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.Rectangle;
  99 import java.awt.event.ActionEvent;
 100 import java.awt.event.ActionListener;
 101 import java.awt.event.FocusEvent;
 102 import java.awt.event.FocusListener;
 103 import java.awt.event.ItemEvent;
 104 import java.awt.event.ItemListener;
 105 import java.awt.event.KeyEvent;
 106 import java.awt.event.KeyListener;
 107 import java.awt.event.WindowAdapter;
 108 import java.awt.event.WindowEvent;
 109 import java.io.IOException;
 110 import java.io.UnsupportedEncodingException;
 111 import java.net.URL;
 112 import java.net.URLEncoder;
 113 import java.util.Arrays;
 114 import java.util.Deque;
 115 import java.util.HashMap;
 116 import java.util.List;
 117 import java.util.Map;
 118 import java.util.StringTokenizer;
 119 import java.util.Vector;
 120
 121 import org.jmol.viewer.Viewer;
 122
 123 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 124         ItemListener, KeyListener, AlignViewControllerGuiI
 125 {
 126   public AlignViewControllerI avc;
 127
 128   public AlignmentPanel alignPanel;
 129
 130   public AlignViewport viewport;
 131
 132   // width and height may be overridden by applet parameters
 133   int frameWidth = 700;
 134
 135   int frameHeight = 500;
 136
 137   String jalviewServletURL;
 138
 139   /*
 140    * Flag for showing autocalculated consensus above or below other consensus
 141    * rows
 142    */
 143   private boolean showAutoCalculatedAbove;
 144
 145   private SequenceAnnotationOrder annotationSortOrder;
 146
 147   /**
 148    * Constructor that creates the frame and adds it to the display.
 149    *
 150    * @param al
 151    * @param applet
 152    * @param title
 153    * @param embedded
 154    */
 155   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 156           boolean embedded)
 157   {
 158     this(al, applet, title, embedded, true);
 159   }
 160
 161   /**
 162    * Constructor that optionally allows the frame to be displayed or only
 163    * created.
 164    *
 165    * @param al
 166    * @param applet
 167    * @param title
 168    * @param embedded
 169    * @param addToDisplay
 170    */
 171   public AlignFrame(AlignmentI al, JalviewLite applet, String title,
 172           boolean embedded, boolean addToDisplay)
 173   {
 174     this(al, null, null, applet, title, embedded, addToDisplay);
 175   }
 176
 177   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 178           HiddenColumns hidden, JalviewLite applet, String title,
 179           boolean embedded)
 180   {
 181     this(al, hiddenSeqs, hidden, applet, title, embedded, true);
 182   }
 183
 184   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 185           HiddenColumns hidden, JalviewLite applet, String title,
 186           boolean embedded, boolean addToDisplay)
 187   {
 188     if (applet != null)
 189     {
 190       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 191     }
 192
 193     try
 194     {
 195       jbInit();
 196     } catch (Exception ex)
 197     {
 198       ex.printStackTrace();
 199     }
 200     // need to get window geometry before we calculate alignment layout
 201     if (applet != null)
 202     {
 203       String param;
 204       try
 205       {
 206         param = applet.getParameter("windowWidth");
 207         if (param != null)
 208         {
 209           int width = Integer.parseInt(param);
 210           frameWidth = width;
 211         }
 212         param = applet.getParameter("windowHeight");
 213         if (param != null)
 214         {
 215           int height = Integer.parseInt(param);
 216           frameHeight = height;
 217         }
 218       } catch (Exception ex)
 219       {
 220       }
 221     }
 222     viewport = new AlignViewport(al, applet);
 223
 224     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 225     {
 226       viewport.hideSequence(hiddenSeqs);
 227     }
 228     if (hidden != null)
 229     {
 230       viewport.getAlignment().setHiddenColumns(hidden);
 231     }
