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         alignPanel.scrollUp(true);
 605       }
 606       else
 607       {
 608         alignPanel.setScrollValues(ranges.getStartRes(),
 609                 2 * ranges.getStartSeq() - ranges.getEndSeq());
 610       }
 611       break;
 612
 613     case KeyEvent.VK_PAGE_DOWN:
 614       if (viewport.getWrapAlignment())
 615       {
 616         alignPanel.scrollUp(false);
 617       }
 618       else
 619       {
 620         alignPanel
 621                 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
 622       }
 623       break;
 624
 625     case KeyEvent.VK_Z:
 626       if (evt.isControlDown())
 627       {
 628         undoMenuItem_actionPerformed();
 629       }
 630       break;
 631
 632     case KeyEvent.VK_Y:
 633       if (evt.isControlDown())
 634       {
 635         redoMenuItem_actionPerformed();
 636       }
 637       break;
 638
 639     case KeyEvent.VK_L:
 640       if (evt.isControlDown())
 641       {
 642         trimAlignment(true);
 643       }
 644       break;
 645
 646     case KeyEvent.VK_R:
 647       if (evt.isControlDown())
 648       {
 649         trimAlignment(false);
 650       }
 651       break;
 652
 653     case KeyEvent.VK_E:
 654       if (evt.isControlDown())
 655       {
 656         if (evt.isShiftDown())
 657         {
 658           this.removeAllGapsMenuItem_actionPerformed();
 659         }
 660         else
 661         {
 662           removeGappedColumnMenuItem_actionPerformed();
 663         }
 664       }
 665       break;
 666     case KeyEvent.VK_I:
 667       if (evt.isControlDown())
 668       {
 669         if (evt.isAltDown())
 670         {
 671           invertColSel_actionPerformed();
 672         }
 673         else
 674         {
 675           invertSequenceMenuItem_actionPerformed();
 676         }
 677       }
 678       break;
 679
 680     case KeyEvent.VK_G:
 681       if (evt.isControlDown())
 682       {
 683         if (evt.isShiftDown())
 684         {
 685           this.unGroup_actionPerformed();
 686         }
 687         else
 688         {
 689           this.createGroup_actionPerformed();
 690         }
 691       }
 692       break;
 693
 694     case KeyEvent.VK_U:
 695       if (evt.isControlDown())
 696       {
 697         this.deleteGroups_actionPerformed();
 698       }
 699       break;
 700
 701     case KeyEvent.VK_T:
 702       if (evt.isControlDown())
 703       {
 704         newView(null);
 705       }
 706       break;
 707
 708     }
 709     alignPanel.paintAlignment(true);
 710   }
 711
 712   /**
 713    * called by key handler and the hide all/show all menu items
 714    *
 715    * @param toggleSeqs
 716    * @param toggleCols
 717    */
 718   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 719   {
 720     boolean hide = false;
 721     SequenceGroup sg = viewport.getSelectionGroup();
 722     if (!toggleSeqs && !toggleCols)
 723     {
 724       // Hide everything by the current selection - this is a hack - we do the
 725       // invert and then hide
 726       // first check that there will be visible columns after the invert.
 727       if (viewport.hasSelectedColumns()
 728               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 729                       .getEndRes()))
 730       {
 731         // now invert the sequence set, if required - empty selection implies
 732         // that no hiding is required.
 733         if (sg != null)
 734         {
 735           invertSequenceMenuItem_actionPerformed();
 736           sg = viewport.getSelectionGroup();
 737           toggleSeqs = true;
 738
 739         }
 740         viewport.expandColSelection(sg, true);
 741         // finally invert the column selection and get the new sequence
 742         // selection and indicate it should be hidden.
 743         invertColSel_actionPerformed();
 744         toggleCols = true;
 745       }
 746     }
 747
 748     if (toggleSeqs)
 749     {
 750       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 751       {
 752         hide = true;
 753         viewport.hideAllSelectedSeqs();
 754       }
 755       else if (!(toggleCols && viewport.hasSelectedColumns()))
 756       {
 757         viewport.showAllHiddenSeqs();
 758       }
 759     }
 760
 761     if (toggleCols)
 762     {
 763       if (viewport.hasSelectedColumns())
 764       {
 765         viewport.hideSelectedColumns();
 766         if (!toggleSeqs)
 767         {
 768           viewport.setSelectionGroup(sg);
 769         }
 770       }
 771       else if (!hide)
 772       {
 773         viewport.showAllHiddenColumns();
 774       }
 775       viewport.sendSelection();
 776     }
 777   }
 778
 779   @Override
 780   public void keyReleased(KeyEvent evt)
 781   {
 782   }
 783
 784   @Override
 785   public void keyTyped(KeyEvent evt)
 786   {
 787   }
 788
 789   @Override
 790   public void itemStateChanged(ItemEvent evt)
 791   {
 792     final Object source = evt.getSource();
 793     if (source == displayNonconservedMenuItem)
 794     {
 795       displayNonconservedMenuItem_actionPerformed();
 796     }
 797     else if (source == colourTextMenuItem)
 798     {
 799       colourTextMenuItem_actionPerformed();
 800     }
 801     else if (source == wrapMenuItem)
 802     {
 803       wrapMenuItem_actionPerformed();
 804     }
 805     else if (source == scaleAbove)
 806     {
 807       viewport.setScaleAboveWrapped(scaleAbove.getState());
 808     }
 809     else if (source == scaleLeft)
 810     {
 811       viewport.setScaleLeftWrapped(scaleLeft.getState());
 812     }
 813     else if (source == scaleRight)
 814     {
 815       viewport.setScaleRightWrapped(scaleRight.getState());
 816     }
 817     else if (source == seqLimits)
 818     {
 819       seqLimits_itemStateChanged();
 820     }
 821     else if (source == viewBoxesMenuItem)
 822     {
 823       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 824     }
 825     else if (source == viewTextMenuItem)
 826     {
 827       viewport.setShowText(viewTextMenuItem.getState());
 828     }
 829     else if (source == renderGapsMenuItem)
 830     {
 831       viewport.setRenderGaps(renderGapsMenuItem.getState());
 832     }
 833     else if (source == annotationPanelMenuItem)
 834     {
 835       boolean showAnnotations = annotationPanelMenuItem.getState();
 836       showAlignmentAnnotations.setEnabled(showAnnotations);
 837       showSequenceAnnotations.setEnabled(showAnnotations);
 838       viewport.setShowAnnotation(showAnnotations);
 839       alignPanel.setAnnotationVisible(showAnnotations);
 840     }
 841     else if (source == sequenceFeatures)
 842     {
 843       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 844       alignPanel.seqPanel.seqCanvas.repaint();
 845     }
 846     else if (source == showAlignmentAnnotations)
 847     {
 848       setAnnotationsVisibility();
 849     }
 850     else if (source == showSequenceAnnotations)
 851     {
 852       setAnnotationsVisibility();
 853     }
 854     else if (source == sortAnnBySequence)
 855     {
 856       boolean newState = sortAnnBySequence.getState();
 857       sortAnnByLabel.setState(false);
 858       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 859               : SequenceAnnotationOrder.NONE);
 860       setViewportAnnotationOrder();
 861     }
 862     else if (source == sortAnnByLabel)
 863     {
 864       boolean newState = sortAnnByLabel.getState();
 865       sortAnnBySequence.setState(false);
 866       setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 867               : SequenceAnnotationOrder.NONE);
 868       setViewportAnnotationOrder();
 869     }
 870     else if (source == showAutoFirst)
 871     {
 872       showAutoLast.setState(!showAutoFirst.getState());
 873       setShowAutoCalculatedAbove(showAutoFirst.getState());
 874       setViewportAnnotationOrder();
 875     }
 876     else if (source == showAutoLast)
 877     {
 878       showAutoFirst.setState(!showAutoLast.getState());
 879       setShowAutoCalculatedAbove(showAutoFirst.getState());
 880       setViewportAnnotationOrder();
 881     }
 882     else if (source == conservationMenuItem)
 883     {
 884       conservationMenuItem_actionPerformed();
 885     }
 886     else if (source == abovePIDThreshold)
 887     {
 888       abovePIDThreshold_actionPerformed();
 889     }
 890     else if (source == applyToAllGroups)
 891     {
 892       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 893     }
 894     else if (source == autoCalculate)
 895     {
 896       viewport.autoCalculateConsensus = autoCalculate.getState();
 897     }
 898     else if (source == sortByTree)
 899     {
 900       viewport.sortByTree = sortByTree.getState();
 901     }
 902     else if (source == this.centreColumnLabelFlag)
 903     {
 904       centreColumnLabelFlag_stateChanged();
 905     }
 906     else if (source == this.followMouseOverFlag)
 907     {
 908       mouseOverFlag_stateChanged();
 909     }
 910     else if (source == showGroupConsensus)
 911     {
 912       showGroupConsensus_actionPerformed();
 913     }
 914     else if (source == showGroupConservation)
 915     {
 916       showGroupConservation_actionPerformed();
 917     }
 918     else if (source == showSequenceLogo)
 919     {
 920       showSequenceLogo_actionPerformed();
 921     }
 922     else if (source == normSequenceLogo)
 923     {
 924       normSequenceLogo_actionPerformed();
 925     }
 926     else if (source == showConsensusHistogram)
 927     {
 928       showConsensusHistogram_actionPerformed();
 929     }
 930     else if (source == applyAutoAnnotationSettings)
 931     {
 932       applyAutoAnnotationSettings_actionPerformed();
 933     }
 934     alignPanel.paintAlignment(true);
 935   }
 936
 937   /**
 938    * Set the visibility state of sequence-related and/or alignment-related
 939    * annotations depending on checkbox selections, and repaint.
 940    *
 941    * @param visible
 942    */
 943   private void setAnnotationsVisibility()
 944   {
 945     boolean showForAlignment = showAlignmentAnnotations.getState();
 946     boolean showForSequences = showSequenceAnnotations.getState();
 947     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 948     {
 949       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 950               .getAlignmentAnnotation())
 951       {
 952         boolean visible = (aa.sequenceRef == null ? showForAlignment
 953                 : showForSequences);
 954         aa.visible = visible;
 955       }
 956     }
 957     alignPanel.validateAnnotationDimensions(true);
 958     validate();
 959     repaint();
 960   }
 961
 962   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 963   {
 964     this.annotationSortOrder = order;
 965   }
 966
 967   /**
 968    * Set flags on the viewport that control annotation ordering
 969    */
 970   private void setViewportAnnotationOrder()
 971   {
 972     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 973     this.alignPanel.av
 974             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 975   }
 976
 977   private void setShowAutoCalculatedAbove(boolean showAbove)
 978   {
 979     this.showAutoCalculatedAbove = showAbove;
 980   }
 981
 982   private void mouseOverFlag_stateChanged()
 983   {
 984     viewport.setFollowHighlight(followMouseOverFlag.getState());
 985     // TODO: could kick the scrollTo mechanism to reset view for current
 986     // searchresults.
