreshold)
 876     {
 877       abovePIDThreshold_actionPerformed();
 878     }
 879     else if (source == applyToAllGroups)
 880     {
 881       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 882     }
 883     else if (source == autoCalculate)
 884     {
 885       viewport.autoCalculateConsensus = autoCalculate.getState();
 886     }
 887     else if (source == sortByTree)
 888     {
 889       viewport.sortByTree = sortByTree.getState();
 890     }
 891     else if (source == this.centreColumnLabelFlag)
 892     {
 893       centreColumnLabelFlag_stateChanged();
 894     }
 895     else if (source == this.followMouseOverFlag)
 896     {
 897       mouseOverFlag_stateChanged();
 898     }
 899     else if (source == showGroupConsensus)
 900     {
 901       showGroupConsensus_actionPerformed();
 902     }
 903     else if (source == showGroupConservation)
 904     {
 905       showGroupConservation_actionPerformed();
 906     }
 907     else if (source == showSequenceLogo)
 908     {
 909       showSequenceLogo_actionPerformed();
 910     }
 911     else if (source == normSequenceLogo)
 912     {
 913       normSequenceLogo_actionPerformed();
 914     }
 915     else if (source == showConsensusHistogram)
 916     {
 917       showConsensusHistogram_actionPerformed();
 918     }
 919     else if (source == applyAutoAnnotationSettings)
 920     {
 921       applyAutoAnnotationSettings_actionPerformed();
 922     }
 923     // TODO: repaint flags set only if warranted
 924     alignPanel.paintAlignment(true, true);
 925   }
 926
 927   /**
 928    * Set the visibility state of sequence-related and/or alignment-related
 929    * annotations depending on checkbox selections, and repaint.
 930    *
 931    * @param visible
 932    */
 933   private void setAnnotationsVisibility()
 934   {
 935     boolean showForAlignment = showAlignmentAnnotations.getState();
 936     boolean showForSequences = showSequenceAnnotations.getState();
 937     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 938     {
 939       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 940               .getAlignmentAnnotation())
 941       {
 942         boolean visible = (aa.sequenceRef == null ? showForAlignment
 943                 : showForSequences);
 944         aa.visible = visible;
 945       }
 946     }
 947     alignPanel.validateAnnotationDimensions(true);
 948     validate();
 949     repaint();
 950   }
 951
 952   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 953   {
 954     this.annotationSortOrder = order;
 955   }
 956
 957   /**
 958    * Set flags on the viewport that control annotation ordering
 959    */
 960   private void setViewportAnnotationOrder()
 961   {
 962     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 963     this.alignPanel.av
 964             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 965   }
 966
 967   private void setShowAutoCalculatedAbove(boolean showAbove)
 968   {
 969     this.showAutoCalculatedAbove = showAbove;
 970   }
 971
 972   private void mouseOverFlag_stateChanged()
 973   {
 974     viewport.setFollowHighlight(followMouseOverFlag.getState());
 975     // TODO: could kick the scrollTo mechanism to reset view for current
 976     // searchresults.
 977   }
 978
 979   private void centreColumnLabelFlag_stateChanged()
 980   {
 981     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 982     this.alignPanel.annotationPanel.repaint();
 983   }
 984
 985   @Override
 986   public void actionPerformed(ActionEvent evt)
 987   {
 988     viewport.applet.currentAlignFrame = this;
 989
 990     Object source = evt.getSource();
 991
 992     if (source == inputText)
 993     {
 994       inputText_actionPerformed();
 995     }
 996     else if (source == loadTree)
 997     {
 998       loadTree_actionPerformed();
 999     }
1000     else if (source == loadApplication)
1001     {
1002       launchFullApplication();
1003     }
1004     else if (source == loadAnnotations)
1005     {
1006       loadAnnotations();
1007     }
1008     else if (source == outputAnnotations)
1009     {
1010       outputAnnotations(true);
1011     }
1012     else if (source == outputFeatures)
1013     {
1014       outputFeatures(true, "Jalview");
1015     }
1016     else if (source == closeMenuItem)
1017     {
1018       closeMenuItem_actionPerformed();
1019     }
1020     else if (source == copy)
1021     {
1022       copy_actionPerformed();
1023     }
1024     else if (source == undoMenuItem)
1025     {
1026       undoMenuItem_actionPerformed();
1027     }
1028     else if (source == redoMenuItem)
1029     {
1030       redoMenuItem_actionPerformed();
1031     }
1032     else if (source == inputText)
1033     {
1034       inputText_actionPerformed();
1035     }
1036     else if (source == closeMenuItem)
1037     {
1038       closeMenuItem_actionPerformed();
1039     }
1040     else if (source == undoMenuItem)
1041     {
1042       undoMenuItem_actionPerformed();
1043     }
1044     else if (source == redoMenuItem)
1045     {
1046       redoMenuItem_actionPerformed();
1047     }
1048     else if (source == copy)
1049     {
1050       copy_actionPerformed();
1051     }
1052     else if (source == pasteNew)
1053     {
1054       pasteNew_actionPerformed();
1055     }
1056     else if (source == pasteThis)
1057     {
1058       pasteThis_actionPerformed();
1059     }
1060     else if (source == cut)
1061     {
1062       cut_actionPerformed();
1063     }
1064     else if (source == delete)
1065     {
1066       delete_actionPerformed();
1067     }
1068     else if (source == createGroup)
1069     {
1070       createGroup_actionPerformed();
1071     }
1072     else if (source == unGroup)
1073     {
1074       unGroup_actionPerformed();
1075     }
1076     else if (source == grpsFromSelection)
1077     {
1078       makeGrpsFromSelection_actionPerformed();
1079     }
1080     else if (source == deleteGroups)
1081     {
1082       deleteGroups_actionPerformed();
1083     }
1084     else if (source == selectAllSequenceMenuItem)
1085     {
1086       selectAllSequenceMenuItem_actionPerformed();
1087     }
1088     else if (source == deselectAllSequenceMenuItem)
1089     {
1090       deselectAllSequenceMenuItem_actionPerformed();
1091     }
1092     else if (source == invertSequenceMenuItem)
1093     {
1094       invertSequenceMenuItem_actionPerformed();
1095       // uncomment to slave sequence selections in split frame
1096       // viewport.sendSelection();
1097     }
1098     else if (source == invertColSel)
1099     {
1100       viewport.invertColumnSelection();
1101       alignPanel.paintAlignment(false, false);
1102       viewport.sendSelection();
1103     }
1104     else if (source == remove2LeftMenuItem)
1105     {
1106       trimAlignment(true);
1107     }
1108     else if (source == remove2RightMenuItem)
1109     {
1110       trimAlignment(false);
1111     }
1112     else if (source == removeGappedColumnMenuItem)
1113     {
1114       removeGappedColumnMenuItem_actionPerformed();
1115     }
1116     else if (source == removeAllGapsMenuItem)
1117     {
1118       removeAllGapsMenuItem_actionPerformed();
1119     }
1120     else if (source == findMenuItem)
1121     {
1122       findMenuItem_actionPerformed();
1123     }
1124     else if (source == font)
1125     {
1126       new FontChooser(alignPanel);
1127     }
1128     else if (source == newView)
1129     {
1130       newView(null);
1131     }
1132     else if (source == showColumns)
1133     {
1134       viewport.showAllHiddenColumns();
1135       alignPanel.paintAlignment(true, true);
1136       viewport.sendSelection();
1137     }
1138     else if (source == showSeqs)
1139     {
1140       viewport.showAllHiddenSeqs();
1141       alignPanel.paintAlignment(true, true);
1142       // uncomment if we want to slave sequence selections in split frame
1143       // viewport.sendSelection();
1144     }
1145     else if (source == hideColumns)
1146     {
1147       viewport.hideSelectedColumns();
1148       alignPanel.paintAlignment(true, true);
1149       viewport.sendSelection();
1150     }
1151     else if (source == hideSequences
1152             && viewport.getSelectionGroup() != null)
1153     {
1154       viewport.hideAllSelectedSeqs();
1155       alignPanel.paintAlignment(true, true);
1156       // uncomment if we want to slave sequence selections in split frame
1157       // viewport.sendSelection();
1158     }
1159     else if (source == hideAllButSelection)
1160     {
1161       toggleHiddenRegions(false, false);
1162       alignPanel.paintAlignment(true, true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == hideAllSelection)
1166     {
1167       SequenceGroup sg = viewport.getSelectionGroup();
1168       viewport.expandColSelection(sg, false);
1169       viewport.hideAllSelectedSeqs();
1170       viewport.hideSelectedColumns();
1171       alignPanel.paintAlignment(true, true);
1172       viewport.sendSelection();
1173     }
1174     else if (source == showAllHidden)
1175     {
1176       viewport.showAllHiddenColumns();
1177       viewport.showAllHiddenSeqs();
1178       alignPanel.paintAlignment(true, true);
1179       viewport.sendSelection();
1180     }
1181     else if (source == showGroupConsensus)
1182     {
1183       showGroupConsensus_actionPerformed();
1184     }
1185     else if (source == showGroupConservation)
1186     {
1187       showGroupConservation_actionPerformed();
1188     }
1189     else if (source == showSequenceLogo)
1190     {
1191       showSequenceLogo_actionPerformed();
1192     }
1193     else if (source == normSequenceLogo)
1194     {
1195       normSequenceLogo_actionPerformed();
1196     }
1197     else if (source == showConsensusHistogram)
1198     {
1199       showConsensusHistogram_actionPerformed();
1200     }
1201     else if (source == applyAutoAnnotationSettings)
1202     {
1203       applyAutoAnnotationSettings_actionPerformed();
1204     }
1205     else if (source == featureSettings)
1206     {
1207       showFeatureSettingsUI();
1208     }
1209     else if (source == alProperties)
1210     {
1211       StringBuffer contents = new jalview.io.AlignmentProperties(
1212               viewport.getAlignment()).formatAsString();
1213       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214       cap.setText(contents.toString());
1215       Frame frame = new Frame();
1216       frame.add(cap);
1217       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218               .formatMessage("label.alignment_properties", new String[]
1219               { getTitle() }), 400, 250);
1220     }
1221     else if (source == overviewMenuItem)
1222     {
1223       overviewMenuItem_actionPerformed();
1224     }
1225     else if (source == noColourmenuItem)
1226     {
1227       changeColour(null);
1228     }
1229     else if (source == clustalColour)
1230     {
1231       abovePIDThreshold.setState(false);
1232       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1233     }
1234     else if (source == zappoColour)
1235     {
1236       changeColour(new ZappoColourScheme());
1237     }
1238     else if (source == taylorColour)
1239     {
1240       changeColour(new TaylorColourScheme());
1241     }
1242     else if (source == hydrophobicityColour)
1243     {
1244       changeColour(new HydrophobicColourScheme());
1245     }
1246     else if (source == helixColour)
1247     {
1248       changeColour(new HelixColourScheme());
1249     }
1250     else if (source == strandColour)
1251     {
1252       changeColour(new StrandColourScheme());
1253     }
1254     else if (source == turnColour)
1255     {
1256       changeColour(new TurnColourScheme());
1257     }
1258     else if (source == buriedColour)
1259     {
1260       changeColour(new BuriedColourScheme());
1261     }
1262     else if (source == nucleotideColour)
1263     {
1264       changeColour(new NucleotideColourScheme());
1265     }
1266     else if (source == purinePyrimidineColour)
1267     {
1268       changeColour(new PurinePyrimidineColourScheme());
1269     }
1270     // else if (source == RNAInteractionColour)
1271     // {
1272     // changeColour(new RNAInteractionColourScheme());
1273     // }
1274     else if (source == RNAHelixColour)
1275     {
1276       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277       // new RNAHelicesColourChooser(viewport, alignPanel);
1278     }
1279     else if (source == modifyPID)
1280     {
1281       modifyPID_actionPerformed();
1282     }
1283     else if (source == modifyConservation)
1284     {
1285       modifyConservation_actionPerformed();
1286     }
1287     else if (source == userDefinedColour)
1288     {
1289       new UserDefinedColours(alignPanel, null);
1290     }
1291     else if (source == PIDColour)
1292     {
1293       changeColour(new PIDColourScheme());
1294     }
