src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
  25 import jalview.analysis.TreeBuilder;
  26 import jalview.analysis.scoremodels.PIDModel;
  27 import jalview.analysis.scoremodels.ScoreModels;
  28 import jalview.api.AlignViewControllerGuiI;
  29 import jalview.api.AlignViewControllerI;
  30 import jalview.api.AlignViewportI;
  31 import jalview.api.FeatureColourI;
  32 import jalview.api.FeatureRenderer;
  33 import jalview.api.FeatureSettingsControllerI;
  34 import jalview.api.SequenceStructureBinding;
  35 import jalview.bin.JalviewLite;
  36 import jalview.commands.CommandI;
  37 import jalview.commands.EditCommand;
  38 import jalview.commands.EditCommand.Action;
  39 import jalview.commands.OrderCommand;
  40 import jalview.commands.RemoveGapColCommand;
  41 import jalview.commands.RemoveGapsCommand;
  42 import jalview.commands.SlideSequencesCommand;
  43 import jalview.commands.TrimRegionCommand;
  44 import jalview.datamodel.Alignment;
  45 import jalview.datamodel.AlignmentAnnotation;
  46 import jalview.datamodel.AlignmentI;
  47 import jalview.datamodel.AlignmentOrder;
  48 import jalview.datamodel.ColumnSelection;
  49 import jalview.datamodel.HiddenColumns;
  50 import jalview.datamodel.PDBEntry;
  51 import jalview.datamodel.Sequence;
  52 import jalview.datamodel.SequenceGroup;
  53 import jalview.datamodel.SequenceI;
  54 import jalview.io.AnnotationFile;
  55 import jalview.io.AppletFormatAdapter;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FeaturesFile;
  58 import jalview.io.FileFormat;
  59 import jalview.io.FileFormatI;
  60 import jalview.io.FileFormats;
  61 import jalview.io.TCoffeeScoreFile;
  62 import jalview.schemes.Blosum62ColourScheme;
  63 import jalview.schemes.BuriedColourScheme;
  64 import jalview.schemes.ClustalxColourScheme;
  65 import jalview.schemes.ColourSchemeI;
  66 import jalview.schemes.HelixColourScheme;
  67 import jalview.schemes.HydrophobicColourScheme;
  68 import jalview.schemes.NucleotideColourScheme;
  69 import jalview.schemes.PIDColourScheme;
  70 import jalview.schemes.PurinePyrimidineColourScheme;
  71 import jalview.schemes.RNAHelicesColour;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.ZappoColourScheme;
  77 import jalview.structure.StructureSelectionManager;
  78 import jalview.structures.models.AAStructureBindingModel;
  79 import jalview.util.MappingUtils;
  80 import jalview.util.MessageManager;
  81 import jalview.viewmodel.AlignmentViewport;
  82 import jalview.viewmodel.ViewportRanges;
  83
  84 import java.awt.BorderLayout;
  85 import java.awt.Canvas;
  86 import java.awt.CheckboxMenuItem;
  87 import java.awt.Color;
  88 import java.awt.FlowLayout;
  89 import java.awt.Font;
  90 import java.awt.FontMetrics;
  91 import java.awt.Frame;
  92 import java.awt.Graphics;
  93 import java.awt.Label;
  94 import java.awt.Menu;
  95 import java.awt.MenuBar;
  96 import java.awt.MenuItem;
  97 import java.awt.Panel;
  98 import java.awt.event.ActionEvent;
  99 import java.awt.event.ActionListener;
 100 import java.awt.event.FocusEvent;
 101 import java.awt.event.FocusListener;
 102 import java.awt.event.ItemEvent;
 103 import java.awt.event.ItemListener;
 104 import java.awt.event.KeyEvent;
 105 import java.awt.event.KeyListener;
 106 import java.awt.event.WindowAdapter;
 107 import java.awt.event.WindowEvent;
 108 import java.io.IOException;
 109 import java.net.URL;
 110 import java.net.URLEncoder;
 111 import java.util.Arrays;
 112 import java.util.Deque;
 113 import java.util.HashMap;
 114 import java.util.List;
 115 import java.util.Map;
 116 import java.util.StringTokenizer;
 117 import java.util.Vector;
 118
 119 import org.jmol.viewer.Viewer;
 120
 121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 122         ItemListener, KeyListener, AlignViewControllerGuiI
 123 {
 124   public AlignViewControllerI avc;
 125
 126   public AlignmentPanel alignPanel;
 127
 128   public AlignViewport viewport;
 129
 130   // width and height may be overridden by applet parameters
 131   int frameWidth = 700;
 132
 133   int frameHeight = 500;
 134
 135   String jalviewServletURL;
 136
 137   /*
 138    * Flag for showing autocalculated consensus above or below other consensus
 139    * rows
 140    */
 141   private boolean showAutoCalculatedAbove;
 142
 143   private SequenceAnnotationOrder annotationSortOrder;
 144
 145   /**
 146    * Constructor that creates the frame and adds it to the display.
 147    *
 148    * @param al
 149    * @param applet
 150    * @param title
 151    * @param embedded
 152    */
 153   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 154           boolean embedded)
 155   {
 156     this(al, applet, title, embedded, true);
 157   }
 158
 159   /**
 160    * Constructor that optionally allows the frame to be displayed or only
 161    * created.
 162    *
 163    * @param al
 164    * @param applet
 165    * @param title
 166    * @param embedded
 167    * @param addToDisplay
 168    */
 169   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 170           boolean embedded, boolean addToDisplay)
 171   {
 172     this(al, null, null, applet, title, embedded, addToDisplay);
 173   }
 174
 175   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 176           HiddenColumns hidden, JalviewLite applet,
 177           String title, boolean embedded)
 178   {
 179     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 180   }
 181
 182   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 183           HiddenColumns hidden, JalviewLite applet,
 184           String title, boolean embedded, boolean addToDisplay)
 185   {
 186     if (applet != null)
 187     {
 188       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 189     }
 190
 191     try
 192     {
 193       jbInit();
 194     } catch (Exception ex)
 195     {
 196       ex.printStackTrace();
 197     }
 198     // need to get window geometry before we calculate alignment layout
 199     if (applet != null)
 200     {
 201       String param;
 202       try
 203       {
 204         param = applet.getParameter("windowWidth");
 205         if (param != null)
 206         {
 207           int width = Integer.parseInt(param);
 208           frameWidth = width;
 209         }
 210         param = applet.getParameter("windowHeight");
 211         if (param != null)
 212         {
 213           int height = Integer.parseInt(param);
 214           frameHeight = height;
 215         }
 216       } catch (Exception ex)
 217       {
 218       }
 219     }
 220     viewport = new AlignViewport(al, applet);
 221
 222     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 223     {
 224       viewport.hideSequence(hiddenSeqs);
 225     }
 226     if (hidden != null)
 227     {
 228       viewport.getAlignment().setHiddenColumns(hidden);
 229     }
 230     viewport.setScaleAboveWrapped(scaleAbove.getState());
 231
 232     alignPanel = new AlignmentPanel(this, viewport);
 233     avc = new jalview.controller.AlignViewController(this, viewport,
 234             alignPanel);
 235     viewport.updateConservation(alignPanel);
 236     viewport.updateConsensus(alignPanel);
 237
 238     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 239     followMouseOverFlag.setState(viewport.isFollowHighlight());
 240     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 241     showGroupConservation.setState(viewport.isShowGroupConservation());
 242     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 243     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 244     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 245     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 246     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 247     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 248     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 249     showAlignmentAnnotations.setState(true);
 250     showSequenceAnnotations.setState(false);
 251
 252     seqLimits.setState(viewport.getShowJVSuffix());
 253
 254     if (applet != null)
 255     {
 256       String param = applet.getParameter("sortBy");
 257       if (param != null)
 258       {
 259         if (param.equalsIgnoreCase("Id"))
 260         {
 261           sortIDMenuItem_actionPerformed();
 262         }
 263         else if (param.equalsIgnoreCase("Pairwise Identity"))
 264         {
 265           sortPairwiseMenuItem_actionPerformed();
 266         }
 267         else if (param.equalsIgnoreCase("Length"))
 268         {
 269           sortLengthMenuItem_actionPerformed();
 270         }
 271       }
 272
 273       param = applet.getParameter("wrap");
 274       if (param != null)
 275       {
 276         if (param.equalsIgnoreCase("true"))
 277         {
 278           wrapMenuItem.setState(true);
 279           wrapMenuItem_actionPerformed();
 280         }
 281       }
 282       param = applet.getParameter("centrecolumnlabels");
 283       if (param != null)
 284       {
 285         centreColumnLabelFlag.setState(true);
 286         centreColumnLabelFlag_stateChanged();
 287       }
 288
 289     }
 290     if (viewport.getAlignment().isNucleotide())
 291     {
 292       conservationMenuItem.setEnabled(false);
 293       clustalColour.setEnabled(false);
 294       BLOSUM62Colour.setEnabled(false);
 295       zappoColour.setEnabled(false);
 296       taylorColour.setEnabled(false);
 297       hydrophobicityColour.setEnabled(false);
 298       helixColour.setEnabled(false);
 299       strandColour.setEnabled(false);
 300       turnColour.setEnabled(false);
 301       buriedColour.setEnabled(false);
 302       viewport.updateStrucConsensus(alignPanel);
 303       if (viewport.getAlignment().hasRNAStructure())
 304       {
 305         RNAHelixColour.setEnabled(true);
 306       }
 307       else
 308       {
 309         RNAHelixColour.setEnabled(false);
 310       }
 311     }
 312     else
 313     {
 314       RNAHelixColour.setEnabled(false);
 315       purinePyrimidineColour.setEnabled(false);
 316       nucleotideColour.setEnabled(false);
 317     }
 318     // Some JVMS send keyevents to Top frame or lowest panel,
 319     // Havent worked out why yet. So add to both this frame and seqCanvas for
 320     // now
 321     this.addKeyListener(this);
 322     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 323     alignPanel.idPanel.idCanvas.addKeyListener(this);
 324     alignPanel.scalePanel.addKeyListener(this);
 325     alignPanel.annotationPanel.addKeyListener(this);
 326     alignPanel.annotationPanelHolder.addKeyListener(this);
 327     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 328     alignPanel.alabels.addKeyListener(this);
 329
 330     setAnnotationsVisibility();
 331
 332     if (addToDisplay)
 333     {
 334       addToDisplay(embedded);
 335     }
 336   }
 337
 338   /**
 339    * @param embedded
 340    */
 341   public void addToDisplay(boolean embedded)
 342   {
 343     createAlignFrameWindow(embedded);
 344     validate();
 345     alignPanel.adjustAnnotationHeight();
 346     alignPanel.paintAlignment(true);
 347   }
 348
 349   public AlignViewport getAlignViewport()
 350   {
 351     return viewport;
 352   }
 353
 354   public SeqCanvas getSeqcanvas()
 355   {
 356     return alignPanel.seqPanel.seqCanvas;
 357   }
 358
 359   /**
 360    * Load a features file onto the alignment
 361    *
 362    * @param file
 363    *          file URL, content, or other resolvable path
 364    * @param type
 365    *          is protocol for accessing data referred to by file
 366    */
 367
 368   public boolean parseFeaturesFile(String file, DataSourceType type)
 369   {
 370     return parseFeaturesFile(file, type, true);
 371   }
 372
 373   /**
 374    * Load a features file onto the alignment
 375    *
 376    * @param file
 377    *          file URL, content, or other resolvable path
 378    * @param sourceType
 379    *          is protocol for accessing data referred to by file
 380    * @param autoenabledisplay
 381    *          when true, display features flag will be automatically enabled if
 382    *          features are loaded
 383    * @return true if data parsed as a features file
 384    */
 385   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 386           boolean autoenabledisplay)
 387   {
 388     boolean featuresFile = false;
 389     try
 390     {
 391       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 392               .getFeatureRenderer().getFeatureColours();
 393       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
 394               "relaxedidmatch", false);
 395       featuresFile = new FeaturesFile(file, sourceType).parse(
 396               viewport.getAlignment(), colours, true, relaxedIdMatching);
 397     } catch (Exception ex)
 398     {
 399       ex.printStackTrace();
 400     }
 401
 402     if (featuresFile)
 403     {
 404       if (autoenabledisplay)
 405       {
 406         viewport.setShowSequenceFeatures(true);
 407         sequenceFeatures.setState(true);
 408       }
 409       if (alignPanel.seqPanel.seqCanvas.fr != null)
 410       {
 411         // update the min/max ranges where necessary
 412         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 413       }
 414       if (viewport.featureSettings != null)
 415       {
 416         viewport.featureSettings.refreshTable();
 417       }
 418       alignPanel.paintAlignment(true);
 419       statusBar.setText(MessageManager
 420               .getString("label.successfully_added_features_alignment"));
 421     }
 422     return featuresFile;
 423   }
 424
 425   @Override
 426   public void keyPressed(KeyEvent evt)
 427   {
 428     ViewportRanges ranges = viewport.getRanges();
 429
 430     if (viewport.cursorMode
 431             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 432                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 433                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 434             && Character.isDigit(evt.getKeyChar()))
 435     {
 436       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 437     }
 438
 439     switch (evt.getKeyCode())
 440     {
 441     case 27: // escape key
 442       deselectAllSequenceMenuItem_actionPerformed();
 443
 444       alignPanel.alabels.cancelDrag();
 445       break;
 446     case KeyEvent.VK_X:
 447       if (evt.isControlDown() || evt.isMetaDown())
 448       {
 449         cut_actionPerformed();
 450       }
 451       break;
 452     case KeyEvent.VK_C:
 453       if (viewport.cursorMode && !evt.isControlDown())
 454       {
 455         alignPanel.seqPanel.setCursorColumn();
 456       }
 457       if (evt.isControlDown() || evt.isMetaDown())
 458       {
 459         copy_actionPerformed();
 460       }
 461       break;
 462     case KeyEvent.VK_V:
 463       if (evt.isControlDown())
 464       {
 465         paste(evt.isShiftDown());
 466       }
 467       break;
 468     case KeyEvent.VK_A:
 469       if (evt.isControlDown() || evt.isMetaDown())
 470       {
 471         selectAllSequenceMenuItem_actionPerformed();
 472       }
 473       break;
 474     case KeyEvent.VK_DOWN:
 475       if (viewport.cursorMode)
 476       {
 477         alignPanel.seqPanel.moveCursor(0, 1);
 478       }
 479       else
 480       {
 481         moveSelectedSequences(false);
 482       }
 483       break;
 484
 485     case KeyEvent.VK_UP:
 486       if (viewport.cursorMode)
 487       {
 488         alignPanel.seqPanel.moveCursor(0, -1);
 489       }
 490       else
 491       {
 492         moveSelectedSequences(true);
 493       }
 494       break;
 495
 496     case KeyEvent.VK_LEFT:
 497       if (evt.isAltDown() || !viewport.cursorMode)
 498       {
 499         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 500       }
 501       else
 502       {
 503         alignPanel.seqPanel.moveCursor(-1, 0);
 504       }
 505       break;
 506
 507     case KeyEvent.VK_RIGHT:
 508       if (evt.isAltDown() || !viewport.cursorMode)
 509       {
 510         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 511       }
 512       else
 513       {
 514         alignPanel.seqPanel.moveCursor(1, 0);
 515       }
 516       break;
 517
 518     case KeyEvent.VK_SPACE:
 519       if (viewport.cursorMode)
 520       {
 521         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 522                 || evt.isShiftDown() || evt.isAltDown());
 523       }
 524       break;
 525
 526     case KeyEvent.VK_DELETE:
 527     case KeyEvent.VK_BACK_SPACE:
 528       if (viewport.cursorMode)
 529       {
 530         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 531                 || evt.isShiftDown() || evt.isAltDown());
 532       }
 533       else
 534       {
 535         cut_actionPerformed();
 536         alignPanel.seqPanel.seqCanvas.repaint();
 537       }
 538       break;
 539
 540     case KeyEvent.VK_S:
 541       if (viewport.cursorMode)
 542       {
 543         alignPanel.seqPanel.setCursorRow();
 544       }
 545       break;
 546     case KeyEvent.VK_P:
 547       if (viewport.cursorMode)
 548       {
 549         alignPanel.seqPanel.setCursorPosition();
 550       }
 551       break;
 552
 553     case KeyEvent.VK_ENTER:
 554     case KeyEvent.VK_COMMA:
 555       if (viewport.cursorMode)
 556       {
 557         alignPanel.seqPanel.setCursorRowAndColumn();
 558       }
 559       break;
 560
 561     case KeyEvent.VK_Q:
 562       if (viewport.cursorMode)
 563       {
 564         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 565       }
 566       break;
 567     case KeyEvent.VK_M:
 568       if (viewport.cursorMode)
 569       {
 570         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 571       }
 572       break;
 573
 574     case KeyEvent.VK_F2:
 575       viewport.cursorMode = !viewport.cursorMode;
 576       statusBar.setText(MessageManager.formatMessage(
 577               "label.keyboard_editing_mode",
 578               new String[] { (viewport.cursorMode ? "on" : "off") }));
 579       if (viewport.cursorMode)
 580       {
 581         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 582         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 583       }
 584       break;
 585
 586     case KeyEvent.VK_F:
 587       if (evt.isControlDown())
 588       {
 589         findMenuItem_actionPerformed();
 590       }
 591       break;
 592
 593     case KeyEvent.VK_H:
 594     {
 595       boolean toggleSeqs = !evt.isControlDown();
 596       boolean toggleCols = !evt.isShiftDown();
 597       toggleHiddenRegions(toggleSeqs, toggleCols);
 598       break;
 599     }
 600
 601     case KeyEvent.VK_PAGE_UP:
 602       if (viewport.getWrapAlignment())
 603       {
 604         ranges.scrollUp(true);
 605       }
 606       else
 607       {
 608         ranges.pageUp();
 609       }
 610       break;
 611
 612     case KeyEvent.VK_PAGE_DOWN:
 613       if (viewport.getWrapAlignment())
 614       {
 615         ranges.scrollUp(false);
 616       }
 617       else
 618       {
 619         ranges.pageDown();
 620       }
 621       break;
 622
 623     case KeyEvent.VK_Z:
 624       if (evt.isControlDown())
 625       {
 626         undoMenuItem_actionPerformed();
 627       }
 628       break;
 629
 630     case KeyEvent.VK_Y:
 631       if (evt.isControlDown())
 632       {
 633         redoMenuItem_actionPerformed();
 634       }
 635       break;
 636
 637     case KeyEvent.VK_L:
 638       if (evt.isControlDown())
 639       {
 640         trimAlignment(true);
 641       }
 642       break;
 643
 644     case KeyEvent.VK_R:
 645       if (evt.isControlDown())
 646       {
 647         trimAlignment(false);
 648       }
 649       break;
 650
 651     case KeyEvent.VK_E:
 652       if (evt.isControlDown())
 653       {
 654         if (evt.isShiftDown())
 655         {
 656           this.removeAllGapsMenuItem_actionPerformed();
 657         }
 658         else
 659         {
 660           removeGappedColumnMenuItem_actionPerformed();
 661         }
 662       }
 663       break;
 664     case KeyEvent.VK_I:
 665       if (evt.isControlDown())
 666       {
 667         if (evt.isAltDown())
 668         {
 669           invertColSel_actionPerformed();
 670         }
 671         else
 672         {
 673           invertSequenceMenuItem_actionPerformed();
 674         }
 675       }
 676       break;
 677
 678     case KeyEvent.VK_G:
 679       if (evt.isControlDown())
 680       {
 681         if (evt.isShiftDown())
 682         {
 683           this.unGroup_actionPerformed();
 684         }
 685         else
 686         {
 687           this.createGroup_actionPerformed();
 688         }
 689       }
 690       break;
 691
 692     case KeyEvent.VK_U:
 693       if (evt.isControlDown())
 694       {
 695         this.deleteGroups_actionPerformed();
 696       }
 697       break;
 698
 699     case KeyEvent.VK_T:
 700       if (evt.isControlDown())
 701       {
 702         newView(null);
 703       }
 704       break;
 705
 706     }
 707     alignPanel.paintAlignment(true);
 708   }
 709
 710   /**
 711    * called by key handler and the hide all/show all menu items
 712    *
 713    * @param toggleSeqs
 714    * @param toggleCols
 715    */
 716   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 717   {
 718     boolean hide = false;
 719     SequenceGroup sg = viewport.getSelectionGroup();
 720     if (!toggleSeqs && !toggleCols)
 721     {
 722       // Hide everything by the current selection - this is a hack - we do the
 723       // invert and then hide
 724       // first check that there will be visible columns after the invert.