 987   }
 988
 989   private void centreColumnLabelFlag_stateChanged()
 990   {
 991     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 992     this.alignPanel.annotationPanel.repaint();
 993   }
 994
 995   @Override
 996   public void actionPerformed(ActionEvent evt)
 997   {
 998     viewport.applet.currentAlignFrame = this;
 999
1000     Object source = evt.getSource();
1001
1002     if (source == inputText)
1003     {
1004       inputText_actionPerformed();
1005     }
1006     else if (source == loadTree)
1007     {
1008       loadTree_actionPerformed();
1009     }
1010     else if (source == loadApplication)
1011     {
1012       launchFullApplication();
1013     }
1014     else if (source == loadAnnotations)
1015     {
1016       loadAnnotations();
1017     }
1018     else if (source == outputAnnotations)
1019     {
1020       outputAnnotations(true);
1021     }
1022     else if (source == outputFeatures)
1023     {
1024       outputFeatures(true, "Jalview");
1025     }
1026     else if (source == closeMenuItem)
1027     {
1028       closeMenuItem_actionPerformed();
1029     }
1030     else if (source == copy)
1031     {
1032       copy_actionPerformed();
1033     }
1034     else if (source == undoMenuItem)
1035     {
1036       undoMenuItem_actionPerformed();
1037     }
1038     else if (source == redoMenuItem)
1039     {
1040       redoMenuItem_actionPerformed();
1041     }
1042     else if (source == inputText)
1043     {
1044       inputText_actionPerformed();
1045     }
1046     else if (source == closeMenuItem)
1047     {
1048       closeMenuItem_actionPerformed();
1049     }
1050     else if (source == undoMenuItem)
1051     {
1052       undoMenuItem_actionPerformed();
1053     }
1054     else if (source == redoMenuItem)
1055     {
1056       redoMenuItem_actionPerformed();
1057     }
1058     else if (source == copy)
1059     {
1060       copy_actionPerformed();
1061     }
1062     else if (source == pasteNew)
1063     {
1064       pasteNew_actionPerformed();
1065     }
1066     else if (source == pasteThis)
1067     {
1068       pasteThis_actionPerformed();
1069     }
1070     else if (source == cut)
1071     {
1072       cut_actionPerformed();
1073     }
1074     else if (source == delete)
1075     {
1076       delete_actionPerformed();
1077     }
1078     else if (source == createGroup)
1079     {
1080       createGroup_actionPerformed();
1081     }
1082     else if (source == unGroup)
1083     {
1084       unGroup_actionPerformed();
1085     }
1086     else if (source == grpsFromSelection)
1087     {
1088       makeGrpsFromSelection_actionPerformed();
1089     }
1090     else if (source == deleteGroups)
1091     {
1092       deleteGroups_actionPerformed();
1093     }
1094     else if (source == selectAllSequenceMenuItem)
1095     {
1096       selectAllSequenceMenuItem_actionPerformed();
1097     }
1098     else if (source == deselectAllSequenceMenuItem)
1099     {
1100       deselectAllSequenceMenuItem_actionPerformed();
1101     }
1102     else if (source == invertSequenceMenuItem)
1103     {
1104       invertSequenceMenuItem_actionPerformed();
1105       // uncomment to slave sequence selections in split frame
1106       // viewport.sendSelection();
1107     }
1108     else if (source == invertColSel)
1109     {
1110       viewport.invertColumnSelection();
1111       alignPanel.paintAlignment(true);
1112       viewport.sendSelection();
1113     }
1114     else if (source == remove2LeftMenuItem)
1115     {
1116       trimAlignment(true);
1117     }
1118     else if (source == remove2RightMenuItem)
1119     {
1120       trimAlignment(false);
1121     }
1122     else if (source == removeGappedColumnMenuItem)
1123     {
1124       removeGappedColumnMenuItem_actionPerformed();
1125     }
1126     else if (source == removeAllGapsMenuItem)
1127     {
1128       removeAllGapsMenuItem_actionPerformed();
1129     }
1130     else if (source == findMenuItem)
1131     {
1132       findMenuItem_actionPerformed();
1133     }
1134     else if (source == font)
1135     {
1136       new FontChooser(alignPanel);
1137     }
1138     else if (source == newView)
1139     {
1140       newView(null);
1141     }
1142     else if (source == showColumns)
1143     {
1144       viewport.showAllHiddenColumns();
1145       alignPanel.paintAlignment(true);
1146       viewport.sendSelection();
1147     }
1148     else if (source == showSeqs)
1149     {
1150       viewport.showAllHiddenSeqs();
1151       alignPanel.paintAlignment(true);
1152       // uncomment if we want to slave sequence selections in split frame
1153       // viewport.sendSelection();
1154     }
1155     else if (source == hideColumns)
1156     {
1157       viewport.hideSelectedColumns();
1158       alignPanel.paintAlignment(true);
1159       viewport.sendSelection();
1160     }
1161     else if (source == hideSequences
1162             && viewport.getSelectionGroup() != null)
1163     {
1164       viewport.hideAllSelectedSeqs();
1165       alignPanel.paintAlignment(true);
1166       // uncomment if we want to slave sequence selections in split frame
1167       // viewport.sendSelection();
1168     }
1169     else if (source == hideAllButSelection)
1170     {
1171       toggleHiddenRegions(false, false);
1172       alignPanel.paintAlignment(true);
1173       viewport.sendSelection();
1174     }
1175     else if (source == hideAllSelection)
1176     {
1177       SequenceGroup sg = viewport.getSelectionGroup();
1178       viewport.expandColSelection(sg, false);
1179       viewport.hideAllSelectedSeqs();
1180       viewport.hideSelectedColumns();
1181       alignPanel.paintAlignment(true);
1182       viewport.sendSelection();
1183     }
1184     else if (source == showAllHidden)
1185     {
1186       viewport.showAllHiddenColumns();
1187       viewport.showAllHiddenSeqs();
1188       alignPanel.paintAlignment(true);
1189       viewport.sendSelection();
1190     }
1191     else if (source == showGroupConsensus)
1192     {
1193       showGroupConsensus_actionPerformed();
1194     }
1195     else if (source == showGroupConservation)
1196     {
1197       showGroupConservation_actionPerformed();
1198     }
1199     else if (source == showSequenceLogo)
1200     {
1201       showSequenceLogo_actionPerformed();
1202     }
1203     else if (source == normSequenceLogo)
1204     {
1205       normSequenceLogo_actionPerformed();
1206     }
1207     else if (source == showConsensusHistogram)
1208     {
1209       showConsensusHistogram_actionPerformed();
1210     }
1211     else if (source == applyAutoAnnotationSettings)
1212     {
1213       applyAutoAnnotationSettings_actionPerformed();
1214     }
1215     else if (source == featureSettings)
1216     {
1217       new FeatureSettings(alignPanel);
1218     }
1219     else if (source == alProperties)
1220     {
1221       StringBuffer contents = new jalview.io.AlignmentProperties(
1222               viewport.getAlignment()).formatAsString();
1223       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1224       cap.setText(contents.toString());
1225       Frame frame = new Frame();
1226       frame.add(cap);
1227       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1228               "label.alignment_properties", new String[] { getTitle() }),
1229               400, 250);
1230     }
1231     else if (source == overviewMenuItem)
1232     {
1233       overviewMenuItem_actionPerformed();
1234     }
1235     else if (source == noColourmenuItem)
1236     {
1237       changeColour(null);
1238     }
1239     else if (source == clustalColour)
1240     {
1241       abovePIDThreshold.setState(false);
1242       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1243     }
1244     else if (source == zappoColour)
1245     {
1246       changeColour(new ZappoColourScheme());
1247     }
1248     else if (source == taylorColour)
1249     {
1250       changeColour(new TaylorColourScheme());
1251     }
1252     else if (source == hydrophobicityColour)
1253     {
1254       changeColour(new HydrophobicColourScheme());
1255     }
1256     else if (source == helixColour)
1257     {
1258       changeColour(new HelixColourScheme());
1259     }
1260     else if (source == strandColour)
1261     {
1262       changeColour(new StrandColourScheme());
1263     }
1264     else if (source == turnColour)
1265     {
1266       changeColour(new TurnColourScheme());
1267     }
1268     else if (source == buriedColour)
1269     {
1270       changeColour(new BuriedColourScheme());
1271     }
1272     else if (source == nucleotideColour)
1273     {
1274       changeColour(new NucleotideColourScheme());
1275     }
1276     else if (source == purinePyrimidineColour)
1277     {
1278       changeColour(new PurinePyrimidineColourScheme());
1279     }
1280     // else if (source == RNAInteractionColour)
1281     // {
1282     // changeColour(new RNAInteractionColourScheme());
1283     // }
1284     else if (source == RNAHelixColour)
1285     {
1286       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1287       // new RNAHelicesColourChooser(viewport, alignPanel);
1288     }
1289     else if (source == modifyPID)
1290     {
1291       modifyPID_actionPerformed();
1292     }
1293     else if (source == modifyConservation)
1294     {
1295       modifyConservation_actionPerformed();
1296     }
1297     else if (source == userDefinedColour)
1298     {
1299       new UserDefinedColours(alignPanel, null);
1300     }
1301     else if (source == PIDColour)
1302     {
1303       changeColour(new PIDColourScheme());
1304     }
1305     else if (source == BLOSUM62Colour)
1306     {
1307       changeColour(new Blosum62ColourScheme());
1308     }
1309     else if (source == tcoffeeColour)
1310     {
1311       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1312     }
1313     else if (source == annotationColour)
1314     {
1315       new AnnotationColourChooser(viewport, alignPanel);
1316     }
1317     else if (source == annotationColumnSelection)
1318     {
1319       new AnnotationColumnChooser(viewport, alignPanel);
1320     }
1321     else if (source == sortPairwiseMenuItem)
1322     {
1323       sortPairwiseMenuItem_actionPerformed();
1324     }
1325     else if (source == sortIDMenuItem)
1326     {
1327       sortIDMenuItem_actionPerformed();
1328     }
1329     else if (source == sortLengthMenuItem)
1330     {
1331       sortLengthMenuItem_actionPerformed();
1332     }
1333     else if (source == sortGroupMenuItem)
1334     {
1335       sortGroupMenuItem_actionPerformed();
1336     }
1337     else if (source == removeRedundancyMenuItem)
1338     {
1339       removeRedundancyMenuItem_actionPerformed();
1340     }
1341     else if (source == pairwiseAlignmentMenuItem)
1342     {
1343       pairwiseAlignmentMenuItem_actionPerformed();
1344     }
1345     else if (source == PCAMenuItem)
1346     {
1347       PCAMenuItem_actionPerformed();
1348     }
1349     else if (source == averageDistanceTreeMenuItem)
1350     {
1351       averageDistanceTreeMenuItem_actionPerformed();
1352     }
1353     else if (source == neighbourTreeMenuItem)
1354     {
1355       neighbourTreeMenuItem_actionPerformed();
1356     }
1357     else if (source == njTreeBlosumMenuItem)
1358     {
1359       njTreeBlosumMenuItem_actionPerformed();
1360     }
1361     else if (source == avDistanceTreeBlosumMenuItem)
1362     {
1363       avTreeBlosumMenuItem_actionPerformed();
1364     }
1365     else if (source == documentation)
1366     {
1367       documentation_actionPerformed();
1368     }
1369     else if (source == about)
1370     {
1371       about_actionPerformed();
1372     }
1373
1374   }
1375
1376   public void inputText_actionPerformed()
1377   {
1378     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1379     Frame frame = new Frame();
1380     frame.add(cap);
1381     jalview.bin.JalviewLite.addFrame(frame,
1382             MessageManager.getString("label.input_cut_paste"), 500, 500);
1383   }
1384
1385   protected void outputText_actionPerformed(ActionEvent e)
1386   {
1387     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388     Frame frame = new Frame();
1389     frame.add(cap);
1390     JalviewLite.addFrame(frame, MessageManager.formatMessage(
1391             "label.alignment_output_command",
1392             new Object[] { e.getActionCommand() }), 600, 500);
1393
1394     FileFormatI fileFormat = FileFormats.getInstance().forName(
1395             e.getActionCommand());
1396     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1397             fileFormat, viewport.getAlignment(),
1398             viewport.getShowJVSuffix()));
1399   }
1400
1401   public void loadAnnotations()
1402   {
1403     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1404     cap.setText(MessageManager
1405             .getString("label.paste_features_annotations_Tcoffee_here"));
1406     cap.setAnnotationImport();
1407     Frame frame = new Frame();
1408     frame.add(cap);
1409     jalview.bin.JalviewLite.addFrame(frame,
1410             MessageManager.getString("action.paste_annotations"), 400, 300);
1411
1412   }
1413
1414   public String outputAnnotations(boolean displayTextbox)
1415   {
1416     String annotation = new AnnotationFile()
1417             .printAnnotationsForView(viewport);
1418
1419     if (displayTextbox)
1420     {
1421       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1422       Frame frame = new Frame();
1423       frame.add(cap);
1424       jalview.bin.JalviewLite.addFrame(frame,
1425               MessageManager.getString("label.annotations"), 600, 500);
1426       cap.setText(annotation);
1427     }
1428
1429     return annotation;
1430   }
1431
1432   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1433   {
1434     if (alignPanel.getFeatureRenderer() != null
1435             && viewport.getFeaturesDisplayed() != null)
1436     {
1437       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1438
1439     }
1440     return null;
1441   }
1442
1443   public String outputFeatures(boolean displayTextbox, String format)
1444   {
1445     String features;
1446     FeaturesFile formatter = new FeaturesFile();
1447     if (format.equalsIgnoreCase("Jalview"))
1448     {
1449       features = formatter.printJalviewFormat(viewport.getAlignment()
1450               .getSequencesArray(), getDisplayedFeatureCols());
1451     }
1452     else
1453     {
1454       features = formatter.printGffFormat(viewport.getAlignment()
1455               .getSequencesArray(), getDisplayedFeatureCols());
1456     }
1457
1458     if (displayTextbox)
1459     {
1460       boolean frimport = false;
1461       if (features == null || features.equals("No Features Visible"))
1462       {
1463         features = "# No features visible - paste some and import them here.";
1464         frimport = true;
1465       }
1466
1467       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1468       if (frimport)
1469       {
1470         cap.setAnnotationImport();
1471       }
1472       Frame frame = new Frame();
1473       frame.add(cap);
1474       jalview.bin.JalviewLite.addFrame(frame,
1475               MessageManager.getString("label.features"), 600, 500);
1476       cap.setText(features);
1477     }
1478     else
1479     {
1480       if (features == null)
1481       {
1482         features = "";
1483       }
1484     }
1485
1486     return features;
1487   }
1488
1489   void launchFullApplication()
1490   {
1491     StringBuffer url = new StringBuffer(jalviewServletURL);
1492
1493     // allow servlet parameters to be passed in applet parameter
1494     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1495             : "?";
1496     url.append(firstSep);
1497
1498     url.append("open="
1499             + appendProtocol(viewport.applet.getParameter("file")));
1500
1501     if (viewport.applet.getParameter("features") != null)
1502     {
1503       url.append("&features=");
1504       url.append(appendProtocol(viewport.applet.getParameter("features")));
1505     }
1506
1507     if (viewport.applet.getParameter("annotations") != null)
1508     {
1509       url.append("&annotations=");
1510       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1511     }
1512
1513     if (viewport.applet.getParameter("jnetfile") != null
1514             || viewport.applet.getParameter("jpredfile") != null)
1515     {
1516       url.append("&annotations=");
1517       url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1518               .getParameter("jnetfile") : viewport.applet
1519               .getParameter("jpredfile")));
1520     }
1521
1522     if (viewport.applet.getParameter("defaultColour") != null)
1523     {
1524       url.append("&colour="
1525               + removeWhiteSpace(viewport.applet
1526                       .getParameter("defaultColour")));
1527     }
1528
1529     if (viewport.applet.getParameter("userDefinedColour") != null)
1530     {
1531       url.append("&colour="
1532               + removeWhiteSpace(viewport.applet
1533                       .getParameter("userDefinedColour")));
1534     }
1535     if (viewport.applet.getParameter("tree") != null)
1536     {
1537       url.append("&tree="
1538               + appendProtocol(viewport.applet.getParameter("tree")));
1539     }
1540     if (viewport.applet.getParameter("treeFile") != null)
1541     {
1542       url.append("&tree="
1543               + appendProtocol(viewport.applet.getParameter("treeFile")));
1544     }
1545
1546     showURL(url.toString(), "FULL_APP");
1547   }
1548
1549   String removeWhiteSpace(String colour)
1550   {
1551     StringBuffer sb = new StringBuffer();
1552     for (int i = 0; i < colour.length(); i++)
1553     {
1554       if (Character.isWhitespace(colour.charAt(i)))
1555       {
1556         sb.append("%20");
1557       }
1558       else
1559       {
1560         sb.append(colour.charAt(i));
1561       }
1562     }
1563
1564     return sb.toString();
1565   }
1566
1567   String appendProtocol(String url)
1568   {
1569     try
1570     {
1571       new URL(url);
1572       url = URLEncoder.encode(url);
1573     }
1574     /*
1575      * When we finally deprecate 1.1 compatibility, we can start to use
1576      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1577      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1578      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1579      * ex.printStackTrace(); }
1580      */
1581     catch (java.net.MalformedURLException ex)
1582     {
1583       url = viewport.applet.getCodeBase() + url;
1584     }
1585     return url;
1586   }
1587
1588   public void closeMenuItem_actionPerformed()
1589   {
1590     PaintRefresher.RemoveComponent(alignPanel);
1591     if (alignPanel.seqPanel != null
1592             && alignPanel.seqPanel.seqCanvas != null)
1593     {
1594       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1595     }
1596     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1597     {
1598       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1599     }
1600
1601     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1602     {
1603       System.exit(0);
1604     }
1605     else
1606     {
1607     }
1608     viewport = null;
1609     alignPanel = null;
1610     this.dispose();
1611   }
1612
1613   /**
1614    * TODO: JAL-1104
1615    */
1616   void updateEditMenuBar()
1617   {
1618
1619     if (viewport.getHistoryList().size() > 0)
1620     {
1621       undoMenuItem.setEnabled(true);
1622       CommandI command = viewport.getHistoryList().peek();
1623       undoMenuItem.setLabel(MessageManager.formatMessage(
1624               "label.undo_command",
1625               new Object[] { command.getDescription() }));
1626     }
1627     else
1628     {
1629       undoMenuItem.setEnabled(false);
1630       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1631     }
1632
1633     if (viewport.getRedoList().size() > 0)
1634     {
1635       redoMenuItem.setEnabled(true);
1636
1637       CommandI command = viewport.getRedoList().peek();
1638       redoMenuItem.setLabel(MessageManager.formatMessage(
1639               "label.redo_command",
1640               new Object[] { command.getDescription() }));
1641     }
1642     else
1643     {
1644       redoMenuItem.setEnabled(false);
1645       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1646     }
1647   }
1648
1649   /**
1650    * TODO: JAL-1104
1651    */
1652   @Override
1653   public void addHistoryItem(CommandI command)
1654   {
1655     if (command.getSize() > 0)
1656     {
1657       viewport.addToHistoryList(command);
1658       viewport.clearRedoList();
1659       updateEditMenuBar();
1660       viewport.updateHiddenColumns();
1661     }
1662   }
1663
1664   /**
1665    * TODO: JAL-1104 DOCUMENT ME!