1295     else if (source == BLOSUM62Colour)
1296     {
1297       changeColour(new Blosum62ColourScheme());
1298     }
1299     else if (source == tcoffeeColour)
1300     {
1301       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1302     }
1303     else if (source == annotationColour)
1304     {
1305       new AnnotationColourChooser(viewport, alignPanel);
1306     }
1307     else if (source == annotationColumnSelection)
1308     {
1309       new AnnotationColumnChooser(viewport, alignPanel);
1310     }
1311     else if (source == sortPairwiseMenuItem)
1312     {
1313       sortPairwiseMenuItem_actionPerformed();
1314     }
1315     else if (source == sortIDMenuItem)
1316     {
1317       sortIDMenuItem_actionPerformed();
1318     }
1319     else if (source == sortLengthMenuItem)
1320     {
1321       sortLengthMenuItem_actionPerformed();
1322     }
1323     else if (source == sortGroupMenuItem)
1324     {
1325       sortGroupMenuItem_actionPerformed();
1326     }
1327     else if (source == removeRedundancyMenuItem)
1328     {
1329       removeRedundancyMenuItem_actionPerformed();
1330     }
1331     else if (source == pairwiseAlignmentMenuItem)
1332     {
1333       pairwiseAlignmentMenuItem_actionPerformed();
1334     }
1335     else if (source == PCAMenuItem)
1336     {
1337       PCAMenuItem_actionPerformed();
1338     }
1339     else if (source == averageDistanceTreeMenuItem)
1340     {
1341       averageDistanceTreeMenuItem_actionPerformed();
1342     }
1343     else if (source == neighbourTreeMenuItem)
1344     {
1345       neighbourTreeMenuItem_actionPerformed();
1346     }
1347     else if (source == njTreeBlosumMenuItem)
1348     {
1349       njTreeBlosumMenuItem_actionPerformed();
1350     }
1351     else if (source == avDistanceTreeBlosumMenuItem)
1352     {
1353       avTreeBlosumMenuItem_actionPerformed();
1354     }
1355     else if (source == documentation)
1356     {
1357       documentation_actionPerformed();
1358     }
1359     else if (source == about)
1360     {
1361       about_actionPerformed();
1362     }
1363
1364   }
1365
1366   public void inputText_actionPerformed()
1367   {
1368     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369     Frame frame = new Frame();
1370     frame.add(cap);
1371     jalview.bin.JalviewLite.addFrame(frame,
1372             MessageManager.getString("label.input_cut_paste"), 500, 500);
1373   }
1374
1375   protected void outputText_actionPerformed(ActionEvent e)
1376   {
1377     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     JalviewLite.addFrame(frame, MessageManager
1381             .formatMessage("label.alignment_output_command", new Object[]
1382             { e.getActionCommand() }), 600, 500);
1383
1384     FileFormatI fileFormat = FileFormats.getInstance()
1385             .forName(e.getActionCommand());
1386     cap.setText(
1387             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1389   }
1390
1391   public void loadAnnotations()
1392   {
1393     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394     cap.setText(MessageManager
1395             .getString("label.paste_features_annotations_Tcoffee_here"));
1396     cap.setAnnotationImport();
1397     Frame frame = new Frame();
1398     frame.add(cap);
1399     jalview.bin.JalviewLite.addFrame(frame,
1400             MessageManager.getString("action.paste_annotations"), 400, 300);
1401
1402   }
1403
1404   public String outputAnnotations(boolean displayTextbox)
1405   {
1406     String annotation = new AnnotationFile()
1407             .printAnnotationsForView(viewport);
1408
1409     if (displayTextbox)
1410     {
1411       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412       Frame frame = new Frame();
1413       frame.add(cap);
1414       jalview.bin.JalviewLite.addFrame(frame,
1415               MessageManager.getString("label.annotations"), 600, 500);
1416       cap.setText(annotation);
1417     }
1418
1419     return annotation;
1420   }
1421
1422   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1423   {
1424     if (alignPanel.getFeatureRenderer() != null
1425             && viewport.getFeaturesDisplayed() != null)
1426     {
1427       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1428
1429     }
1430     return null;
1431   }
1432
1433   private List<String> getDisplayedFeatureGroups()
1434   {
1435     if (alignPanel.getFeatureRenderer() != null
1436             && viewport.getFeaturesDisplayed() != null)
1437     {
1438       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1439
1440     }
1441     return null;
1442   }
1443
1444   public String outputFeatures(boolean displayTextbox, String format)
1445   {
1446     String features;
1447     FeaturesFile formatter = new FeaturesFile();
1448     if (format.equalsIgnoreCase("Jalview"))
1449     {
1450       features = formatter.printJalviewFormat(
1451               viewport.getAlignment().getSequencesArray(),
1452               alignPanel.getFeatureRenderer(), true, false);
1453     }
1454     else
1455     {
1456       features = formatter.printGffFormat(
1457               viewport.getAlignment().getSequencesArray(),
1458               alignPanel.getFeatureRenderer(), true, false);
1459     }
1460
1461     if (displayTextbox)
1462     {
1463       boolean frimport = false;
1464       if (features == null || features.equals("No Features Visible"))
1465       {
1466         features = "# No features visible - paste some and import them here.";
1467         frimport = true;
1468       }
1469
1470       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1471       if (frimport)
1472       {
1473         cap.setAnnotationImport();
1474       }
1475       Frame frame = new Frame();
1476       frame.add(cap);
1477       jalview.bin.JalviewLite.addFrame(frame,
1478               MessageManager.getString("label.features"), 600, 500);
1479       cap.setText(features);
1480     }
1481     else
1482     {
1483       if (features == null)
1484       {
1485         features = "";
1486       }
1487     }
1488
1489     return features;
1490   }
1491
1492   void launchFullApplication()
1493   {
1494     StringBuffer url = new StringBuffer(jalviewServletURL);
1495
1496     // allow servlet parameters to be passed in applet parameter
1497     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1498             : "?";
1499     url.append(firstSep);
1500
1501     url.append(
1502             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1503
1504     if (viewport.applet.getParameter("features") != null)
1505     {
1506       url.append("&features=");
1507       url.append(appendProtocol(viewport.applet.getParameter("features")));
1508     }
1509
1510     if (viewport.applet.getParameter("annotations") != null)
1511     {
1512       url.append("&annotations=");
1513       url.append(
1514               appendProtocol(viewport.applet.getParameter("annotations")));
1515     }
1516
1517     if (viewport.applet.getParameter("jnetfile") != null
1518             || viewport.applet.getParameter("jpredfile") != null)
1519     {
1520       url.append("&annotations=");
1521       url.append(appendProtocol(
1522               viewport.applet.getParameter("jnetfile") != null
1523                       ? viewport.applet.getParameter("jnetfile")
1524                       : viewport.applet.getParameter("jpredfile")));
1525     }
1526
1527     if (viewport.applet.getParameter("defaultColour") != null)
1528     {
1529       url.append("&colour=" + removeWhiteSpace(
1530               viewport.applet.getParameter("defaultColour")));
1531     }
1532
1533     if (viewport.applet.getParameter("userDefinedColour") != null)
1534     {
1535       url.append("&colour=" + removeWhiteSpace(
1536               viewport.applet.getParameter("userDefinedColour")));
1537     }
1538     if (viewport.applet.getParameter("tree") != null)
1539     {
1540       url.append("&tree="
1541               + appendProtocol(viewport.applet.getParameter("tree")));
1542     }
1543     if (viewport.applet.getParameter("treeFile") != null)
1544     {
1545       url.append("&tree="
1546               + appendProtocol(viewport.applet.getParameter("treeFile")));
1547     }
1548
1549     showURL(url.toString(), "FULL_APP");
1550   }
1551
1552   String removeWhiteSpace(String colour)
1553   {
1554     StringBuffer sb = new StringBuffer();
1555     for (int i = 0; i < colour.length(); i++)
1556     {
1557       if (Character.isWhitespace(colour.charAt(i)))
1558       {
1559         sb.append("%20");
1560       }
1561       else
1562       {
1563         sb.append(colour.charAt(i));
1564       }
1565     }
1566
1567     return sb.toString();
1568   }
1569
1570   String appendProtocol(String url)
1571   {
1572     try
1573     {
1574       new URL(url);
1575       url = URLEncoder.encode(url, "UTF-8");
1576     }
1577     /*
1578      * When we finally deprecate 1.1 compatibility, we can start to use
1579      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582      * ex.printStackTrace(); }
1583      */
1584     catch (java.net.MalformedURLException ex)
1585     {
1586       url = viewport.applet.getCodeBase() + url;
1587     } catch (UnsupportedEncodingException ex)
1588     {
1589       System.err.println(
1590               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1591                       + url);
1592       ex.printStackTrace();
1593     }
1594     return url;
1595   }
1596
1597   public void closeMenuItem_actionPerformed()
1598   {
1599     PaintRefresher.RemoveComponent(alignPanel);
1600     if (alignPanel.seqPanel != null
1601             && alignPanel.seqPanel.seqCanvas != null)
1602     {
1603       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1604     }
1605     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1606     {
1607       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1608     }
1609
1610     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1611     {
1612       System.exit(0);
1613     }
1614
1615     viewport = null;
1616     if (alignPanel != null && alignPanel.overviewPanel != null)
1617     {
1618       alignPanel.overviewPanel.dispose();
1619     }
1620     alignPanel = null;
1621     this.dispose();
1622   }
1623
1624   /**
1625    * TODO: JAL-1104
1626    */
1627   void updateEditMenuBar()
1628   {
1629
1630     if (viewport.getHistoryList().size() > 0)
1631     {
1632       undoMenuItem.setEnabled(true);
1633       CommandI command = viewport.getHistoryList().peek();
1634       undoMenuItem.setLabel(MessageManager
1635               .formatMessage("label.undo_command", new Object[]
1636               { command.getDescription() }));
1637     }
1638     else
1639     {
1640       undoMenuItem.setEnabled(false);
1641       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1642     }
1643
1644     if (viewport.getRedoList().size() > 0)
1645     {
1646       redoMenuItem.setEnabled(true);
1647
1648       CommandI command = viewport.getRedoList().peek();
1649       redoMenuItem.setLabel(MessageManager
1650               .formatMessage("label.redo_command", new Object[]
1651               { command.getDescription() }));
1652     }
1653     else
1654     {
1655       redoMenuItem.setEnabled(false);
1656       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1657     }
1658   }
1659
1660   /**
1661    * TODO: JAL-1104
1662    */
1663   @Override
1664   public void addHistoryItem(CommandI command)
1665   {
1666     if (command.getSize() > 0)
1667     {
1668       viewport.addToHistoryList(command);
1669       viewport.clearRedoList();
1670       updateEditMenuBar();
1671       viewport.updateHiddenColumns();
1672     }
1673   }
1674
1675   /**
1676    * TODO: JAL-1104 DOCUMENT ME!
1677    *
1678    * @param e
1679    *          DOCUMENT ME!
1680    */
1681   protected void undoMenuItem_actionPerformed()
1682   {
1683     if (viewport.getHistoryList().isEmpty())
1684     {
1685       return;
1686     }
1687
1688     CommandI command = viewport.getHistoryList().pop();
1689     viewport.addToRedoList(command);
1690     command.undoCommand(null);
1691
1692     AlignmentViewport originalSource = getOriginatingSource(command);
1693     // JBPNote Test
1694     if (originalSource != viewport)
1695     {
1696       System.err
1697               .println("Warning: Viewport object mismatch whilst undoing");
1698     }
1699     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1700                                           // viewport.getColumnSelection().getHiddenColumns()
1701                                           // != null;
1702     updateEditMenuBar();
1703     originalSource.firePropertyChange("alignment", null,
1704             originalSource.getAlignment().getSequences());
1705   }
1706
1707   /**
1708    * TODO: JAL-1104 DOCUMENT ME!
1709    *
1710    * @param e
1711    *          DOCUMENT ME!