 725       if (viewport.hasSelectedColumns()
 726               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 727                       .getEndRes()))
 728       {
 729         // now invert the sequence set, if required - empty selection implies
 730         // that no hiding is required.
 731         if (sg != null)
 732         {
 733           invertSequenceMenuItem_actionPerformed();
 734           sg = viewport.getSelectionGroup();
 735           toggleSeqs = true;
 736
 737         }
 738         viewport.expandColSelection(sg, true);
 739         // finally invert the column selection and get the new sequence
 740         // selection and indicate it should be hidden.
 741         invertColSel_actionPerformed();
 742         toggleCols = true;
 743       }
 744     }
 745
 746     if (toggleSeqs)
 747     {
 748       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 749       {
 750         hide = true;
 751         viewport.hideAllSelectedSeqs();
 752       }
 753       else if (!(toggleCols && viewport.hasSelectedColumns()))
 754       {
 755         viewport.showAllHiddenSeqs();
 756       }
 757     }
 758
 759     if (toggleCols)
 760     {
 761       if (viewport.hasSelectedColumns())
 762       {
 763         viewport.hideSelectedColumns();
 764         if (!toggleSeqs)
 765         {
 766           viewport.setSelectionGroup(sg);
 767         }
 768       }
 769       else if (!hide)
 770       {
 771         viewport.showAllHiddenColumns();
 772       }
 773       viewport.sendSelection();
 774     }
 775   }
 776
 777   @Override
 778   public void keyReleased(KeyEvent evt)
 779   {
 780   }
 781
 782   @Override
 783   public void keyTyped(KeyEvent evt)
 784   {
 785   }
 786
 787   @Override
 788   public void itemStateChanged(ItemEvent evt)
 789   {
 790     final Object source = evt.getSource();
 791     if (source == displayNonconservedMenuItem)
 792     {
 793       displayNonconservedMenuItem_actionPerformed();
 794     }
 795     else if (source == colourTextMenuItem)
 796     {
 797       colourTextMenuItem_actionPerformed();
 798     }
 799     else if (source == wrapMenuItem)
 800     {
 801       wrapMenuItem_actionPerformed();
 802     }
 803     else if (source == scaleAbove)
 804     {
 805       viewport.setScaleAboveWrapped(scaleAbove.getState());
 806     }
 807     else if (source == scaleLeft)
 808     {
 809       viewport.setScaleLeftWrapped(scaleLeft.getState());
 810     }
 811     else if (source == scaleRight)
 812     {
 813       viewport.setScaleRightWrapped(scaleRight.getState());
 814     }
 815     else if (source == seqLimits)
 816     {
 817       seqLimits_itemStateChanged();
 818     }
 819     else if (source == viewBoxesMenuItem)
 820     {
 821       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 822     }
 823     else if (source == viewTextMenuItem)
 824     {
 825       viewport.setShowText(viewTextMenuItem.getState());
 826     }
 827     else if (source == renderGapsMenuItem)
 828     {
 829       viewport.setRenderGaps(renderGapsMenuItem.getState());
 830     }
 831     else if (source == annotationPanelMenuItem)
 832     {
 833       boolean showAnnotations = annotationPanelMenuItem.getState();
 834       showAlignmentAnnotations.setEnabled(showAnnotations);
 835       showSequenceAnnotations.setEnabled(showAnnotations);
 836       viewport.setShowAnnotation(showAnnotations);
 837       alignPanel.setAnnotationVisible(showAnnotations);
 838     }
 839     else if (source == sequenceFeatures)
 840     {
 841       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 842       alignPanel.seqPanel.seqCanvas.repaint();
 843     }
 844     else if (source == showAlignmentAnnotations)
 845     {
 846       setAnnotationsVisibility();
 847     }
 848     else if (source == showSequenceAnnotations)
 849     {
 850       setAnnotationsVisibility();
 851     }
 852     else if (source == sortAnnBySequence)
 853     {
 854       boolean newState = sortAnnBySequence.getState();
 855       sortAnnByLabel.setState(false);
 856       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 857               : SequenceAnnotationOrder.NONE);
 858       setViewportAnnotationOrder();
 859     }
 860     else if (source == sortAnnByLabel)
 861     {
 862       boolean newState = sortAnnByLabel.getState();
 863       sortAnnBySequence.setState(false);
 864       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 865               : SequenceAnnotationOrder.NONE);
 866       setViewportAnnotationOrder();
 867     }
 868     else if (source == showAutoFirst)
 869     {
 870       showAutoLast.setState(!showAutoFirst.getState());
 871       setShowAutoCalculatedAbove(showAutoFirst.getState());
 872       setViewportAnnotationOrder();
 873     }
 874     else if (source == showAutoLast)
 875     {
 876       showAutoFirst.setState(!showAutoLast.getState());
 877       setShowAutoCalculatedAbove(showAutoFirst.getState());
 878       setViewportAnnotationOrder();
 879     }
 880     else if (source == conservationMenuItem)
 881     {
 882       conservationMenuItem_actionPerformed();
 883     }
 884     else if (source == abovePIDThreshold)
 885     {
 886       abovePIDThreshold_actionPerformed();
 887     }
 888     else if (source == applyToAllGroups)
 889     {
 890       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 891     }
 892     else if (source == autoCalculate)
 893     {
 894       viewport.autoCalculateConsensus = autoCalculate.getState();
 895     }
 896     else if (source == sortByTree)
 897     {
 898       viewport.sortByTree = sortByTree.getState();
 899     }
 900     else if (source == this.centreColumnLabelFlag)
 901     {
 902       centreColumnLabelFlag_stateChanged();
 903     }
 904     else if (source == this.followMouseOverFlag)
 905     {
 906       mouseOverFlag_stateChanged();
 907     }
 908     else if (source == showGroupConsensus)
 909     {
 910       showGroupConsensus_actionPerformed();
 911     }
 912     else if (source == showGroupConservation)
 913     {
 914       showGroupConservation_actionPerformed();
 915     }
 916     else if (source == showSequenceLogo)
 917     {
 918       showSequenceLogo_actionPerformed();
 919     }
 920     else if (source == normSequenceLogo)
 921     {
 922       normSequenceLogo_actionPerformed();
 923     }
 924     else if (source == showConsensusHistogram)
 925     {
 926       showConsensusHistogram_actionPerformed();
 927     }
 928     else if (source == applyAutoAnnotationSettings)
 929     {
 930       applyAutoAnnotationSettings_actionPerformed();
 931     }
 932     alignPanel.paintAlignment(true);
 933   }
 934
 935   /**
 936    * Set the visibility state of sequence-related and/or alignment-related
 937    * annotations depending on checkbox selections, and repaint.
 938    *
 939    * @param visible
 940    */
 941   private void setAnnotationsVisibility()
 942   {
 943     boolean showForAlignment = showAlignmentAnnotations.getState();
 944     boolean showForSequences = showSequenceAnnotations.getState();
 945     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 946     {
 947       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 948               .getAlignmentAnnotation())
 949       {
 950         boolean visible = (aa.sequenceRef == null ? showForAlignment
 951                 : showForSequences);
 952         aa.visible = visible;
 953       }
 954     }
 955     alignPanel.validateAnnotationDimensions(true);
 956     validate();
 957     repaint();
 958   }
 959
 960   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 961   {
 962     this.annotationSortOrder = order;
 963   }
 964
 965   /**
 966    * Set flags on the viewport that control annotation ordering
 967    */
 968   private void setViewportAnnotationOrder()
 969   {
 970     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 971     this.alignPanel.av
 972             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 973   }
 974
 975   private void setShowAutoCalculatedAbove(boolean showAbove)
 976   {
 977     this.showAutoCalculatedAbove = showAbove;
 978   }
 979
 980   private void mouseOverFlag_stateChanged()
 981   {
 982     viewport.setFollowHighlight(followMouseOverFlag.getState());
 983     // TODO: could kick the scrollTo mechanism to reset view for current
 984     // searchresults.
