src/jalview/appletgui/AlignFrame.java

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