1712    */
1713   protected void redoMenuItem_actionPerformed()
1714   {
1715     if (viewport.getRedoList().isEmpty())
1716     {
1717       return;
1718     }
1719
1720     CommandI command = viewport.getRedoList().pop();
1721     viewport.addToHistoryList(command);
1722     command.doCommand(null);
1723
1724     AlignmentViewport originalSource = getOriginatingSource(command);
1725     // JBPNote Test
1726     if (originalSource != viewport)
1727     {
1728       System.err
1729               .println("Warning: Viewport object mismatch whilst re-doing");
1730     }
1731     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1732                                           // viewport.getColumnSelection().getHiddenColumns()
1733                                           // != null;
1734
1735     updateEditMenuBar();
1736     originalSource.firePropertyChange("alignment", null,
1737             originalSource.getAlignment().getSequences());
1738   }
1739
1740   AlignmentViewport getOriginatingSource(CommandI command)
1741   {
1742     AlignmentViewport originalSource = null;
1743     // For sequence removal and addition, we need to fire
1744     // the property change event FROM the viewport where the
1745     // original alignment was altered
1746     AlignmentI al = null;
1747     if (command instanceof EditCommand)
1748     {
1749       EditCommand editCommand = (EditCommand) command;
1750       al = editCommand.getAlignment();
1751       Vector comps = PaintRefresher.components
1752               .get(viewport.getSequenceSetId());
1753       for (int i = 0; i < comps.size(); i++)
1754       {
1755         if (comps.elementAt(i) instanceof AlignmentPanel)
1756         {
1757           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1758           {
1759             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1760             break;
1761           }
1762         }
1763       }
1764     }
1765
1766     if (originalSource == null)
1767     {
1768       // The original view is closed, we must validate
1769       // the current view against the closed view first
1770       if (al != null)
1771       {
1772         PaintRefresher.validateSequences(al, viewport.getAlignment());
1773       }
1774
1775       originalSource = viewport;
1776     }
1777
1778     return originalSource;
1779   }
1780
1781   /**
1782    * Move the currently selected sequences up or down one position in the
1783    * alignment
1784    *
1785    * @param up
1786    */
1787   public void moveSelectedSequences(boolean up)
1788   {
1789     SequenceGroup sg = viewport.getSelectionGroup();
1790     if (sg == null)
1791     {
1792       return;
1793     }
1794     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1795             up ? null : viewport.getHiddenRepSequences(), up);
1796     alignPanel.paintAlignment(true, false);
1797
1798     /*
1799      * Also move cDNA/protein complement sequences
1800      */
1801     AlignViewportI complement = viewport.getCodingComplement();
1802     if (complement != null)
1803     {
1804       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1805               viewport, complement);
1806       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1807               up ? null : complement.getHiddenRepSequences(), up);
1808       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1809               false);
1810     }
1811   }
1812
1813   synchronized void slideSequences(boolean right, int size)
1814   {
1815     List<SequenceI> sg = new Vector<>();
1816     if (viewport.cursorMode)
1817     {
1818       sg.add(viewport.getAlignment()
1819               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1820     }
1821     else if (viewport.getSelectionGroup() != null
1822             && viewport.getSelectionGroup().getSize() != viewport
1823                     .getAlignment().getHeight())
1824     {
1825       sg = viewport.getSelectionGroup()
1826               .getSequences(viewport.getHiddenRepSequences());
1827     }
1828
1829     if (sg.size() < 1)
1830     {
1831       return;
1832     }
1833
1834     Vector<SequenceI> invertGroup = new Vector();
1835
1836     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1837     {
1838       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1839       {
1840         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1841       }
1842     }
1843
1844     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1845
1846     SequenceI[] seqs2 = invertGroup
1847             .toArray(new SequenceI[invertGroup.size()]);
1848     for (int i = 0; i < invertGroup.size(); i++)
1849     {
1850       seqs2[i] = invertGroup.elementAt(i);
1851     }
1852
1853     SlideSequencesCommand ssc;
1854     if (right)
1855     {
1856       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1857               viewport.getGapCharacter());
1858     }
1859     else
1860     {
1861       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1862               viewport.getGapCharacter());
1863     }
1864
1865     int groupAdjustment = 0;
1866     if (ssc.getGapsInsertedBegin() && right)
1867     {
1868       if (viewport.cursorMode)
1869       {
1870         alignPanel.seqPanel.moveCursor(size, 0);
1871       }
1872       else
1873       {
1874         groupAdjustment = size;
1875       }
1876     }
1877     else if (!ssc.getGapsInsertedBegin() && !right)
1878     {
1879       if (viewport.cursorMode)
1880       {
1881         alignPanel.seqPanel.moveCursor(-size, 0);
1882       }
1883       else
1884       {
1885         groupAdjustment = -size;
1886       }
1887     }
1888
1889     if (groupAdjustment != 0)
1890     {
1891       viewport.getSelectionGroup().setStartRes(
1892               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1893       viewport.getSelectionGroup().setEndRes(
1894               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1895     }
1896
1897     boolean appendHistoryItem = false;
1898     Deque<CommandI> historyList = viewport.getHistoryList();
1899     if (historyList != null && historyList.size() > 0
1900             && historyList.peek() instanceof SlideSequencesCommand)
1901     {
1902       appendHistoryItem = ssc.appendSlideCommand(
1903               (SlideSequencesCommand) historyList.peek());
1904     }
1905
1906     if (!appendHistoryItem)
1907     {
1908       addHistoryItem(ssc);
1909     }
1910
1911     repaint();
1912   }
1913
1914   static StringBuffer copiedSequences;
1915
1916   static HiddenColumns copiedHiddenColumns;
1917
1918   protected void copy_actionPerformed()
1919   {
1920     if (viewport.getSelectionGroup() == null)
1921     {
1922       return;
1923     }
1924
1925     SequenceGroup sg = viewport.getSelectionGroup();
1926     copiedSequences = new StringBuffer();
1927     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1928     for (int i = 0; i < sg.getSize(); i++)
1929     {
1930       SequenceI seq = sg.getSequenceAt(i);
1931       int index = viewport.getAlignment().findIndex(seq);
1932       orderedSeqs.put(index, seq);
1933     }
1934
1935     int index = 0, startRes, endRes;
1936     char ch;
1937
1938     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1939     {
1940       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1941       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1942
1943       // create new HiddenColumns object with copy of hidden regions
1944       // between startRes and endRes, offset by startRes
1945       copiedHiddenColumns = new HiddenColumns(
1946               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1947               hiddenCutoff, hiddenOffset);
1948     }
1949     else
1950     {
1951       copiedHiddenColumns = null;
1952     }
1953
1954     for (int i = 0; i < sg.getSize(); i++)
1955     {
1956       SequenceI seq = null;
1957
1958       while (seq == null)
1959       {
1960         if (orderedSeqs.containsKey(index))
1961         {
1962           seq = orderedSeqs.get(index);
1963           index++;
1964           break;
1965         }
1966         else
1967         {
1968           index++;
1969         }
1970       }
1971
1972       // FIND START RES
1973       // Returns residue following index if gap
1974       startRes = seq.findPosition(sg.getStartRes());
1975
1976       // FIND END RES
1977       // Need to find the residue preceeding index if gap
1978       endRes = 0;
1979
1980       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1981       {
1982         ch = seq.getCharAt(j);
1983         if (!jalview.util.Comparison.isGap((ch)))
1984         {
1985           endRes++;
1986         }
1987       }
1988
1989       if (endRes > 0)
1990       {
1991         endRes += seq.getStart() - 1;
1992       }
1993
1994       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1995               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1996                       sg.getEndRes() + 1)
1997               + "\n");
1998     }
1999
2000   }
2001
2002   protected void pasteNew_actionPerformed()
2003   {
2004     paste(true);
2005   }
2006
2007   protected void pasteThis_actionPerformed()
2008   {
2009     paste(false);
2010   }
2011
2012   void paste(boolean newAlignment)
2013   {
2014     try
2015     {
2016       if (copiedSequences == null)
2017       {
2018         return;
2019       }
2020
2021       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2022               "\t");
2023       Vector seqs = new Vector();
2024       while (st.hasMoreElements())
2025       {
2026         String name = st.nextToken();
2027         int start = Integer.parseInt(st.nextToken());
2028         int end = Integer.parseInt(st.nextToken());
2029         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2030       }
2031       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2032       for (int i = 0; i < seqs.size(); i++)
2033       {
2034         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2035       }
2036
2037       if (newAlignment)
2038       {
2039         String newtitle = MessageManager
2040                 .getString("label.copied_sequences");
2041         if (getTitle().startsWith(
2042                 MessageManager.getString("label.copied_sequences")))
2043         {
2044           newtitle = getTitle();
2045         }
2046         else
2047         {
2048           newtitle = newtitle.concat(MessageManager
2049                   .formatMessage("label.from_msname", new String[]
2050                   { getTitle() }));
2051         }
2052         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2053                 viewport.applet, newtitle, false);
2054         af.viewport.setHiddenColumns(copiedHiddenColumns);
2055
2056         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2057                 frameHeight);
2058       }
2059       else
2060       {
2061         addSequences(newSeqs);
2062       }
2063
2064     } catch (Exception ex)
2065     {
2066     } // could be anything being pasted in here
2067
2068   }
2069
2070   void addSequences(SequenceI[] seqs)
2071   {
2072     for (int i = 0; i < seqs.length; i++)
2073     {
2074       viewport.getAlignment().addSequence(seqs[i]);
2075     }
2076
2077     // !newAlignment
2078     addHistoryItem(new EditCommand(
2079             MessageManager.getString("label.add_sequences"), Action.PASTE,
2080             seqs, 0, viewport.getAlignment().getWidth(),
2081             viewport.getAlignment()));
2082
2083     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2084                                                                              // 2019.04.18
2085     viewport.getAlignment().getWidth();
2086     viewport.firePropertyChange("alignment", null,
2087             viewport.getAlignment().getSequences());
2088
2089   }
2090
2091   protected void cut_actionPerformed()
2092   {
2093     copy_actionPerformed();
2094     delete_actionPerformed();
2095   }
2096
2097   protected void delete_actionPerformed()
2098   {
2099
2100     SequenceGroup sg = viewport.getSelectionGroup();
2101     if (sg == null)
2102     {
2103       return;
2104     }
2105
2106     Vector seqs = new Vector();
2107     SequenceI seq;
2108     for (int i = 0; i < sg.getSize(); i++)
2109     {
2110       seq = sg.getSequenceAt(i);
2111       seqs.addElement(seq);
2112     }
2113
2114     /*
2115      * If the cut affects all sequences, warn, remove highlighted columns
2116      */
2117     if (sg.getSize() == viewport.getAlignment().getHeight())
2118     {
2119       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2120               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2121       if (isEntireAlignWidth)
2122       {
2123         String title = MessageManager.getString("label.delete_all");
2124         Panel infoPanel = new Panel();
2125         infoPanel.setLayout(new FlowLayout());
2126         infoPanel.add(
2127                 new Label(MessageManager.getString("warn.delete_all")));
2128
2129         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2130         dialog.setMainPanel(infoPanel);
2131         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2132         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2133         dialog.setVisible(true);
2134
2135         if (!dialog.accept)
2136         {
2137           return;
2138         }
2139       }
2140       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2141               sg.getEndRes() + 1);
2142     }
2143
2144     SequenceI[] cut = new SequenceI[seqs.size()];
2145     for (int i = 0; i < seqs.size(); i++)
2146     {
2147       cut[i] = (SequenceI) seqs.elementAt(i);
2148     }
2149
2150     /*
2151      * //ADD HISTORY ITEM
2152      */
2153     addHistoryItem(new EditCommand(
2154             MessageManager.getString("label.cut_sequences"), Action.CUT,
2155             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2156             viewport.getAlignment()));
2157
2158     viewport.setSelectionGroup(null);
2159     viewport.getAlignment().deleteGroup(sg);
2160
2161     viewport.firePropertyChange("alignment", null,
2162             viewport.getAlignment().getSequences());
2163
2164     if (viewport.getAlignment().getHeight() < 1)
2165     {
2166       this.setVisible(false);
2167     }
2168     viewport.sendSelection();
2169   }
2170
2171   /**
2172    * group consensus toggled
2173    *
2174    */
2175   protected void showGroupConsensus_actionPerformed()
2176   {
2177     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2178     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179
2180   }
2181
2182   /**
2183    * group conservation toggled.
2184    */
2185   protected void showGroupConservation_actionPerformed()
2186   {
2187     viewport.setShowGroupConservation(showGroupConservation.getState());
2188     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189   }
2190
2191   /*
2192    * (non-Javadoc)
2193    *
2194    * @see
2195    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2196    * .event.ActionEvent)
2197    */
2198   protected void showConsensusHistogram_actionPerformed()
2199   {
2200     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2201     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2202   }
2203
2204   /*
2205    * (non-Javadoc)
2206    *
2207    * @see
2208    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2209    * .event.ActionEvent)
2210    */
2211   protected void showSequenceLogo_actionPerformed()
2212   {
2213     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2214     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2215   }
2216
2217   protected void normSequenceLogo_actionPerformed()
2218   {
2219     showSequenceLogo.setState(true);
2220     viewport.setShowSequenceLogo(true);
2221     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2222     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223   }
2224
2225   protected void applyAutoAnnotationSettings_actionPerformed()
2226   {
2227     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2228   }
2229
2230   protected void makeGrpsFromSelection_actionPerformed()
2231   {
2232     if (avc.makeGroupsFromSelection())
2233     {
2234       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2235       alignPanel.updateAnnotation();
2236       alignPanel.paintAlignment(true, true);
2237     }
2238   }
2239
2240   protected void createGroup_actionPerformed()
2241   {
2242     avc.createGroup();
2243   }
2244
2245   protected void unGroup_actionPerformed()
2246   {
2247     if (avc.unGroup())
2248     {
2249       alignPanel.alignmentChanged();
2250     }
2251   }
2252
2253   protected void deleteGroups_actionPerformed()
2254   {
2255     if (avc.deleteGroups())
2256     {
2257       alignPanel.alignmentChanged();
2258     }
2259   }
2260
2261   public void selectAllSequenceMenuItem_actionPerformed()
2262   {
2263     SequenceGroup sg = new SequenceGroup();
2264     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2265     {
2266       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2267     }
2268     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2269     viewport.setSelectionGroup(sg);
2270     // JAL-2034 - should delegate to
2271     // alignPanel to decide if overview needs
2272     // updating.
2273     alignPanel.paintAlignment(false, false);
2274     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2275     viewport.sendSelection();
2276   }
2277
2278   public void deselectAllSequenceMenuItem_actionPerformed()
2279   {
2280     if (viewport.cursorMode)
2281     {
2282       alignPanel.seqPanel.keyboardNo1 = null;
2283       alignPanel.seqPanel.keyboardNo2 = null;
2284     }
2285     viewport.setSelectionGroup(null);
2286     viewport.getColumnSelection().clear();
2287     viewport.setSelectionGroup(null);
2288     alignPanel.idPanel.idCanvas.searchResults = null;
2289     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2290     // JAL-2034 - should delegate to
2291     // alignPanel to decide if overview needs
2292     // updating.