 232     viewport.setScaleAboveWrapped(scaleAbove.getState());
 233
 234     alignPanel = new AlignmentPanel(this, viewport);
 235     avc = new jalview.controller.AlignViewController(this, viewport,
 236             alignPanel);
 237     viewport.updateConservation(alignPanel);
 238     viewport.updateConsensus(alignPanel);
 239
 240     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 241     followMouseOverFlag.setState(viewport.isFollowHighlight());
 242     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 243     showGroupConservation.setState(viewport.isShowGroupConservation());
 244     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 245     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 246     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 247     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 248     annotationPanelMenuItem.setState(viewport.isShowAnnotation());
 249     showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
 250     showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
 251     showAlignmentAnnotations.setState(true);
 252     showSequenceAnnotations.setState(false);
 253
 254     seqLimits.setState(viewport.getShowJVSuffix());
 255
 256     if (applet != null)
 257     {
 258       String param = applet.getParameter("sortBy");
 259       if (param != null)
 260       {
 261         if (param.equalsIgnoreCase("Id"))
 262         {
 263           sortIDMenuItem_actionPerformed();
 264         }
 265         else if (param.equalsIgnoreCase("Pairwise Identity"))
 266         {
 267           sortPairwiseMenuItem_actionPerformed();
 268         }
 269         else if (param.equalsIgnoreCase("Length"))
 270         {
 271           sortLengthMenuItem_actionPerformed();
 272         }
 273       }
 274
 275       param = applet.getParameter("wrap");
 276       if (param != null)
 277       {
 278         if (param.equalsIgnoreCase("true"))
 279         {
 280           wrapMenuItem.setState(true);
 281           wrapMenuItem_actionPerformed();
 282         }
 283       }
 284       param = applet.getParameter("centrecolumnlabels");
 285       if (param != null)
 286       {
 287         centreColumnLabelFlag.setState(true);
 288         centreColumnLabelFlag_stateChanged();
 289       }
 290
 291     }
 292     if (viewport.getAlignment().isNucleotide())
 293     {
 294       conservationMenuItem.setEnabled(false);
 295       clustalColour.setEnabled(false);
 296       BLOSUM62Colour.setEnabled(false);
 297       zappoColour.setEnabled(false);
 298       taylorColour.setEnabled(false);
 299       hydrophobicityColour.setEnabled(false);
 300       helixColour.setEnabled(false);
 301       strandColour.setEnabled(false);
 302       turnColour.setEnabled(false);
 303       buriedColour.setEnabled(false);
 304       viewport.updateStrucConsensus(alignPanel);
 305       if (viewport.getAlignment().hasRNAStructure())
 306       {
 307         RNAHelixColour.setEnabled(true);
 308       }
 309       else
 310       {
 311         RNAHelixColour.setEnabled(false);
 312       }
 313     }
 314     else
 315     {
 316       RNAHelixColour.setEnabled(false);
 317       purinePyrimidineColour.setEnabled(false);
 318       nucleotideColour.setEnabled(false);
 319     }
 320     // Some JVMS send keyevents to Top frame or lowest panel,
 321     // Havent worked out why yet. So add to both this frame and seqCanvas for
 322     // now
 323     this.addKeyListener(this);
 324     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 325     alignPanel.idPanel.idCanvas.addKeyListener(this);
 326     alignPanel.scalePanel.addKeyListener(this);
 327     alignPanel.annotationPanel.addKeyListener(this);
 328     alignPanel.annotationPanelHolder.addKeyListener(this);
 329     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 330     alignPanel.alabels.addKeyListener(this);
 331
 332     setAnnotationsVisibility();
 333
 334     if (addToDisplay)
 335     {
 336       addToDisplay(embedded);
 337     }
 338   }
 339
 340   /**
 341    * @param embedded
 342    */