 985   }
 986
 987   private void centreColumnLabelFlag_stateChanged()
 988   {
 989     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 990     this.alignPanel.annotationPanel.repaint();
 991   }
 992
 993   @Override
 994   public void actionPerformed(ActionEvent evt)
 995   {
 996     viewport.applet.currentAlignFrame = this;
 997
 998     Object source = evt.getSource();
 999
1000     if (source == inputText)
1001     {
1002       inputText_actionPerformed();
1003     }
1004     else if (source == loadTree)
1005     {
1006       loadTree_actionPerformed();
1007     }
1008     else if (source == loadApplication)
1009     {
1010       launchFullApplication();
1011     }
1012     else if (source == loadAnnotations)
1013     {
1014       loadAnnotations();
1015     }
1016     else if (source == outputAnnotations)
1017     {
1018       outputAnnotations(true);
1019     }
1020     else if (source == outputFeatures)
1021     {
1022       outputFeatures(true, "Jalview");
1023     }
1024     else if (source == closeMenuItem)
1025     {
1026       closeMenuItem_actionPerformed();
1027     }
1028     else if (source == copy)
1029     {
1030       copy_actionPerformed();
1031     }
1032     else if (source == undoMenuItem)
1033     {
1034       undoMenuItem_actionPerformed();
1035     }
1036     else if (source == redoMenuItem)
1037     {
1038       redoMenuItem_actionPerformed();
1039     }
1040     else if (source == inputText)
1041     {
1042       inputText_actionPerformed();
1043     }
1044     else if (source == closeMenuItem)
1045     {
1046       closeMenuItem_actionPerformed();
1047     }
1048     else if (source == undoMenuItem)
1049     {
1050       undoMenuItem_actionPerformed();
1051     }
1052     else if (source == redoMenuItem)
1053     {
1054       redoMenuItem_actionPerformed();
1055     }
1056     else if (source == copy)
1057     {
1058       copy_actionPerformed();
1059     }
1060     else if (source == pasteNew)
1061     {
1062       pasteNew_actionPerformed();
1063     }
1064     else if (source == pasteThis)
1065     {
1066       pasteThis_actionPerformed();
1067     }
1068     else if (source == cut)
1069     {
1070       cut_actionPerformed();
1071     }
1072     else if (source == delete)
1073     {
1074       delete_actionPerformed();
1075     }
1076     else if (source == createGroup)
1077     {
1078       createGroup_actionPerformed();
1079     }
1080     else if (source == unGroup)
1081     {
1082       unGroup_actionPerformed();
1083     }
1084     else if (source == grpsFromSelection)
1085     {
1086       makeGrpsFromSelection_actionPerformed();
1087     }
1088     else if (source == deleteGroups)
1089     {
1090       deleteGroups_actionPerformed();
1091     }
1092     else if (source == selectAllSequenceMenuItem)
1093     {
1094       selectAllSequenceMenuItem_actionPerformed();
1095     }
1096     else if (source == deselectAllSequenceMenuItem)
1097     {
1098       deselectAllSequenceMenuItem_actionPerformed();
1099     }
1100     else if (source == invertSequenceMenuItem)
1101     {
1102       invertSequenceMenuItem_actionPerformed();
1103       // uncomment to slave sequence selections in split frame
1104       // viewport.sendSelection();
1105     }
1106     else if (source == invertColSel)
1107     {
1108       viewport.invertColumnSelection();
1109       alignPanel.paintAlignment(true);
1110       viewport.sendSelection();
1111     }
1112     else if (source == remove2LeftMenuItem)
1113     {
1114       trimAlignment(true);
1115     }
1116     else if (source == remove2RightMenuItem)
1117     {
1118       trimAlignment(false);
1119     }
1120     else if (source == removeGappedColumnMenuItem)
1121     {
1122       removeGappedColumnMenuItem_actionPerformed();
1123     }
1124     else if (source == removeAllGapsMenuItem)
1125     {
1126       removeAllGapsMenuItem_actionPerformed();
1127     }
1128     else if (source == findMenuItem)
1129     {
1130       findMenuItem_actionPerformed();
1131     }
1132     else if (source == font)
1133     {
1134       new FontChooser(alignPanel);
1135     }
1136     else if (source == newView)
1137     {
1138       newView(null);
1139     }
1140     else if (source == showColumns)
1141     {
1142       viewport.showAllHiddenColumns();
1143       alignPanel.paintAlignment(true);
1144       viewport.sendSelection();
1145     }
1146     else if (source == showSeqs)
1147     {
1148       viewport.showAllHiddenSeqs();
1149       alignPanel.paintAlignment(true);
1150       // uncomment if we want to slave sequence selections in split frame
1151       // viewport.sendSelection();
1152     }
1153     else if (source == hideColumns)
1154     {
1155       viewport.hideSelectedColumns();
1156       alignPanel.paintAlignment(true);
1157       viewport.sendSelection();
1158     }
1159     else if (source == hideSequences
1160             && viewport.getSelectionGroup() != null)
1161     {
1162       viewport.hideAllSelectedSeqs();
1163       alignPanel.paintAlignment(true);
1164       // uncomment if we want to slave sequence selections in split frame
1165       // viewport.sendSelection();
1166     }
1167     else if (source == hideAllButSelection)
1168     {
1169       toggleHiddenRegions(false, false);
1170       alignPanel.paintAlignment(true);
1171       viewport.sendSelection();
1172     }
1173     else if (source == hideAllSelection)
1174     {
1175       SequenceGroup sg = viewport.getSelectionGroup();
1176       viewport.expandColSelection(sg, false);
1177       viewport.hideAllSelectedSeqs();
1178       viewport.hideSelectedColumns();
1179       alignPanel.paintAlignment(true);
1180       viewport.sendSelection();
1181     }
1182     else if (source == showAllHidden)
1183     {
1184       viewport.showAllHiddenColumns();
1185       viewport.showAllHiddenSeqs();
1186       alignPanel.paintAlignment(true);
1187       viewport.sendSelection();
1188     }
1189     else if (source == showGroupConsensus)
1190     {
1191       showGroupConsensus_actionPerformed();
1192     }
1193     else if (source == showGroupConservation)
1194     {
1195       showGroupConservation_actionPerformed();
1196     }
1197     else if (source == showSequenceLogo)
1198     {
1199       showSequenceLogo_actionPerformed();
1200     }
1201     else if (source == normSequenceLogo)
1202     {
1203       normSequenceLogo_actionPerformed();
1204     }
1205     else if (source == showConsensusHistogram)
1206     {
1207       showConsensusHistogram_actionPerformed();
1208     }
1209     else if (source == applyAutoAnnotationSettings)
1210     {
1211       applyAutoAnnotationSettings_actionPerformed();
1212     }
1213     else if (source == featureSettings)
1214     {
1215       new FeatureSettings(alignPanel);
1216     }
1217     else if (source == alProperties)
1218     {
1219       StringBuffer contents = new jalview.io.AlignmentProperties(
1220               viewport.getAlignment()).formatAsString();
1221       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1222       cap.setText(contents.toString());
1223       Frame frame = new Frame();
1224       frame.add(cap);
1225       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1226               "label.alignment_properties", new String[] { getTitle() }),
1227               400, 250);
1228     }
1229     else if (source == overviewMenuItem)
1230     {
1231       overviewMenuItem_actionPerformed();
1232     }
1233     else if (source == noColourmenuItem)
1234     {
1235       changeColour(null);
1236     }
1237     else if (source == clustalColour)
1238     {
1239       abovePIDThreshold.setState(false);
1240       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1241     }
1242     else if (source == zappoColour)
1243     {
1244       changeColour(new ZappoColourScheme());
1245     }
1246     else if (source == taylorColour)
1247     {
1248       changeColour(new TaylorColourScheme());
1249     }
1250     else if (source == hydrophobicityColour)
1251     {
1252       changeColour(new HydrophobicColourScheme());
1253     }
1254     else if (source == helixColour)
1255     {
1256       changeColour(new HelixColourScheme());
1257     }
1258     else if (source == strandColour)
1259     {
1260       changeColour(new StrandColourScheme());
1261     }
1262     else if (source == turnColour)
1263     {
1264       changeColour(new TurnColourScheme());
1265     }
1266     else if (source == buriedColour)
1267     {
1268       changeColour(new BuriedColourScheme());
1269     }
1270     else if (source == nucleotideColour)
1271     {
1272       changeColour(new NucleotideColourScheme());
1273     }
1274     else if (source == purinePyrimidineColour)
1275     {
1276       changeColour(new PurinePyrimidineColourScheme());
1277     }
1278     // else if (source == RNAInteractionColour)
1279     // {
1280     // changeColour(new RNAInteractionColourScheme());
1281     // }
1282     else if (source == RNAHelixColour)
1283     {
1284       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1285       // new RNAHelicesColourChooser(viewport, alignPanel);
1286     }
1287     else if (source == modifyPID)
1288     {
1289       modifyPID_actionPerformed();
1290     }
1291     else if (source == modifyConservation)
1292     {
1293       modifyConservation_actionPerformed();
1294     }
1295     else if (source == userDefinedColour)
1296     {
1297       new UserDefinedColours(alignPanel, null);
1298     }
1299     else if (source == PIDColour)
1300     {
1301       changeColour(new PIDColourScheme());
1302     }
1303     else if (source == BLOSUM62Colour)
1304     {
1305       changeColour(new Blosum62ColourScheme());
1306     }
1307     else if (source == tcoffeeColour)
1308     {
1309       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1310     }
1311     else if (source == annotationColour)
1312     {
1313       new AnnotationColourChooser(viewport, alignPanel);
1314     }
1315     else if (source == annotationColumnSelection)
1316     {
1317       new AnnotationColumnChooser(viewport, alignPanel);
1318     }
1319     else if (source == sortPairwiseMenuItem)
1320     {
1321       sortPairwiseMenuItem_actionPerformed();
1322     }
1323     else if (source == sortIDMenuItem)
1324     {
1325       sortIDMenuItem_actionPerformed();
1326     }
1327     else if (source == sortLengthMenuItem)
1328     {
1329       sortLengthMenuItem_actionPerformed();
1330     }
1331     else if (source == sortGroupMenuItem)
1332     {
1333       sortGroupMenuItem_actionPerformed();
1334     }
1335     else if (source == removeRedundancyMenuItem)
1336     {
1337       removeRedundancyMenuItem_actionPerformed();
1338     }
1339     else if (source == pairwiseAlignmentMenuItem)
1340     {
1341       pairwiseAlignmentMenuItem_actionPerformed();
1342     }
1343     else if (source == PCAMenuItem)
1344     {
1345       PCAMenuItem_actionPerformed();
1346     }
1347     else if (source == averageDistanceTreeMenuItem)
1348     {
1349       averageDistanceTreeMenuItem_actionPerformed();
1350     }
1351     else if (source == neighbourTreeMenuItem)
1352     {
1353       neighbourTreeMenuItem_actionPerformed();
1354     }
1355     else if (source == njTreeBlosumMenuItem)
1356     {
1357       njTreeBlosumMenuItem_actionPerformed();
1358     }
1359     else if (source == avDistanceTreeBlosumMenuItem)
1360     {
1361       avTreeBlosumMenuItem_actionPerformed();
1362     }
1363     else if (source == documentation)
1364     {
1365       documentation_actionPerformed();
1366     }
1367     else if (source == about)
1368     {
1369       about_actionPerformed();
1370     }
1371
1372   }
1373
1374   public void inputText_actionPerformed()
1375   {
1376     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377     Frame frame = new Frame();
1378     frame.add(cap);
1379     jalview.bin.JalviewLite.addFrame(frame,
1380             MessageManager.getString("label.input_cut_paste"), 500, 500);
1381   }
1382
1383   protected void outputText_actionPerformed(ActionEvent e)
1384   {
1385     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1386     Frame frame = new Frame();
1387     frame.add(cap);
1388     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1389             "label.alignment_output_command",
1390             new Object[] { e.getActionCommand() }), 600, 500);
1391
1392     FileFormatI fileFormat = FileFormats.getInstance().forName(
1393             e.getActionCommand());
1394     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1395             fileFormat, viewport.getAlignment(),
1396             viewport.getShowJVSuffix()));
1397   }
1398
1399   public void loadAnnotations()
1400   {
1401     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1402     cap.setText(MessageManager
1403             .getString("label.paste_features_annotations_Tcoffee_here"));
1404     cap.setAnnotationImport();
1405     Frame frame = new Frame();
1406     frame.add(cap);
1407     jalview.bin.JalviewLite.addFrame(frame,
1408             MessageManager.getString("action.paste_annotations"), 400, 300);
1409
1410   }
1411
1412   public String outputAnnotations(boolean displayTextbox)
1413   {
1414     String annotation = new AnnotationFile()
1415             .printAnnotationsForView(viewport);
1416
1417     if (displayTextbox)
1418     {
1419       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1420       Frame frame = new Frame();
1421       frame.add(cap);
1422       jalview.bin.JalviewLite.addFrame(frame,
1423               MessageManager.getString("label.annotations"), 600, 500);
1424       cap.setText(annotation);
1425     }
1426
1427     return annotation;
1428   }
1429
1430   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1431   {
1432     if (alignPanel.getFeatureRenderer() != null
1433             && viewport.getFeaturesDisplayed() != null)
1434     {
1435       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1436
1437     }
1438     return null;
1439   }
1440
1441   public String outputFeatures(boolean displayTextbox, String format)
1442   {
1443     String features;
1444     FeaturesFile formatter = new FeaturesFile();
1445     if (format.equalsIgnoreCase("Jalview"))
1446     {
1447       features = formatter.printJalviewFormat(viewport.getAlignment()
1448               .getSequencesArray(), getDisplayedFeatureCols());
1449     }
1450     else
1451     {
1452       features = formatter.printGffFormat(viewport.getAlignment()
1453               .getSequencesArray(), getDisplayedFeatureCols());
1454     }
1455
1456     if (displayTextbox)
1457     {
1458       boolean frimport = false;
1459       if (features == null || features.equals("No Features Visible"))
1460       {
1461         features = "# No features visible - paste some and import them here.";
1462         frimport = true;
1463       }
1464
1465       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1466       if (frimport)
1467       {
1468         cap.setAnnotationImport();
1469       }
1470       Frame frame = new Frame();
1471       frame.add(cap);
1472       jalview.bin.JalviewLite.addFrame(frame,
1473               MessageManager.getString("label.features"), 600, 500);
1474       cap.setText(features);
1475     }
1476     else
1477     {
1478       if (features == null)
1479       {
1480         features = "";
1481       }
1482     }
1483
1484     return features;
1485   }
1486
1487   void launchFullApplication()
1488   {
1489     StringBuffer url = new StringBuffer(jalviewServletURL);
1490
1491     // allow servlet parameters to be passed in applet parameter
1492     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1493             : "?";
1494     url.append(firstSep);
1495
1496     url.append("open="
1497             + appendProtocol(viewport.applet.getParameter("file")));
1498
1499     if (viewport.applet.getParameter("features") != null)
1500     {
1501       url.append("&features=");
1502       url.append(appendProtocol(viewport.applet.getParameter("features")));
1503     }
1504
1505     if (viewport.applet.getParameter("annotations") != null)
1506     {
1507       url.append("&annotations=");
1508       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1509     }
1510
1511     if (viewport.applet.getParameter("jnetfile") != null
1512             || viewport.applet.getParameter("jpredfile") != null)
1513     {
1514       url.append("&annotations=");
1515       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1516               .getParameter("jnetfile") : viewport.applet
1517               .getParameter("jpredfile")));
1518     }
1519
1520     if (viewport.applet.getParameter("defaultColour") != null)
1521     {
1522       url.append("&colour="
1523               + removeWhiteSpace(viewport.applet
1524                       .getParameter("defaultColour")));
1525     }
1526
1527     if (viewport.applet.getParameter("userDefinedColour") != null)
1528     {
1529       url.append("&colour="
1530               + removeWhiteSpace(viewport.applet
1531                       .getParameter("userDefinedColour")));
1532     }
1533     if (viewport.applet.getParameter("tree") != null)
1534     {
1535       url.append("&tree="
1536               + appendProtocol(viewport.applet.getParameter("tree")));
1537     }
1538     if (viewport.applet.getParameter("treeFile") != null)
1539     {
1540       url.append("&tree="
1541               + appendProtocol(viewport.applet.getParameter("treeFile")));
1542     }
1543
1544     showURL(url.toString(), "FULL_APP");
1545   }
1546
1547   String removeWhiteSpace(String colour)
1548   {
1549     StringBuffer sb = new StringBuffer();
1550     for (int i = 0; i < colour.length(); i++)
1551     {
1552       if (Character.isWhitespace(colour.charAt(i)))
1553       {
1554         sb.append("%20");
1555       }
1556       else
1557       {
1558         sb.append(colour.charAt(i));
1559       }
1560     }
1561
1562     return sb.toString();
1563   }
1564
1565   String appendProtocol(String url)
1566   {
1567     try
1568     {
1569       new URL(url);
1570       url = URLEncoder.encode(url);
1571     }
1572     /*
1573      * When we finally deprecate 1.1 compatibility, we can start to use
1574      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1575      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1576      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1577      * ex.printStackTrace(); }
1578      */
1579     catch (java.net.MalformedURLException ex)
1580     {
1581       url = viewport.applet.getCodeBase() + url;
1582     }
1583     return url;
1584   }
1585
1586   public void closeMenuItem_actionPerformed()
1587   {
1588     PaintRefresher.RemoveComponent(alignPanel);
1589     if (alignPanel.seqPanel != null
1590             && alignPanel.seqPanel.seqCanvas != null)
1591     {
1592       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1593     }
1594     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1595     {
1596       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1597     }
1598
1599     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1600     {
1601       System.exit(0);
1602     }
1603     else
1604     {
1605     }
1606     viewport = null;
1607     alignPanel = null;
1608     this.dispose();
1609   }
1610
1611   /**
1612    * TODO: JAL-1104
1613    */
1614   void updateEditMenuBar()
1615   {
1616
1617     if (viewport.getHistoryList().size() > 0)
1618     {
1619       undoMenuItem.setEnabled(true);
1620       CommandI command = viewport.getHistoryList().peek();
1621       undoMenuItem.setLabel(MessageManager.formatMessage(
1622               "label.undo_command",
1623               new Object[] { command.getDescription() }));
1624     }
1625     else
1626     {
1627       undoMenuItem.setEnabled(false);
1628       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1629     }
1630
1631     if (viewport.getRedoList().size() > 0)
1632     {
1633       redoMenuItem.setEnabled(true);
1634
1635       CommandI command = viewport.getRedoList().peek();
1636       redoMenuItem.setLabel(MessageManager.formatMessage(
1637               "label.redo_command",
1638               new Object[] { command.getDescription() }));
1639     }
1640     else
1641     {
1642       redoMenuItem.setEnabled(false);
1643       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1644     }
1645   }
1646
1647   /**
1648    * TODO: JAL-1104
1649    */
1650   @Override
1651   public void addHistoryItem(CommandI command)
1652   {
1653     if (command.getSize() > 0)
1654     {
1655       viewport.addToHistoryList(command);
1656       viewport.clearRedoList();
1657       updateEditMenuBar();
1658       viewport.updateHiddenColumns();
1659     }
1660   }
1661
1662   /**
1663    * TODO: JAL-1104 DOCUMENT ME!
1664    *
1665    * @param e
1666    *          DOCUMENT ME!
1667    */
1668   protected void undoMenuItem_actionPerformed()
1669   {
1670     if (viewport.getHistoryList().isEmpty())
1671     {
1672       return;
1673     }
1674
1675     CommandI command = viewport.getHistoryList().pop();
1676     viewport.addToRedoList(command);
1677     command.undoCommand(null);
1678
1679     AlignmentViewport originalSource = getOriginatingSource(command);
1680     // JBPNote Test
1681     if (originalSource != viewport)
1682     {
1683       System.err
1684               .println("Warning: Viewport object mismatch whilst undoing");
1685     }
1686     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1687                                           // viewport.getColumnSelection().getHiddenColumns()
1688                                           // != null;
1689     updateEditMenuBar();
1690     originalSource.firePropertyChange("alignment", null, originalSource
1691             .getAlignment().getSequences());
1692   }
1693
1694   /**
1695    * TODO: JAL-1104 DOCUMENT ME!