2293     alignPanel.paintAlignment(false, false);
2294     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2295     viewport.sendSelection();
2296   }
2297
2298   public void invertSequenceMenuItem_actionPerformed()
2299   {
2300     SequenceGroup sg = viewport.getSelectionGroup();
2301     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2302     {
2303       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2304     }
2305
2306     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2307     viewport.sendSelection();
2308   }
2309
2310   public void invertColSel_actionPerformed()
2311   {
2312     viewport.invertColumnSelection();
2313     alignPanel.paintAlignment(true, false);
2314     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2315     viewport.sendSelection();
2316   }
2317
2318   void trimAlignment(boolean trimLeft)
2319   {
2320     AlignmentI al = viewport.getAlignment();
2321     ViewportRanges ranges = viewport.getRanges();
2322     ColumnSelection colSel = viewport.getColumnSelection();
2323     int column;
2324
2325     if (!colSel.isEmpty())
2326     {
2327       if (trimLeft)
2328       {
2329         column = colSel.getMin();
2330       }
2331       else
2332       {
2333         column = colSel.getMax();
2334       }
2335
2336       SequenceI[] seqs;
2337       if (viewport.getSelectionGroup() != null)
2338       {
2339         seqs = viewport.getSelectionGroup()
2340                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2341       }
2342       else
2343       {
2344         seqs = al.getSequencesArray();
2345       }
2346
2347       TrimRegionCommand trimRegion;
2348       if (trimLeft)
2349       {
2350         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2351                 column, al);
2352         ranges.setStartRes(0);
2353       }
2354       else
2355       {
2356         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2357                 column, al);
2358       }
2359
2360       setStatus(MessageManager.formatMessage("label.removed_columns",
2361               new String[]
2362               { Integer.valueOf(trimRegion.getSize()).toString() }));
2363       addHistoryItem(trimRegion);
2364
2365       for (SequenceGroup sg : al.getGroups())
2366       {
2367         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2368                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2369         {
2370           al.deleteGroup(sg);
2371         }
2372       }
2373
2374       viewport.firePropertyChange("alignment", null, al.getSequences());
2375     }
2376   }
2377
2378   public void removeGappedColumnMenuItem_actionPerformed()
2379   {
2380     AlignmentI al = viewport.getAlignment();
2381     ViewportRanges ranges = viewport.getRanges();
2382     int start = 0;
2383     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2384
2385     SequenceI[] seqs;
2386     if (viewport.getSelectionGroup() != null)
2387     {
2388       seqs = viewport.getSelectionGroup()
2389               .getSequencesAsArray(viewport.getHiddenRepSequences());
2390       start = viewport.getSelectionGroup().getStartRes();
2391       end = viewport.getSelectionGroup().getEndRes();
2392     }
2393     else
2394     {
2395       seqs = viewport.getAlignment().getSequencesArray();
2396     }
2397
2398     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2399             "Remove Gapped Columns", seqs, start, end,
2400             viewport.getAlignment());
2401
2402     addHistoryItem(removeGapCols);
2403
2404     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2405             new String[]
2406             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2407
2408     // This is to maintain viewport position on first residue
2409     // of first sequence
2410     SequenceI seq = al.getSequenceAt(0);
2411     int startRes = seq.findPosition(ranges.getStartRes());
2412     // ShiftList shifts;
2413     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2414     // edit.alColumnChanges=shifts.getInverse();
2415     // if (viewport.hasHiddenColumns)
2416     // viewport.getColumnSelection().compensateForEdits(shifts);
2417     ranges.setStartRes(seq.findIndex(startRes) - 1);
2418     viewport.firePropertyChange("alignment", null, al.getSequences());
2419
2420   }
2421
2422   public void removeAllGapsMenuItem_actionPerformed()
2423   {
2424     AlignmentI al = viewport.getAlignment();
2425     ViewportRanges ranges = viewport.getRanges();
2426     int start = 0;
2427     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2428
2429     SequenceI[] seqs;
2430     if (viewport.getSelectionGroup() != null)
2431     {
2432       seqs = viewport.getSelectionGroup()
2433               .getSequencesAsArray(viewport.getHiddenRepSequences());
2434       start = viewport.getSelectionGroup().getStartRes();
2435       end = viewport.getSelectionGroup().getEndRes();
2436     }
2437     else
2438     {
2439       seqs = viewport.getAlignment().getSequencesArray();
2440     }
2441
2442     // This is to maintain viewport position on first residue
2443     // of first sequence
2444     SequenceI seq = al.getSequenceAt(0);
2445     int startRes = seq.findPosition(ranges.getStartRes());
2446
2447     addHistoryItem(
2448             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2449
2450     ranges.setStartRes(seq.findIndex(startRes) - 1);
2451
2452     viewport.firePropertyChange("alignment", null, al.getSequences());
2453
2454   }
2455
2456   public void findMenuItem_actionPerformed()
2457   {
2458     new Finder(alignPanel);
2459   }
2460
2461   /**
2462    * create a new view derived from the current view
2463    *
2464    * @param viewtitle
2465    * @return frame for the new view
2466    */
2467   public AlignFrame newView(String viewtitle)
2468   {
2469     AlignmentI newal;
2470     if (viewport.hasHiddenRows())
2471     {
2472       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2473               .getFullAlignment().getSequencesArray());
2474     }
2475     else
2476     {
2477       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2478     }
2479
2480     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2481     {
2482       for (int i = 0; i < viewport.getAlignment()
2483               .getAlignmentAnnotation().length; i++)
2484       {
2485         if (!viewport.getAlignment()
2486                 .getAlignmentAnnotation()[i].autoCalculated)
2487         {
2488           newal.addAnnotation(
2489                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2490         }
2491       }
2492     }
2493
2494     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2495
2496     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2497     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2498     PaintRefresher.Register(newaf.alignPanel,
2499             newaf.alignPanel.av.getSequenceSetId());
2500
2501     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2502             newaf.alignPanel.av.getSequenceSetId());
2503     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2504             newaf.alignPanel.av.getSequenceSetId());
2505
2506     Vector comps = PaintRefresher.components
2507             .get(viewport.getSequenceSetId());
2508     int viewSize = -1;
2509     for (int i = 0; i < comps.size(); i++)
2510     {
2511       if (comps.elementAt(i) instanceof AlignmentPanel)
2512       {
2513         viewSize++;
2514       }
2515     }
2516
2517     String title = new String(this.getTitle());
2518     if (viewtitle != null)
2519     {
2520       title = viewtitle + " ( " + title + ")";
2521     }
2522     else
2523     {
2524       if (title.indexOf("(View") > -1)
2525       {
2526         title = title.substring(0, title.indexOf("(View"));
2527       }
2528       title += "(View " + viewSize + ")";
2529     }
2530
2531     newaf.setTitle(title.toString());
2532
2533     newaf.viewport.setHistoryList(viewport.getHistoryList());
2534     newaf.viewport.setRedoList(viewport.getRedoList());
2535     return newaf;
2536   }
2537
2538   /**
2539    *
2540    * @return list of feature groups on the view
2541    */
2542   public String[] getFeatureGroups()
2543   {
2544     FeatureRenderer fr = null;
2545     if (alignPanel != null
2546             && (fr = alignPanel.getFeatureRenderer()) != null)
2547     {
2548       List<String> gps = fr.getFeatureGroups();
2549       String[] _gps = gps.toArray(new String[gps.size()]);
2550       return _gps;
2551     }
2552     return null;
2553   }
2554
2555   /**
2556    * get sequence feature groups that are hidden or shown
2557    *
2558    * @param visible
2559    *          true is visible
2560    * @return list
2561    */
2562   public String[] getFeatureGroupsOfState(boolean visible)
2563   {
2564     FeatureRenderer fr = null;
2565     if (alignPanel != null
2566             && (fr = alignPanel.getFeatureRenderer()) != null)
2567     {
2568       List<String> gps = fr.getGroups(visible);
2569       String[] _gps = gps.toArray(new String[gps.size()]);
2570       return _gps;
2571     }
2572     return null;
2573   }
2574
2575   /**
2576    * Change the display state for the given feature groups
2577    *
2578    * @param groups
2579    *          list of group strings
2580    * @param state
2581    *          visible or invisible
2582    */
2583   public void setFeatureGroupState(String[] groups, boolean state)
2584   {
2585     FeatureRenderer fr = null;
2586     this.sequenceFeatures.setState(true);
2587     viewport.setShowSequenceFeatures(true);
2588     if (alignPanel != null
2589             && (fr = alignPanel.getFeatureRenderer()) != null)
2590     {
2591
2592       fr.setGroupVisibility(Arrays.asList(groups), state);
2593       alignPanel.seqPanel.seqCanvas.repaint();
2594       if (alignPanel.overviewPanel != null)
2595       {
2596         alignPanel.overviewPanel.updateOverviewImage();
2597       }
2598     }
2599   }
2600
2601   public void seqLimits_itemStateChanged()
2602   {
2603     viewport.setShowJVSuffix(seqLimits.getState());
2604     alignPanel.fontChanged();
2605     alignPanel.paintAlignment(true, false);
2606   }
2607
2608   protected void colourTextMenuItem_actionPerformed()
2609   {
2610     viewport.setColourText(colourTextMenuItem.getState());
2611     alignPanel.paintAlignment(false, false);
2612   }
2613
2614   protected void displayNonconservedMenuItem_actionPerformed()
2615   {
2616     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2617     alignPanel.paintAlignment(false, false);
2618   }
2619
2620   protected void wrapMenuItem_actionPerformed()
2621   {
2622     viewport.setWrapAlignment(wrapMenuItem.getState());
2623     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2624     scaleAbove.setEnabled(wrapMenuItem.getState());
2625     scaleLeft.setEnabled(wrapMenuItem.getState());
2626     scaleRight.setEnabled(wrapMenuItem.getState());
2627     alignPanel.paintAlignment(true, false);
2628   }
2629
2630   public void overviewMenuItem_actionPerformed()
2631   {
2632     if (alignPanel.overviewPanel != null)
2633     {
2634       return;
2635     }
2636
2637     Frame frame = new Frame();
2638     final OverviewPanel overview = new OverviewPanel(alignPanel);
2639     frame.add(overview);
2640     // +50 must allow for applet frame window
2641     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2642             .formatMessage("label.overview_params", new String[]
2643             { this.getTitle() }), overview.getPreferredSize().width,
2644             overview.getPreferredSize().height + 50);
2645
2646     frame.pack();
2647     final AlignmentPanel ap = alignPanel;
2648     frame.addWindowListener(new WindowAdapter()
2649     {
2650       @Override
2651       public void windowClosing(WindowEvent e)
2652       {
2653         overview.dispose();
2654         if (ap != null)
2655         {
2656           ap.setOverviewPanel(null);
2657         }
2658       };
2659     });
2660
2661     alignPanel.setOverviewPanel(overview);
2662
2663   }
2664
2665   @Override
2666   public void changeColour(ColourSchemeI cs)
2667   {
2668     viewport.setGlobalColourScheme(cs);
2669
2670     alignPanel.paintAlignment(true, true);
2671   }
2672
2673   protected void modifyPID_actionPerformed()
2674   {
2675     if (viewport.getAbovePIDThreshold()
2676             && viewport.getGlobalColourScheme() != null)
2677     {
2678       SliderPanel.setPIDSliderSource(alignPanel,
2679               viewport.getResidueShading(), alignPanel.getViewName());
2680       SliderPanel.showPIDSlider();
2681     }
2682   }
2683
2684   protected void modifyConservation_actionPerformed()
2685   {
2686     if (viewport.getConservationSelected()
2687             && viewport.getGlobalColourScheme() != null)
2688     {
2689       SliderPanel.setConservationSlider(alignPanel,
2690               viewport.getResidueShading(), alignPanel.getViewName());
2691       SliderPanel.showConservationSlider();
2692     }
2693   }
2694
2695   protected void conservationMenuItem_actionPerformed()
2696   {
2697     boolean selected = conservationMenuItem.getState();
2698     modifyConservation.setEnabled(selected);
2699     viewport.setConservationSelected(selected);
2700     viewport.getResidueShading().setConservationApplied(selected);
2701
2702     changeColour(viewport.getGlobalColourScheme());
2703
2704     if (selected)
2705     {
2706       modifyConservation_actionPerformed();
2707     }
2708     else
2709     {
2710       SliderPanel.hideConservationSlider();
2711     }
2712   }
2713
2714   public void abovePIDThreshold_actionPerformed()
2715   {
2716     boolean selected = abovePIDThreshold.getState();
2717     modifyPID.setEnabled(selected);
2718     viewport.setAbovePIDThreshold(selected);
2719     if (!selected)
2720     {
2721       viewport.getResidueShading().setThreshold(0,
2722               viewport.isIgnoreGapsConsensus());
2723     }
2724
2725     changeColour(viewport.getGlobalColourScheme());
2726
2727     if (selected)
2728     {
2729       modifyPID_actionPerformed();
2730     }
2731     else
2732     {
2733       SliderPanel.hidePIDSlider();
2734     }
2735   }
2736
2737   public void sortPairwiseMenuItem_actionPerformed()
2738   {
2739     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2740     AlignmentSorter.sortByPID(viewport.getAlignment(),
2741             viewport.getAlignment().getSequenceAt(0));
2742
2743     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2744             viewport.getAlignment()));
2745     alignPanel.paintAlignment(true, false);
2746   }
2747
2748   public void sortIDMenuItem_actionPerformed()
2749   {
2750     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2751     AlignmentSorter.sortByID(viewport.getAlignment());
2752     addHistoryItem(
2753             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2754     alignPanel.paintAlignment(true, false);
2755   }
2756
2757   public void sortLengthMenuItem_actionPerformed()
2758   {
2759     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2760     AlignmentSorter.sortByLength(viewport.getAlignment());
2761     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2762             viewport.getAlignment()));
2763     alignPanel.paintAlignment(true, false);
2764   }
2765
2766   public void sortGroupMenuItem_actionPerformed()
2767   {
2768     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2769     AlignmentSorter.sortByGroup(viewport.getAlignment());
2770     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2771             viewport.getAlignment()));
2772     alignPanel.paintAlignment(true, false);
2773
2774   }
2775
2776   public void removeRedundancyMenuItem_actionPerformed()
2777   {
2778     new RedundancyPanel(alignPanel);
2779   }
2780
2781   public void pairwiseAlignmentMenuItem_actionPerformed()
2782   {
2783     if (viewport.getSelectionGroup() != null
2784             && viewport.getSelectionGroup().getSize() > 1)
2785     {
2786       Frame frame = new Frame();
2787       frame.add(new PairwiseAlignPanel(alignPanel));
2788       jalview.bin.JalviewLite.addFrame(frame,
2789               MessageManager.getString("action.pairwise_alignment"), 600,
2790               500);
2791     }
2792   }
2793
2794   public void PCAMenuItem_actionPerformed()
2795   {
2796     // are the sequences aligned?