 343   public void addToDisplay(boolean embedded)
 344   {
 345     createAlignFrameWindow(embedded);
 346     validate();
 347     alignPanel.adjustAnnotationHeight();
 348     alignPanel.paintAlignment(true, true);
 349   }
 350
 351   public AlignViewport getAlignViewport()
 352   {
 353     return viewport;
 354   }
 355
 356   public SeqCanvas getSeqcanvas()
 357   {
 358     return alignPanel.seqPanel.seqCanvas;
 359   }
 360
 361   /**
 362    * Load a features file onto the alignment
 363    *
 364    * @param file
 365    *          file URL, content, or other resolvable path
 366    * @param type
 367    *          is protocol for accessing data referred to by file
 368    */
 369
 370   public boolean parseFeaturesFile(String file, DataSourceType type)
 371   {
 372     return parseFeaturesFile(file, type, true);
 373   }
 374
 375   /**
 376    * Load a features file onto the alignment
 377    *
 378    * @param file
 379    *          file URL, content, or other resolvable path
 380    * @param sourceType
 381    *          is protocol for accessing data referred to by file
 382    * @param autoenabledisplay
 383    *          when true, display features flag will be automatically enabled if
 384    *          features are loaded
 385    * @return true if data parsed as a features file
 386    */
 387   public boolean parseFeaturesFile(String file, DataSourceType sourceType,
 388           boolean autoenabledisplay)
 389   {
 390     boolean featuresFile = false;
 391     try
 392     {
 393       Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
 394               .getFeatureRenderer().getFeatureColours();
 395       boolean relaxedIdMatching = viewport.applet
 396               .getDefaultParameter("relaxedidmatch", false);
 397       featuresFile = new FeaturesFile(file, sourceType).parse(
 398               viewport.getAlignment(), colours, true, relaxedIdMatching);
 399     } catch (Exception ex)
 400     {
 401       ex.printStackTrace();
 402     }
 403
 404     if (featuresFile)
 405     {
 406       if (autoenabledisplay)
 407       {
 408         viewport.setShowSequenceFeatures(true);
 409         sequenceFeatures.setState(true);
 410       }
 411       if (alignPanel.seqPanel.seqCanvas.fr != null)
 412       {
 413         // update the min/max ranges where necessary
 414         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 415       }
 416       if (viewport.featureSettings != null)
 417       {
 418         viewport.featureSettings.refreshTable();
 419       }
 420       alignPanel.paintAlignment(true, true);
 421       setStatus(MessageManager
 422               .getString("label.successfully_added_features_alignment"));
 423     }
 424     return featuresFile;
 425   }
 426
 427   @Override
 428   public void keyPressed(KeyEvent evt)
 429   {
 430     ViewportRanges ranges = viewport.getRanges();
 431
 432     if (viewport.cursorMode
 433             && ((evt.getKeyCode() >= KeyEvent.VK_0
 434                     && evt.getKeyCode() <= KeyEvent.VK_9)
 435                     || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 436                             && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 437             && Character.isDigit(evt.getKeyChar()))
 438     {
 439       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 440     }
 441
 442     switch (evt.getKeyCode())
 443     {
 444     case 27: // escape key
 445       deselectAllSequenceMenuItem_actionPerformed();
 446
 447       alignPanel.alabels.cancelDrag();
 448       break;
 449     case KeyEvent.VK_X:
 450       if (evt.isControlDown() || evt.isMetaDown())
 451       {
 452         cut_actionPerformed();
 453       }
 454       break;
 455     case KeyEvent.VK_C:
 456       if (viewport.cursorMode && !evt.isControlDown())
 457       {
 458         alignPanel.seqPanel.setCursorColumn();
 459       }
 460       if (evt.isControlDown() || evt.isMetaDown())
 461       {
 462         copy_actionPerformed();
 463       }
 464       break;
 465     case KeyEvent.VK_V:
 466       if (evt.isControlDown())
 467       {
 468         paste(evt.isShiftDown());
 469       }
 470       break;
 471     case KeyEvent.VK_A:
 472       if (evt.isControlDown() || evt.isMetaDown())
 473       {
 474         selectAllSequenceMenuItem_actionPerformed();
 475       }
 476       break;
 477     case KeyEvent.VK_DOWN:
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.moveCursor(0, 1);
 481       }
 482       else
 483       {
 484         moveSelectedSequences(false);
 485       }
 486       break;
 487
 488     case KeyEvent.VK_UP:
 489       if (viewport.cursorMode)
 490       {
 491         alignPanel.seqPanel.moveCursor(0, -1);
 492       }
 493       else
 494       {
 495         moveSelectedSequences(true);
 496       }
 497       break;
 498
 499     case KeyEvent.VK_LEFT:
 500       if (evt.isAltDown() || !viewport.cursorMode)
 501       {
 502         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 503       }
 504       else
 505       {
 506         alignPanel.seqPanel.moveCursor(-1, 0);
 507       }
 508       break;
 509
 510     case KeyEvent.VK_RIGHT:
 511       if (evt.isAltDown() || !viewport.cursorMode)
 512       {
 513         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 514       }
 515       else
 516       {
 517         alignPanel.seqPanel.moveCursor(1, 0);
 518       }
 519       break;
 520
 521     case KeyEvent.VK_SPACE:
 522       if (viewport.cursorMode)
 523       {
 524         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 525                 || evt.isShiftDown() || evt.isAltDown());
 526       }
 527       break;
 528
 529     case KeyEvent.VK_DELETE:
 530     case KeyEvent.VK_BACK_SPACE:
 531       if (viewport.cursorMode)
 532       {
 533         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 534                 || evt.isShiftDown() || evt.isAltDown());
 535       }
 536       else
 537       {
 538         cut_actionPerformed();
 539         alignPanel.seqPanel.seqCanvas.repaint();
 540       }
 541       break;
 542
 543     case KeyEvent.VK_S:
 544       if (viewport.cursorMode)
 545       {
 546         alignPanel.seqPanel.setCursorRow();
 547       }
 548       break;
 549     case KeyEvent.VK_P:
 550       if (viewport.cursorMode)
 551       {
 552         alignPanel.seqPanel.setCursorPosition();
 553       }
 554       break;
 555
 556     case KeyEvent.VK_ENTER:
 557     case KeyEvent.VK_COMMA:
 558       if (viewport.cursorMode)
 559       {
 560         alignPanel.seqPanel.setCursorRowAndColumn();
 561       }
 562       break;
 563
 564     case KeyEvent.VK_Q:
 565       if (viewport.cursorMode)
 566       {
 567         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 568       }
 569       break;
 570     case KeyEvent.VK_M:
 571       if (viewport.cursorMode)
 572       {
 573         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 574       }
 575       break;
 576
 577     case KeyEvent.VK_F2:
 578       viewport.cursorMode = !viewport.cursorMode;
 579       setStatus(MessageManager
 580               .formatMessage("label.keyboard_editing_mode", new String[]
 581               { (viewport.cursorMode ? "on" : "off") }));
 582       if (viewport.cursorMode)
 583       {
 584         alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
 585         alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
 586       }
 587       break;
 588
 589     case KeyEvent.VK_F:
 590       if (evt.isControlDown())
 591       {
 592         findMenuItem_actionPerformed();
 593       }
 594       break;
 595
 596     case KeyEvent.VK_H:
 597     {
 598       boolean toggleSeqs = !evt.isControlDown();
 599       boolean toggleCols = !evt.isShiftDown();
 600       toggleHiddenRegions(toggleSeqs, toggleCols);
 601       break;
 602     }
 603
 604     case KeyEvent.VK_PAGE_UP:
 605       ranges.pageUp();
 606       break;
 607
 608     case KeyEvent.VK_PAGE_DOWN:
 609       ranges.pageDown();
 610       break;
 611
 612     case KeyEvent.VK_Z:
 613       if (evt.isControlDown())
 614       {
