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