2797     if (!viewport.getAlignment().isAligned(false))
2798     {
2799       SequenceI current;
2800       int Width = viewport.getAlignment().getWidth();
2801
2802       for (int i = 0; i < viewport.getAlignment().getSequences()
2803               .size(); i++)
2804       {
2805         current = viewport.getAlignment().getSequenceAt(i);
2806
2807         if (current.getLength() < Width)
2808         {
2809           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2810         }
2811       }
2812       alignPanel.paintAlignment(false, false);
2813     }
2814
2815     if ((viewport.getSelectionGroup() != null
2816             && viewport.getSelectionGroup().getSize() < 4
2817             && viewport.getSelectionGroup().getSize() > 0)
2818             || viewport.getAlignment().getHeight() < 4)
2819     {
2820       return;
2821     }
2822
2823     try
2824     {
2825       new PCAPanel(viewport);
2826     } catch (java.lang.OutOfMemoryError ex)
2827     {
2828     }
2829
2830   }
2831
2832   public void averageDistanceTreeMenuItem_actionPerformed()
2833   {
2834     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2835             "Average distance tree using PID");
2836   }
2837
2838   public void neighbourTreeMenuItem_actionPerformed()
2839   {
2840     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2841             "Neighbour joining tree using PID");
2842   }
2843
2844   protected void njTreeBlosumMenuItem_actionPerformed()
2845   {
2846     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2847             ScoreModels.getInstance().getBlosum62().getName(),
2848             "Neighbour joining tree using BLOSUM62");
2849   }
2850
2851   protected void avTreeBlosumMenuItem_actionPerformed()
2852   {
2853     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2854             ScoreModels.getInstance().getBlosum62().getName(),
2855             "Average distance tree using BLOSUM62");
2856   }
2857
2858   void newTreePanel(String type, String pwType, String title)
2859   {
2860     // are the sequences aligned?
2861     if (!viewport.getAlignment().isAligned(false))
2862     {
2863       SequenceI current;
2864       int Width = viewport.getAlignment().getWidth();
2865
2866       for (int i = 0; i < viewport.getAlignment().getSequences()
2867               .size(); i++)
2868       {
2869         current = viewport.getAlignment().getSequenceAt(i);
2870
2871         if (current.getLength() < Width)
2872         {
2873           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2874         }
2875       }
2876       alignPanel.paintAlignment(false, false);
2877
2878     }
2879
2880     if ((viewport.getSelectionGroup() != null
2881             && viewport.getSelectionGroup().getSize() > 1)
2882             || (viewport.getAlignment().getHeight() > 1))
2883     {
2884       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2885
2886       addTreeMenuItem(tp, title);
2887
2888       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2889     }
2890   }
2891
2892   void loadTree_actionPerformed()
2893   {
2894     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2895     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2896     cap.setTreeImport();
2897     Frame frame = new Frame();
2898     frame.add(cap);
2899     jalview.bin.JalviewLite.addFrame(frame,
2900             MessageManager.getString("label.paste_newick_file"), 400, 300);
2901   }
2902
2903   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2904   {
2905     TreePanel tp = new TreePanel(alignPanel, treeFile,
2906             MessageManager.getString("label.load_tree_from_file"), tree);
2907     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2908     addTreeMenuItem(tp, treeFile);
2909   }
2910
2911   /**
2912    * sort the alignment using the given treePanel
2913    *
2914    * @param treePanel
2915    *          tree used to sort view
2916    * @param title
2917    *          string used for undo event name
2918    */
2919   public void sortByTree(TreePanel treePanel, String title)
2920   {
2921     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2922     AlignmentSorter.sortByTree(viewport.getAlignment(),
2923             treePanel.getTree());
2924     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2925     // HistoryItem.SORT));
2926     addHistoryItem(new OrderCommand(MessageManager
2927             .formatMessage("label.order_by_params", new String[]
2928             { title }), oldOrder, viewport.getAlignment()));
2929     alignPanel.paintAlignment(true, false);
2930   }
2931
2932   /**
2933    * Do any automatic reordering of the alignment and add the necessary bits to
2934    * the menu structure for the new tree
2935    *
2936    * @param treePanel
2937    * @param title
2938    */
2939   protected void addTreeMenuItem(final TreePanel treePanel,
2940           final String title)
2941   {
2942     final MenuItem item = new MenuItem(title);
2943     sortByTreeMenu.add(item);
2944     item.addActionListener(new java.awt.event.ActionListener()
2945     {
2946       @Override
2947       public void actionPerformed(ActionEvent evt)
2948       {
2949         sortByTree(treePanel, title); // treePanel.getTitle());
2950       }
2951     });
2952
2953     treePanel.addWindowListener(new WindowAdapter()
2954     {
2955       @Override
2956       public void windowOpened(WindowEvent e)
2957       {
2958         if (viewport.sortByTree)
2959         {
2960           sortByTree(treePanel, title);
2961         }
2962         super.windowOpened(e);
2963       }
2964
2965       @Override
2966       public void windowClosing(WindowEvent e)
2967       {
2968         sortByTreeMenu.remove(item);
2969       };
2970     });
2971   }
2972
2973   public boolean sortBy(AlignmentOrder alorder, String undoname)
2974   {
2975     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2976     if (viewport.applet.debug)
2977     {
2978       System.err.println("Sorting " + alorder.getOrder().size()
2979               + " in alignment '" + getTitle() + "'");
2980     }
2981     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2982     if (undoname != null)
2983     {
2984       addHistoryItem(new OrderCommand(undoname, oldOrder,
2985               viewport.getAlignment()));
2986     }
2987     alignPanel.paintAlignment(true, false);
2988     return true;
2989   }
2990
2991   protected void documentation_actionPerformed()
2992   {
2993     alignPanel.av.applet.openJalviewHelpUrl();
2994   }
2995
2996   protected void about_actionPerformed()
2997   {
2998
2999     class AboutPanel extends Canvas
3000     {
3001       String version;
3002
3003       String builddate;
3004
3005       public AboutPanel(String version, String builddate)
3006       {
3007         this.version = version;
3008         this.builddate = builddate;
3009       }
3010
3011       @Override
3012       public void paint(Graphics g)
3013       {
3014         g.setColor(Color.white);
3015         g.fillRect(0, 0, getSize().width, getSize().height);
3016         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3017         FontMetrics fm = g.getFontMetrics();
3018         int fh = fm.getHeight();
3019         int y = 5, x = 7;
3020         g.setColor(Color.black);
3021         // TODO: update this text for each release or centrally store it for
3022         // lite and application
3023         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3024         g.drawString(MessageManager
3025                 .formatMessage("label.jalviewLite_release", new String[]
3026                 { version }), x, y += fh);
3027         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3028         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3029                 new String[]
3030                 { builddate }), x, y += fh);
3031         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3032         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3033                 y += fh * 1.5);
3034         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3035                 x + 50, y += fh + 8);
3036         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3037                 x, y += fh);
3038         g.drawString(MessageManager
3039                 .getString("label.jalview_distribution_lists"), x, y += fh);
3040         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3041                 x, y += fh + 8);
3042         g.drawString(
3043                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3044                 y += fh);
3045         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3046                 x, y += fh);
3047         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3048                 x, y += fh);
3049       }
3050     }
3051
3052     Frame frame = new Frame();
3053     frame.add(new AboutPanel(JalviewLite.getVersion(),
3054             JalviewLite.getBuildDate()));
3055     jalview.bin.JalviewLite.addFrame(frame,
3056             MessageManager.getString("label.jalview"), 580, 220);
3057
3058   }
3059
3060   public void showURL(String url, String target)
3061   {
3062     if (viewport.applet == null)
3063     {
3064       System.out.println("Not running as applet - no browser available.");
3065     }
3066     else
3067     {
3068       viewport.applet.showURL(url, target);
3069     }
3070   }
3071
3072   // ////////////////////////////////////////////////////////////////////////////////
3073   // JBuilder Graphics here
3074
3075   MenuBar alignFrameMenuBar = new MenuBar();
3076
3077   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3078
3079   MenuItem loadApplication = new MenuItem(
3080           MessageManager.getString("label.view_full_application"));
3081
3082   MenuItem loadTree = new MenuItem(
3083           MessageManager.getString("label.load_associated_tree"));
3084
3085   MenuItem loadAnnotations = new MenuItem(
3086           MessageManager.getString("label.load_features_annotations"));
3087
3088   MenuItem outputFeatures = new MenuItem(
3089           MessageManager.getString("label.export_features"));
3090
3091   MenuItem outputAnnotations = new MenuItem(
3092           MessageManager.getString("label.export_annotations"));
3093
3094   MenuItem closeMenuItem = new MenuItem(
3095           MessageManager.getString("action.close"));
3096
3097   MenuItem selectAllSequenceMenuItem = new MenuItem(
3098           MessageManager.getString("action.select_all"));
3099
3100   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3101           MessageManager.getString("action.deselect_all"));
3102
3103   MenuItem invertSequenceMenuItem = new MenuItem(
3104           MessageManager.getString("action.invert_selection"));
3105
3106   MenuItem remove2LeftMenuItem = new MenuItem();
3107
3108   MenuItem remove2RightMenuItem = new MenuItem();
3109
3110   MenuItem removeGappedColumnMenuItem = new MenuItem();
3111
3112   MenuItem removeAllGapsMenuItem = new MenuItem();
3113
3114   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3115
3116   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3117
3118   MenuItem sortPairwiseMenuItem = new MenuItem();
3119
3120   MenuItem sortIDMenuItem = new MenuItem();
3121
3122   MenuItem sortLengthMenuItem = new MenuItem();
3123
3124   MenuItem sortGroupMenuItem = new MenuItem();
3125
3126   MenuItem removeRedundancyMenuItem = new MenuItem();
3127
3128   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3129
3130   MenuItem PCAMenuItem = new MenuItem();
3131
3132   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3133
3134   MenuItem neighbourTreeMenuItem = new MenuItem();
3135
3136   BorderLayout borderLayout1 = new BorderLayout();
3137
3138   public Label statusBar = new Label();
3139
3140   MenuItem clustalColour = new MenuItem();
3141
3142   MenuItem zappoColour = new MenuItem();
3143
3144   MenuItem taylorColour = new MenuItem();
3145
3146   MenuItem hydrophobicityColour = new MenuItem();
3147
3148   MenuItem helixColour = new MenuItem();
3149
3150   MenuItem strandColour = new MenuItem();
3151
3152   MenuItem turnColour = new MenuItem();
3153
3154   MenuItem buriedColour = new MenuItem();
3155
3156   MenuItem purinePyrimidineColour = new MenuItem();
3157
3158   // MenuItem RNAInteractionColour = new MenuItem();
3159
3160   MenuItem RNAHelixColour = new MenuItem();
3161
3162   MenuItem userDefinedColour = new MenuItem();
3163
3164   MenuItem PIDColour = new MenuItem();
3165
3166   MenuItem BLOSUM62Colour = new MenuItem();
3167
3168   MenuItem tcoffeeColour = new MenuItem();
3169
3170   MenuItem njTreeBlosumMenuItem = new MenuItem();
3171
3172   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3173
3174   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3175
3176   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3177
3178   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3179
3180   MenuItem alProperties = new MenuItem(
3181           MessageManager.getString("label.alignment_props"));
3182
3183   MenuItem overviewMenuItem = new MenuItem();
3184
3185   MenuItem undoMenuItem = new MenuItem();
3186
3187   MenuItem redoMenuItem = new MenuItem();
3188
3189   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3190
3191   MenuItem noColourmenuItem = new MenuItem();
3192
3193   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3194
3195   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3196
3197   MenuItem findMenuItem = new MenuItem();
3198
3199   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3200
3201   MenuItem nucleotideColour = new MenuItem();
3202
3203   MenuItem deleteGroups = new MenuItem();
3204
3205   MenuItem grpsFromSelection = new MenuItem();
3206
3207   MenuItem createGroup = new MenuItem();
3208
3209   MenuItem unGroup = new MenuItem();
3210
3211   MenuItem delete = new MenuItem();
3212
3213   MenuItem copy = new MenuItem();
3214
3215   MenuItem cut = new MenuItem();
3216
3217   Menu pasteMenu = new Menu();
3218