1666    *
1667    * @param e
1668    *          DOCUMENT ME!
1669    */
1670   protected void undoMenuItem_actionPerformed()
1671   {
1672     if (viewport.getHistoryList().isEmpty())
1673     {
1674       return;
1675     }
1676
1677     CommandI command = viewport.getHistoryList().pop();
1678     viewport.addToRedoList(command);
1679     command.undoCommand(null);
1680
1681     AlignmentViewport originalSource = getOriginatingSource(command);
1682     // JBPNote Test
1683     if (originalSource != viewport)
1684     {
1685       System.err
1686               .println("Warning: Viewport object mismatch whilst undoing");
1687     }
1688     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1689                                           // viewport.getColumnSelection().getHiddenColumns()
1690                                           // != null;
1691     updateEditMenuBar();
1692     originalSource.firePropertyChange("alignment", null, originalSource
1693             .getAlignment().getSequences());
1694   }
1695
1696   /**
1697    * TODO: JAL-1104 DOCUMENT ME!
1698    *
1699    * @param e
1700    *          DOCUMENT ME!
1701    */
1702   protected void redoMenuItem_actionPerformed()
1703   {
1704     if (viewport.getRedoList().isEmpty())
1705     {
1706       return;
1707     }
1708
1709     CommandI command = viewport.getRedoList().pop();
1710     viewport.addToHistoryList(command);
1711     command.doCommand(null);
1712
1713     AlignmentViewport originalSource = getOriginatingSource(command);
1714     // JBPNote Test
1715     if (originalSource != viewport)
1716     {
1717       System.err
1718               .println("Warning: Viewport object mismatch whilst re-doing");
1719     }
1720     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1721                                           // viewport.getColumnSelection().getHiddenColumns()
1722                                           // != null;
1723
1724     updateEditMenuBar();
1725     originalSource.firePropertyChange("alignment", null, originalSource
1726             .getAlignment().getSequences());
1727   }
1728
1729   AlignmentViewport getOriginatingSource(CommandI command)
1730   {
1731     AlignmentViewport originalSource = null;
1732     // For sequence removal and addition, we need to fire
1733     // the property change event FROM the viewport where the
1734     // original alignment was altered
1735     AlignmentI al = null;
1736     if (command instanceof EditCommand)
1737     {
1738       EditCommand editCommand = (EditCommand) command;
1739       al = editCommand.getAlignment();
1740       Vector comps = (Vector) PaintRefresher.components.get(viewport
1741               .getSequenceSetId());
1742       for (int i = 0; i < comps.size(); i++)
1743       {
1744         if (comps.elementAt(i) instanceof AlignmentPanel)
1745         {
1746           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1747           {
1748             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1749             break;
1750           }
1751         }
1752       }
1753     }
1754
1755     if (originalSource == null)
1756     {
1757       // The original view is closed, we must validate
1758       // the current view against the closed view first
1759       if (al != null)
1760       {
1761         PaintRefresher.validateSequences(al, viewport.getAlignment());
1762       }
1763
1764       originalSource = viewport;
1765     }
1766
1767     return originalSource;
1768   }
1769
1770   /**
1771    * Move the currently selected sequences up or down one position in the
1772    * alignment
1773    *
1774    * @param up
1775    */
1776   public void moveSelectedSequences(boolean up)
1777   {
1778     SequenceGroup sg = viewport.getSelectionGroup();
1779     if (sg == null)
1780     {
1781       return;
1782     }
1783     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1784             up ? null : viewport.getHiddenRepSequences(), up);
1785     alignPanel.paintAlignment(true);
1786
1787     /*
1788      * Also move cDNA/protein complement sequences
1789      */
1790     AlignViewportI complement = viewport.getCodingComplement();
1791     if (complement != null)
1792     {
1793       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1794               viewport, complement);
1795       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1796               up ? null : complement.getHiddenRepSequences(), up);
1797       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1798     }
1799   }
1800
1801   synchronized void slideSequences(boolean right, int size)
1802   {
1803     List<SequenceI> sg = new Vector<SequenceI>();
1804     if (viewport.cursorMode)
1805     {
1806       sg.add(viewport.getAlignment().getSequenceAt(
1807               alignPanel.seqPanel.seqCanvas.cursorY));
1808     }
1809     else if (viewport.getSelectionGroup() != null
1810             && viewport.getSelectionGroup().getSize() != viewport
1811                     .getAlignment().getHeight())
1812     {
1813       sg = viewport.getSelectionGroup().getSequences(
1814               viewport.getHiddenRepSequences());
1815     }
1816
1817     if (sg.size() < 1)
1818     {
1819       return;
1820     }
1821
1822     Vector<SequenceI> invertGroup = new Vector();
1823
1824     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1825     {
1826       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1827       {
1828         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1829       }
1830     }
1831
1832     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1833
1834     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1835             .size()]);
1836     for (int i = 0; i < invertGroup.size(); i++)
1837     {
1838       seqs2[i] = invertGroup.elementAt(i);
1839     }
1840
1841     SlideSequencesCommand ssc;
1842     if (right)
1843     {
1844       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1845               size, viewport.getGapCharacter());
1846     }
1847     else
1848     {
1849       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1850               size, viewport.getGapCharacter());
1851     }
1852
1853     int groupAdjustment = 0;
1854     if (ssc.getGapsInsertedBegin() && right)
1855     {
1856       if (viewport.cursorMode)
1857       {
1858         alignPanel.seqPanel.moveCursor(size, 0);
1859       }
1860       else
1861       {
1862         groupAdjustment = size;
1863       }
1864     }
1865     else if (!ssc.getGapsInsertedBegin() && !right)
1866     {
1867       if (viewport.cursorMode)
1868       {
1869         alignPanel.seqPanel.moveCursor(-size, 0);
1870       }
1871       else
1872       {
1873         groupAdjustment = -size;
1874       }
1875     }
1876
1877     if (groupAdjustment != 0)
1878     {
1879       viewport.getSelectionGroup().setStartRes(
1880               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1881       viewport.getSelectionGroup().setEndRes(
1882               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1883     }
1884
1885     boolean appendHistoryItem = false;
1886     Deque<CommandI> historyList = viewport.getHistoryList();
1887     if (historyList != null && historyList.size() > 0
1888             && historyList.peek() instanceof SlideSequencesCommand)
1889     {
1890       appendHistoryItem = ssc
1891               .appendSlideCommand((SlideSequencesCommand) historyList
1892                       .peek());
1893     }
1894
1895     if (!appendHistoryItem)
1896     {
1897       addHistoryItem(ssc);
1898     }
1899
1900     repaint();
1901   }
1902
1903   static StringBuffer copiedSequences;
1904
1905   static Vector copiedHiddenColumns;
1906
1907   protected void copy_actionPerformed()
1908   {
1909     if (viewport.getSelectionGroup() == null)
1910     {
1911       return;
1912     }
1913
1914     SequenceGroup sg = viewport.getSelectionGroup();
1915     copiedSequences = new StringBuffer();
1916     Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1917     for (int i = 0; i < sg.getSize(); i++)
1918     {
1919       SequenceI seq = sg.getSequenceAt(i);
1920       int index = viewport.getAlignment().findIndex(seq);
1921       orderedSeqs.put(index, seq);
1922     }
1923
1924     int index = 0, startRes, endRes;
1925     char ch;
1926
1927     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1928     {
1929       copiedHiddenColumns = new Vector();
1930       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1931       for (int[] region : viewport.getAlignment().getHiddenColumns()
1932               .getListOfCols())
1933       {
1934         copiedHiddenColumns.addElement(new int[] {
1935             region[0] - hiddenOffset, region[1] - hiddenOffset });
1936       }
1937     }
1938     else
1939     {
1940       copiedHiddenColumns = null;
1941     }
1942
1943     for (int i = 0; i < sg.getSize(); i++)
1944     {
1945       SequenceI seq = null;
1946
1947       while (seq == null)
1948       {
1949         if (orderedSeqs.containsKey(index))
1950         {
1951           seq = orderedSeqs.get(index);
1952           index++;
1953           break;
1954         }
1955         else
1956         {
1957           index++;
1958         }
1959       }
1960
1961       // FIND START RES
1962       // Returns residue following index if gap
1963       startRes = seq.findPosition(sg.getStartRes());
1964
1965       // FIND END RES
1966       // Need to find the residue preceeding index if gap
1967       endRes = 0;
1968
1969       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1970       {
1971         ch = seq.getCharAt(j);
1972         if (!jalview.util.Comparison.isGap((ch)))
1973         {
1974           endRes++;
1975         }
1976       }
1977
1978       if (endRes > 0)
1979       {
1980         endRes += seq.getStart() - 1;
1981       }
1982
1983       copiedSequences.append(seq.getName()
1984               + "\t"
1985               + startRes
1986               + "\t"
1987               + endRes
1988               + "\t"
1989               + seq.getSequenceAsString(sg.getStartRes(),
1990                       sg.getEndRes() + 1) + "\n");
1991     }
1992
1993   }
1994
1995   protected void pasteNew_actionPerformed()
1996   {
1997     paste(true);
1998   }
1999
2000   protected void pasteThis_actionPerformed()
2001   {
2002     paste(false);
2003   }
2004
2005   void paste(boolean newAlignment)
2006   {
2007     try
2008     {
2009
2010       if (copiedSequences == null)
2011       {
2012         return;
2013       }
2014
2015       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2016       Vector seqs = new Vector();
2017       while (st.hasMoreElements())
2018       {
2019         String name = st.nextToken();
2020         int start = Integer.parseInt(st.nextToken());
2021         int end = Integer.parseInt(st.nextToken());
2022         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2023       }
2024       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2025       for (int i = 0; i < seqs.size(); i++)
2026       {
2027         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2028       }
2029
2030       if (newAlignment)
2031       {
2032         String newtitle = MessageManager
2033                 .getString("label.copied_sequences");
2034         if (getTitle().startsWith(
2035                 MessageManager.getString("label.copied_sequences")))
2036         {
2037           newtitle = getTitle();
2038         }
2039         else
2040         {
2041           newtitle = newtitle.concat(MessageManager.formatMessage(
2042                   "label.from_msname", new String[] { getTitle() }));
2043         }
2044         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2045                 viewport.applet, newtitle, false);
2046         if (copiedHiddenColumns != null)
2047         {
2048           for (int i = 0; i < copiedHiddenColumns.size(); i++)
2049           {
2050             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2051             af.viewport.hideColumns(region[0], region[1]);
2052           }
2053         }
2054
2055         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2056                 frameHeight);
2057       }
2058       else
2059       {
2060         addSequences(newSeqs);
2061       }
2062
2063     } catch (Exception ex)
2064     {
2065     } // could be anything being pasted in here
2066
2067   }
2068
2069   void addSequences(SequenceI[] seqs)
2070   {
2071     for (int i = 0; i < seqs.length; i++)
2072     {
2073       viewport.getAlignment().addSequence(seqs[i]);
2074     }
2075
2076     // !newAlignment
2077     addHistoryItem(new EditCommand(
2078             MessageManager.getString("label.add_sequences"), Action.PASTE,
2079             seqs, 0, viewport.getAlignment().getWidth(),
2080             viewport.getAlignment()));
2081
2082     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2083     viewport.getAlignment().getWidth();
2084     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2085             .getSequences());
2086
2087   }
2088
2089   protected void cut_actionPerformed()
2090   {
2091     copy_actionPerformed();
2092     delete_actionPerformed();
2093   }
2094
2095   protected void delete_actionPerformed()
2096   {
2097
2098     SequenceGroup sg = viewport.getSelectionGroup();
2099     if (sg == null)
2100     {
2101       return;
2102     }
2103
2104     Vector seqs = new Vector();
2105     SequenceI seq;
2106     for (int i = 0; i < sg.getSize(); i++)
2107     {
2108       seq = sg.getSequenceAt(i);
2109       seqs.addElement(seq);
2110     }
2111
2112     /*
2113      * If the cut affects all sequences, warn, remove highlighted columns
2114      */
2115     if (sg.getSize() == viewport.getAlignment().getHeight())
2116     {
2117       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2118               .getAlignment().getWidth()) ? true : false;
2119       if (isEntireAlignWidth)
2120       {
2121         String title = MessageManager.getString("label.delete_all");
2122         Panel infoPanel = new Panel();
2123         infoPanel.setLayout(new FlowLayout());
2124         infoPanel
2125                 .add(new Label(MessageManager.getString("warn.delete_all")));
2126
2127         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2128         dialog.setMainPanel(infoPanel);
2129         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2130         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2131         dialog.setVisible(true);
2132
2133         if (!dialog.accept)
2134         {
2135           return;
2136         }
2137       }
2138       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2139               sg.getEndRes() + 1);
2140     }
2141
2142     SequenceI[] cut = new SequenceI[seqs.size()];
2143     for (int i = 0; i < seqs.size(); i++)
2144     {
2145       cut[i] = (SequenceI) seqs.elementAt(i);
2146     }
2147
2148     /*
2149      * //ADD HISTORY ITEM
2150      */
2151     addHistoryItem(new EditCommand(
2152             MessageManager.getString("label.cut_sequences"), Action.CUT,
2153             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2154             viewport.getAlignment()));
2155
2156     viewport.setSelectionGroup(null);
2157     viewport.getAlignment().deleteGroup(sg);
2158
2159     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2160             .getSequences());
2161
2162     if (viewport.getAlignment().getHeight() < 1)
2163     {
2164       this.setVisible(false);
2165     }
2166     viewport.sendSelection();
2167   }
2168
2169   /**
2170    * group consensus toggled
2171    *
2172    */
2173   protected void showGroupConsensus_actionPerformed()
2174   {
2175     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2176     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177
2178   }
2179
2180   /**
2181    * group conservation toggled.