1696    *
1697    * @param e
1698    *          DOCUMENT ME!
1699    */
1700   protected void redoMenuItem_actionPerformed()
1701   {
1702     if (viewport.getRedoList().isEmpty())
1703     {
1704       return;
1705     }
1706
1707     CommandI command = viewport.getRedoList().pop();
1708     viewport.addToHistoryList(command);
1709     command.doCommand(null);
1710
1711     AlignmentViewport originalSource = getOriginatingSource(command);
1712     // JBPNote Test
1713     if (originalSource != viewport)
1714     {
1715       System.err
1716               .println("Warning: Viewport object mismatch whilst re-doing");
1717     }
1718     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1719                                           // viewport.getColumnSelection().getHiddenColumns()
1720                                           // != null;
1721
1722     updateEditMenuBar();
1723     originalSource.firePropertyChange("alignment", null, originalSource
1724             .getAlignment().getSequences());
1725   }
1726
1727   AlignmentViewport getOriginatingSource(CommandI command)
1728   {
1729     AlignmentViewport originalSource = null;
1730     // For sequence removal and addition, we need to fire
1731     // the property change event FROM the viewport where the
1732     // original alignment was altered
1733     AlignmentI al = null;
1734     if (command instanceof EditCommand)
1735     {
1736       EditCommand editCommand = (EditCommand) command;
1737       al = editCommand.getAlignment();
1738       Vector comps = (Vector) PaintRefresher.components.get(viewport
1739               .getSequenceSetId());
1740       for (int i = 0; i < comps.size(); i++)
1741       {
1742         if (comps.elementAt(i) instanceof AlignmentPanel)
1743         {
1744           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1745           {
1746             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1747             break;
1748           }
1749         }
1750       }
1751     }
1752
1753     if (originalSource == null)
1754     {
1755       // The original view is closed, we must validate
1756       // the current view against the closed view first
1757       if (al != null)
1758       {
1759         PaintRefresher.validateSequences(al, viewport.getAlignment());
1760       }
1761
1762       originalSource = viewport;
1763     }
1764
1765     return originalSource;
1766   }
1767
1768   /**
1769    * Move the currently selected sequences up or down one position in the
1770    * alignment
1771    *
1772    * @param up
1773    */
1774   public void moveSelectedSequences(boolean up)
1775   {
1776     SequenceGroup sg = viewport.getSelectionGroup();
1777     if (sg == null)
1778     {
1779       return;
1780     }
1781     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1782             up ? null : viewport.getHiddenRepSequences(), up);
1783     alignPanel.paintAlignment(true);
1784
1785     /*
1786      * Also move cDNA/protein complement sequences
1787      */
1788     AlignViewportI complement = viewport.getCodingComplement();
1789     if (complement != null)
1790     {
1791       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1792               viewport, complement);
1793       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1794               up ? null : complement.getHiddenRepSequences(), up);
1795       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1796     }
1797   }
1798
1799   synchronized void slideSequences(boolean right, int size)
1800   {
1801     List<SequenceI> sg = new Vector<>();
1802     if (viewport.cursorMode)
1803     {
1804       sg.add(viewport.getAlignment().getSequenceAt(
1805               alignPanel.seqPanel.seqCanvas.cursorY));
1806     }
1807     else if (viewport.getSelectionGroup() != null
1808             && viewport.getSelectionGroup().getSize() != viewport
1809                     .getAlignment().getHeight())
1810     {
1811       sg = viewport.getSelectionGroup().getSequences(
1812               viewport.getHiddenRepSequences());
1813     }
1814
1815     if (sg.size() < 1)
1816     {
1817       return;
1818     }
1819
1820     Vector<SequenceI> invertGroup = new Vector();
1821
1822     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1823     {
1824       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1825       {
1826         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1827       }
1828     }
1829
1830     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1831
1832     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1833             .size()]);
1834     for (int i = 0; i < invertGroup.size(); i++)
1835     {
1836       seqs2[i] = invertGroup.elementAt(i);
1837     }
1838
1839     SlideSequencesCommand ssc;
1840     if (right)
1841     {
1842       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1843               size, viewport.getGapCharacter());
1844     }
1845     else
1846     {
1847       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1848               size, viewport.getGapCharacter());
1849     }
1850
1851     int groupAdjustment = 0;
1852     if (ssc.getGapsInsertedBegin() && right)
1853     {
1854       if (viewport.cursorMode)
1855       {
1856         alignPanel.seqPanel.moveCursor(size, 0);
1857       }
1858       else
1859       {
1860         groupAdjustment = size;
1861       }
1862     }
1863     else if (!ssc.getGapsInsertedBegin() && !right)
1864     {
1865       if (viewport.cursorMode)
1866       {
1867         alignPanel.seqPanel.moveCursor(-size, 0);
1868       }
1869       else
1870       {
1871         groupAdjustment = -size;
1872       }
1873     }
1874
1875     if (groupAdjustment != 0)
1876     {
1877       viewport.getSelectionGroup().setStartRes(
1878               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1879       viewport.getSelectionGroup().setEndRes(
1880               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1881     }
1882
1883     boolean appendHistoryItem = false;
1884     Deque<CommandI> historyList = viewport.getHistoryList();
1885     if (historyList != null && historyList.size() > 0
1886             && historyList.peek() instanceof SlideSequencesCommand)
1887     {
1888       appendHistoryItem = ssc
1889               .appendSlideCommand((SlideSequencesCommand) historyList
1890                       .peek());
1891     }
1892
1893     if (!appendHistoryItem)
1894     {
1895       addHistoryItem(ssc);
1896     }
1897
1898     repaint();
1899   }
1900
1901   static StringBuffer copiedSequences;
1902
1903   static Vector copiedHiddenColumns;
1904
1905   protected void copy_actionPerformed()
1906   {
1907     if (viewport.getSelectionGroup() == null)
1908     {
1909       return;
1910     }
1911
1912     SequenceGroup sg = viewport.getSelectionGroup();
1913     copiedSequences = new StringBuffer();
1914     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1915     for (int i = 0; i < sg.getSize(); i++)
1916     {
1917       SequenceI seq = sg.getSequenceAt(i);
1918       int index = viewport.getAlignment().findIndex(seq);
1919       orderedSeqs.put(index, seq);
1920     }
1921
1922     int index = 0, startRes, endRes;
1923     char ch;
1924
1925     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1926     {
1927       copiedHiddenColumns = new Vector();
1928       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1929       for (int[] region : viewport.getAlignment().getHiddenColumns())
1930       {
1931         copiedHiddenColumns.addElement(new int[] {
1932             region[0] - hiddenOffset, region[1] - hiddenOffset });
1933       }
1934     }
1935     else
1936     {
1937       copiedHiddenColumns = null;
1938     }
1939
1940     for (int i = 0; i < sg.getSize(); i++)
1941     {
1942       SequenceI seq = null;
1943
1944       while (seq == null)
1945       {
1946         if (orderedSeqs.containsKey(index))
1947         {
1948           seq = orderedSeqs.get(index);
1949           index++;
1950           break;
1951         }
1952         else
1953         {
1954           index++;
1955         }
1956       }
1957
1958       // FIND START RES
1959       // Returns residue following index if gap
1960       startRes = seq.findPosition(sg.getStartRes());
1961
1962       // FIND END RES
1963       // Need to find the residue preceeding index if gap
1964       endRes = 0;
1965
1966       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1967       {
1968         ch = seq.getCharAt(j);
1969         if (!jalview.util.Comparison.isGap((ch)))
1970         {
1971           endRes++;
1972         }
1973       }
1974
1975       if (endRes > 0)
1976       {
1977         endRes += seq.getStart() - 1;
1978       }
1979
1980       copiedSequences.append(seq.getName()
1981               + "\t"
1982               + startRes
1983               + "\t"
1984               + endRes
1985               + "\t"
1986               + seq.getSequenceAsString(sg.getStartRes(),
1987                       sg.getEndRes() + 1) + "\n");
1988     }
1989
1990   }
1991
1992   protected void pasteNew_actionPerformed()
1993   {
1994     paste(true);
1995   }
1996
1997   protected void pasteThis_actionPerformed()
1998   {
1999     paste(false);
2000   }
2001
2002   void paste(boolean newAlignment)
2003   {
2004     try
2005     {
2006
2007       if (copiedSequences == null)
2008       {
2009         return;
2010       }
2011
2012       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2013       Vector seqs = new Vector();
2014       while (st.hasMoreElements())
2015       {
2016         String name = st.nextToken();
2017         int start = Integer.parseInt(st.nextToken());
2018         int end = Integer.parseInt(st.nextToken());
2019         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2020       }
2021       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2022       for (int i = 0; i < seqs.size(); i++)
2023       {
2024         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2025       }
2026
2027       if (newAlignment)
2028       {
2029         String newtitle = MessageManager
2030                 .getString("label.copied_sequences");
2031         if (getTitle().startsWith(
2032                 MessageManager.getString("label.copied_sequences")))
2033         {
2034           newtitle = getTitle();
2035         }
2036         else
2037         {
2038           newtitle = newtitle.concat(MessageManager.formatMessage(
2039                   "label.from_msname", new String[] { getTitle() }));
2040         }
2041         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2042                 viewport.applet, newtitle, false);
2043         if (copiedHiddenColumns != null)
2044         {
2045           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2046           {
2047             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2048             af.viewport.hideColumns(region[0], region[1]);
2049           }
2050         }
2051
2052         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2053                 frameHeight);
2054       }
2055       else
2056       {
2057         addSequences(newSeqs);
2058       }
2059
2060     } catch (Exception ex)
2061     {
2062     } // could be anything being pasted in here
2063
2064   }
2065
2066   void addSequences(SequenceI[] seqs)
2067   {
2068     for (int i = 0; i < seqs.length; i++)
2069     {
2070       viewport.getAlignment().addSequence(seqs[i]);
2071     }
2072
2073     // !newAlignment
2074     addHistoryItem(new EditCommand(
2075             MessageManager.getString("label.add_sequences"), Action.PASTE,
2076             seqs, 0, viewport.getAlignment().getWidth(),
2077             viewport.getAlignment()));
2078
2079     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2080     viewport.getAlignment().getWidth();
2081     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082             .getSequences());
2083
2084   }
2085
2086   protected void cut_actionPerformed()
2087   {
2088     copy_actionPerformed();
2089     delete_actionPerformed();
2090   }
2091
2092   protected void delete_actionPerformed()
2093   {
2094
2095     SequenceGroup sg = viewport.getSelectionGroup();
2096     if (sg == null)
2097     {
2098       return;
2099     }
2100
2101     Vector seqs = new Vector();
2102     SequenceI seq;
2103     for (int i = 0; i < sg.getSize(); i++)
2104     {
2105       seq = sg.getSequenceAt(i);
2106       seqs.addElement(seq);
2107     }
2108
2109     /*
2110      * If the cut affects all sequences, warn, remove highlighted columns
2111      */
2112     if (sg.getSize() == viewport.getAlignment().getHeight())
2113     {
2114       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2115               .getAlignment().getWidth()) ? true : false;
2116       if (isEntireAlignWidth)
2117       {
2118         String title = MessageManager.getString("label.delete_all");
2119         Panel infoPanel = new Panel();
2120         infoPanel.setLayout(new FlowLayout());
2121         infoPanel
2122                 .add(new Label(MessageManager.getString("warn.delete_all")));
2123
2124         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2125         dialog.setMainPanel(infoPanel);
2126         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2127         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2128         dialog.setVisible(true);
2129
2130         if (!dialog.accept)
2131         {
2132           return;
2133         }
2134       }
2135       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2136               sg.getEndRes() + 1);
2137     }
2138
2139     SequenceI[] cut = new SequenceI[seqs.size()];
2140     for (int i = 0; i < seqs.size(); i++)
2141     {
2142       cut[i] = (SequenceI) seqs.elementAt(i);
2143     }
2144
2145     /*
2146      * //ADD HISTORY ITEM
2147      */
2148     addHistoryItem(new EditCommand(
2149             MessageManager.getString("label.cut_sequences"), Action.CUT,
2150             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2151             viewport.getAlignment()));
2152
2153     viewport.setSelectionGroup(null);
2154     viewport.getAlignment().deleteGroup(sg);
2155
2156     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2157             .getSequences());
2158
2159     if (viewport.getAlignment().getHeight() < 1)
2160     {
2161       this.setVisible(false);
2162     }
2163     viewport.sendSelection();
2164   }
2165
2166   /**
2167    * group consensus toggled
2168    *
2169    */
2170   protected void showGroupConsensus_actionPerformed()
2171   {
2172     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2173     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174
2175   }
2176
2177   /**
2178    * group conservation toggled.
2179    */
2180   protected void showGroupConservation_actionPerformed()
2181   {
2182     viewport.setShowGroupConservation(showGroupConservation.getState());
2183     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2184   }
2185
2186   /*
2187    * (non-Javadoc)
2188    *
2189    * @see
2190    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2191    * .event.ActionEvent)
2192    */
2193   protected void showConsensusHistogram_actionPerformed()
2194   {
2195     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2196     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2197   }
2198
2199   /*
2200    * (non-Javadoc)
2201    *
2202    * @see
2203    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2204    * .event.ActionEvent)
2205    */
2206   protected void showSequenceLogo_actionPerformed()
2207   {
2208     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2209     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210   }
2211
2212   protected void normSequenceLogo_actionPerformed()
2213   {
2214     showSequenceLogo.setState(true);
2215     viewport.setShowSequenceLogo(true);
2216     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2217     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2218   }
2219
2220   protected void applyAutoAnnotationSettings_actionPerformed()
2221   {
2222     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223   }
2224
2225   protected void makeGrpsFromSelection_actionPerformed()
2226   {
2227     if (avc.makeGroupsFromSelection())
2228     {
2229       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2230       alignPanel.updateAnnotation();
2231       alignPanel.paintAlignment(true);
2232     }
2233   }
2234
2235   protected void createGroup_actionPerformed()
2236   {
2237     avc.createGroup();
2238   }
2239
2240   protected void unGroup_actionPerformed()
2241   {
2242     if (avc.unGroup())
2243     {
2244       alignPanel.alignmentChanged();
2245     }
2246   }
2247
2248   protected void deleteGroups_actionPerformed()
2249   {
2250     if (avc.deleteGroups())
2251     {
2252       alignPanel.alignmentChanged();
2253     }
2254   }
2255
2256   public void selectAllSequenceMenuItem_actionPerformed()
2257   {
2258     SequenceGroup sg = new SequenceGroup();
2259     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2260     {
2261       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2262     }
2263     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2264     viewport.setSelectionGroup(sg);
2265     // JAL-2034 - should delegate to
2266     // alignPanel to decide if overview needs
2267     // updating.
2268     alignPanel.paintAlignment(false);
2269     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2270     viewport.sendSelection();
2271   }
2272
2273   public void deselectAllSequenceMenuItem_actionPerformed()
2274   {
2275     if (viewport.cursorMode)
2276     {
2277       alignPanel.seqPanel.keyboardNo1 = null;
2278       alignPanel.seqPanel.keyboardNo2 = null;
2279     }
2280     viewport.setSelectionGroup(null);
2281     viewport.getColumnSelection().clear();
2282     viewport.setSelectionGroup(null);
2283     alignPanel.idPanel.idCanvas.searchResults = null;
2284     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2285     // JAL-2034 - should delegate to
2286     // alignPanel to decide if overview needs
2287     // updating.