3219   MenuItem pasteNew = new MenuItem();
3220
3221   MenuItem pasteThis = new MenuItem();
3222
3223   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3224
3225   MenuItem font = new MenuItem();
3226
3227   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3228
3229   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3230
3231   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3232
3233   MenuItem modifyPID = new MenuItem();
3234
3235   MenuItem modifyConservation = new MenuItem();
3236
3237   CheckboxMenuItem autoCalculate = null;
3238
3239   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3240           "Sort Alignment With New Tree", true);
3241
3242   Menu sortByTreeMenu = new Menu();
3243
3244   MenuItem inputText = new MenuItem();
3245
3246   MenuItem documentation = new MenuItem();
3247
3248   MenuItem about = new MenuItem();
3249
3250   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3257
3258   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3259
3260   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3261
3262   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3263
3264   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3265
3266   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3267
3268   /**
3269    * Initialise menus and other items
3270    *
3271    * @throws Exception
3272    */
3273   private void jbInit() throws Exception
3274   {
3275     setMenuBar(alignFrameMenuBar);
3276
3277     /*
3278      * Configure File menu items and actions
3279      */
3280     inputText
3281             .setLabel(MessageManager.getString("label.input_from_textbox"));
3282     inputText.addActionListener(this);
3283     Menu outputTextboxMenu = new Menu(
3284             MessageManager.getString("label.out_to_textbox"));
3285     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3286     {
3287       MenuItem item = new MenuItem(ff);
3288
3289       item.addActionListener(new java.awt.event.ActionListener()
3290       {
3291         @Override
3292         public void actionPerformed(ActionEvent e)
3293         {
3294           outputText_actionPerformed(e);
3295         }
3296       });
3297
3298       outputTextboxMenu.add(item);
3299     }
3300     closeMenuItem.addActionListener(this);
3301     loadApplication.addActionListener(this);
3302     loadTree.addActionListener(this);
3303     loadAnnotations.addActionListener(this);
3304     outputFeatures.addActionListener(this);
3305     outputAnnotations.addActionListener(this);
3306
3307     /*
3308      * Configure Edit menu items and actions
3309      */
3310     undoMenuItem.setEnabled(false);
3311     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3312     undoMenuItem.addActionListener(this);
3313     redoMenuItem.setEnabled(false);
3314     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3315     redoMenuItem.addActionListener(this);
3316     copy.setLabel(MessageManager.getString("action.copy"));
3317     copy.addActionListener(this);
3318     cut.setLabel(MessageManager.getString("action.cut"));
3319     cut.addActionListener(this);
3320     delete.setLabel(MessageManager.getString("action.delete"));
3321     delete.addActionListener(this);
3322     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3323     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3324     pasteNew.addActionListener(this);
3325     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3326     pasteThis.addActionListener(this);
3327     remove2LeftMenuItem
3328             .setLabel(MessageManager.getString("action.remove_left"));
3329     remove2LeftMenuItem.addActionListener(this);
3330     remove2RightMenuItem
3331             .setLabel(MessageManager.getString("action.remove_right"));
3332     remove2RightMenuItem.addActionListener(this);
3333     removeGappedColumnMenuItem.setLabel(
3334             MessageManager.getString("action.remove_empty_columns"));
3335     removeGappedColumnMenuItem.addActionListener(this);
3336     removeAllGapsMenuItem
3337             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3338     removeAllGapsMenuItem.addActionListener(this);
3339     removeRedundancyMenuItem
3340             .setLabel(MessageManager.getString("action.remove_redundancy"));
3341     removeRedundancyMenuItem.addActionListener(this);
3342
3343     /*
3344      * Configure Select menu items and actions
3345      */
3346     findMenuItem.setLabel(MessageManager.getString("action.find"));
3347     findMenuItem.addActionListener(this);
3348     selectAllSequenceMenuItem.addActionListener(this);
3349     deselectAllSequenceMenuItem.addActionListener(this);
3350     invertSequenceMenuItem.setLabel(
3351             MessageManager.getString("action.invert_sequence_selection"));
3352     invertSequenceMenuItem.addActionListener(this);
3353     invertColSel.setLabel(
3354             MessageManager.getString("action.invert_column_selection"));
3355     invertColSel.addActionListener(this);
3356     deleteGroups
3357             .setLabel(MessageManager.getString("action.undefine_groups"));
3358     deleteGroups.addActionListener(this);
3359     grpsFromSelection.setLabel(
3360             MessageManager.getString("action.make_groups_selection"));
3361     grpsFromSelection.addActionListener(this);
3362     createGroup.setLabel(MessageManager.getString("action.create_group"));
3363     createGroup.addActionListener(this);
3364     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3365     unGroup.addActionListener(this);
3366
3367     annotationColumnSelection.setLabel(
3368             MessageManager.getString("action.select_by_annotation"));
3369     annotationColumnSelection.addActionListener(this);
3370
3371     /*
3372      * Configure View menu items and actions
3373      */
3374     newView.setLabel(MessageManager.getString("action.new_view"));
3375     newView.addActionListener(this);
3376     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3377     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3378     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3379     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3380     hideColumns
3381             .setLabel(MessageManager.getString("label.selected_columns"));
3382     hideSequences
3383             .setLabel(MessageManager.getString("label.selected_sequences"));
3384     hideAllButSelection.setLabel(
3385             MessageManager.getString("label.all_but_selected_region"));
3386     hideAllSelection
3387             .setLabel(MessageManager.getString("label.selected_region"));
3388     showAllHidden.setLabel(
3389             MessageManager.getString("label.all_sequences_columns"));
3390     showColumns.addActionListener(this);
3391     showSeqs.addActionListener(this);
3392     hideColumns.addActionListener(this);
3393     hideSequences.addActionListener(this);
3394     hideAllButSelection.addActionListener(this);
3395     hideAllSelection.addActionListener(this);
3396     showAllHidden.addActionListener(this);
3397     featureSettings
3398             .setLabel(MessageManager.getString("action.feature_settings"));
3399     featureSettings.addActionListener(this);
3400     sequenceFeatures.setLabel(
3401             MessageManager.getString("label.show_sequence_features"));
3402     sequenceFeatures.addItemListener(this);
3403     sequenceFeatures.setState(false);
3404     followMouseOverFlag.setLabel(
3405             MessageManager.getString("label.automatic_scrolling"));
3406     followMouseOverFlag.addItemListener(this);
3407     alProperties.addActionListener(this);
3408     overviewMenuItem
3409             .setLabel(MessageManager.getString("label.overview_window"));
3410     overviewMenuItem.addActionListener(this);
3411
3412     /*
3413      * Configure Annotations menu items and actions
3414      */
3415     annotationPanelMenuItem
3416             .setLabel(MessageManager.getString("label.show_annotations"));
3417     annotationPanelMenuItem.addItemListener(this);
3418     showGroupConsensus
3419             .setLabel(MessageManager.getString("label.group_consensus"));
3420     showGroupConservation
3421             .setLabel(MessageManager.getString("label.group_conservation"));
3422     showConsensusHistogram.setLabel(
3423             MessageManager.getString("label.show_consensus_histogram"));
3424     showSequenceLogo.setLabel(
3425             MessageManager.getString("label.show_consensus_logo"));
3426     normSequenceLogo.setLabel(
3427             MessageManager.getString("label.norm_consensus_logo"));
3428     applyAutoAnnotationSettings
3429             .setLabel(MessageManager.getString("label.apply_all_groups"));
3430     applyAutoAnnotationSettings.setState(true);
3431     Menu autoAnnMenu = new Menu(
3432             MessageManager.getString("label.autocalculated_annotation"));
3433     showGroupConsensus.addItemListener(this);
3434     showGroupConservation.addItemListener(this);
3435     showConsensusHistogram.addItemListener(this);
3436     showSequenceLogo.addItemListener(this);
3437     normSequenceLogo.addItemListener(this);
3438     applyAutoAnnotationSettings.addItemListener(this);
3439     showAlignmentAnnotations = new CheckboxMenuItem(
3440             MessageManager.getString("label.show_all_al_annotations"));
3441     showSequenceAnnotations = new CheckboxMenuItem(
3442             MessageManager.getString("label.show_all_seq_annotations"));
3443     sortAnnBySequence = new CheckboxMenuItem(
3444             MessageManager.getString("label.sort_annotations_by_sequence"));
3445     sortAnnByLabel = new CheckboxMenuItem(
3446             MessageManager.getString("label.sort_annotations_by_label"));
3447     showAutoFirst = new CheckboxMenuItem(
3448             MessageManager.getString("label.show_first"));
3449     showAutoFirst.setState(false); // pending applet parameter
3450     setShowAutoCalculatedAbove(showAutoFirst.getState());
3451     showAutoLast = new CheckboxMenuItem(
3452             MessageManager.getString("label.show_last"));
3453     showAutoLast.setState(!showAutoFirst.getState());
3454     showAlignmentAnnotations.addItemListener(this);
3455     showSequenceAnnotations.addItemListener(this);
3456     sortAnnBySequence.addItemListener(this);
3457     sortAnnByLabel.addItemListener(this);
3458     showAutoFirst.addItemListener(this);
3459     showAutoLast.addItemListener(this);
3460
3461     /*
3462      * Configure Format menu items and actions
3463      */
3464     font.setLabel(MessageManager.getString("action.font"));
3465     font.addActionListener(this);
3466     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3467     scaleAbove.setState(true);
3468     scaleAbove.setEnabled(false);
3469     scaleAbove.addItemListener(this);
3470     scaleLeft.setEnabled(false);
3471     scaleLeft.setState(true);
3472     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3473     scaleLeft.addItemListener(this);
3474     scaleRight.setEnabled(false);
3475     scaleRight.setState(true);
3476     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3477     scaleRight.addItemListener(this);
3478     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3479     viewBoxesMenuItem.setState(true);
3480     viewBoxesMenuItem.addItemListener(this);
3481     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3482     viewTextMenuItem.setState(true);
3483     viewTextMenuItem.addItemListener(this);
3484     colourTextMenuItem
3485             .setLabel(MessageManager.getString("label.colour_text"));
3486     colourTextMenuItem.addItemListener(this);
3487     displayNonconservedMenuItem
3488             .setLabel(MessageManager.getString("label.show_non_conserved"));
3489     displayNonconservedMenuItem.addItemListener(this);
3490     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3491     wrapMenuItem.addItemListener(this);
3492     renderGapsMenuItem
3493             .setLabel(MessageManager.getString("action.show_gaps"));
3494     renderGapsMenuItem.setState(true);
3495     renderGapsMenuItem.addItemListener(this);
3496     centreColumnLabelFlag.setLabel(
3497             MessageManager.getString("label.centre_column_labels"));
3498     centreColumnLabelFlag.addItemListener(this);
3499     seqLimits.setState(true);
3500     seqLimits.setLabel(
3501             MessageManager.getString("label.show_sequence_limits"));
3502     seqLimits.addItemListener(this);
3503
3504     /*
3505      * Configure Colour menu items and actions
3506      */
3507     applyToAllGroups.setLabel(
3508             MessageManager.getString("label.apply_colour_to_all_groups"));
3509     applyToAllGroups.setState(true);
3510     applyToAllGroups.addItemListener(this);
3511     clustalColour.setLabel(
3512             MessageManager.getString("label.colourScheme_clustal"));
3513     clustalColour.addActionListener(this);
3514     zappoColour
3515             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3516     zappoColour.addActionListener(this);
3517     taylorColour.setLabel(
3518             MessageManager.getString("label.colourScheme_taylor"));
3519     taylorColour.addActionListener(this);
3520     hydrophobicityColour.setLabel(
3521             MessageManager.getString("label.colourScheme_hydrophobic"));
3522     hydrophobicityColour.addActionListener(this);
3523     helixColour.setLabel(
3524             MessageManager.getString("label.colourScheme_helixpropensity"));
3525     helixColour.addActionListener(this);
3526     strandColour.setLabel(MessageManager
3527             .getString("label.colourScheme_strandpropensity"));
3528     strandColour.addActionListener(this);
3529     turnColour.setLabel(
3530             MessageManager.getString("label.colourScheme_turnpropensity"));
3531     turnColour.addActionListener(this);
3532     buriedColour.setLabel(
3533             MessageManager.getString("label.colourScheme_buriedindex"));
3534     buriedColour.addActionListener(this);
3535     purinePyrimidineColour.setLabel(MessageManager