2182    */
2183   protected void showGroupConservation_actionPerformed()
2184   {
2185     viewport.setShowGroupConservation(showGroupConservation.getState());
2186     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187   }
2188
2189   /*
2190    * (non-Javadoc)
2191    *
2192    * @see
2193    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2194    * .event.ActionEvent)
2195    */
2196   protected void showConsensusHistogram_actionPerformed()
2197   {
2198     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2199     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2200   }
2201
2202   /*
2203    * (non-Javadoc)
2204    *
2205    * @see
2206    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2207    * .event.ActionEvent)
2208    */
2209   protected void showSequenceLogo_actionPerformed()
2210   {
2211     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2212     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2213   }
2214
2215   protected void normSequenceLogo_actionPerformed()
2216   {
2217     showSequenceLogo.setState(true);
2218     viewport.setShowSequenceLogo(true);
2219     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2220     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2221   }
2222
2223   protected void applyAutoAnnotationSettings_actionPerformed()
2224   {
2225     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2226   }
2227
2228   protected void makeGrpsFromSelection_actionPerformed()
2229   {
2230     if (avc.makeGroupsFromSelection())
2231     {
2232       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2233       alignPanel.updateAnnotation();
2234       alignPanel.paintAlignment(true);
2235     }
2236   }
2237
2238   protected void createGroup_actionPerformed()
2239   {
2240     avc.createGroup();
2241   }
2242
2243   protected void unGroup_actionPerformed()
2244   {
2245     if (avc.unGroup())
2246     {
2247       alignPanel.alignmentChanged();
2248     }
2249   }
2250
2251   protected void deleteGroups_actionPerformed()
2252   {
2253     if (avc.deleteGroups())
2254     {
2255       alignPanel.alignmentChanged();
2256     }
2257   }
2258
2259   public void selectAllSequenceMenuItem_actionPerformed()
2260   {
2261     SequenceGroup sg = new SequenceGroup();
2262     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263     {
2264       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2265     }
2266     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2267     viewport.setSelectionGroup(sg);
2268     // JAL-2034 - should delegate to
2269     // alignPanel to decide if overview needs
2270     // updating.
2271     alignPanel.paintAlignment(false);
2272     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273     viewport.sendSelection();
2274   }
2275
2276   public void deselectAllSequenceMenuItem_actionPerformed()
2277   {
2278     if (viewport.cursorMode)
2279     {
2280       alignPanel.seqPanel.keyboardNo1 = null;
2281       alignPanel.seqPanel.keyboardNo2 = null;
2282     }
2283     viewport.setSelectionGroup(null);
2284     viewport.getColumnSelection().clear();
2285     viewport.setSelectionGroup(null);
2286     alignPanel.idPanel.idCanvas.searchResults = null;
2287     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2288     // JAL-2034 - should delegate to
2289     // alignPanel to decide if overview needs
2290     // updating.
2291     alignPanel.paintAlignment(false);
2292     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293     viewport.sendSelection();
2294   }
2295
2296   public void invertSequenceMenuItem_actionPerformed()
2297   {
2298     SequenceGroup sg = viewport.getSelectionGroup();
2299     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2300     {
2301       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2302     }
2303
2304     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2305     viewport.sendSelection();
2306   }
2307
2308   public void invertColSel_actionPerformed()
2309   {
2310     viewport.invertColumnSelection();
2311     alignPanel.paintAlignment(true);
2312     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2313     viewport.sendSelection();
2314   }
2315
2316   void trimAlignment(boolean trimLeft)
2317   {
2318     AlignmentI al = viewport.getAlignment();
2319     ViewportRanges ranges = viewport.getRanges();
2320     ColumnSelection colSel = viewport.getColumnSelection();
2321     int column;
2322
2323     if (!colSel.isEmpty())
2324     {
2325       if (trimLeft)
2326       {
2327         column = colSel.getMin();
2328       }
2329       else
2330       {
2331         column = colSel.getMax();
2332       }
2333
2334       SequenceI[] seqs;
2335       if (viewport.getSelectionGroup() != null)
2336       {
2337         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338                 viewport.getHiddenRepSequences());
2339       }
2340       else
2341       {
2342         seqs = al.getSequencesArray();
2343       }
2344
2345       TrimRegionCommand trimRegion;
2346       if (trimLeft)
2347       {
2348         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2349                 column, al);
2350         ranges.setStartRes(0);
2351       }
2352       else
2353       {
2354         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2355                 column, al);
2356       }
2357
2358       statusBar.setText(MessageManager.formatMessage(
2359               "label.removed_columns",
2360               new String[] { Integer.valueOf(trimRegion.getSize())
2361                       .toString() }));
2362       addHistoryItem(trimRegion);
2363
2364       for (SequenceGroup sg : al.getGroups())
2365       {
2366         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2367                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2368         {
2369           al.deleteGroup(sg);
2370         }
2371       }
2372
2373       viewport.firePropertyChange("alignment", null, al.getSequences());
2374     }
2375   }
2376
2377   public void removeGappedColumnMenuItem_actionPerformed()
2378   {
2379     AlignmentI al = viewport.getAlignment();
2380     ViewportRanges ranges = viewport.getRanges();
2381     int start = 0;
2382     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2383
2384     SequenceI[] seqs;
2385     if (viewport.getSelectionGroup() != null)
2386     {
2387       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2388               viewport.getHiddenRepSequences());
2389       start = viewport.getSelectionGroup().getStartRes();
2390       end = viewport.getSelectionGroup().getEndRes();
2391     }
2392     else
2393     {
2394       seqs = viewport.getAlignment().getSequencesArray();
2395     }
2396
2397     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2398             "Remove Gapped Columns", seqs, start, end,
2399             viewport.getAlignment());
2400
2401     addHistoryItem(removeGapCols);
2402
2403     statusBar.setText(MessageManager.formatMessage(
2404             "label.removed_empty_columns",
2405             new String[] { Integer.valueOf(removeGapCols.getSize())
2406                     .toString() }));
2407
2408     // This is to maintain viewport position on first residue
2409     // of first sequence
2410     SequenceI seq = al.getSequenceAt(0);
2411     int startRes = seq.findPosition(ranges.getStartRes());
2412     // ShiftList shifts;
2413     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2414     // edit.alColumnChanges=shifts.getInverse();
2415     // if (viewport.hasHiddenColumns)
2416     // viewport.getColumnSelection().compensateForEdits(shifts);
2417     ranges.setStartRes(seq.findIndex(startRes) - 1);
2418     viewport.firePropertyChange("alignment", null, al.getSequences());
2419
2420   }
2421
2422   public void removeAllGapsMenuItem_actionPerformed()
2423   {
2424     AlignmentI al = viewport.getAlignment();
2425     ViewportRanges ranges = viewport.getRanges();
2426     int start = 0;
2427     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2428
2429     SequenceI[] seqs;
2430     if (viewport.getSelectionGroup() != null)
2431     {
2432       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2433               viewport.getHiddenRepSequences());
2434       start = viewport.getSelectionGroup().getStartRes();
2435       end = viewport.getSelectionGroup().getEndRes();
2436     }
2437     else
2438     {
2439       seqs = viewport.getAlignment().getSequencesArray();
2440     }
2441
2442     // This is to maintain viewport position on first residue
2443     // of first sequence
2444     SequenceI seq = al.getSequenceAt(0);
2445     int startRes = seq.findPosition(ranges.getStartRes());
2446
2447     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2448             al));
2449
2450     ranges.setStartRes(seq.findIndex(startRes) - 1);
2451
2452     viewport.firePropertyChange("alignment", null, al.getSequences());
2453
2454   }
2455
2456   public void findMenuItem_actionPerformed()
2457   {
2458     new Finder(alignPanel);
2459   }
2460
2461   /**
2462    * create a new view derived from the current view
2463    *
2464    * @param viewtitle
2465    * @return frame for the new view
2466    */
2467   public AlignFrame newView(String viewtitle)
2468   {
2469     AlignmentI newal;
2470     if (viewport.hasHiddenRows())
2471     {
2472       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2473               .getFullAlignment().getSequencesArray());
2474     }
2475     else
2476     {
2477       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2478     }
2479
2480     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2481     {
2482       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2483       {
2484         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2485         {
2486           newal.addAnnotation(viewport.getAlignment()
2487                   .getAlignmentAnnotation()[i]);
2488         }
2489       }
2490     }
2491
2492     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2493
2494     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2495     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2496     PaintRefresher.Register(newaf.alignPanel,
2497             newaf.alignPanel.av.getSequenceSetId());
2498
2499     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2500             newaf.alignPanel.av.getSequenceSetId());
2501     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2502             newaf.alignPanel.av.getSequenceSetId());
2503
2504     Vector comps = (Vector) PaintRefresher.components.get(viewport
2505             .getSequenceSetId());
2506     int viewSize = -1;
2507     for (int i = 0; i < comps.size(); i++)
2508     {
2509       if (comps.elementAt(i) instanceof AlignmentPanel)
2510       {
2511         viewSize++;
2512       }
2513     }
2514
2515     String title = new String(this.getTitle());
2516     if (viewtitle != null)
2517     {
2518       title = viewtitle + " ( " + title + ")";
2519     }
2520     else
2521     {
2522       if (title.indexOf("(View") > -1)
2523       {
2524         title = title.substring(0, title.indexOf("(View"));
2525       }
2526       title += "(View " + viewSize + ")";
2527     }
2528
2529     newaf.setTitle(title.toString());
2530
2531     newaf.viewport.setHistoryList(viewport.getHistoryList());
2532     newaf.viewport.setRedoList(viewport.getRedoList());
2533     return newaf;
2534   }
2535
2536   /**
2537    *
2538    * @return list of feature groups on the view
2539    */
2540   public String[] getFeatureGroups()
2541   {
2542     FeatureRenderer fr = null;
2543     if (alignPanel != null
2544             && (fr = alignPanel.getFeatureRenderer()) != null)
2545     {
2546       List<String> gps = fr.getFeatureGroups();
2547       String[] _gps = gps.toArray(new String[gps.size()]);
2548       return _gps;
2549     }
2550     return null;
2551   }
2552
2553   /**
2554    * get sequence feature groups that are hidden or shown
2555    *
2556    * @param visible
2557    *          true is visible
2558    * @return list
2559    */
2560   public String[] getFeatureGroupsOfState(boolean visible)
2561   {
2562     FeatureRenderer fr = null;
2563     if (alignPanel != null
2564             && (fr = alignPanel.getFeatureRenderer()) != null)
2565     {
2566       List<String> gps = fr.getGroups(visible);
2567       String[] _gps = gps.toArray(new String[gps.size()]);
2568       return _gps;
2569     }
2570     return null;
2571   }
2572
2573   /**
2574    * Change the display state for the given feature groups
2575    *
2576    * @param groups
2577    *          list of group strings
2578    * @param state
2579    *          visible or invisible
2580    */
2581   public void setFeatureGroupState(String[] groups, boolean state)
2582   {
2583     FeatureRenderer fr = null;
2584     this.sequenceFeatures.setState(true);
2585     viewport.setShowSequenceFeatures(true);
2586     if (alignPanel != null
2587             && (fr = alignPanel.getFeatureRenderer()) != null)
2588     {
2589
2590       fr.setGroupVisibility(Arrays.asList(groups), state);
2591       alignPanel.seqPanel.seqCanvas.repaint();
2592       if (alignPanel.overviewPanel != null)
2593       {
2594         alignPanel.overviewPanel.updateOverviewImage();
2595       }
2596     }
2597   }
2598
2599   public void seqLimits_itemStateChanged()
2600   {
2601     viewport.setShowJVSuffix(seqLimits.getState());
2602     alignPanel.fontChanged();
2603     alignPanel.paintAlignment(true);
2604   }
2605
2606   protected void colourTextMenuItem_actionPerformed()
2607   {
2608     viewport.setColourText(colourTextMenuItem.getState());
2609     alignPanel.paintAlignment(true);
2610   }
2611
2612   protected void displayNonconservedMenuItem_actionPerformed()
2613   {
2614     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2615     alignPanel.paintAlignment(true);
2616   }
2617
2618   protected void wrapMenuItem_actionPerformed()
2619   {
2620     viewport.setWrapAlignment(wrapMenuItem.getState());
2621     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2622     scaleAbove.setEnabled(wrapMenuItem.getState());
2623     scaleLeft.setEnabled(wrapMenuItem.getState());
2624     scaleRight.setEnabled(wrapMenuItem.getState());
2625     alignPanel.paintAlignment(true);
2626   }
2627
2628   public void overviewMenuItem_actionPerformed()
2629   {
2630     if (alignPanel.overviewPanel != null)
2631     {
2632       return;
2633     }
2634
2635     Frame frame = new Frame();
2636     OverviewPanel overview = new OverviewPanel(alignPanel);
2637     frame.add(overview);
2638     // +50 must allow for applet frame window
2639     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2640             "label.overview_params", new String[] { this.getTitle() }),
2641             overview.getPreferredSize().width,
2642             overview.getPreferredSize().height + 50);
2643
2644     frame.pack();
2645     final AlignmentPanel ap = alignPanel;
2646     frame.addWindowListener(new WindowAdapter()
2647     {
2648       @Override
2649       public void windowClosing(WindowEvent e)
2650       {
2651         if (ap != null)
2652         {
2653           ap.setOverviewPanel(null);
2654         }
2655       };
2656     });
2657
2658     alignPanel.setOverviewPanel(overview);
2659
2660   }
2661
2662   @Override
2663   public void changeColour(ColourSchemeI cs)