2288     alignPanel.paintAlignment(false);
2289     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2290     viewport.sendSelection();
2291   }
2292
2293   public void invertSequenceMenuItem_actionPerformed()
2294   {
2295     SequenceGroup sg = viewport.getSelectionGroup();
2296     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2297     {
2298       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2299     }
2300
2301     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2302     viewport.sendSelection();
2303   }
2304
2305   public void invertColSel_actionPerformed()
2306   {
2307     viewport.invertColumnSelection();
2308     alignPanel.paintAlignment(true);
2309     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2310     viewport.sendSelection();
2311   }
2312
2313   void trimAlignment(boolean trimLeft)
2314   {
2315     AlignmentI al = viewport.getAlignment();
2316     ViewportRanges ranges = viewport.getRanges();
2317     ColumnSelection colSel = viewport.getColumnSelection();
2318     int column;
2319
2320     if (!colSel.isEmpty())
2321     {
2322       if (trimLeft)
2323       {
2324         column = colSel.getMin();
2325       }
2326       else
2327       {
2328         column = colSel.getMax();
2329       }
2330
2331       SequenceI[] seqs;
2332       if (viewport.getSelectionGroup() != null)
2333       {
2334         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335                 viewport.getHiddenRepSequences());
2336       }
2337       else
2338       {
2339         seqs = al.getSequencesArray();
2340       }
2341
2342       TrimRegionCommand trimRegion;
2343       if (trimLeft)
2344       {
2345         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2346                 column, al);
2347         ranges.setStartRes(0);
2348       }
2349       else
2350       {
2351         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2352                 column, al);
2353       }
2354
2355       statusBar.setText(MessageManager.formatMessage(
2356               "label.removed_columns",
2357               new String[] { Integer.valueOf(trimRegion.getSize())
2358                       .toString() }));
2359       addHistoryItem(trimRegion);
2360
2361       for (SequenceGroup sg : al.getGroups())
2362       {
2363         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2364                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2365         {
2366           al.deleteGroup(sg);
2367         }
2368       }
2369
2370       viewport.firePropertyChange("alignment", null, al.getSequences());
2371     }
2372   }
2373
2374   public void removeGappedColumnMenuItem_actionPerformed()
2375   {
2376     AlignmentI al = viewport.getAlignment();
2377     ViewportRanges ranges = viewport.getRanges();
2378     int start = 0;
2379     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2380
2381     SequenceI[] seqs;
2382     if (viewport.getSelectionGroup() != null)
2383     {
2384       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2385               viewport.getHiddenRepSequences());
2386       start = viewport.getSelectionGroup().getStartRes();
2387       end = viewport.getSelectionGroup().getEndRes();
2388     }
2389     else
2390     {
2391       seqs = viewport.getAlignment().getSequencesArray();
2392     }
2393
2394     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2395             "Remove Gapped Columns", seqs, start, end,
2396             viewport.getAlignment());
2397
2398     addHistoryItem(removeGapCols);
2399
2400     statusBar.setText(MessageManager.formatMessage(
2401             "label.removed_empty_columns",
2402             new String[] { Integer.valueOf(removeGapCols.getSize())
2403                     .toString() }));
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = al.getSequenceAt(0);
2408     int startRes = seq.findPosition(ranges.getStartRes());
2409     // ShiftList shifts;
2410     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411     // edit.alColumnChanges=shifts.getInverse();
2412     // if (viewport.hasHiddenColumns)
2413     // viewport.getColumnSelection().compensateForEdits(shifts);
2414     ranges.setStartRes(seq.findIndex(startRes) - 1);
2415     viewport.firePropertyChange("alignment", null, al.getSequences());
2416
2417   }
2418
2419   public void removeAllGapsMenuItem_actionPerformed()
2420   {
2421     AlignmentI al = viewport.getAlignment();
2422     ViewportRanges ranges = viewport.getRanges();
2423     int start = 0;
2424     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2425
2426     SequenceI[] seqs;
2427     if (viewport.getSelectionGroup() != null)
2428     {
2429       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2430               viewport.getHiddenRepSequences());
2431       start = viewport.getSelectionGroup().getStartRes();
2432       end = viewport.getSelectionGroup().getEndRes();
2433     }
2434     else
2435     {
2436       seqs = viewport.getAlignment().getSequencesArray();
2437     }
2438
2439     // This is to maintain viewport position on first residue
2440     // of first sequence
2441     SequenceI seq = al.getSequenceAt(0);
2442     int startRes = seq.findPosition(ranges.getStartRes());
2443
2444     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2445             al));
2446
2447     ranges.setStartRes(seq.findIndex(startRes) - 1);
2448
2449     viewport.firePropertyChange("alignment", null, al.getSequences());
2450
2451   }
2452
2453   public void findMenuItem_actionPerformed()
2454   {
2455     new Finder(alignPanel);
2456   }
2457
2458   /**
2459    * create a new view derived from the current view
2460    *
2461    * @param viewtitle
2462    * @return frame for the new view
2463    */
2464   public AlignFrame newView(String viewtitle)
2465   {
2466     AlignmentI newal;
2467     if (viewport.hasHiddenRows())
2468     {
2469       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470               .getFullAlignment().getSequencesArray());
2471     }
2472     else
2473     {
2474       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2475     }
2476
2477     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2478     {
2479       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2480       {
2481         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2482         {
2483           newal.addAnnotation(viewport.getAlignment()
2484                   .getAlignmentAnnotation()[i]);
2485         }
2486       }
2487     }
2488
2489     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2490
2491     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2492     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2493     PaintRefresher.Register(newaf.alignPanel,
2494             newaf.alignPanel.av.getSequenceSetId());
2495
2496     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2497             newaf.alignPanel.av.getSequenceSetId());
2498     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2499             newaf.alignPanel.av.getSequenceSetId());
2500
2501     Vector comps = (Vector) PaintRefresher.components.get(viewport
2502             .getSequenceSetId());
2503     int viewSize = -1;
2504     for (int i = 0; i < comps.size(); i++)
2505     {
2506       if (comps.elementAt(i) instanceof AlignmentPanel)
2507       {
2508         viewSize++;
2509       }
2510     }
2511
2512     String title = new String(this.getTitle());
2513     if (viewtitle != null)
2514     {
2515       title = viewtitle + " ( " + title + ")";
2516     }
2517     else
2518     {
2519       if (title.indexOf("(View") > -1)
2520       {
2521         title = title.substring(0, title.indexOf("(View"));
2522       }
2523       title += "(View " + viewSize + ")";
2524     }
2525
2526     newaf.setTitle(title.toString());
2527
2528     newaf.viewport.setHistoryList(viewport.getHistoryList());
2529     newaf.viewport.setRedoList(viewport.getRedoList());
2530     return newaf;
2531   }
2532
2533   /**
2534    *
2535    * @return list of feature groups on the view
2536    */
2537   public String[] getFeatureGroups()
2538   {
2539     FeatureRenderer fr = null;
2540     if (alignPanel != null
2541             && (fr = alignPanel.getFeatureRenderer()) != null)
2542     {
2543       List<String> gps = fr.getFeatureGroups();
2544       String[] _gps = gps.toArray(new String[gps.size()]);
2545       return _gps;
2546     }
2547     return null;
2548   }
2549
2550   /**
2551    * get sequence feature groups that are hidden or shown
2552    *
2553    * @param visible
2554    *          true is visible
2555    * @return list
2556    */
2557   public String[] getFeatureGroupsOfState(boolean visible)
2558   {
2559     FeatureRenderer fr = null;
2560     if (alignPanel != null
2561             && (fr = alignPanel.getFeatureRenderer()) != null)
2562     {
2563       List<String> gps = fr.getGroups(visible);
2564       String[] _gps = gps.toArray(new String[gps.size()]);
2565       return _gps;
2566     }
2567     return null;
2568   }
2569
2570   /**
2571    * Change the display state for the given feature groups
2572    *
2573    * @param groups
2574    *          list of group strings
2575    * @param state
2576    *          visible or invisible
2577    */
2578   public void setFeatureGroupState(String[] groups, boolean state)
2579   {
2580     FeatureRenderer fr = null;
2581     this.sequenceFeatures.setState(true);
2582     viewport.setShowSequenceFeatures(true);
2583     if (alignPanel != null
2584             && (fr = alignPanel.getFeatureRenderer()) != null)
2585     {
2586
2587       fr.setGroupVisibility(Arrays.asList(groups), state);
2588       alignPanel.seqPanel.seqCanvas.repaint();
2589       if (alignPanel.overviewPanel != null)
2590       {
2591         alignPanel.overviewPanel.updateOverviewImage();
2592       }
2593     }
2594   }
2595
2596   public void seqLimits_itemStateChanged()
2597   {
2598     viewport.setShowJVSuffix(seqLimits.getState());
2599     alignPanel.fontChanged();
2600     alignPanel.paintAlignment(true);
2601   }
2602
2603   protected void colourTextMenuItem_actionPerformed()
2604   {
2605     viewport.setColourText(colourTextMenuItem.getState());
2606     alignPanel.paintAlignment(true);
2607   }
2608
2609   protected void displayNonconservedMenuItem_actionPerformed()
2610   {
2611     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2612     alignPanel.paintAlignment(true);
2613   }
2614
2615   protected void wrapMenuItem_actionPerformed()
2616   {
2617     viewport.setWrapAlignment(wrapMenuItem.getState());
2618     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2619     scaleAbove.setEnabled(wrapMenuItem.getState());
2620     scaleLeft.setEnabled(wrapMenuItem.getState());
2621     scaleRight.setEnabled(wrapMenuItem.getState());
2622     alignPanel.paintAlignment(true);
2623   }
2624
2625   public void overviewMenuItem_actionPerformed()
2626   {
2627     if (alignPanel.overviewPanel != null)
2628     {
2629       return;
2630     }
2631
2632     Frame frame = new Frame();
2633     OverviewPanel overview = new OverviewPanel(alignPanel);
2634     frame.add(overview);
2635     // +50 must allow for applet frame window
2636     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2637             "label.overview_params", new String[] { this.getTitle() }),
2638             overview.getPreferredSize().width,
2639             overview.getPreferredSize().height + 50);
2640
2641     frame.pack();
2642     final AlignmentPanel ap = alignPanel;
2643     frame.addWindowListener(new WindowAdapter()
2644     {
2645       @Override
2646       public void windowClosing(WindowEvent e)
2647       {
2648         if (ap != null)
2649         {
2650           ap.setOverviewPanel(null);
2651         }
2652       };
2653     });
2654
2655     alignPanel.setOverviewPanel(overview);
2656
2657   }
2658
2659   @Override
2660   public void changeColour(ColourSchemeI cs)
2661   {
2662     viewport.setGlobalColourScheme(cs);
2663
2664     alignPanel.paintAlignment(true);
2665   }
2666
2667   protected void modifyPID_actionPerformed()
2668   {
2669     if (viewport.getAbovePIDThreshold()
2670             && viewport.getGlobalColourScheme() != null)
2671     {
2672       SliderPanel.setPIDSliderSource(alignPanel,
2673               viewport.getResidueShading(), alignPanel.getViewName());
2674       SliderPanel.showPIDSlider();
2675     }
2676   }
2677
2678   protected void modifyConservation_actionPerformed()
2679   {
2680     if (viewport.getConservationSelected()
2681             && viewport.getGlobalColourScheme() != null)
2682     {
2683       SliderPanel.setConservationSlider(alignPanel,
2684               viewport.getResidueShading(), alignPanel.getViewName());
2685       SliderPanel.showConservationSlider();
2686     }
2687   }
2688
2689   protected void conservationMenuItem_actionPerformed()
2690   {
2691     boolean selected = conservationMenuItem.getState();
2692     modifyConservation.setEnabled(selected);
2693     viewport.setConservationSelected(selected);
2694     viewport.getResidueShading().setConservationApplied(selected);
2695
2696     changeColour(viewport.getGlobalColourScheme());
2697
2698     if (selected)
2699     {
2700       modifyConservation_actionPerformed();
2701     }
2702     else
2703     {
2704       SliderPanel.hideConservationSlider();
2705     }
2706   }
2707
2708   public void abovePIDThreshold_actionPerformed()
2709   {
2710     boolean selected = abovePIDThreshold.getState();
2711     modifyPID.setEnabled(selected);
2712     viewport.setAbovePIDThreshold(selected);
2713     if (!selected)
2714     {
2715       viewport.getResidueShading().setThreshold(0,
2716               viewport.isIgnoreGapsConsensus());
2717     }
2718
2719     changeColour(viewport.getGlobalColourScheme());
2720
2721     if (selected)
2722     {
2723       modifyPID_actionPerformed();
2724     }
2725     else
2726     {
2727       SliderPanel.hidePIDSlider();
2728     }
2729   }
2730
2731   public void sortPairwiseMenuItem_actionPerformed()
2732   {
2733     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2735             .getAlignment().getSequenceAt(0));
2736
2737     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2738             viewport.getAlignment()));
2739     alignPanel.paintAlignment(true);
2740   }
2741
2742   public void sortIDMenuItem_actionPerformed()
2743   {
2744     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2745     AlignmentSorter.sortByID(viewport.getAlignment());
2746     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2747             viewport.getAlignment()));
2748     alignPanel.paintAlignment(true);
2749   }
2750
2751   public void sortLengthMenuItem_actionPerformed()
2752   {
2753     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2754     AlignmentSorter.sortByLength(viewport.getAlignment());
2755     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2756             viewport.getAlignment()));
2757     alignPanel.paintAlignment(true);
2758   }
2759
2760   public void sortGroupMenuItem_actionPerformed()
2761   {
2762     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2763     AlignmentSorter.sortByGroup(viewport.getAlignment());
2764     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2765             viewport.getAlignment()));
2766     alignPanel.paintAlignment(true);
2767
2768   }
2769
2770   public void removeRedundancyMenuItem_actionPerformed()
2771   {
2772     new RedundancyPanel(alignPanel);
2773   }
2774
2775   public void pairwiseAlignmentMenuItem_actionPerformed()
2776   {
2777     if (viewport.getSelectionGroup() != null
2778             && viewport.getSelectionGroup().getSize() > 1)
2779     {
2780       Frame frame = new Frame();
2781       frame.add(new PairwiseAlignPanel(alignPanel));
2782       jalview.bin.JalviewLite.addFrame(frame,
2783               MessageManager.getString("action.pairwise_alignment"), 600,
2784               500);
2785     }
2786   }
2787
2788   public void PCAMenuItem_actionPerformed()
2789   {
2790     // are the sequences aligned?
2791     if (!viewport.getAlignment().isAligned(false))
2792     {
2793       SequenceI current;
2794       int Width = viewport.getAlignment().getWidth();
2795
2796       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2797       {
2798         current = viewport.getAlignment().getSequenceAt(i);
2799
2800         if (current.getLength() < Width)
2801         {
2802           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2803         }
2804       }
2805       alignPanel.paintAlignment(true);
2806     }
2807
2808     if ((viewport.getSelectionGroup() != null
2809             && viewport.getSelectionGroup().getSize() < 4 && viewport
2810             .getSelectionGroup().getSize() > 0)
2811             || viewport.getAlignment().getHeight() < 4)
2812     {
2813       return;
2814     }
2815
2816     try
2817     {
2818       new PCAPanel(viewport);
2819     } catch (java.lang.OutOfMemoryError ex)
2820     {
2821     }
2822
2823   }
2824
2825   public void averageDistanceTreeMenuItem_actionPerformed()
2826   {
2827     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2828             "Average distance tree using PID");
2829   }
2830
2831   public void neighbourTreeMenuItem_actionPerformed()
2832   {
2833     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2834             "Neighbour joining tree using PID");
2835   }
2836
2837   protected void njTreeBlosumMenuItem_actionPerformed()
2838   {
2839     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2840             .getBlosum62().getName(),
2841             "Neighbour joining tree using BLOSUM62");
2842   }
2843
2844   protected void avTreeBlosumMenuItem_actionPerformed()
2845   {
2846     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2847             .getBlosum62().getName(),
2848             "Average distance tree using BLOSUM62");
2849   }
2850
2851   void newTreePanel(String type, String pwType, String title)
2852   {
2853     // are the sequences aligned?