3536             .getString("label.colourScheme_purine/pyrimidine"));
3537     purinePyrimidineColour.addActionListener(this);
3538     // RNAInteractionColour.setLabel(MessageManager
3539     // .getString("label.rna_interaction"));
3540     // RNAInteractionColour.addActionListener(this);
3541     RNAHelixColour.setLabel(
3542             MessageManager.getString("label.colourScheme_rnahelices"));
3543     RNAHelixColour.addActionListener(this);
3544     userDefinedColour
3545             .setLabel(MessageManager.getString("action.user_defined"));
3546     userDefinedColour.addActionListener(this);
3547     PIDColour.setLabel(
3548             MessageManager.getString("label.colourScheme_%identity"));
3549     PIDColour.addActionListener(this);
3550     BLOSUM62Colour.setLabel(
3551             MessageManager.getString("label.colourScheme_blosum62"));
3552     BLOSUM62Colour.addActionListener(this);
3553     tcoffeeColour.setLabel(
3554             MessageManager.getString("label.colourScheme_t-coffeescores"));
3555     // it will be enabled only if a score file is provided
3556     tcoffeeColour.setEnabled(false);
3557     tcoffeeColour.addActionListener(this);
3558     conservationMenuItem
3559             .setLabel(MessageManager.getString("action.by_conservation"));
3560     conservationMenuItem.addItemListener(this);
3561     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3562     noColourmenuItem.addActionListener(this);
3563     abovePIDThreshold.setLabel(
3564             MessageManager.getString("label.above_identity_threshold"));
3565     abovePIDThreshold.addItemListener(this);
3566     nucleotideColour.setLabel(
3567             MessageManager.getString("label.colourScheme_nucleotide"));
3568     nucleotideColour.addActionListener(this);
3569     modifyPID.setLabel(
3570             MessageManager.getString("label.modify_identity_threshold"));
3571     modifyPID.setEnabled(abovePIDThreshold.getState());
3572     modifyPID.addActionListener(this);
3573     modifyConservation.setLabel(MessageManager
3574             .getString("label.modify_conservation_threshold"));
3575     modifyConservation.setEnabled(conservationMenuItem.getState());
3576     modifyConservation.addActionListener(this);
3577     annotationColour
3578             .setLabel(MessageManager.getString("action.by_annotation"));
3579     annotationColour.addActionListener(this);
3580
3581     /*
3582      * Configure Calculate menu items and actions
3583      */
3584     sortPairwiseMenuItem
3585             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3586     sortPairwiseMenuItem.addActionListener(this);
3587     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3588     sortIDMenuItem.addActionListener(this);
3589     sortLengthMenuItem
3590             .setLabel(MessageManager.getString("action.by_length"));
3591     sortLengthMenuItem.addActionListener(this);
3592     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3593     sortGroupMenuItem.addActionListener(this);
3594     pairwiseAlignmentMenuItem.setLabel(
3595             MessageManager.getString("action.pairwise_alignment"));
3596     pairwiseAlignmentMenuItem.addActionListener(this);
3597     PCAMenuItem.setLabel(
3598             MessageManager.getString("label.principal_component_analysis"));
3599     PCAMenuItem.addActionListener(this);
3600     autoCalculate = new CheckboxMenuItem(
3601             MessageManager.getString("label.autocalculate_consensus"),
3602             true);
3603     averageDistanceTreeMenuItem.setLabel(
3604             MessageManager.getString("label.average_distance_identity"));
3605     averageDistanceTreeMenuItem.addActionListener(this);
3606     neighbourTreeMenuItem.setLabel(
3607             MessageManager.getString("label.neighbour_joining_identity"));
3608     neighbourTreeMenuItem.addActionListener(this);
3609     avDistanceTreeBlosumMenuItem.setLabel(
3610             MessageManager.getString("label.average_distance_blosum62"));
3611     avDistanceTreeBlosumMenuItem.addActionListener(this);
3612     njTreeBlosumMenuItem
3613             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3614     njTreeBlosumMenuItem.addActionListener(this);
3615     sortByTreeMenu
3616             .setLabel(MessageManager.getString("action.by_tree_order"));
3617     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3618     Menu calculateTreeMenu = new Menu(
3619             MessageManager.getString("action.calculate_tree"));
3620     autoCalculate.addItemListener(this);
3621     sortByTree.addItemListener(this);
3622
3623     /*
3624      * Configure Help menu items and actions
3625      */
3626     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3627     documentation.setLabel(MessageManager.getString("label.documentation"));
3628     documentation.addActionListener(this);
3629     about.setLabel(MessageManager.getString("label.about"));
3630     about.addActionListener(this);
3631
3632     /*
3633      * Add top level menus to frame
3634      */
3635     alignFrameMenuBar.add(fileMenu);
3636     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3637     alignFrameMenuBar.add(editMenu);
3638     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3639     alignFrameMenuBar.add(selectMenu);
3640     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3641     alignFrameMenuBar.add(viewMenu);
3642     Menu annotationsMenu = new Menu(
3643             MessageManager.getString("action.annotations"));
3644     alignFrameMenuBar.add(annotationsMenu);
3645     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3646     alignFrameMenuBar.add(formatMenu);
3647     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3648     alignFrameMenuBar.add(colourMenu);
3649     Menu calculateMenu = new Menu(
3650             MessageManager.getString("action.calculate"));
3651     alignFrameMenuBar.add(calculateMenu);
3652     alignFrameMenuBar.add(helpMenu);
3653
3654     /*
3655      * File menu
3656      */
3657     fileMenu.add(inputText);
3658     fileMenu.add(loadTree);
3659     fileMenu.add(loadAnnotations);
3660     fileMenu.addSeparator();
3661     fileMenu.add(outputTextboxMenu);
3662     fileMenu.add(outputFeatures);
3663     fileMenu.add(outputAnnotations);
3664     if (jalviewServletURL != null)
3665     {
3666       fileMenu.add(loadApplication);
3667     }
3668     fileMenu.addSeparator();
3669     fileMenu.add(closeMenuItem);
3670
3671     /*
3672      * Edit menu
3673      */
3674     editMenu.add(undoMenuItem);
3675     editMenu.add(redoMenuItem);
3676     editMenu.add(cut);
3677     editMenu.add(copy);
3678     pasteMenu.add(pasteNew);
3679     pasteMenu.add(pasteThis);
3680     editMenu.add(pasteMenu);
3681     editMenu.add(delete);
3682     editMenu.addSeparator();
3683     editMenu.add(remove2LeftMenuItem);
3684     editMenu.add(remove2RightMenuItem);
3685     editMenu.add(removeGappedColumnMenuItem);
3686     editMenu.add(removeAllGapsMenuItem);
3687     editMenu.add(removeRedundancyMenuItem);
3688
3689     /*
3690      * Select menu
3691      */
3692     selectMenu.add(findMenuItem);
3693     selectMenu.addSeparator();
3694     selectMenu.add(selectAllSequenceMenuItem);
3695     selectMenu.add(deselectAllSequenceMenuItem);
3696     selectMenu.add(invertSequenceMenuItem);
3697     selectMenu.add(invertColSel);
3698     selectMenu.add(createGroup);
3699     selectMenu.add(unGroup);
3700     selectMenu.add(grpsFromSelection);
3701     selectMenu.add(deleteGroups);
3702     selectMenu.add(annotationColumnSelection);
3703
3704     /*
3705      * View menu
3706      */
3707     viewMenu.add(newView);
3708     viewMenu.addSeparator();
3709     showMenu.add(showColumns);
3710     showMenu.add(showSeqs);
3711     showMenu.add(showAllHidden);
3712     viewMenu.add(showMenu);
3713     hideMenu.add(hideColumns);
3714     hideMenu.add(hideSequences);
3715     hideMenu.add(hideAllSelection);
3716     hideMenu.add(hideAllButSelection);
3717     viewMenu.add(hideMenu);
3718     viewMenu.addSeparator();
3719     viewMenu.add(followMouseOverFlag);
3720     viewMenu.addSeparator();
3721     viewMenu.add(sequenceFeatures);
3722     viewMenu.add(featureSettings);
3723     viewMenu.addSeparator();
3724     viewMenu.add(alProperties);
3725     viewMenu.addSeparator();
3726     viewMenu.add(overviewMenuItem);
3727
3728     /*
3729      * Annotations menu
3730      */
3731     annotationsMenu.add(annotationPanelMenuItem);
3732     annotationsMenu.addSeparator();
3733     annotationsMenu.add(showAlignmentAnnotations);
3734     annotationsMenu.add(showSequenceAnnotations);
3735     annotationsMenu.add(sortAnnBySequence);
3736     annotationsMenu.add(sortAnnByLabel);
3737     annotationsMenu.addSeparator();
3738     autoAnnMenu.add(showAutoFirst);
3739     autoAnnMenu.add(showAutoLast);
3740     autoAnnMenu.addSeparator();
3741     autoAnnMenu.add(applyAutoAnnotationSettings);
3742     autoAnnMenu.add(showConsensusHistogram);
3743     autoAnnMenu.add(showSequenceLogo);
3744     autoAnnMenu.add(normSequenceLogo);
3745     autoAnnMenu.addSeparator();
3746     autoAnnMenu.add(showGroupConservation);
3747     autoAnnMenu.add(showGroupConsensus);
3748     annotationsMenu.add(autoAnnMenu);
3749
3750     /*
3751      * Format menu
3752      */
3753     formatMenu.add(font);
3754     formatMenu.add(seqLimits);
3755     formatMenu.add(wrapMenuItem);
3756     formatMenu.add(scaleAbove);
3757     formatMenu.add(scaleLeft);
3758     formatMenu.add(scaleRight);
3759     formatMenu.add(viewBoxesMenuItem);
3760     formatMenu.add(viewTextMenuItem);
3761     formatMenu.add(colourTextMenuItem);
3762     formatMenu.add(displayNonconservedMenuItem);
3763     formatMenu.add(renderGapsMenuItem);
3764     formatMenu.add(centreColumnLabelFlag);
3765
3766     /*
3767      * Colour menu
3768      */
3769     colourMenu.add(applyToAllGroups);
3770     colourMenu.addSeparator();
3771     colourMenu.add(noColourmenuItem);
3772     colourMenu.add(clustalColour);
3773     colourMenu.add(BLOSUM62Colour);
3774     colourMenu.add(PIDColour);
3775     colourMenu.add(zappoColour);
3776     colourMenu.add(taylorColour);
3777     colourMenu.add(hydrophobicityColour);
3778     colourMenu.add(helixColour);
3779     colourMenu.add(strandColour);
3780     colourMenu.add(turnColour);
3781     colourMenu.add(buriedColour);
3782     colourMenu.add(nucleotideColour);
3783     colourMenu.add(purinePyrimidineColour);
3784     // colourMenu.add(RNAInteractionColour);
3785     colourMenu.add(tcoffeeColour);
3786     colourMenu.add(userDefinedColour);
3787     colourMenu.addSeparator();
3788     colourMenu.add(conservationMenuItem);
3789     colourMenu.add(modifyConservation);
3790     colourMenu.add(abovePIDThreshold);
3791     colourMenu.add(modifyPID);
3792     colourMenu.add(annotationColour);
3793     colourMenu.add(RNAHelixColour);
3794
3795     /*
3796      * Calculate menu
3797      */
3798     sortMenu.add(sortIDMenuItem);
3799     sortMenu.add(sortLengthMenuItem);
3800     sortMenu.add(sortByTreeMenu);
3801     sortMenu.add(sortGroupMenuItem);
3802     sortMenu.add(sortPairwiseMenuItem);
3803     calculateMenu.add(sortMenu);
3804     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3805     calculateTreeMenu.add(neighbourTreeMenuItem);
3806     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3807     calculateTreeMenu.add(njTreeBlosumMenuItem);
3808     calculateMenu.add(calculateTreeMenu);
3809     calculateMenu.addSeparator();
3810     calculateMenu.add(pairwiseAlignmentMenuItem);
3811     calculateMenu.add(PCAMenuItem);
3812     calculateMenu.add(autoCalculate);
3813     calculateMenu.add(sortByTree);
3814
3815     /*
3816      * Help menu
3817      */
3818     helpMenu.add(documentation);
3819     helpMenu.add(about);
3820
3821     /*
3822      * Status bar
3823      */
3824     statusBar.setBackground(Color.white);
3825     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3826     setStatus(MessageManager.getString("label.status_bar"));
3827     this.add(statusBar, BorderLayout.SOUTH);
3828   }
3829
3830   @Override
3831   public void setStatus(String string)
3832   {
3833     statusBar.setText(string);
3834   };
3835
3836   MenuItem featureSettings = new MenuItem();
3837
3838   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3839
3840   MenuItem annotationColour = new MenuItem();
3841
3842   MenuItem annotationColumnSelection = new MenuItem();
3843
3844   MenuItem invertColSel = new MenuItem();
3845
3846   MenuItem showColumns = new MenuItem();
3847
3848   MenuItem showSeqs = new MenuItem();
3849
3850   MenuItem hideColumns = new MenuItem();
3851
3852   MenuItem hideSequences = new MenuItem();
3853
3854   MenuItem hideAllButSelection = new MenuItem();
3855
3856   MenuItem hideAllSelection = new MenuItem();
3857
3858   MenuItem showAllHidden = new MenuItem();
3859
3860   MenuItem newView = new MenuItem();
3861
3862   private CheckboxMenuItem showAlignmentAnnotations;
3863
3864   private CheckboxMenuItem showSequenceAnnotations;
3865
3866   private CheckboxMenuItem sortAnnBySequence;
3867
3868   private CheckboxMenuItem sortAnnByLabel;
3869
3870   private CheckboxMenuItem showAutoFirst;
3871
3872   private CheckboxMenuItem showAutoLast;
3873
3874   private SplitFrame splitFrame;
3875
3876   /**
3877    * Attach the alignFrame panels after embedding menus, if necessary. This used
3878    * to be called setEmbedded, but is now creates the dropdown menus in a
3879    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3880    *
3881    * @param reallyEmbedded
3882    *          true to attach the view to the applet area on the page rather than
3883    *          in a new window
3884    */
3885   public void createAlignFrameWindow(boolean reallyEmbedded)
3886   {
3887     if (reallyEmbedded)
3888     {
3889       embedAlignFrameInApplet(viewport.applet);
3890     }
3891     else
3892     {
3893       // //////
3894       // test and embed menu bar if necessary.
