src/jalview/appletgui/AlignFrame.java

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