2664   {
2665     viewport.setGlobalColourScheme(cs);
2666
2667     alignPanel.paintAlignment(true);
2668   }
2669
2670   protected void modifyPID_actionPerformed()
2671   {
2672     if (viewport.getAbovePIDThreshold()
2673             && viewport.getGlobalColourScheme() != null)
2674     {
2675       SliderPanel.setPIDSliderSource(alignPanel,
2676               viewport.getResidueShading(), alignPanel.getViewName());
2677       SliderPanel.showPIDSlider();
2678     }
2679   }
2680
2681   protected void modifyConservation_actionPerformed()
2682   {
2683     if (viewport.getConservationSelected()
2684             && viewport.getGlobalColourScheme() != null)
2685     {
2686       SliderPanel.setConservationSlider(alignPanel,
2687               viewport.getResidueShading(), alignPanel.getViewName());
2688       SliderPanel.showConservationSlider();
2689     }
2690   }
2691
2692   protected void conservationMenuItem_actionPerformed()
2693   {
2694     boolean selected = conservationMenuItem.getState();
2695     modifyConservation.setEnabled(selected);
2696     viewport.setConservationSelected(selected);
2697     viewport.getResidueShading().setConservationApplied(selected);
2698
2699     changeColour(viewport.getGlobalColourScheme());
2700
2701     if (selected)
2702     {
2703       modifyConservation_actionPerformed();
2704     }
2705     else
2706     {
2707       SliderPanel.hideConservationSlider();
2708     }
2709   }
2710
2711   public void abovePIDThreshold_actionPerformed()
2712   {
2713     boolean selected = abovePIDThreshold.getState();
2714     modifyPID.setEnabled(selected);
2715     viewport.setAbovePIDThreshold(selected);
2716     if (!selected)
2717     {
2718       viewport.getResidueShading().setThreshold(0,
2719               viewport.isIgnoreGapsConsensus());
2720     }
2721
2722     changeColour(viewport.getGlobalColourScheme());
2723
2724     if (selected)
2725     {
2726       modifyPID_actionPerformed();
2727     }
2728     else
2729     {
2730       SliderPanel.hidePIDSlider();
2731     }
2732   }
2733
2734   public void sortPairwiseMenuItem_actionPerformed()
2735   {
2736     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2738             .getAlignment().getSequenceAt(0));
2739
2740     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2741             viewport.getAlignment()));
2742     alignPanel.paintAlignment(true);
2743   }
2744
2745   public void sortIDMenuItem_actionPerformed()
2746   {
2747     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2748     AlignmentSorter.sortByID(viewport.getAlignment());
2749     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2750             viewport.getAlignment()));
2751     alignPanel.paintAlignment(true);
2752   }
2753
2754   public void sortLengthMenuItem_actionPerformed()
2755   {
2756     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2757     AlignmentSorter.sortByLength(viewport.getAlignment());
2758     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2759             viewport.getAlignment()));
2760     alignPanel.paintAlignment(true);
2761   }
2762
2763   public void sortGroupMenuItem_actionPerformed()
2764   {
2765     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2766     AlignmentSorter.sortByGroup(viewport.getAlignment());
2767     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2768             viewport.getAlignment()));
2769     alignPanel.paintAlignment(true);
2770
2771   }
2772
2773   public void removeRedundancyMenuItem_actionPerformed()
2774   {
2775     new RedundancyPanel(alignPanel);
2776   }
2777
2778   public void pairwiseAlignmentMenuItem_actionPerformed()
2779   {
2780     if (viewport.getSelectionGroup() != null
2781             && viewport.getSelectionGroup().getSize() > 1)
2782     {
2783       Frame frame = new Frame();
2784       frame.add(new PairwiseAlignPanel(alignPanel));
2785       jalview.bin.JalviewLite.addFrame(frame,
2786               MessageManager.getString("action.pairwise_alignment"), 600,
2787               500);
2788     }
2789   }
2790
2791   public void PCAMenuItem_actionPerformed()
2792   {
2793     // are the sequences aligned?
2794     if (!viewport.getAlignment().isAligned(false))
2795     {
2796       SequenceI current;
2797       int Width = viewport.getAlignment().getWidth();
2798
2799       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2800       {
2801         current = viewport.getAlignment().getSequenceAt(i);
2802
2803         if (current.getLength() < Width)
2804         {
2805           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2806         }
2807       }
2808       alignPanel.paintAlignment(true);
2809     }
2810
2811     if ((viewport.getSelectionGroup() != null
2812             && viewport.getSelectionGroup().getSize() < 4 && viewport
2813             .getSelectionGroup().getSize() > 0)
2814             || viewport.getAlignment().getHeight() < 4)
2815     {
2816       return;
2817     }
2818
2819     try
2820     {
2821       new PCAPanel(viewport);
2822     } catch (java.lang.OutOfMemoryError ex)
2823     {
2824     }
2825
2826   }
2827
2828   public void averageDistanceTreeMenuItem_actionPerformed()
2829   {
2830     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2831             "Average distance tree using PID");
2832   }
2833
2834   public void neighbourTreeMenuItem_actionPerformed()
2835   {
2836     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2837             "Neighbour joining tree using PID");
2838   }
2839
2840   protected void njTreeBlosumMenuItem_actionPerformed()
2841   {
2842     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2843             .getBlosum62().getName(),
2844             "Neighbour joining tree using BLOSUM62");
2845   }
2846
2847   protected void avTreeBlosumMenuItem_actionPerformed()
2848   {
2849     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2850             .getBlosum62().getName(),
2851             "Average distance tree using BLOSUM62");
2852   }
2853
2854   void newTreePanel(String type, String pwType, String title)
2855   {
2856     // are the sequences aligned?
2857     if (!viewport.getAlignment().isAligned(false))
2858     {
2859       SequenceI current;
2860       int Width = viewport.getAlignment().getWidth();
2861
2862       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2863       {
2864         current = viewport.getAlignment().getSequenceAt(i);
2865
2866         if (current.getLength() < Width)
2867         {
2868           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2869         }
2870       }
2871       alignPanel.paintAlignment(true);
2872
2873     }
2874
2875     if ((viewport.getSelectionGroup() != null && viewport
2876             .getSelectionGroup().getSize() > 1)
2877             || (viewport.getAlignment().getHeight() > 1))
2878     {
2879       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2880
2881       addTreeMenuItem(tp, title);
2882
2883       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2884     }
2885   }
2886
2887   void loadTree_actionPerformed()
2888   {
2889     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2890     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2891     cap.setTreeImport();
2892     Frame frame = new Frame();
2893     frame.add(cap);
2894     jalview.bin.JalviewLite.addFrame(frame,
2895             MessageManager.getString("label.paste_newick_file"), 400, 300);
2896   }
2897
2898   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2899   {
2900     TreePanel tp = new TreePanel(alignPanel, treeFile,
2901             MessageManager.getString("label.load_tree_from_file"), tree);
2902     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2903     addTreeMenuItem(tp, treeFile);
2904   }
2905
2906   /**
2907    * sort the alignment using the given treePanel
2908    *
2909    * @param treePanel
2910    *          tree used to sort view
2911    * @param title
2912    *          string used for undo event name
2913    */
2914   public void sortByTree(TreePanel treePanel, String title)
2915   {
2916     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2917     AlignmentSorter
2918             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2919     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2920     // HistoryItem.SORT));
2921     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2922             "label.order_by_params", new String[] { title }), oldOrder,
2923             viewport.getAlignment()));
2924     alignPanel.paintAlignment(true);
2925   }
2926
2927   /**
2928    * Do any automatic reordering of the alignment and add the necessary bits to
2929    * the menu structure for the new tree
2930    *
2931    * @param treePanel
2932    * @param title
2933    */
2934   protected void addTreeMenuItem(final TreePanel treePanel,
2935           final String title)
2936   {
2937     final MenuItem item = new MenuItem(title);
2938     sortByTreeMenu.add(item);
2939     item.addActionListener(new java.awt.event.ActionListener()
2940     {
2941       @Override
2942       public void actionPerformed(ActionEvent evt)
2943       {
2944         sortByTree(treePanel, title); // treePanel.getTitle());
2945       }
2946     });
2947
2948     treePanel.addWindowListener(new WindowAdapter()
2949     {
2950       @Override
2951       public void windowOpened(WindowEvent e)
2952       {
2953         if (viewport.sortByTree)
2954         {
2955           sortByTree(treePanel, title);
2956         }
2957         super.windowOpened(e);
2958       }
2959
2960       @Override
2961       public void windowClosing(WindowEvent e)
2962       {
2963         sortByTreeMenu.remove(item);
2964       };
2965     });
2966   }
2967
2968   public boolean sortBy(AlignmentOrder alorder, String undoname)
2969   {
2970     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2971     if (viewport.applet.debug)
2972     {
2973       System.err.println("Sorting " + alorder.getOrder().size()
2974               + " in alignment '" + getTitle() + "'");
2975     }
2976     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2977     if (undoname != null)
2978     {
2979       addHistoryItem(new OrderCommand(undoname, oldOrder,
2980               viewport.getAlignment()));
2981     }
2982     alignPanel.paintAlignment(true);
2983     return true;
2984   }
2985
2986   protected void documentation_actionPerformed()
2987   {
2988     alignPanel.av.applet.openJalviewHelpUrl();
2989   }
2990
2991   protected void about_actionPerformed()
2992   {
2993
2994     class AboutPanel extends Canvas
2995     {
2996       String version;
2997
2998       String builddate;
2999
3000       public AboutPanel(String version, String builddate)
3001       {
3002         this.version = version;
3003         this.builddate = builddate;
3004       }
3005
3006       @Override
3007       public void paint(Graphics g)
3008       {
3009         g.setColor(Color.white);
3010         g.fillRect(0, 0, getSize().width, getSize().height);
3011         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3012         FontMetrics fm = g.getFontMetrics();
3013         int fh = fm.getHeight();
3014         int y = 5, x = 7;
3015         g.setColor(Color.black);
3016         // TODO: update this text for each release or centrally store it for
3017         // lite and application
3018         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3019         g.drawString(MessageManager.formatMessage(
3020                 "label.jalviewLite_release", new String[] { version }), x,
3021                 y += fh);
3022         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3023         g.drawString(MessageManager.formatMessage(
3024                 "label.jaview_build_date", new String[] { builddate }), x,
3025                 y += fh);
3026         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3027         g.drawString(MessageManager.getString("label.jalview_authors_1"),
3028                 x, y += fh * 1.5);
3029         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3030                 x + 50, y += fh + 8);
3031         g.drawString(
3032                 MessageManager.getString("label.jalview_dev_managers"), x,
3033                 y += fh);
3034         g.drawString(MessageManager
3035                 .getString("label.jalview_distribution_lists"), x, y += fh);
3036         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3037                 x, y += fh + 8);
3038         g.drawString(
3039                 MessageManager.getString("label.jalview_cite_1_authors"),
3040                 x, y += fh);
3041         g.drawString(
3042                 MessageManager.getString("label.jalview_cite_1_title"), x,
3043                 y += fh);
3044         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3045                 x, y += fh);
3046       }
3047     }
3048
3049     Frame frame = new Frame();
3050     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3051             .getBuildDate()));
3052     jalview.bin.JalviewLite.addFrame(frame,
3053             MessageManager.getString("label.jalview"), 580, 220);
3054
3055   }
3056
3057   public void showURL(String url, String target)
3058   {
3059     if (viewport.applet == null)
3060     {
3061       System.out.println("Not running as applet - no browser available.");
3062     }
3063     else
3064     {
3065       viewport.applet.showURL(url, target);
3066     }
3067   }
3068
3069   // ////////////////////////////////////////////////////////////////////////////////
3070   // JBuilder Graphics here
3071
3072   MenuBar alignFrameMenuBar = new MenuBar();
3073
3074   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3075
3076   MenuItem loadApplication = new MenuItem(
3077           MessageManager.getString("label.view_full_application"));
3078
3079   MenuItem loadTree = new MenuItem(
3080           MessageManager.getString("label.load_associated_tree"));
3081
3082   MenuItem loadAnnotations = new MenuItem(
3083           MessageManager.getString("label.load_features_annotations"));
3084
3085   MenuItem outputFeatures = new MenuItem(
3086           MessageManager.getString("label.export_features"));
3087
3088   MenuItem outputAnnotations = new MenuItem(
3089           MessageManager.getString("label.export_annotations"));
3090
3091   MenuItem closeMenuItem = new MenuItem(
3092           MessageManager.getString("action.close"));
3093
3094   MenuItem selectAllSequenceMenuItem = new MenuItem(
3095           MessageManager.getString("action.select_all"));
3096
3097   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3098           MessageManager.getString("action.deselect_all"));
3099
3100   MenuItem invertSequenceMenuItem = new MenuItem(
3101           MessageManager.getString("action.invert_selection"));
3102
3103   MenuItem remove2LeftMenuItem = new MenuItem();
3104
3105   MenuItem remove2RightMenuItem = new MenuItem();
3106
3107   MenuItem removeGappedColumnMenuItem = new MenuItem();
3108
3109   MenuItem removeAllGapsMenuItem = new MenuItem();
3110
3111   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3112
3113   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3114
3115   MenuItem sortPairwiseMenuItem = new MenuItem();
3116
3117   MenuItem sortIDMenuItem = new MenuItem();
3118
3119   MenuItem sortLengthMenuItem = new MenuItem();
3120
3121   MenuItem sortGroupMenuItem = new MenuItem();