2854     if (!viewport.getAlignment().isAligned(false))
2855     {
2856       SequenceI current;
2857       int Width = viewport.getAlignment().getWidth();
2858
2859       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2860       {
2861         current = viewport.getAlignment().getSequenceAt(i);
2862
2863         if (current.getLength() < Width)
2864         {
2865           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2866         }
2867       }
2868       alignPanel.paintAlignment(true);
2869
2870     }
2871
2872     if ((viewport.getSelectionGroup() != null && viewport
2873             .getSelectionGroup().getSize() > 1)
2874             || (viewport.getAlignment().getHeight() > 1))
2875     {
2876       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2877
2878       addTreeMenuItem(tp, title);
2879
2880       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2881     }
2882   }
2883
2884   void loadTree_actionPerformed()
2885   {
2886     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2887     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2888     cap.setTreeImport();
2889     Frame frame = new Frame();
2890     frame.add(cap);
2891     jalview.bin.JalviewLite.addFrame(frame,
2892             MessageManager.getString("label.paste_newick_file"), 400, 300);
2893   }
2894
2895   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2896   {
2897     TreePanel tp = new TreePanel(alignPanel, treeFile,
2898             MessageManager.getString("label.load_tree_from_file"), tree);
2899     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2900     addTreeMenuItem(tp, treeFile);
2901   }
2902
2903   /**
2904    * sort the alignment using the given treePanel
2905    *
2906    * @param treePanel
2907    *          tree used to sort view
2908    * @param title
2909    *          string used for undo event name
2910    */
2911   public void sortByTree(TreePanel treePanel, String title)
2912   {
2913     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2914     AlignmentSorter
2915             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2916     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2917     // HistoryItem.SORT));
2918     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2919             "label.order_by_params", new String[] { title }), oldOrder,
2920             viewport.getAlignment()));
2921     alignPanel.paintAlignment(true);
2922   }
2923
2924   /**
2925    * Do any automatic reordering of the alignment and add the necessary bits to
2926    * the menu structure for the new tree
2927    *
2928    * @param treePanel
2929    * @param title
2930    */
2931   protected void addTreeMenuItem(final TreePanel treePanel,
2932           final String title)
2933   {
2934     final MenuItem item = new MenuItem(title);
2935     sortByTreeMenu.add(item);
2936     item.addActionListener(new java.awt.event.ActionListener()
2937     {
2938       @Override
2939       public void actionPerformed(ActionEvent evt)
2940       {
2941         sortByTree(treePanel, title); // treePanel.getTitle());
2942       }
2943     });
2944
2945     treePanel.addWindowListener(new WindowAdapter()
2946     {
2947       @Override
2948       public void windowOpened(WindowEvent e)
2949       {
2950         if (viewport.sortByTree)
2951         {
2952           sortByTree(treePanel, title);
2953         }
2954         super.windowOpened(e);
2955       }
2956
2957       @Override
2958       public void windowClosing(WindowEvent e)
2959       {
2960         sortByTreeMenu.remove(item);
2961       };
2962     });
2963   }
2964
2965   public boolean sortBy(AlignmentOrder alorder, String undoname)
2966   {
2967     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2968     if (viewport.applet.debug)
2969     {
2970       System.err.println("Sorting " + alorder.getOrder().size()
2971               + " in alignment '" + getTitle() + "'");
2972     }
2973     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2974     if (undoname != null)
2975     {
2976       addHistoryItem(new OrderCommand(undoname, oldOrder,
2977               viewport.getAlignment()));
2978     }
2979     alignPanel.paintAlignment(true);
2980     return true;
2981   }
2982
2983   protected void documentation_actionPerformed()
2984   {
2985     alignPanel.av.applet.openJalviewHelpUrl();
2986   }
2987
2988   protected void about_actionPerformed()
2989   {
2990
2991     class AboutPanel extends Canvas
2992     {
2993       String version;
2994
2995       String builddate;
2996
2997       public AboutPanel(String version, String builddate)
2998       {
2999         this.version = version;
3000         this.builddate = builddate;
3001       }
3002
3003       @Override
3004       public void paint(Graphics g)
3005       {
3006         g.setColor(Color.white);
3007         g.fillRect(0, 0, getSize().width, getSize().height);
3008         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3009         FontMetrics fm = g.getFontMetrics();
3010         int fh = fm.getHeight();
3011         int y = 5, x = 7;
3012         g.setColor(Color.black);
3013         // TODO: update this text for each release or centrally store it for
3014         // lite and application
3015         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3016         g.drawString(MessageManager.formatMessage(
3017                 "label.jalviewLite_release", new String[] { version }), x,
3018                 y += fh);
3019         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3020         g.drawString(MessageManager.formatMessage(
3021                 "label.jaview_build_date", new String[] { builddate }), x,
3022                 y += fh);
3023         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3024         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3025                 x, y += fh * 1.5);
3026         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3027                 x + 50, y += fh + 8);
3028         g.drawString(
3029                 MessageManager.getString("label.jalview_dev_managers"), x,
3030                 y += fh);
3031         g.drawString(MessageManager
3032                 .getString("label.jalview_distribution_lists"), x, y += fh);
3033         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3034                 x, y += fh + 8);
3035         g.drawString(
3036                 MessageManager.getString("label.jalview_cite_1_authors"),
3037                 x, y += fh);
3038         g.drawString(
3039                 MessageManager.getString("label.jalview_cite_1_title"), x,
3040                 y += fh);
3041         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3042                 x, y += fh);
3043       }
3044     }
3045
3046     Frame frame = new Frame();
3047     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3048             .getBuildDate()));
3049     jalview.bin.JalviewLite.addFrame(frame,
3050             MessageManager.getString("label.jalview"), 580, 220);
3051
3052   }
3053
3054   public void showURL(String url, String target)
3055   {
3056     if (viewport.applet == null)
3057     {
3058       System.out.println("Not running as applet - no browser available.");
3059     }
3060     else
3061     {
3062       viewport.applet.showURL(url, target);
3063     }
3064   }
3065
3066   // ////////////////////////////////////////////////////////////////////////////////
3067   // JBuilder Graphics here
3068
3069   MenuBar alignFrameMenuBar = new MenuBar();
3070
3071   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3072
3073   MenuItem loadApplication = new MenuItem(
3074           MessageManager.getString("label.view_full_application"));
3075
3076   MenuItem loadTree = new MenuItem(
3077           MessageManager.getString("label.load_associated_tree"));
3078
3079   MenuItem loadAnnotations = new MenuItem(
3080           MessageManager.getString("label.load_features_annotations"));
3081
3082   MenuItem outputFeatures = new MenuItem(
3083           MessageManager.getString("label.export_features"));
3084
3085   MenuItem outputAnnotations = new MenuItem(
3086           MessageManager.getString("label.export_annotations"));
3087
3088   MenuItem closeMenuItem = new MenuItem(
3089           MessageManager.getString("action.close"));
3090
3091   MenuItem selectAllSequenceMenuItem = new MenuItem(
3092           MessageManager.getString("action.select_all"));
3093
3094   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3095           MessageManager.getString("action.deselect_all"));
3096
3097   MenuItem invertSequenceMenuItem = new MenuItem(
3098           MessageManager.getString("action.invert_selection"));
3099
3100   MenuItem remove2LeftMenuItem = new MenuItem();
3101
3102   MenuItem remove2RightMenuItem = new MenuItem();
3103
3104   MenuItem removeGappedColumnMenuItem = new MenuItem();
3105
3106   MenuItem removeAllGapsMenuItem = new MenuItem();
3107
3108   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3109
3110   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3111
3112   MenuItem sortPairwiseMenuItem = new MenuItem();
3113
3114   MenuItem sortIDMenuItem = new MenuItem();
3115
3116   MenuItem sortLengthMenuItem = new MenuItem();
3117
3118   MenuItem sortGroupMenuItem = new MenuItem();
3119
3120   MenuItem removeRedundancyMenuItem = new MenuItem();
3121
3122   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3123
3124   MenuItem PCAMenuItem = new MenuItem();
3125
3126   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3127
3128   MenuItem neighbourTreeMenuItem = new MenuItem();
3129
3130   BorderLayout borderLayout1 = new BorderLayout();
3131
3132   public Label statusBar = new Label();
3133
3134   MenuItem clustalColour = new MenuItem();
3135
3136   MenuItem zappoColour = new MenuItem();
3137
3138   MenuItem taylorColour = new MenuItem();
3139
3140   MenuItem hydrophobicityColour = new MenuItem();
3141
3142   MenuItem helixColour = new MenuItem();
3143
3144   MenuItem strandColour = new MenuItem();
3145
3146   MenuItem turnColour = new MenuItem();
3147
3148   MenuItem buriedColour = new MenuItem();
3149
3150   MenuItem purinePyrimidineColour = new MenuItem();
3151
3152   // MenuItem RNAInteractionColour = new MenuItem();
3153
3154   MenuItem RNAHelixColour = new MenuItem();
3155
3156   MenuItem userDefinedColour = new MenuItem();
3157
3158   MenuItem PIDColour = new MenuItem();
3159
3160   MenuItem BLOSUM62Colour = new MenuItem();
3161
3162   MenuItem tcoffeeColour = new MenuItem();
3163
3164   MenuItem njTreeBlosumMenuItem = new MenuItem();
3165
3166   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3167
3168   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3169
3170   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3171
3172   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3173
3174   MenuItem alProperties = new MenuItem(
3175           MessageManager.getString("label.alignment_props"));
3176
3177   MenuItem overviewMenuItem = new MenuItem();
3178
3179   MenuItem undoMenuItem = new MenuItem();
3180
3181   MenuItem redoMenuItem = new MenuItem();
3182
3183   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3184
3185   MenuItem noColourmenuItem = new MenuItem();
3186
3187   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3188
3189   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3190
3191   MenuItem findMenuItem = new MenuItem();
3192
3193   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3194
3195   MenuItem nucleotideColour = new MenuItem();
3196
3197   MenuItem deleteGroups = new MenuItem();
3198
3199   MenuItem grpsFromSelection = new MenuItem();
3200
3201   MenuItem createGroup = new MenuItem();
3202
3203   MenuItem unGroup = new MenuItem();
3204
3205   MenuItem delete = new MenuItem();
3206
3207   MenuItem copy = new MenuItem();
3208
3209   MenuItem cut = new MenuItem();
3210
3211   Menu pasteMenu = new Menu();
3212
3213   MenuItem pasteNew = new MenuItem();
3214
3215   MenuItem pasteThis = new MenuItem();
3216
3217   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3218
3219   MenuItem font = new MenuItem();
3220
3221   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3222
3223   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3224
3225   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3226
3227   MenuItem modifyPID = new MenuItem();
3228
3229   MenuItem modifyConservation = new MenuItem();
3230
3231   CheckboxMenuItem autoCalculate = null;
3232
3233   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3234           "Sort Alignment With New Tree", true);
3235
3236   Menu sortByTreeMenu = new Menu();
3237
3238   MenuItem inputText = new MenuItem();
3239
3240   MenuItem documentation = new MenuItem();
3241
3242   MenuItem about = new MenuItem();
3243
3244   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3245
3246   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3247
3248   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3249
3250   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3251
3252   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3253
3254   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3255
3256   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3257
3258   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3259
3260   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3261
3262   /**
3263    * Initialise menus and other items
3264    *
3265    * @throws Exception
3266    */
3267   private void jbInit() throws Exception
3268   {
3269     setMenuBar(alignFrameMenuBar);
3270
3271     /*
3272      * Configure File menu items and actions
3273      */
3274     inputText
3275             .setLabel(MessageManager.getString("label.input_from_textbox"));
3276     inputText.addActionListener(this);
3277     Menu outputTextboxMenu = new Menu(
3278             MessageManager.getString("label.out_to_textbox"));
3279     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3280     {
3281       MenuItem item = new MenuItem(ff);
3282
3283       item.addActionListener(new java.awt.event.ActionListener()
3284       {
3285         @Override
3286         public void actionPerformed(ActionEvent e)
3287         {
3288           outputText_actionPerformed(e);
3289         }
3290       });
3291
3292       outputTextboxMenu.add(item);
3293     }
3294     closeMenuItem.addActionListener(this);
3295     loadApplication.addActionListener(this);
3296     loadTree.addActionListener(this);
3297     loadAnnotations.addActionListener(this);
3298     outputFeatures.addActionListener(this);
3299     outputAnnotations.addActionListener(this);
3300
3301     /*
3302      * Configure Edit menu items and actions
3303      */
3304     undoMenuItem.setEnabled(false);
3305     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3306     undoMenuItem.addActionListener(this);
3307     redoMenuItem.setEnabled(false);
3308     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3309     redoMenuItem.addActionListener(this);
3310     copy.setLabel(MessageManager.getString("action.copy"));
3311     copy.addActionListener(this);
3312     cut.setLabel(MessageManager.getString("action.cut"));
3313     cut.addActionListener(this);
3314     delete.setLabel(MessageManager.getString("action.delete"));
3315     delete.addActionListener(this);
3316     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3317     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3318     pasteNew.addActionListener(this);
3319     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3320     pasteThis.addActionListener(this);
3321     remove2LeftMenuItem.setLabel(MessageManager
3322             .getString("action.remove_left"));
3323     remove2LeftMenuItem.addActionListener(this);
3324     remove2RightMenuItem.setLabel(MessageManager
3325             .getString("action.remove_right"));
3326     remove2RightMenuItem.addActionListener(this);
3327     removeGappedColumnMenuItem.setLabel(MessageManager
3328             .getString("action.remove_empty_columns"));
3329     removeGappedColumnMenuItem.addActionListener(this);
3330     removeAllGapsMenuItem.setLabel(MessageManager
3331             .getString("action.remove_all_gaps"));
3332     removeAllGapsMenuItem.addActionListener(this);
3333     removeRedundancyMenuItem.setLabel(MessageManager
3334             .getString("action.remove_redundancy"));
3335     removeRedundancyMenuItem.addActionListener(this);
3336
3337     /*
3338      * Configure Select menu items and actions
3339      */
3340     findMenuItem.setLabel(MessageManager.getString("action.find"));
3341     findMenuItem.addActionListener(this);
3342     selectAllSequenceMenuItem.addActionListener(this);
3343     deselectAllSequenceMenuItem.addActionListener(this);
3344     invertSequenceMenuItem.setLabel(MessageManager
3345             .getString("action.invert_sequence_selection"));
3346     invertSequenceMenuItem.addActionListener(this);
3347     invertColSel.setLabel(MessageManager
3348             .getString("action.invert_column_selection"));
3349     invertColSel.addActionListener(this);
3350     deleteGroups.setLabel(MessageManager
3351             .getString("action.undefine_groups"));
3352     deleteGroups.addActionListener(this);
3353     grpsFromSelection.setLabel(MessageManager
3354             .getString("action.make_groups_selection"));
3355     grpsFromSelection.addActionListener(this);
3356     createGroup.setLabel(MessageManager.getString("action.create_group"));
3357     createGroup.addActionListener(this);
3358     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3359     unGroup.addActionListener(this);
3360
3361     annotationColumnSelection.setLabel(MessageManager
3362             .getString("action.select_by_annotation"));
3363     annotationColumnSelection.addActionListener(this);
3364
3365     /*
3366      * Configure View menu items and actions
3367      */
3368     newView.setLabel(MessageManager.getString("action.new_view"));
3369     newView.addActionListener(this);
3370     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3371     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3372     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3373     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3374     hideColumns
3375             .setLabel(MessageManager.getString("label.selected_columns"));
3376     hideSequences.setLabel(MessageManager
3377             .getString("label.selected_sequences"));
3378     hideAllButSelection.setLabel(MessageManager
3379             .getString("label.all_but_selected_region"));
3380     hideAllSelection.setLabel(MessageManager
3381             .getString("label.selected_region"));
3382     showAllHidden.setLabel(MessageManager
3383             .getString("label.all_sequences_columns"));
3384     showColumns.addActionListener(this);
3385     showSeqs.addActionListener(this);
3386     hideColumns.addActionListener(this);
3387     hideSequences.addActionListener(this);
3388     hideAllButSelection.addActionListener(this);
3389     hideAllSelection.addActionListener(this);
3390     showAllHidden.addActionListener(this);
3391     featureSettings.setLabel(MessageManager
3392             .getString("action.feature_settings"));
3393     featureSettings.addActionListener(this);
3394     sequenceFeatures.setLabel(MessageManager
3395             .getString("label.show_sequence_features"));
3396     sequenceFeatures.addItemListener(this);
3397     sequenceFeatures.setState(false);
3398     followMouseOverFlag.setLabel(MessageManager
3399             .getString("label.automatic_scrolling"));
3400     followMouseOverFlag.addItemListener(this);
3401     alProperties.addActionListener(this);
3402     overviewMenuItem.setLabel(MessageManager
3403             .getString("label.overview_window"));
3404     overviewMenuItem.addActionListener(this);
3405
3406     /*
3407      * Configure Annotations menu items and actions
3408      */
3409     annotationPanelMenuItem.setLabel(MessageManager
3410             .getString("label.show_annotations"));