3895       //
3896       if (embedMenuIfNeeded(alignPanel))
3897       {
3898         /*
3899          * adjust for status bar height too. ? pointless as overridden by layout
3900          * manager
3901          */
3902         alignPanel.setSize(getSize().width,
3903                 getSize().height - statusBar.getHeight());
3904       }
3905       add(statusBar, BorderLayout.SOUTH);
3906       add(alignPanel, BorderLayout.CENTER);
3907       // and register with the applet so it can pass external API calls to us
3908       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3909               frameHeight);
3910     }
3911   }
3912
3913   /**
3914    * Add the components of this AlignFrame to the applet container.
3915    *
3916    * @param theApplet
3917    */
3918   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3919   {
3920     // ////
3921     // Explicitly build the embedded menu panel for the on-page applet
3922     //
3923     // view cannot be closed if its actually on the page
3924     fileMenu.remove(closeMenuItem);
3925     fileMenu.remove(3); // Remove Separator
3926     // construct embedded menu, using default font
3927     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3928     // and actually add the components to the applet area
3929     theApplet.setLayout(new BorderLayout());
3930     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3931     theApplet.add(statusBar, BorderLayout.SOUTH);
3932     // TODO should size be left to the layout manager?
3933     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3934             - embeddedMenu.getHeight() - statusBar.getHeight());
3935     theApplet.add(alignPanel, BorderLayout.CENTER);
3936     final AlignFrame me = this;
3937     theApplet.addFocusListener(new FocusListener()
3938     {
3939
3940       @Override
3941       public void focusLost(FocusEvent e)
3942       {
3943         if (theApplet.currentAlignFrame == me)
3944         {
3945           theApplet.currentAlignFrame = null;
3946         }
3947       }
3948
3949       @Override
3950       public void focusGained(FocusEvent e)
3951       {
3952         theApplet.currentAlignFrame = me;
3953       }
3954     });
3955     theApplet.validate();
3956   }
3957
3958   /**
3959    * create a new binding between structures in an existing jmol viewer instance
3960    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3961    * this does not open a new Jmol window, or modify the display of the
3962    * structures in the original jmol window. Note This method doesn't work
3963    * without an additional javascript library to exchange messages between the
3964    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3965    *
3966    * @param jmolViewer
3967    *          JmolViewer instance
3968    * @param sequenceIds
3969    *          - sequence Ids to search for associations
3970    */
3971   public SequenceStructureBinding addStructureViewInstance(
3972           Object jmolviewer, String[] sequenceIds)
3973   {
3974     Viewer viewer = null;
3975     try
3976     {
3977       viewer = (Viewer) jmolviewer;
3978     } catch (ClassCastException ex)
3979     {
3980       System.err.println(
3981               "Unsupported viewer object :" + jmolviewer.getClass());
3982     }
3983     if (viewer == null)
3984     {
3985       System.err.println("Can't use this object as a structure viewer:"
3986               + jmolviewer.getClass());
3987       return null;
3988     }
3989     SequenceI[] seqs = null;
3990     if (sequenceIds == null || sequenceIds.length == 0)
3991     {
3992       seqs = viewport.getAlignment().getSequencesArray();
3993     }
3994     else
3995     {
3996       Vector sqi = new Vector();
3997       AlignmentI al = viewport.getAlignment();
3998       for (int sid = 0; sid < sequenceIds.length; sid++)
3999       {
4000         SequenceI sq = al.findName(sequenceIds[sid]);
4001         if (sq != null)
4002         {
4003           sqi.addElement(sq);
4004         }
4005       }
4006       if (sqi.size() > 0)
4007       {
4008         seqs = new SequenceI[sqi.size()];
4009         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4010         {
4011           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4012         }
4013       }
4014       else
4015       {
4016         return null;
4017       }
4018     }
4019     AAStructureBindingModel jmv = null;
4020     // TODO: search for a jmv that involves viewer
4021     if (jmv == null)
4022     { // create a new viewer/jalview binding.
4023       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4024     }
4025     return jmv;
4026
4027   }
4028
4029   /**
4030    * bind a pdb file to a sequence in the current view
4031    *
4032    * @param sequenceId
4033    *          - sequenceId within the dataset.
4034    * @param pdbEntryString
4035    *          - the short name for the PDB file
4036    * @param pdbFile
4037    *          - pdb file - either a URL or a valid PDB file.
4038    * @return true if binding was as success TODO: consider making an exception
4039    *         structure for indicating when PDB parsing or sequenceId location
4040    *         fails.
4041    */
4042   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4043           String pdbFile)
4044   {
4045     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4046     boolean needtoadd = false;
4047     if (toaddpdb != null)
4048     {
4049       Vector pdbe = toaddpdb.getAllPDBEntries();
4050       PDBEntry pdbentry = null;
4051       if (pdbe != null && pdbe.size() > 0)
4052       {
4053         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4054         {
4055           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4056           if (!pdbentry.getId().equals(pdbEntryString)
4057                   && !pdbentry.getFile().equals(pdbFile))
4058           {
4059             pdbentry = null;
4060           }
4061           else
4062           {
4063             continue;
4064           }
4065         }
4066       }
4067       if (pdbentry == null)
4068       {
4069         pdbentry = new PDBEntry();
4070         pdbentry.setId(pdbEntryString);
4071         pdbentry.setFile(pdbFile);
4072         needtoadd = true; // add this new entry to sequence.
4073       }
4074       // resolve data source
4075       // TODO: this code should be a refactored to an io package
4076       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4077               FileFormat.PDB);
4078       if (protocol == null)
4079       {
4080         return false;
4081       }
4082       if (needtoadd)
4083       {
4084         pdbentry.setProperty("protocol", protocol);
4085         toaddpdb.addPDBId(pdbentry);
4086         alignPanel.getStructureSelectionManager()
4087                 .registerPDBEntry(pdbentry);
4088       }
4089     }
4090     return true;
4091   }
4092
4093   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4094   {
4095     if (seqs != null)
4096     {
4097       Vector sequences = new Vector();
4098       for (int i = 0; i < seqs.length; i++)
4099       {
4100         if (seqs[i] != null)
4101         {
4102           sequences
4103                   .addElement(new Object[]
4104                   { seqs[i], (chains != null) ? chains[i] : null });
4105         }
4106       }
4107       seqs = new SequenceI[sequences.size()];
4108       chains = new String[sequences.size()];
4109       for (int i = 0, isize = sequences.size(); i < isize; i++)
4110       {
4111         Object[] oj = (Object[]) sequences.elementAt(i);
4112
4113         seqs[i] = (SequenceI) oj[0];
4114         chains[i] = (String) oj[1];
4115       }
4116     }
4117     return new Object[] { seqs, chains };
4118
4119   }
4120
4121   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4122           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4123   {
4124     // Scrub any null sequences from the array
4125     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4126     seqs = (SequenceI[]) sqch[0];
4127     chains = (String[]) sqch[1];
4128     if (seqs == null || seqs.length == 0)
4129     {
4130       System.err.println(
4131               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4132     }
4133     if (protocol == null)
4134     {
4135       String sourceType = (String) pdb.getProperty("protocol");
4136       try
4137       {
4138         protocol = DataSourceType.valueOf(sourceType);
4139       } catch (IllegalArgumentException e)
4140       {
4141         // ignore
4142       }
4143       if (protocol == null)
4144       {
4145         System.err.println("Couldn't work out protocol to open structure: "
4146                 + pdb.getId());
4147         return;
4148       }
4149     }
4150     if (applet.useXtrnalSviewer)
4151     {
4152       // register the association(s) and quit, don't create any windows.
4153       if (StructureSelectionManager.getStructureSelectionManager(applet)
4154               .setMapping(seqs, chains, pdb.getFile(), protocol,
4155                       null) == null)
4156       {
4157         System.err.println("Failed to map " + pdb.getFile() + " ("
4158                 + protocol + ") to any sequences");
4159       }
4160       return;
4161     }
4162     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4163     {
4164       // can only do alignments with Jmol
4165       // find the last jmol window assigned to this alignment
4166       AppletJmol ajm = null, tajm;
4167       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4168       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4169       {
4170         tajm = (AppletJmol) jmols.elementAt(i);
4171         if (tajm.ap.alignFrame == this)
4172         {
4173           ajm = tajm;
4174           break;
4175         }
4176       }
4177       if (ajm != null)
4178       {
4179         System.err.println(
4180                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4181         // try and add the pdb structure
4182         // ajm.addS
4183         ajm = null;
4184       }
4185     }
4186     // otherwise, create a new window
4187     if (applet.jmolAvailable)
4188     {
4189       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4190       applet.lastFrameX += 40;
4191       applet.lastFrameY += 40;
4192     }
4193     else
4194     {
4195       new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4196     }
4197
4198   }
4199
4200   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4201           SequenceI[][] seqs, String[][] chains, String[] protocols)
4202   {
4203     // TODO Auto-generated method stub
4204     System.err.println("Aligned Structure View: Not yet implemented.");
4205   }
4206
4207   /**
4208    * modify the current selection, providing the user has not made a selection
4209    * already.
4210    *
4211    * @param sel
4212    *          - sequences from this alignment
4213    * @param csel
4214    *          - columns to be selected on the alignment
4215    */
4216   public void select(SequenceGroup sel, ColumnSelection csel,
4217           HiddenColumns hidden)
4218   {
4219     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4220   }
4221
4222   public void scrollTo(int row, int column)
4223   {
4224     alignPanel.seqPanel.scrollTo(row, column);
4225   }
4226
4227   public void scrollToRow(int row)
4228   {
4229     alignPanel.seqPanel.scrollToRow(row);
4230   }
4231
4232   public void scrollToColumn(int column)
4233   {
4234     alignPanel.seqPanel.scrollToColumn(column);
4235   }
4236
4237   /**
4238    * @return the alignments unique ID.
4239    */
4240   public String getSequenceSetId()
4241   {
4242     return viewport.getSequenceSetId();
4243   }
4244
4245   /**
4246    * Load the (T-Coffee) score file from the specified url
4247    *
4248    * @param source
4249    *          File/URL/T-COFFEE score file contents
4250    * @throws IOException
4251    * @return true if alignment was annotated with data from source
4252    */
4253   public boolean loadScoreFile(String source) throws IOException
4254   {
4255
4256     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4257             AppletFormatAdapter.checkProtocol(source));
4258     if (!file.isValid())
4259     {
4260       // TODO: raise dialog for gui
4261       System.err.println("Problems parsing T-Coffee scores: "
4262               + file.getWarningMessage());
4263       System.err.println("Origin was:\n" + source);
4264       return false;
4265     }
4266
4267     /*
4268      * check that the score matrix matches the alignment dimensions
4269      */
4270     AlignmentI aln;
4271     if ((aln = viewport.getAlignment()) != null
4272             && (aln.getHeight() != file.getHeight()
4273                     || aln.getWidth() != file.getWidth()))
4274     {
4275       // TODO: raise a dialog box here rather than bomb out.
4276       System.err.println(
4277               "The scores matrix does not match the alignment dimensions");
4278
4279     }
4280
4281     // TODO add parameter to indicate if matching should be done
4282     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4283     {
4284       alignPanel.fontChanged();
4285       tcoffeeColour.setEnabled(true);
4286       // switch to this color
4287       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288       return true;
4289     }
4290     else
4291     {
4292       System.err.println("Problems resolving T-Coffee scores:");
4293       if (file.getWarningMessage() != null)
4294       {
4295         System.err.println(file.getWarningMessage());
4296       }
4297     }
4298     return false;
4299   }
4300
4301   public SplitFrame getSplitFrame()
4302   {
4303     return this.splitFrame;
4304   }
4305
4306   public void setSplitFrame(SplitFrame sf)
4307   {
4308     this.splitFrame = sf;
4309   }
4310
4311   // may not need this
4312   @Override
4313   public void setShowSeqFeatures(boolean b)
4314   {
4315     // showSeqFeatures.setSelected(b);
4316     viewport.setShowSequenceFeatures(b);
4317
4318   }
4319
4320   @Override
4321   public void setMenusForViewport()
4322   {
4323     // setMenusFromViewport(viewport);
4324
4325   }
4326
4327   @Override
4328   public void refreshFeatureUI(boolean enableIfNecessary)
4329   {
4330     if (enableIfNecessary)
4331     {
4332       sequenceFeatures.setState(true);
4333       alignPanel.av.setShowSequenceFeatures(true);
4334     }
4335   }
4336
4337   @Override
4338   public FeatureSettingsControllerI getFeatureSettingsUI()
4339   {
4340     return alignPanel.av.featureSettings;
4341   }
4342
4343   @Override
4344   public FeatureSettingsControllerI showFeatureSettingsUI()
4345   {
4346     return new FeatureSettings(alignPanel);
4347   }
4348
4349   private Rectangle fs_bounds = null;
4350
4351   @Override
4352   public void setFeatureSettingsGeometry(Rectangle bounds)
4353   {
4354     fs_bounds = bounds;
4355   }
4356
4357   @Override
4358   public Rectangle getFeatureSettingsGeometry()
4359   {
4360     return fs_bounds;
4361   }
4362
4363 }