3122
3123   MenuItem removeRedundancyMenuItem = new MenuItem();
3124
3125   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3126
3127   MenuItem PCAMenuItem = new MenuItem();
3128
3129   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3130
3131   MenuItem neighbourTreeMenuItem = new MenuItem();
3132
3133   BorderLayout borderLayout1 = new BorderLayout();
3134
3135   public Label statusBar = new Label();
3136
3137   MenuItem clustalColour = new MenuItem();
3138
3139   MenuItem zappoColour = new MenuItem();
3140
3141   MenuItem taylorColour = new MenuItem();
3142
3143   MenuItem hydrophobicityColour = new MenuItem();
3144
3145   MenuItem helixColour = new MenuItem();
3146
3147   MenuItem strandColour = new MenuItem();
3148
3149   MenuItem turnColour = new MenuItem();
3150
3151   MenuItem buriedColour = new MenuItem();
3152
3153   MenuItem purinePyrimidineColour = new MenuItem();
3154
3155   // MenuItem RNAInteractionColour = new MenuItem();
3156
3157   MenuItem RNAHelixColour = new MenuItem();
3158
3159   MenuItem userDefinedColour = new MenuItem();
3160
3161   MenuItem PIDColour = new MenuItem();
3162
3163   MenuItem BLOSUM62Colour = new MenuItem();
3164
3165   MenuItem tcoffeeColour = new MenuItem();
3166
3167   MenuItem njTreeBlosumMenuItem = new MenuItem();
3168
3169   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3170
3171   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3174
3175   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3176
3177   MenuItem alProperties = new MenuItem(
3178           MessageManager.getString("label.alignment_props"));
3179
3180   MenuItem overviewMenuItem = new MenuItem();
3181
3182   MenuItem undoMenuItem = new MenuItem();
3183
3184   MenuItem redoMenuItem = new MenuItem();
3185
3186   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3187
3188   MenuItem noColourmenuItem = new MenuItem();
3189
3190   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3191
3192   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3193
3194   MenuItem findMenuItem = new MenuItem();
3195
3196   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3197
3198   MenuItem nucleotideColour = new MenuItem();
3199
3200   MenuItem deleteGroups = new MenuItem();
3201
3202   MenuItem grpsFromSelection = new MenuItem();
3203
3204   MenuItem createGroup = new MenuItem();
3205
3206   MenuItem unGroup = new MenuItem();
3207
3208   MenuItem delete = new MenuItem();
3209
3210   MenuItem copy = new MenuItem();
3211
3212   MenuItem cut = new MenuItem();
3213
3214   Menu pasteMenu = new Menu();
3215
3216   MenuItem pasteNew = new MenuItem();
3217
3218   MenuItem pasteThis = new MenuItem();
3219
3220   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3221
3222   MenuItem font = new MenuItem();
3223
3224   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3225
3226   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3227
3228   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3229
3230   MenuItem modifyPID = new MenuItem();
3231
3232   MenuItem modifyConservation = new MenuItem();
3233
3234   CheckboxMenuItem autoCalculate = null;
3235
3236   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3237           "Sort Alignment With New Tree", true);
3238
3239   Menu sortByTreeMenu = new Menu();
3240
3241   MenuItem inputText = new MenuItem();
3242
3243   MenuItem documentation = new MenuItem();
3244
3245   MenuItem about = new MenuItem();
3246
3247   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3248
3249   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3250
3251   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3252
3253   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3254
3255   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3256
3257   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3258
3259   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3260
3261   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3262
3263   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3264
3265   /**
3266    * Initialise menus and other items
3267    *
3268    * @throws Exception
3269    */
3270   private void jbInit() throws Exception
3271   {
3272     setMenuBar(alignFrameMenuBar);
3273
3274     /*
3275      * Configure File menu items and actions
3276      */
3277     inputText
3278             .setLabel(MessageManager.getString("label.input_from_textbox"));
3279     inputText.addActionListener(this);
3280     Menu outputTextboxMenu = new Menu(
3281             MessageManager.getString("label.out_to_textbox"));
3282     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3283     {
3284       MenuItem item = new MenuItem(ff);
3285
3286       item.addActionListener(new java.awt.event.ActionListener()
3287       {
3288         @Override
3289         public void actionPerformed(ActionEvent e)
3290         {
3291           outputText_actionPerformed(e);
3292         }
3293       });
3294
3295       outputTextboxMenu.add(item);
3296     }
3297     closeMenuItem.addActionListener(this);
3298     loadApplication.addActionListener(this);
3299     loadTree.addActionListener(this);
3300     loadAnnotations.addActionListener(this);
3301     outputFeatures.addActionListener(this);
3302     outputAnnotations.addActionListener(this);
3303
3304     /*
3305      * Configure Edit menu items and actions
3306      */
3307     undoMenuItem.setEnabled(false);
3308     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3309     undoMenuItem.addActionListener(this);
3310     redoMenuItem.setEnabled(false);
3311     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3312     redoMenuItem.addActionListener(this);
3313     copy.setLabel(MessageManager.getString("action.copy"));
3314     copy.addActionListener(this);
3315     cut.setLabel(MessageManager.getString("action.cut"));
3316     cut.addActionListener(this);
3317     delete.setLabel(MessageManager.getString("action.delete"));
3318     delete.addActionListener(this);
3319     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3320     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3321     pasteNew.addActionListener(this);
3322     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3323     pasteThis.addActionListener(this);
3324     remove2LeftMenuItem.setLabel(MessageManager
3325             .getString("action.remove_left"));
3326     remove2LeftMenuItem.addActionListener(this);
3327     remove2RightMenuItem.setLabel(MessageManager
3328             .getString("action.remove_right"));
3329     remove2RightMenuItem.addActionListener(this);
3330     removeGappedColumnMenuItem.setLabel(MessageManager
3331             .getString("action.remove_empty_columns"));
3332     removeGappedColumnMenuItem.addActionListener(this);
3333     removeAllGapsMenuItem.setLabel(MessageManager
3334             .getString("action.remove_all_gaps"));
3335     removeAllGapsMenuItem.addActionListener(this);
3336     removeRedundancyMenuItem.setLabel(MessageManager
3337             .getString("action.remove_redundancy"));
3338     removeRedundancyMenuItem.addActionListener(this);
3339
3340     /*
3341      * Configure Select menu items and actions
3342      */
3343     findMenuItem.setLabel(MessageManager.getString("action.find"));
3344     findMenuItem.addActionListener(this);
3345     selectAllSequenceMenuItem.addActionListener(this);
3346     deselectAllSequenceMenuItem.addActionListener(this);
3347     invertSequenceMenuItem.setLabel(MessageManager
3348             .getString("action.invert_sequence_selection"));
3349     invertSequenceMenuItem.addActionListener(this);
3350     invertColSel.setLabel(MessageManager
3351             .getString("action.invert_column_selection"));
3352     invertColSel.addActionListener(this);
3353     deleteGroups.setLabel(MessageManager
3354             .getString("action.undefine_groups"));
3355     deleteGroups.addActionListener(this);
3356     grpsFromSelection.setLabel(MessageManager
3357             .getString("action.make_groups_selection"));
3358     grpsFromSelection.addActionListener(this);
3359     createGroup.setLabel(MessageManager.getString("action.create_group"));
3360     createGroup.addActionListener(this);
3361     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3362     unGroup.addActionListener(this);
3363
3364     annotationColumnSelection.setLabel(MessageManager
3365             .getString("action.select_by_annotation"));
3366     annotationColumnSelection.addActionListener(this);
3367
3368     /*
3369      * Configure View menu items and actions
3370      */
3371     newView.setLabel(MessageManager.getString("action.new_view"));
3372     newView.addActionListener(this);
3373     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3374     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3375     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3376     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3377     hideColumns
3378             .setLabel(MessageManager.getString("label.selected_columns"));
3379     hideSequences.setLabel(MessageManager
3380             .getString("label.selected_sequences"));
3381     hideAllButSelection.setLabel(MessageManager
3382             .getString("label.all_but_selected_region"));
3383     hideAllSelection.setLabel(MessageManager
3384             .getString("label.selected_region"));
3385     showAllHidden.setLabel(MessageManager
3386             .getString("label.all_sequences_columns"));
3387     showColumns.addActionListener(this);
3388     showSeqs.addActionListener(this);
3389     hideColumns.addActionListener(this);
3390     hideSequences.addActionListener(this);
3391     hideAllButSelection.addActionListener(this);
3392     hideAllSelection.addActionListener(this);
3393     showAllHidden.addActionListener(this);
3394     featureSettings.setLabel(MessageManager
3395             .getString("action.feature_settings"));
3396     featureSettings.addActionListener(this);
3397     sequenceFeatures.setLabel(MessageManager
3398             .getString("label.show_sequence_features"));
3399     sequenceFeatures.addItemListener(this);
3400     sequenceFeatures.setState(false);
3401     followMouseOverFlag.setLabel(MessageManager
3402             .getString("label.automatic_scrolling"));
3403     followMouseOverFlag.addItemListener(this);
3404     alProperties.addActionListener(this);
3405     overviewMenuItem.setLabel(MessageManager
3406             .getString("label.overview_window"));
3407     overviewMenuItem.addActionListener(this);
3408
3409     /*
3410      * Configure Annotations menu items and actions
3411      */
3412     annotationPanelMenuItem.setLabel(MessageManager
3413             .getString("label.show_annotations"));
3414     annotationPanelMenuItem.addItemListener(this);
3415     showGroupConsensus.setLabel(MessageManager
3416             .getString("label.group_consensus"));
3417     showGroupConservation.setLabel(MessageManager
3418             .getString("label.group_conservation"));
3419     showConsensusHistogram.setLabel(MessageManager
3420             .getString("label.show_consensus_histogram"));
3421     showSequenceLogo.setLabel(MessageManager
3422             .getString("label.show_consensus_logo"));
3423     normSequenceLogo.setLabel(MessageManager
3424             .getString("label.norm_consensus_logo"));
3425     applyAutoAnnotationSettings.setLabel(MessageManager
3426             .getString("label.apply_all_groups"));
3427     applyAutoAnnotationSettings.setState(true);
3428     Menu autoAnnMenu = new Menu(
3429             MessageManager.getString("label.autocalculated_annotation"));
3430     showGroupConsensus.addItemListener(this);
3431     showGroupConservation.addItemListener(this);
3432     showConsensusHistogram.addItemListener(this);
3433     showSequenceLogo.addItemListener(this);
3434     normSequenceLogo.addItemListener(this);
3435     applyAutoAnnotationSettings.addItemListener(this);
3436     showAlignmentAnnotations = new CheckboxMenuItem(
3437             MessageManager.getString("label.show_all_al_annotations"));
3438     showSequenceAnnotations = new CheckboxMenuItem(
3439             MessageManager.getString("label.show_all_seq_annotations"));
3440     sortAnnBySequence = new CheckboxMenuItem(
3441             MessageManager.getString("label.sort_annotations_by_sequence"));
3442     sortAnnByLabel = new CheckboxMenuItem(
3443             MessageManager.getString("label.sort_annotations_by_label"));
3444     showAutoFirst = new CheckboxMenuItem(
3445             MessageManager.getString("label.show_first"));
3446     showAutoFirst.setState(false); // pending applet parameter
3447     setShowAutoCalculatedAbove(showAutoFirst.getState());
3448     showAutoLast = new CheckboxMenuItem(
3449             MessageManager.getString("label.show_last"));
3450     showAutoLast.setState(!showAutoFirst.getState());
3451     showAlignmentAnnotations.addItemListener(this);
3452     showSequenceAnnotations.addItemListener(this);
3453     sortAnnBySequence.addItemListener(this);
3454     sortAnnByLabel.addItemListener(this);
3455     showAutoFirst.addItemListener(this);
3456     showAutoLast.addItemListener(this);
3457
3458     /*
3459      * Configure Format menu items and actions
3460      */
3461     font.setLabel(MessageManager.getString("action.font"));
3462     font.addActionListener(this);
3463     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3464     scaleAbove.setState(true);
3465     scaleAbove.setEnabled(false);
3466     scaleAbove.addItemListener(this);
3467     scaleLeft.setEnabled(false);
3468     scaleLeft.setState(true);
3469     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3470     scaleLeft.addItemListener(this);
3471     scaleRight.setEnabled(false);
3472     scaleRight.setState(true);
3473     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3474     scaleRight.addItemListener(this);
3475     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3476     viewBoxesMenuItem.setState(true);
3477     viewBoxesMenuItem.addItemListener(this);
3478     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3479     viewTextMenuItem.setState(true);
3480     viewTextMenuItem.addItemListener(this);
3481     colourTextMenuItem.setLabel(MessageManager
3482             .getString("label.colour_text"));
3483     colourTextMenuItem.addItemListener(this);
3484     displayNonconservedMenuItem.setLabel(MessageManager
3485             .getString("label.show_non_conserved"));
3486     displayNonconservedMenuItem.addItemListener(this);
3487     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3488     wrapMenuItem.addItemListener(this);
3489     renderGapsMenuItem.setLabel(MessageManager
3490             .getString("action.show_gaps"));
3491     renderGapsMenuItem.setState(true);
3492     renderGapsMenuItem.addItemListener(this);
3493     centreColumnLabelFlag.setLabel(MessageManager
3494             .getString("label.centre_column_labels"));
3495     centreColumnLabelFlag.addItemListener(this);
3496     seqLimits.setState(true);
3497     seqLimits.setLabel(MessageManager
3498             .getString("label.show_sequence_limits"));
3499     seqLimits.addItemListener(this);
3500
3501     /*
3502      * Configure Colour menu items and actions
3503      */
3504     applyToAllGroups.setLabel(MessageManager
3505             .getString("label.apply_colour_to_all_groups"));