3411     annotationPanelMenuItem.addItemListener(this);
3412     showGroupConsensus.setLabel(MessageManager
3413             .getString("label.group_consensus"));
3414     showGroupConservation.setLabel(MessageManager
3415             .getString("label.group_conservation"));
3416     showConsensusHistogram.setLabel(MessageManager
3417             .getString("label.show_consensus_histogram"));
3418     showSequenceLogo.setLabel(MessageManager
3419             .getString("label.show_consensus_logo"));
3420     normSequenceLogo.setLabel(MessageManager
3421             .getString("label.norm_consensus_logo"));
3422     applyAutoAnnotationSettings.setLabel(MessageManager
3423             .getString("label.apply_all_groups"));
3424     applyAutoAnnotationSettings.setState(true);
3425     Menu autoAnnMenu = new Menu(
3426             MessageManager.getString("label.autocalculated_annotation"));
3427     showGroupConsensus.addItemListener(this);
3428     showGroupConservation.addItemListener(this);
3429     showConsensusHistogram.addItemListener(this);
3430     showSequenceLogo.addItemListener(this);
3431     normSequenceLogo.addItemListener(this);
3432     applyAutoAnnotationSettings.addItemListener(this);
3433     showAlignmentAnnotations = new CheckboxMenuItem(
3434             MessageManager.getString("label.show_all_al_annotations"));
3435     showSequenceAnnotations = new CheckboxMenuItem(
3436             MessageManager.getString("label.show_all_seq_annotations"));
3437     sortAnnBySequence = new CheckboxMenuItem(
3438             MessageManager.getString("label.sort_annotations_by_sequence"));
3439     sortAnnByLabel = new CheckboxMenuItem(
3440             MessageManager.getString("label.sort_annotations_by_label"));
3441     showAutoFirst = new CheckboxMenuItem(
3442             MessageManager.getString("label.show_first"));
3443     showAutoFirst.setState(false); // pending applet parameter
3444     setShowAutoCalculatedAbove(showAutoFirst.getState());
3445     showAutoLast = new CheckboxMenuItem(
3446             MessageManager.getString("label.show_last"));
3447     showAutoLast.setState(!showAutoFirst.getState());
3448     showAlignmentAnnotations.addItemListener(this);
3449     showSequenceAnnotations.addItemListener(this);
3450     sortAnnBySequence.addItemListener(this);
3451     sortAnnByLabel.addItemListener(this);
3452     showAutoFirst.addItemListener(this);
3453     showAutoLast.addItemListener(this);
3454
3455     /*
3456      * Configure Format menu items and actions
3457      */
3458     font.setLabel(MessageManager.getString("action.font"));
3459     font.addActionListener(this);
3460     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3461     scaleAbove.setState(true);
3462     scaleAbove.setEnabled(false);
3463     scaleAbove.addItemListener(this);
3464     scaleLeft.setEnabled(false);
3465     scaleLeft.setState(true);
3466     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3467     scaleLeft.addItemListener(this);
3468     scaleRight.setEnabled(false);
3469     scaleRight.setState(true);
3470     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3471     scaleRight.addItemListener(this);
3472     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3473     viewBoxesMenuItem.setState(true);
3474     viewBoxesMenuItem.addItemListener(this);
3475     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3476     viewTextMenuItem.setState(true);
3477     viewTextMenuItem.addItemListener(this);
3478     colourTextMenuItem.setLabel(MessageManager
3479             .getString("label.colour_text"));
3480     colourTextMenuItem.addItemListener(this);
3481     displayNonconservedMenuItem.setLabel(MessageManager
3482             .getString("label.show_non_conserved"));
3483     displayNonconservedMenuItem.addItemListener(this);
3484     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3485     wrapMenuItem.addItemListener(this);
3486     renderGapsMenuItem.setLabel(MessageManager
3487             .getString("action.show_gaps"));
3488     renderGapsMenuItem.setState(true);
3489     renderGapsMenuItem.addItemListener(this);
3490     centreColumnLabelFlag.setLabel(MessageManager
3491             .getString("label.centre_column_labels"));
3492     centreColumnLabelFlag.addItemListener(this);
3493     seqLimits.setState(true);
3494     seqLimits.setLabel(MessageManager
3495             .getString("label.show_sequence_limits"));
3496     seqLimits.addItemListener(this);
3497
3498     /*
3499      * Configure Colour menu items and actions
3500      */
3501     applyToAllGroups.setLabel(MessageManager
3502             .getString("label.apply_colour_to_all_groups"));
3503     applyToAllGroups.setState(true);
3504     applyToAllGroups.addItemListener(this);
3505     clustalColour.setLabel(MessageManager
3506             .getString("label.colourScheme_clustal"));
3507     clustalColour.addActionListener(this);
3508     zappoColour.setLabel(MessageManager
3509             .getString("label.colourScheme_zappo"));
3510     zappoColour.addActionListener(this);
3511     taylorColour.setLabel(MessageManager
3512             .getString("label.colourScheme_taylor"));
3513     taylorColour.addActionListener(this);
3514     hydrophobicityColour.setLabel(MessageManager
3515             .getString("label.colourScheme_hydrophobic"));
3516     hydrophobicityColour.addActionListener(this);
3517     helixColour.setLabel(MessageManager
3518             .getString("label.colourScheme_helix_propensity"));
3519     helixColour.addActionListener(this);
3520     strandColour.setLabel(MessageManager
3521             .getString("label.colourScheme_strand_propensity"));
3522     strandColour.addActionListener(this);
3523     turnColour.setLabel(MessageManager
3524             .getString("label.colourScheme_turn_propensity"));
3525     turnColour.addActionListener(this);
3526     buriedColour.setLabel(MessageManager
3527             .getString("label.colourScheme_buried_index"));
3528     buriedColour.addActionListener(this);
3529     purinePyrimidineColour.setLabel(MessageManager
3530             .getString("label.colourScheme_purine/pyrimidine"));
3531     purinePyrimidineColour.addActionListener(this);
3532     // RNAInteractionColour.setLabel(MessageManager
3533     // .getString("label.rna_interaction"));
3534     // RNAInteractionColour.addActionListener(this);
3535     RNAHelixColour.setLabel(MessageManager
3536             .getString("label.colourScheme_rna_helices"));
3537     RNAHelixColour.addActionListener(this);
3538     userDefinedColour.setLabel(MessageManager
3539             .getString("action.user_defined"));
3540     userDefinedColour.addActionListener(this);
3541     PIDColour.setLabel(MessageManager
3542             .getString("label.colourScheme_%_identity"));
3543     PIDColour.addActionListener(this);
3544     BLOSUM62Colour.setLabel(MessageManager
3545             .getString("label.colourScheme_blosum62"));
3546     BLOSUM62Colour.addActionListener(this);
3547     tcoffeeColour.setLabel(MessageManager
3548             .getString("label.colourScheme_t-coffee_scores"));
3549     // it will be enabled only if a score file is provided
3550     tcoffeeColour.setEnabled(false);
3551     tcoffeeColour.addActionListener(this);
3552     conservationMenuItem.setLabel(MessageManager
3553             .getString("action.by_conservation"));
3554     conservationMenuItem.addItemListener(this);
3555     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3556     noColourmenuItem.addActionListener(this);
3557     abovePIDThreshold.setLabel(MessageManager
3558             .getString("label.above_identity_threshold"));
3559     abovePIDThreshold.addItemListener(this);
3560     nucleotideColour.setLabel(MessageManager
3561             .getString("label.colourScheme_nucleotide"));
3562     nucleotideColour.addActionListener(this);
3563     modifyPID.setLabel(MessageManager
3564             .getString("label.modify_identity_threshold"));
3565     modifyPID.setEnabled(abovePIDThreshold.getState());
3566     modifyPID.addActionListener(this);
3567     modifyConservation.setLabel(MessageManager
3568             .getString("label.modify_conservation_threshold"));
3569     modifyConservation.setEnabled(conservationMenuItem.getState());
3570     modifyConservation.addActionListener(this);
3571     annotationColour.setLabel(MessageManager
3572             .getString("action.by_annotation"));
3573     annotationColour.addActionListener(this);
3574
3575     /*
3576      * Configure Calculate menu items and actions
3577      */
3578     sortPairwiseMenuItem.setLabel(MessageManager
3579             .getString("action.by_pairwise_id"));
3580     sortPairwiseMenuItem.addActionListener(this);
3581     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3582     sortIDMenuItem.addActionListener(this);
3583     sortLengthMenuItem.setLabel(MessageManager
3584             .getString("action.by_length"));
3585     sortLengthMenuItem.addActionListener(this);
3586     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3587     sortGroupMenuItem.addActionListener(this);
3588     pairwiseAlignmentMenuItem.setLabel(MessageManager
3589             .getString("action.pairwise_alignment"));
3590     pairwiseAlignmentMenuItem.addActionListener(this);
3591     PCAMenuItem.setLabel(MessageManager
3592             .getString("label.principal_component_analysis"));
3593     PCAMenuItem.addActionListener(this);
3594     autoCalculate = new CheckboxMenuItem(
3595             MessageManager.getString("label.autocalculate_consensus"), true);
3596     averageDistanceTreeMenuItem.setLabel(MessageManager
3597             .getString("label.average_distance_identity"));
3598     averageDistanceTreeMenuItem.addActionListener(this);
3599     neighbourTreeMenuItem.setLabel(MessageManager
3600             .getString("label.neighbour_joining_identity"));
3601     neighbourTreeMenuItem.addActionListener(this);
3602     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3603             .getString("label.average_distance_blosum62"));
3604     avDistanceTreeBlosumMenuItem.addActionListener(this);
3605     njTreeBlosumMenuItem.setLabel(MessageManager
3606             .getString("label.neighbour_blosum62"));
3607     njTreeBlosumMenuItem.addActionListener(this);
3608     sortByTreeMenu.setLabel(MessageManager
3609             .getString("action.by_tree_order"));
3610     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3611     Menu calculateTreeMenu = new Menu(
3612             MessageManager.getString("action.calculate_tree"));
3613     autoCalculate.addItemListener(this);
3614     sortByTree.addItemListener(this);
3615
3616     /*
3617      * Configure Help menu items and actions
3618      */
3619     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3620     documentation.setLabel(MessageManager.getString("label.documentation"));
3621     documentation.addActionListener(this);
3622     about.setLabel(MessageManager.getString("label.about"));
3623     about.addActionListener(this);
3624
3625     /*
3626      * Add top level menus to frame
3627      */
3628     alignFrameMenuBar.add(fileMenu);
3629     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3630     alignFrameMenuBar.add(editMenu);
3631     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3632     alignFrameMenuBar.add(selectMenu);
3633     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3634     alignFrameMenuBar.add(viewMenu);
3635     Menu annotationsMenu = new Menu(
3636             MessageManager.getString("action.annotations"));
3637     alignFrameMenuBar.add(annotationsMenu);
3638     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3639     alignFrameMenuBar.add(formatMenu);
3640     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3641     alignFrameMenuBar.add(colourMenu);
3642     Menu calculateMenu = new Menu(
3643             MessageManager.getString("action.calculate"));
3644     alignFrameMenuBar.add(calculateMenu);
3645     alignFrameMenuBar.add(helpMenu);
3646
3647     /*
3648      * File menu
3649      */
3650     fileMenu.add(inputText);
3651     fileMenu.add(loadTree);
3652     fileMenu.add(loadAnnotations);
3653     fileMenu.addSeparator();
3654     fileMenu.add(outputTextboxMenu);
3655     fileMenu.add(outputFeatures);
3656     fileMenu.add(outputAnnotations);
3657     if (jalviewServletURL != null)
3658     {
3659       fileMenu.add(loadApplication);
3660     }
3661     fileMenu.addSeparator();
3662     fileMenu.add(closeMenuItem);
3663
3664     /*
3665      * Edit menu
3666      */
3667     editMenu.add(undoMenuItem);
3668     editMenu.add(redoMenuItem);
3669     editMenu.add(cut);
3670     editMenu.add(copy);
3671     pasteMenu.add(pasteNew);
3672     pasteMenu.add(pasteThis);
3673     editMenu.add(pasteMenu);
3674     editMenu.add(delete);
3675     editMenu.addSeparator();
3676     editMenu.add(remove2LeftMenuItem);
3677     editMenu.add(remove2RightMenuItem);
3678     editMenu.add(removeGappedColumnMenuItem);
3679     editMenu.add(removeAllGapsMenuItem);
3680     editMenu.add(removeRedundancyMenuItem);
3681
3682     /*
3683      * Select menu
3684      */
3685     selectMenu.add(findMenuItem);
3686     selectMenu.addSeparator();
3687     selectMenu.add(selectAllSequenceMenuItem);
3688     selectMenu.add(deselectAllSequenceMenuItem);
3689     selectMenu.add(invertSequenceMenuItem);
3690     selectMenu.add(invertColSel);
3691     selectMenu.add(createGroup);
3692     selectMenu.add(unGroup);
3693     selectMenu.add(grpsFromSelection);
3694     selectMenu.add(deleteGroups);
3695     selectMenu.add(annotationColumnSelection);
3696
3697     /*
3698      * View menu
3699      */
3700     viewMenu.add(newView);
3701     viewMenu.addSeparator();
3702     showMenu.add(showColumns);
3703     showMenu.add(showSeqs);
3704     showMenu.add(showAllHidden);
3705     viewMenu.add(showMenu);
3706     hideMenu.add(hideColumns);
3707     hideMenu.add(hideSequences);
3708     hideMenu.add(hideAllSelection);
3709     hideMenu.add(hideAllButSelection);
3710     viewMenu.add(hideMenu);
3711     viewMenu.addSeparator();
3712     viewMenu.add(followMouseOverFlag);
3713     viewMenu.addSeparator();
3714     viewMenu.add(sequenceFeatures);
3715     viewMenu.add(featureSettings);
3716     viewMenu.addSeparator();
3717     viewMenu.add(alProperties);
3718     viewMenu.addSeparator();
3719     viewMenu.add(overviewMenuItem);
3720
3721     /*
3722      * Annotations menu
3723      */
3724     annotationsMenu.add(annotationPanelMenuItem);
3725     annotationsMenu.addSeparator();
3726     annotationsMenu.add(showAlignmentAnnotations);
3727     annotationsMenu.add(showSequenceAnnotations);
3728     annotationsMenu.add(sortAnnBySequence);
3729     annotationsMenu.add(sortAnnByLabel);
3730     annotationsMenu.addSeparator();
3731     autoAnnMenu.add(showAutoFirst);
3732     autoAnnMenu.add(showAutoLast);
3733     autoAnnMenu.addSeparator();
3734     autoAnnMenu.add(applyAutoAnnotationSettings);
3735     autoAnnMenu.add(showConsensusHistogram);
3736     autoAnnMenu.add(showSequenceLogo);
3737     autoAnnMenu.add(normSequenceLogo);
3738     autoAnnMenu.addSeparator();
3739     autoAnnMenu.add(showGroupConservation);
3740     autoAnnMenu.add(showGroupConsensus);
3741     annotationsMenu.add(autoAnnMenu);
3742
3743     /*
3744      * Format menu
3745      */
3746     formatMenu.add(font);
3747     formatMenu.add(seqLimits);
3748     formatMenu.add(wrapMenuItem);
3749     formatMenu.add(scaleAbove);
3750     formatMenu.add(scaleLeft);
3751     formatMenu.add(scaleRight);
3752     formatMenu.add(viewBoxesMenuItem);
3753     formatMenu.add(viewTextMenuItem);
3754     formatMenu.add(colourTextMenuItem);
3755     formatMenu.add(displayNonconservedMenuItem);
3756     formatMenu.add(renderGapsMenuItem);
3757     formatMenu.add(centreColumnLabelFlag);
3758
3759     /*
3760      * Colour menu
3761      */
3762     colourMenu.add(applyToAllGroups);
3763     colourMenu.addSeparator();
3764     colourMenu.add(noColourmenuItem);
3765     colourMenu.add(clustalColour);
3766     colourMenu.add(BLOSUM62Colour);
3767     colourMenu.add(PIDColour);
3768     colourMenu.add(zappoColour);
3769     colourMenu.add(taylorColour);
3770     colourMenu.add(hydrophobicityColour);
3771     colourMenu.add(helixColour);
3772     colourMenu.add(strandColour);
3773     colourMenu.add(turnColour);
3774     colourMenu.add(buriedColour);
3775     colourMenu.add(nucleotideColour);
3776     colourMenu.add(purinePyrimidineColour);
3777     // colourMenu.add(RNAInteractionColour);
3778     colourMenu.add(tcoffeeColour);
3779     colourMenu.add(userDefinedColour);
3780     colourMenu.addSeparator();
3781     colourMenu.add(conservationMenuItem);
3782     colourMenu.add(modifyConservation);
3783     colourMenu.add(abovePIDThreshold);
3784     colourMenu.add(modifyPID);
3785     colourMenu.add(annotationColour);
3786     colourMenu.add(RNAHelixColour);
3787
3788     /*
3789      * Calculate menu
3790      */
3791     sortMenu.add(sortIDMenuItem);
3792     sortMenu.add(sortLengthMenuItem);
3793     sortMenu.add(sortByTreeMenu);
3794     sortMenu.add(sortGroupMenuItem);
3795     sortMenu.add(sortPairwiseMenuItem);
3796     calculateMenu.add(sortMenu);
3797     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3798     calculateTreeMenu.add(neighbourTreeMenuItem);
3799     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3800     calculateTreeMenu.add(njTreeBlosumMenuItem);
3801     calculateMenu.add(calculateTreeMenu);
3802     calculateMenu.addSeparator();
3803     calculateMenu.add(pairwiseAlignmentMenuItem);
3804     calculateMenu.add(PCAMenuItem);
3805     calculateMenu.add(autoCalculate);
3806     calculateMenu.add(sortByTree);
3807
3808     /*
3809      * Help menu
3810      */
3811     helpMenu.add(documentation);
3812     helpMenu.add(about);
3813
3814     /*
3815      * Status bar
3816      */
3817     statusBar.setBackground(Color.white);
3818     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3819     statusBar.setText(MessageManager.getString("label.status_bar"));
3820     this.add(statusBar, BorderLayout.SOUTH);
3821   }
3822
3823   @Override
3824   public void setStatus(String string)
3825   {
3826     statusBar.setText(string);
3827   };
3828
3829   MenuItem featureSettings = new MenuItem();
3830
3831   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3832
3833   MenuItem annotationColour = new MenuItem();
3834
3835   MenuItem annotationColumnSelection = new MenuItem();
3836
3837   MenuItem invertColSel = new MenuItem();
3838
3839   MenuItem showColumns = new MenuItem();
3840
3841   MenuItem showSeqs = new MenuItem();
3842
3843   MenuItem hideColumns = new MenuItem();
3844
3845   MenuItem hideSequences = new MenuItem();
3846
3847   MenuItem hideAllButSelection = new MenuItem();
3848
3849   MenuItem hideAllSelection = new MenuItem();
3850
3851   MenuItem showAllHidden = new MenuItem();
3852
3853   MenuItem newView = new MenuItem();
3854
3855   private CheckboxMenuItem showAlignmentAnnotations;
3856
3857   private CheckboxMenuItem showSequenceAnnotations;
3858
3859   private CheckboxMenuItem sortAnnBySequence;
3860
3861   private CheckboxMenuItem sortAnnByLabel;
3862
3863   private CheckboxMenuItem showAutoFirst;
3864
3865   private CheckboxMenuItem showAutoLast;
3866
3867   private SplitFrame splitFrame;
3868
3869   /**
3870    * Attach the alignFrame panels after embedding menus, if necessary. This used
3871    * to be called setEmbedded, but is now creates the dropdown menus in a
3872    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3873    *
3874    * @param reallyEmbedded
3875    *          true to attach the view to the applet area on the page rather than
3876    *          in a new window
3877    */
3878   public void createAlignFrameWindow(boolean reallyEmbedded)
3879   {
3880     if (reallyEmbedded)
3881     {
3882       embedAlignFrameInApplet(viewport.applet);
3883     }
3884     else
3885     {
3886       // //////
3887       // test and embed menu bar if necessary.