3506     applyToAllGroups.setState(true);
3507     applyToAllGroups.addItemListener(this);
3508     clustalColour.setLabel(MessageManager
3509             .getString("label.colourScheme_clustal"));
3510     clustalColour.addActionListener(this);
3511     zappoColour.setLabel(MessageManager
3512             .getString("label.colourScheme_zappo"));
3513     zappoColour.addActionListener(this);
3514     taylorColour.setLabel(MessageManager
3515             .getString("label.colourScheme_taylor"));
3516     taylorColour.addActionListener(this);
3517     hydrophobicityColour.setLabel(MessageManager
3518             .getString("label.colourScheme_hydrophobic"));
3519     hydrophobicityColour.addActionListener(this);
3520     helixColour.setLabel(MessageManager
3521             .getString("label.colourScheme_helix_propensity"));
3522     helixColour.addActionListener(this);
3523     strandColour.setLabel(MessageManager
3524             .getString("label.colourScheme_strand_propensity"));
3525     strandColour.addActionListener(this);
3526     turnColour.setLabel(MessageManager
3527             .getString("label.colourScheme_turn_propensity"));
3528     turnColour.addActionListener(this);
3529     buriedColour.setLabel(MessageManager
3530             .getString("label.colourScheme_buried_index"));
3531     buriedColour.addActionListener(this);
3532     purinePyrimidineColour.setLabel(MessageManager
3533             .getString("label.colourScheme_purine/pyrimidine"));
3534     purinePyrimidineColour.addActionListener(this);
3535     // RNAInteractionColour.setLabel(MessageManager
3536     // .getString("label.rna_interaction"));
3537     // RNAInteractionColour.addActionListener(this);
3538     RNAHelixColour.setLabel(MessageManager
3539             .getString("label.colourScheme_rna_helices"));
3540     RNAHelixColour.addActionListener(this);
3541     userDefinedColour.setLabel(MessageManager
3542             .getString("action.user_defined"));
3543     userDefinedColour.addActionListener(this);
3544     PIDColour.setLabel(MessageManager
3545             .getString("label.colourScheme_%_identity"));
3546     PIDColour.addActionListener(this);
3547     BLOSUM62Colour.setLabel(MessageManager
3548             .getString("label.colourScheme_blosum62"));
3549     BLOSUM62Colour.addActionListener(this);
3550     tcoffeeColour.setLabel(MessageManager
3551             .getString("label.colourScheme_t-coffee_scores"));
3552     // it will be enabled only if a score file is provided
3553     tcoffeeColour.setEnabled(false);
3554     tcoffeeColour.addActionListener(this);
3555     conservationMenuItem.setLabel(MessageManager
3556             .getString("action.by_conservation"));
3557     conservationMenuItem.addItemListener(this);
3558     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3559     noColourmenuItem.addActionListener(this);
3560     abovePIDThreshold.setLabel(MessageManager
3561             .getString("label.above_identity_threshold"));
3562     abovePIDThreshold.addItemListener(this);
3563     nucleotideColour.setLabel(MessageManager
3564             .getString("label.colourScheme_nucleotide"));
3565     nucleotideColour.addActionListener(this);
3566     modifyPID.setLabel(MessageManager
3567             .getString("label.modify_identity_threshold"));
3568     modifyPID.setEnabled(abovePIDThreshold.getState());
3569     modifyPID.addActionListener(this);
3570     modifyConservation.setLabel(MessageManager
3571             .getString("label.modify_conservation_threshold"));
3572     modifyConservation.setEnabled(conservationMenuItem.getState());
3573     modifyConservation.addActionListener(this);
3574     annotationColour.setLabel(MessageManager
3575             .getString("action.by_annotation"));
3576     annotationColour.addActionListener(this);
3577
3578     /*
3579      * Configure Calculate menu items and actions
3580      */
3581     sortPairwiseMenuItem.setLabel(MessageManager
3582             .getString("action.by_pairwise_id"));
3583     sortPairwiseMenuItem.addActionListener(this);
3584     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3585     sortIDMenuItem.addActionListener(this);
3586     sortLengthMenuItem.setLabel(MessageManager
3587             .getString("action.by_length"));
3588     sortLengthMenuItem.addActionListener(this);
3589     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3590     sortGroupMenuItem.addActionListener(this);
3591     pairwiseAlignmentMenuItem.setLabel(MessageManager
3592             .getString("action.pairwise_alignment"));
3593     pairwiseAlignmentMenuItem.addActionListener(this);
3594     PCAMenuItem.setLabel(MessageManager
3595             .getString("label.principal_component_analysis"));
3596     PCAMenuItem.addActionListener(this);
3597     autoCalculate = new CheckboxMenuItem(
3598             MessageManager.getString("label.autocalculate_consensus"), true);
3599     averageDistanceTreeMenuItem.setLabel(MessageManager
3600             .getString("label.average_distance_identity"));
3601     averageDistanceTreeMenuItem.addActionListener(this);
3602     neighbourTreeMenuItem.setLabel(MessageManager
3603             .getString("label.neighbour_joining_identity"));
3604     neighbourTreeMenuItem.addActionListener(this);
3605     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3606             .getString("label.average_distance_blosum62"));
3607     avDistanceTreeBlosumMenuItem.addActionListener(this);
3608     njTreeBlosumMenuItem.setLabel(MessageManager
3609             .getString("label.neighbour_blosum62"));
3610     njTreeBlosumMenuItem.addActionListener(this);
3611     sortByTreeMenu.setLabel(MessageManager
3612             .getString("action.by_tree_order"));
3613     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3614     Menu calculateTreeMenu = new Menu(
3615             MessageManager.getString("action.calculate_tree"));
3616     autoCalculate.addItemListener(this);
3617     sortByTree.addItemListener(this);
3618
3619     /*
3620      * Configure Help menu items and actions
3621      */
3622     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3623     documentation.setLabel(MessageManager.getString("label.documentation"));
3624     documentation.addActionListener(this);
3625     about.setLabel(MessageManager.getString("label.about"));
3626     about.addActionListener(this);
3627
3628     /*
3629      * Add top level menus to frame
3630      */
3631     alignFrameMenuBar.add(fileMenu);
3632     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3633     alignFrameMenuBar.add(editMenu);
3634     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3635     alignFrameMenuBar.add(selectMenu);
3636     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3637     alignFrameMenuBar.add(viewMenu);
3638     Menu annotationsMenu = new Menu(
3639             MessageManager.getString("action.annotations"));
3640     alignFrameMenuBar.add(annotationsMenu);
3641     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3642     alignFrameMenuBar.add(formatMenu);
3643     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3644     alignFrameMenuBar.add(colourMenu);
3645     Menu calculateMenu = new Menu(
3646             MessageManager.getString("action.calculate"));
3647     alignFrameMenuBar.add(calculateMenu);
3648     alignFrameMenuBar.add(helpMenu);
3649
3650     /*
3651      * File menu
3652      */
3653     fileMenu.add(inputText);
3654     fileMenu.add(loadTree);
3655     fileMenu.add(loadAnnotations);
3656     fileMenu.addSeparator();
3657     fileMenu.add(outputTextboxMenu);
3658     fileMenu.add(outputFeatures);
3659     fileMenu.add(outputAnnotations);
3660     if (jalviewServletURL != null)
3661     {
3662       fileMenu.add(loadApplication);
3663     }
3664     fileMenu.addSeparator();
3665     fileMenu.add(closeMenuItem);
3666
3667     /*
3668      * Edit menu
3669      */
3670     editMenu.add(undoMenuItem);
3671     editMenu.add(redoMenuItem);
3672     editMenu.add(cut);
3673     editMenu.add(copy);
3674     pasteMenu.add(pasteNew);
3675     pasteMenu.add(pasteThis);
3676     editMenu.add(pasteMenu);
3677     editMenu.add(delete);
3678     editMenu.addSeparator();
3679     editMenu.add(remove2LeftMenuItem);
3680     editMenu.add(remove2RightMenuItem);
3681     editMenu.add(removeGappedColumnMenuItem);
3682     editMenu.add(removeAllGapsMenuItem);
3683     editMenu.add(removeRedundancyMenuItem);
3684
3685     /*
3686      * Select menu
3687      */
3688     selectMenu.add(findMenuItem);
3689     selectMenu.addSeparator();
3690     selectMenu.add(selectAllSequenceMenuItem);
3691     selectMenu.add(deselectAllSequenceMenuItem);
3692     selectMenu.add(invertSequenceMenuItem);
3693     selectMenu.add(invertColSel);
3694     selectMenu.add(createGroup);
3695     selectMenu.add(unGroup);
3696     selectMenu.add(grpsFromSelection);
3697     selectMenu.add(deleteGroups);
3698     selectMenu.add(annotationColumnSelection);
3699
3700     /*
3701      * View menu
3702      */
3703     viewMenu.add(newView);
3704     viewMenu.addSeparator();
3705     showMenu.add(showColumns);
3706     showMenu.add(showSeqs);
3707     showMenu.add(showAllHidden);
3708     viewMenu.add(showMenu);
3709     hideMenu.add(hideColumns);
3710     hideMenu.add(hideSequences);
3711     hideMenu.add(hideAllSelection);
3712     hideMenu.add(hideAllButSelection);
3713     viewMenu.add(hideMenu);
3714     viewMenu.addSeparator();
3715     viewMenu.add(followMouseOverFlag);
3716     viewMenu.addSeparator();
3717     viewMenu.add(sequenceFeatures);
3718     viewMenu.add(featureSettings);
3719     viewMenu.addSeparator();
3720     viewMenu.add(alProperties);
3721     viewMenu.addSeparator();
3722     viewMenu.add(overviewMenuItem);
3723
3724     /*
3725      * Annotations menu
3726      */
3727     annotationsMenu.add(annotationPanelMenuItem);
3728     annotationsMenu.addSeparator();
3729     annotationsMenu.add(showAlignmentAnnotations);
3730     annotationsMenu.add(showSequenceAnnotations);
3731     annotationsMenu.add(sortAnnBySequence);
3732     annotationsMenu.add(sortAnnByLabel);
3733     annotationsMenu.addSeparator();
3734     autoAnnMenu.add(showAutoFirst);
3735     autoAnnMenu.add(showAutoLast);
3736     autoAnnMenu.addSeparator();
3737     autoAnnMenu.add(applyAutoAnnotationSettings);
3738     autoAnnMenu.add(showConsensusHistogram);
3739     autoAnnMenu.add(showSequenceLogo);
3740     autoAnnMenu.add(normSequenceLogo);
3741     autoAnnMenu.addSeparator();
3742     autoAnnMenu.add(showGroupConservation);
3743     autoAnnMenu.add(showGroupConsensus);
3744     annotationsMenu.add(autoAnnMenu);
3745
3746     /*
3747      * Format menu
3748      */
3749     formatMenu.add(font);
3750     formatMenu.add(seqLimits);
3751     formatMenu.add(wrapMenuItem);
3752     formatMenu.add(scaleAbove);
3753     formatMenu.add(scaleLeft);
3754     formatMenu.add(scaleRight);
3755     formatMenu.add(viewBoxesMenuItem);
3756     formatMenu.add(viewTextMenuItem);
3757     formatMenu.add(colourTextMenuItem);
3758     formatMenu.add(displayNonconservedMenuItem);
3759     formatMenu.add(renderGapsMenuItem);
3760     formatMenu.add(centreColumnLabelFlag);
3761
3762     /*
3763      * Colour menu
3764      */
3765     colourMenu.add(applyToAllGroups);
3766     colourMenu.addSeparator();
3767     colourMenu.add(noColourmenuItem);
3768     colourMenu.add(clustalColour);
3769     colourMenu.add(BLOSUM62Colour);
3770     colourMenu.add(PIDColour);
3771     colourMenu.add(zappoColour);
3772     colourMenu.add(taylorColour);
3773     colourMenu.add(hydrophobicityColour);
3774     colourMenu.add(helixColour);
3775     colourMenu.add(strandColour);
3776     colourMenu.add(turnColour);
3777     colourMenu.add(buriedColour);
3778     colourMenu.add(nucleotideColour);
3779     colourMenu.add(purinePyrimidineColour);
3780     // colourMenu.add(RNAInteractionColour);
3781     colourMenu.add(tcoffeeColour);
3782     colourMenu.add(userDefinedColour);
3783     colourMenu.addSeparator();
3784     colourMenu.add(conservationMenuItem);
3785     colourMenu.add(modifyConservation);
3786     colourMenu.add(abovePIDThreshold);
3787     colourMenu.add(modifyPID);
3788     colourMenu.add(annotationColour);
3789     colourMenu.add(RNAHelixColour);
3790
3791     /*
3792      * Calculate menu
3793      */
3794     sortMenu.add(sortIDMenuItem);
3795     sortMenu.add(sortLengthMenuItem);
3796     sortMenu.add(sortByTreeMenu);
3797     sortMenu.add(sortGroupMenuItem);
3798     sortMenu.add(sortPairwiseMenuItem);
3799     calculateMenu.add(sortMenu);
3800     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3801     calculateTreeMenu.add(neighbourTreeMenuItem);
3802     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3803     calculateTreeMenu.add(njTreeBlosumMenuItem);
3804     calculateMenu.add(calculateTreeMenu);
3805     calculateMenu.addSeparator();
3806     calculateMenu.add(pairwiseAlignmentMenuItem);
3807     calculateMenu.add(PCAMenuItem);
3808     calculateMenu.add(autoCalculate);
3809     calculateMenu.add(sortByTree);
3810
3811     /*
3812      * Help menu
3813      */
3814     helpMenu.add(documentation);
3815     helpMenu.add(about);
3816
3817     /*
3818      * Status bar
3819      */
3820     statusBar.setBackground(Color.white);
3821     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3822     statusBar.setText(MessageManager.getString("label.status_bar"));
3823     this.add(statusBar, BorderLayout.SOUTH);
3824   }
3825
3826   @Override
3827   public void setStatus(String string)
3828   {
3829     statusBar.setText(string);
3830   };
3831
3832   MenuItem featureSettings = new MenuItem();
3833
3834   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3835
3836   MenuItem annotationColour = new MenuItem();
3837
3838   MenuItem annotationColumnSelection = new MenuItem();
3839
3840   MenuItem invertColSel = new MenuItem();
3841
3842   MenuItem showColumns = new MenuItem();
3843
3844   MenuItem showSeqs = new MenuItem();
3845
3846   MenuItem hideColumns = new MenuItem();
3847
3848   MenuItem hideSequences = new MenuItem();
3849
3850   MenuItem hideAllButSelection = new MenuItem();
3851
3852   MenuItem hideAllSelection = new MenuItem();
3853
3854   MenuItem showAllHidden = new MenuItem();
3855
3856   MenuItem newView = new MenuItem();
3857
3858   private CheckboxMenuItem showAlignmentAnnotations;
3859
3860   private CheckboxMenuItem showSequenceAnnotations;
3861
3862   private CheckboxMenuItem sortAnnBySequence;
3863
3864   private CheckboxMenuItem sortAnnByLabel;
3865
3866   private CheckboxMenuItem showAutoFirst;
3867
3868   private CheckboxMenuItem showAutoLast;
3869
3870   private SplitFrame splitFrame;
3871
3872   /**
3873    * Attach the alignFrame panels after embedding menus, if necessary. This used
3874    * to be called setEmbedded, but is now creates the dropdown menus in a
3875    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3876    *
3877    * @param reallyEmbedded
3878    *          true to attach the view to the applet area on the page rather than
3879    *          in a new window
3880    */
3881   public void createAlignFrameWindow(boolean reallyEmbedded)
3882   {
3883     if (reallyEmbedded)
3884     {
3885       embedAlignFrameInApplet(viewport.applet);
3886     }
3887     else
3888     {
3889       // //////
3890       // test and embed menu bar if necessary.
3891       //
3892       if (embedMenuIfNeeded(alignPanel))
3893       {
3894         /*
3895          * adjust for status bar height too. ? pointless as overridden by layout
3896          * manager
3897          */
3898         alignPanel.setSize(getSize().width,
3899                 getSize().height - statusBar.getHeight());
3900       }
3901       add(statusBar, BorderLayout.SOUTH);
3902       add(alignPanel, BorderLayout.CENTER);
3903       // and register with the applet so it can pass external API calls to us
3904       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3905               frameHeight);
3906     }
3907   }
3908
3909   /**
3910    * Add the components of this AlignFrame to the applet container.
3911    *
3912    * @param theApplet
3913    */
3914   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3915   {
3916     // ////
3917     // Explicitly build the embedded menu panel for the on-page applet
3918     //
3919     // view cannot be closed if its actually on the page
3920     fileMenu.remove(closeMenuItem);
3921     fileMenu.remove(3); // Remove Separator
3922     // construct embedded menu, using default font
3923     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3924     // and actually add the components to the applet area
3925     theApplet.setLayout(new BorderLayout());
3926     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3927     theApplet.add(statusBar, BorderLayout.SOUTH);
3928     // TODO should size be left to the layout manager?
3929     alignPanel.setSize(theApplet.getSize().width,
3930             theApplet.getSize().height - embeddedMenu.getHeight()
3931                     - statusBar.getHeight());
3932     theApplet.add(alignPanel, BorderLayout.CENTER);
3933     final AlignFrame me = this;
3934     theApplet.addFocusListener(new FocusListener()
3935     {
3936
3937       @Override
3938       public void focusLost(FocusEvent e)
3939       {
3940         if (theApplet.currentAlignFrame == me)
3941         {
3942           theApplet.currentAlignFrame = null;
3943         }
3944       }
3945
3946       @Override
3947       public void focusGained(FocusEvent e)
3948       {
3949         theApplet.currentAlignFrame = me;
3950       }
3951     });
3952     theApplet.validate();
3953   }
3954
3955   /**
3956    * create a new binding between structures in an existing jmol viewer instance
3957    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3958    * this does not open a new Jmol window, or modify the display of the
3959    * structures in the original jmol window. Note This method doesn't work
3960    * without an additional javascript library to exchange messages between the
3961    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3962    *
3963    * @param viewer
3964    *          JmolViewer instance
3965    * @param sequenceIds
3966    *          - sequence Ids to search for associations
3967    */
3968   public SequenceStructureBinding addStructureViewInstance(
3969           Object jmolviewer, String[] sequenceIds)
3970   {
3971     Viewer viewer = null;
3972     try
3973     {
3974       viewer = (Viewer) jmolviewer;
3975     } catch (ClassCastException ex)
3976     {
3977       System.err.println("Unsupported viewer object :"
3978               + jmolviewer.getClass());
3979     }
3980     if (viewer == null)
3981     {
3982       System.err.println("Can't use this object as a structure viewer:"
3983               + jmolviewer.getClass());
3984       return null;
3985     }
3986     SequenceI[] seqs = null;
3987     if (sequenceIds == null || sequenceIds.length == 0)
3988     {
3989       seqs = viewport.getAlignment().getSequencesArray();
3990     }
3991     else
3992     {
3993       Vector sqi = new Vector();
3994       AlignmentI al = viewport.getAlignment();
3995       for (int sid = 0; sid < sequenceIds.length; sid++)
3996       {
3997         SequenceI sq = al.findName(sequenceIds[sid]);
3998         if (sq != null)
3999         {
4000           sqi.addElement(sq);
4001         }
4002       }
4003       if (sqi.size() > 0)
4004       {
4005         seqs = new SequenceI[sqi.size()];
4006         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4007         {
4008           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4009         }
4010       }
4011       else
4012       {
4013         return null;
4014       }
4015     }
4016     AAStructureBindingModel jmv = null;
4017     // TODO: search for a jmv that involves viewer
4018     if (jmv == null)
4019     { // create a new viewer/jalview binding.
4020       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4021     }
4022     return jmv;
4023
4024   }
4025
4026   /**
4027    * bind a pdb file to a sequence in the current view
4028    *
4029    * @param sequenceId
4030    *          - sequenceId within the dataset.
4031    * @param pdbEntryString
4032    *          - the short name for the PDB file
4033    * @param pdbFile
4034    *          - pdb file - either a URL or a valid PDB file.
4035    * @return true if binding was as success TODO: consider making an exception
4036    *         structure for indicating when PDB parsing or sequenceId location
4037    *         fails.
4038    */
4039   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4040           String pdbFile)
4041   {
4042     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4043     boolean needtoadd = false;
4044     if (toaddpdb != null)
4045     {
4046       Vector pdbe = toaddpdb.getAllPDBEntries();
4047       PDBEntry pdbentry = null;
4048       if (pdbe != null && pdbe.size() > 0)
4049       {
4050         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4051         {
4052           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4053           if (!pdbentry.getId().equals(pdbEntryString)
4054                   && !pdbentry.getFile().equals(pdbFile))
4055           {
4056             pdbentry = null;
4057           }
4058           else
4059           {
4060             continue;
4061           }
4062         }
4063       }
4064       if (pdbentry == null)
4065       {
4066         pdbentry = new PDBEntry();
4067         pdbentry.setId(pdbEntryString);
4068         pdbentry.setFile(pdbFile);
4069         needtoadd = true; // add this new entry to sequence.
4070       }
4071       // resolve data source
4072       // TODO: this code should be a refactored to an io package
4073       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4074               pdbFile, FileFormat.PDB);
4075       if (protocol == null)
4076       {
4077         return false;
4078       }
4079       if (needtoadd)
4080       {
4081         pdbentry.setProperty("protocol", protocol);
4082         toaddpdb.addPDBId(pdbentry);
4083         alignPanel.getStructureSelectionManager()
4084                 .registerPDBEntry(pdbentry);
4085       }
4086     }
4087     return true;
4088   }
4089
4090   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4091   {
4092     if (seqs != null)
4093     {
4094       Vector sequences = new Vector();
4095       for (int i = 0; i < seqs.length; i++)
4096       {
4097         if (seqs[i] != null)
4098         {
4099           sequences.addElement(new Object[] { seqs[i],
4100               (chains != null) ? chains[i] : null });
4101         }
4102       }
4103       seqs = new SequenceI[sequences.size()];
4104       chains = new String[sequences.size()];
4105       for (int i = 0, isize = sequences.size(); i < isize; i++)
4106       {
4107         Object[] oj = (Object[]) sequences.elementAt(i);
4108
4109         seqs[i] = (SequenceI) oj[0];
4110         chains[i] = (String) oj[1];
4111       }
4112     }
4113     return new Object[] { seqs, chains };
4114
4115   }
4116
4117   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4118           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4119   {
4120     // Scrub any null sequences from the array
4121     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4122     seqs = (SequenceI[]) sqch[0];
4123     chains = (String[]) sqch[1];
4124     if (seqs == null || seqs.length == 0)
4125     {
4126       System.err
4127               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4128     }
4129     if (protocol == null)
4130     {
4131       String sourceType = (String) pdb.getProperty("protocol");
4132       try
4133       {
4134         protocol = DataSourceType.valueOf(sourceType);
4135       } catch (IllegalArgumentException e)
4136       {
4137         // ignore
4138       }
4139       if (protocol == null)
4140       {
4141         System.err.println("Couldn't work out protocol to open structure: "
4142                 + pdb.getId());
4143         return;
4144       }
4145     }
4146     if (applet.useXtrnalSviewer)
4147     {
4148       // register the association(s) and quit, don't create any windows.
4149       if (StructureSelectionManager.getStructureSelectionManager(applet)
4150               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4151       {
4152         System.err.println("Failed to map " + pdb.getFile() + " ("
4153                 + protocol + ") to any sequences");
4154       }
4155       return;
4156     }
4157     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4158     {
4159       // can only do alignments with Jmol
4160       // find the last jmol window assigned to this alignment
4161       AppletJmol ajm = null, tajm;
4162       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4163       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4164       {
4165         tajm = (AppletJmol) jmols.elementAt(i);
4166         if (tajm.ap.alignFrame == this)
4167         {
4168           ajm = tajm;
4169           break;
4170         }
4171       }
4172       if (ajm != null)
4173       {
4174         System.err
4175                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4176         // try and add the pdb structure
4177         // ajm.addS
4178         ajm = null;
4179       }
4180     }
4181     // otherwise, create a new window
4182     if (applet.jmolAvailable)
4183     {
4184       new AppletJmol(pdb, seqs, chains, alignPanel,
4185               protocol);
4186       applet.lastFrameX += 40;
4187       applet.lastFrameY += 40;
4188     }
4189     else
4190     {
4191       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4192     }
4193
4194   }
4195
4196   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4197           SequenceI[][] seqs, String[][] chains, String[] protocols)
4198   {
4199     // TODO Auto-generated method stub
4200     System.err.println("Aligned Structure View: Not yet implemented.");
4201   }
4202
4203   /**
4204    * modify the current selection, providing the user has not made a selection
4205    * already.
4206    *
4207    * @param sel
4208    *          - sequences from this alignment
4209    * @param csel
4210    *          - columns to be selected on the alignment
4211    */
4212   public void select(SequenceGroup sel, ColumnSelection csel,
4213           HiddenColumns hidden)
4214   {
4215     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4216   }
4217
4218   public void scrollTo(int row, int column)
4219   {
4220     alignPanel.seqPanel.scrollTo(row, column);
4221   }
4222
4223   public void scrollToRow(int row)
4224   {
4225     alignPanel.seqPanel.scrollToRow(row);
4226   }
4227
4228   public void scrollToColumn(int column)
4229   {
4230     alignPanel.seqPanel.scrollToColumn(column);
4231   }
4232
4233   /**
4234    * @return the alignments unique ID.
4235    */
4236   public String getSequenceSetId()
4237   {
4238     return viewport.getSequenceSetId();
4239   }
4240
4241   /**
4242    * Load the (T-Coffee) score file from the specified url
4243    *
4244    * @param source
4245    *          File/URL/T-COFFEE score file contents
4246    * @throws IOException
4247    * @return true if alignment was annotated with data from source
4248    */
4249   public boolean loadScoreFile(String source) throws IOException
4250   {
4251
4252     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4253             AppletFormatAdapter.checkProtocol(source));
4254     if (!file.isValid())
4255     {
4256       // TODO: raise dialog for gui
4257       System.err.println("Problems parsing T-Coffee scores: "
4258               + file.getWarningMessage());
4259       System.err.println("Origin was:\n" + source);
4260       return false;
4261     }
4262
4263     /*
4264      * check that the score matrix matches the alignment dimensions
4265      */
4266     AlignmentI aln;
4267     if ((aln = viewport.getAlignment()) != null
4268             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4269                     .getWidth()))
4270     {
4271       // TODO: raise a dialog box here rather than bomb out.
4272       System.err
4273               .println("The scores matrix does not match the alignment dimensions");
4274
4275     }
4276
4277     // TODO add parameter to indicate if matching should be done
4278     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4279     {
4280       alignPanel.fontChanged();
4281       tcoffeeColour.setEnabled(true);
4282       // switch to this color
4283       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4284       return true;
4285     }
4286     else
4287     {
4288       System.err.println("Problems resolving T-Coffee scores:");
4289       if (file.getWarningMessage() != null)
4290       {
4291         System.err.println(file.getWarningMessage());
4292       }
4293     }
4294     return false;
4295   }
4296
4297   public SplitFrame getSplitFrame()
4298   {
4299     return this.splitFrame;
4300   }
4301
4302   public void setSplitFrame(SplitFrame sf)
4303   {
4304     this.splitFrame = sf;
4305   }
4306
4307   // may not need this
4308   @Override
4309   public void setShowSeqFeatures(boolean b)
4310   {
4311     // showSeqFeatures.setSelected(b);
4312     viewport.setShowSequenceFeatures(b);
4313
4314   }
4315
4316   @Override
4317   public void setMenusForViewport()
4318   {
4319     // setMenusFromViewport(viewport);
4320
4321   }
4322
4323   @Override
4324   public void refreshFeatureUI(boolean enableIfNecessary)
4325   {
4326     if (enableIfNecessary)
4327     {
4328       sequenceFeatures.setState(true);
4329       alignPanel.av.setShowSequenceFeatures(true);
4330     }
4331   }
4332
4333   @Override
4334   public FeatureSettingsControllerI getFeatureSettingsUI()
4335   {
4336     return alignPanel.av.featureSettings;
4337   }
4338
4339 }