3888       //
3889       if (embedMenuIfNeeded(alignPanel))
3890       {
3891         /*
3892          * adjust for status bar height too. ? pointless as overridden by layout
3893          * manager
3894          */
3895         alignPanel.setSize(getSize().width,
3896                 getSize().height - statusBar.getHeight());
3897       }
3898       add(statusBar, BorderLayout.SOUTH);
3899       add(alignPanel, BorderLayout.CENTER);
3900       // and register with the applet so it can pass external API calls to us
3901       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3902               frameHeight);
3903     }
3904   }
3905
3906   /**
3907    * Add the components of this AlignFrame to the applet container.
3908    *
3909    * @param theApplet
3910    */
3911   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3912   {
3913     // ////
3914     // Explicitly build the embedded menu panel for the on-page applet
3915     //
3916     // view cannot be closed if its actually on the page
3917     fileMenu.remove(closeMenuItem);
3918     fileMenu.remove(3); // Remove Separator
3919     // construct embedded menu, using default font
3920     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3921     // and actually add the components to the applet area
3922     theApplet.setLayout(new BorderLayout());
3923     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3924     theApplet.add(statusBar, BorderLayout.SOUTH);
3925     // TODO should size be left to the layout manager?
3926     alignPanel.setSize(theApplet.getSize().width,
3927             theApplet.getSize().height - embeddedMenu.getHeight()
3928                     - statusBar.getHeight());
3929     theApplet.add(alignPanel, BorderLayout.CENTER);
3930     final AlignFrame me = this;
3931     theApplet.addFocusListener(new FocusListener()
3932     {
3933
3934       @Override
3935       public void focusLost(FocusEvent e)
3936       {
3937         if (theApplet.currentAlignFrame == me)
3938         {
3939           theApplet.currentAlignFrame = null;
3940         }
3941       }
3942
3943       @Override
3944       public void focusGained(FocusEvent e)
3945       {
3946         theApplet.currentAlignFrame = me;
3947       }
3948     });
3949     theApplet.validate();
3950   }
3951
3952   /**
3953    * create a new binding between structures in an existing jmol viewer instance
3954    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3955    * this does not open a new Jmol window, or modify the display of the
3956    * structures in the original jmol window. Note This method doesn't work
3957    * without an additional javascript library to exchange messages between the
3958    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3959    *
3960    * @param viewer
3961    *          JmolViewer instance
3962    * @param sequenceIds
3963    *          - sequence Ids to search for associations
3964    */
3965   public SequenceStructureBinding addStructureViewInstance(
3966           Object jmolviewer, String[] sequenceIds)
3967   {
3968     Viewer viewer = null;
3969     try
3970     {
3971       viewer = (Viewer) jmolviewer;
3972     } catch (ClassCastException ex)
3973     {
3974       System.err.println("Unsupported viewer object :"
3975               + jmolviewer.getClass());
3976     }
3977     if (viewer == null)
3978     {
3979       System.err.println("Can't use this object as a structure viewer:"
3980               + jmolviewer.getClass());
3981       return null;
3982     }
3983     SequenceI[] seqs = null;
3984     if (sequenceIds == null || sequenceIds.length == 0)
3985     {
3986       seqs = viewport.getAlignment().getSequencesArray();
3987     }
3988     else
3989     {
3990       Vector sqi = new Vector();
3991       AlignmentI al = viewport.getAlignment();
3992       for (int sid = 0; sid < sequenceIds.length; sid++)
3993       {
3994         SequenceI sq = al.findName(sequenceIds[sid]);
3995         if (sq != null)
3996         {
3997           sqi.addElement(sq);
3998         }
3999       }
4000       if (sqi.size() > 0)
4001       {
4002         seqs = new SequenceI[sqi.size()];
4003         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4004         {
4005           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4006         }
4007       }
4008       else
4009       {
4010         return null;
4011       }
4012     }
4013     AAStructureBindingModel jmv = null;
4014     // TODO: search for a jmv that involves viewer
4015     if (jmv == null)
4016     { // create a new viewer/jalview binding.
4017       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4018     }
4019     return jmv;
4020
4021   }
4022
4023   /**
4024    * bind a pdb file to a sequence in the current view
4025    *
4026    * @param sequenceId
4027    *          - sequenceId within the dataset.
4028    * @param pdbEntryString
4029    *          - the short name for the PDB file
4030    * @param pdbFile
4031    *          - pdb file - either a URL or a valid PDB file.
4032    * @return true if binding was as success TODO: consider making an exception
4033    *         structure for indicating when PDB parsing or sequenceId location
4034    *         fails.
4035    */
4036   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4037           String pdbFile)
4038   {
4039     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4040     boolean needtoadd = false;
4041     if (toaddpdb != null)
4042     {
4043       Vector pdbe = toaddpdb.getAllPDBEntries();
4044       PDBEntry pdbentry = null;
4045       if (pdbe != null && pdbe.size() > 0)
4046       {
4047         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4048         {
4049           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4050           if (!pdbentry.getId().equals(pdbEntryString)
4051                   && !pdbentry.getFile().equals(pdbFile))
4052           {
4053             pdbentry = null;
4054           }
4055           else
4056           {
4057             continue;
4058           }
4059         }
4060       }
4061       if (pdbentry == null)
4062       {
4063         pdbentry = new PDBEntry();
4064         pdbentry.setId(pdbEntryString);
4065         pdbentry.setFile(pdbFile);
4066         needtoadd = true; // add this new entry to sequence.
4067       }
4068       // resolve data source
4069       // TODO: this code should be a refactored to an io package
4070       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4071               pdbFile, FileFormat.PDB);
4072       if (protocol == null)
4073       {
4074         return false;
4075       }
4076       if (needtoadd)
4077       {
4078         pdbentry.setProperty("protocol", protocol);
4079         toaddpdb.addPDBId(pdbentry);
4080         alignPanel.getStructureSelectionManager()
4081                 .registerPDBEntry(pdbentry);
4082       }
4083     }
4084     return true;
4085   }
4086
4087   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4088   {
4089     if (seqs != null)
4090     {
4091       Vector sequences = new Vector();
4092       for (int i = 0; i < seqs.length; i++)
4093       {
4094         if (seqs[i] != null)
4095         {
4096           sequences.addElement(new Object[] { seqs[i],
4097               (chains != null) ? chains[i] : null });
4098         }
4099       }
4100       seqs = new SequenceI[sequences.size()];
4101       chains = new String[sequences.size()];
4102       for (int i = 0, isize = sequences.size(); i < isize; i++)
4103       {
4104         Object[] oj = (Object[]) sequences.elementAt(i);
4105
4106         seqs[i] = (SequenceI) oj[0];
4107         chains[i] = (String) oj[1];
4108       }
4109     }
4110     return new Object[] { seqs, chains };
4111
4112   }
4113
4114   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4115           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4116   {
4117     // Scrub any null sequences from the array
4118     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4119     seqs = (SequenceI[]) sqch[0];
4120     chains = (String[]) sqch[1];
4121     if (seqs == null || seqs.length == 0)
4122     {
4123       System.err
4124               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4125     }
4126     if (protocol == null)
4127     {
4128       String sourceType = (String) pdb.getProperty("protocol");
4129       try
4130       {
4131         protocol = DataSourceType.valueOf(sourceType);
4132       } catch (IllegalArgumentException e)
4133       {
4134         // ignore
4135       }
4136       if (protocol == null)
4137       {
4138         System.err.println("Couldn't work out protocol to open structure: "
4139                 + pdb.getId());
4140         return;
4141       }
4142     }
4143     if (applet.useXtrnalSviewer)
4144     {
4145       // register the association(s) and quit, don't create any windows.
4146       if (StructureSelectionManager.getStructureSelectionManager(applet)
4147               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4148       {
4149         System.err.println("Failed to map " + pdb.getFile() + " ("
4150                 + protocol + ") to any sequences");
4151       }
4152       return;
4153     }
4154     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4155     {
4156       // can only do alignments with Jmol
4157       // find the last jmol window assigned to this alignment
4158       AppletJmol ajm = null, tajm;
4159       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4160       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4161       {
4162         tajm = (AppletJmol) jmols.elementAt(i);
4163         if (tajm.ap.alignFrame == this)
4164         {
4165           ajm = tajm;
4166           break;
4167         }
4168       }
4169       if (ajm != null)
4170       {
4171         System.err
4172                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4173         // try and add the pdb structure
4174         // ajm.addS
4175         ajm = null;
4176       }
4177     }
4178     // otherwise, create a new window
4179     if (applet.jmolAvailable)
4180     {
4181       new AppletJmol(pdb, seqs, chains, alignPanel,
4182               protocol);
4183       applet.lastFrameX += 40;
4184       applet.lastFrameY += 40;
4185     }
4186     else
4187     {
4188       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4189     }
4190
4191   }
4192
4193   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4194           SequenceI[][] seqs, String[][] chains, String[] protocols)
4195   {
4196     // TODO Auto-generated method stub
4197     System.err.println("Aligned Structure View: Not yet implemented.");
4198   }
4199
4200   /**
4201    * modify the current selection, providing the user has not made a selection
4202    * already.
4203    *
4204    * @param sel
4205    *          - sequences from this alignment
4206    * @param csel
4207    *          - columns to be selected on the alignment
4208    */
4209   public void select(SequenceGroup sel, ColumnSelection csel,
4210           HiddenColumns hidden)
4211   {
4212     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4213   }
4214
4215   public void scrollTo(int row, int column)
4216   {
4217     alignPanel.seqPanel.scrollTo(row, column);
4218   }
4219
4220   public void scrollToRow(int row)
4221   {
4222     alignPanel.seqPanel.scrollToRow(row);
4223   }
4224
4225   public void scrollToColumn(int column)
4226   {
4227     alignPanel.seqPanel.scrollToColumn(column);
4228   }
4229
4230   /**
4231    * @return the alignments unique ID.
4232    */
4233   public String getSequenceSetId()
4234   {
4235     return viewport.getSequenceSetId();
4236   }
4237
4238   /**
4239    * Load the (T-Coffee) score file from the specified url
4240    *
4241    * @param source
4242    *          File/URL/T-COFFEE score file contents
4243    * @throws IOException
4244    * @return true if alignment was annotated with data from source
4245    */
4246   public boolean loadScoreFile(String source) throws IOException
4247   {
4248
4249     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4250             AppletFormatAdapter.checkProtocol(source));
4251     if (!file.isValid())
4252     {
4253       // TODO: raise dialog for gui
4254       System.err.println("Problems parsing T-Coffee scores: "
4255               + file.getWarningMessage());
4256       System.err.println("Origin was:\n" + source);
4257       return false;
4258     }
4259
4260     /*
4261      * check that the score matrix matches the alignment dimensions
4262      */
4263     AlignmentI aln;
4264     if ((aln = viewport.getAlignment()) != null
4265             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4266                     .getWidth()))
4267     {
4268       // TODO: raise a dialog box here rather than bomb out.
4269       System.err
4270               .println("The scores matrix does not match the alignment dimensions");
4271
4272     }
4273
4274     // TODO add parameter to indicate if matching should be done
4275     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4276     {
4277       alignPanel.fontChanged();
4278       tcoffeeColour.setEnabled(true);
4279       // switch to this color
4280       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4281       return true;
4282     }
4283     else
4284     {
4285       System.err.println("Problems resolving T-Coffee scores:");
4286       if (file.getWarningMessage() != null)
4287       {
4288         System.err.println(file.getWarningMessage());
4289       }
4290     }
4291     return false;
4292   }
4293
4294   public SplitFrame getSplitFrame()
4295   {
4296     return this.splitFrame;
4297   }
4298
4299   public void setSplitFrame(SplitFrame sf)
4300   {
4301     this.splitFrame = sf;
4302   }
4303
4304   // may not need this
4305   @Override
4306   public void setShowSeqFeatures(boolean b)
4307   {
4308     // showSeqFeatures.setSelected(b);
4309     viewport.setShowSequenceFeatures(b);
4310
4311   }
4312
4313   @Override
4314   public void setMenusForViewport()
4315   {
4316     // setMenusFromViewport(viewport);
4317
4318   }
4319
4320   @Override
4321   public void refreshFeatureUI(boolean enableIfNecessary)
4322   {
4323     if (enableIfNecessary)
4324     {
4325       sequenceFeatures.setState(true);
4326       alignPanel.av.setShowSequenceFeatures(true);
4327     }
4328   }
4329
4330   @Override
4331   public FeatureSettingsControllerI getFeatureSettingsUI()
4332   {
4333     return alignPanel.av.featureSettings;
4334   }
4335
4336 }