 615         undoMenuItem_actionPerformed();
 616       }
 617       break;
 618
 619     case KeyEvent.VK_Y:
 620       if (evt.isControlDown())
 621       {
 622         redoMenuItem_actionPerformed();
 623       }
 624       break;
 625
 626     case KeyEvent.VK_L:
 627       if (evt.isControlDown())
 628       {
 629         trimAlignment(true);
 630       }
 631       break;
 632
 633     case KeyEvent.VK_R:
 634       if (evt.isControlDown())
 635       {
 636         trimAlignment(false);
 637       }
 638       break;
 639
 640     case KeyEvent.VK_E:
 641       if (evt.isControlDown())
 642       {
 643         if (evt.isShiftDown())
 644         {
 645           this.removeAllGapsMenuItem_actionPerformed();
 646         }
 647         else
 648         {
 649           removeGappedColumnMenuItem_actionPerformed();
 650         }
 651       }
 652       break;
 653     case KeyEvent.VK_I:
 654       if (evt.isControlDown())
 655       {
 656         if (evt.isAltDown())
 657         {
 658           invertColSel_actionPerformed();
 659         }
 660         else
 661         {
 662           invertSequenceMenuItem_actionPerformed();
 663         }
 664       }
 665       break;
 666
 667     case KeyEvent.VK_G:
 668       if (evt.isControlDown())
 669       {
 670         if (evt.isShiftDown())
 671         {
 672           this.unGroup_actionPerformed();
 673         }
 674         else
 675         {
 676           this.createGroup_actionPerformed();
 677         }
 678       }
 679       break;
 680
 681     case KeyEvent.VK_U:
 682       if (evt.isControlDown())
 683       {
 684         this.deleteGroups_actionPerformed();
 685       }
 686       break;
 687
 688     case KeyEvent.VK_T:
 689       if (evt.isControlDown())
 690       {
 691         newView(null);
 692       }
 693       break;
 694
 695     }
 696     // TODO: repaint flags set only if the keystroke warrants it
 697     alignPanel.paintAlignment(true, true);
 698   }
 699
 700   /**
 701    * called by key handler and the hide all/show all menu items
 702    *
 703    * @param toggleSeqs
 704    * @param toggleCols
 705    */
 706   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 707   {
 708     boolean hide = false;
 709     SequenceGroup sg = viewport.getSelectionGroup();
 710     if (!toggleSeqs && !toggleCols)
 711     {
 712       // Hide everything by the current selection - this is a hack - we do the
 713       // invert and then hide
 714       // first check that there will be visible columns after the invert.
 715       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
 716               && sg.getStartRes() <= sg.getEndRes()))
 717       {
 718         // now invert the sequence set, if required - empty selection implies
 719         // that no hiding is required.
 720         if (sg != null)
 721         {
 722           invertSequenceMenuItem_actionPerformed();
 723           sg = viewport.getSelectionGroup();
 724           toggleSeqs = true;
 725
 726         }
 727         viewport.expandColSelection(sg, true);
 728         // finally invert the column selection and get the new sequence
 729         // selection and indicate it should be hidden.
 730         invertColSel_actionPerformed();
 731         toggleCols = true;
 732       }
 733     }
 734
 735     if (toggleSeqs)
 736     {
 737       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 738       {
 739         hide = true;
 740         viewport.hideAllSelectedSeqs();
 741       }
 742       else if (!(toggleCols && viewport.hasSelectedColumns()))
 743       {
 744         viewport.showAllHiddenSeqs();
 745       }
 746     }
 747
 748     if (toggleCols)
 749     {
 750       if (viewport.hasSelectedColumns())
 751       {
 752         viewport.hideSelectedColumns();
 753         if (!toggleSeqs)
 754         {
 755           viewport.setSelectionGroup(sg);
 756         }
 757       }
 758       else if (!hide)
 759       {
 760         viewport.showAllHiddenColumns();
 761       }
 762       viewport.sendSelection();
 763     }
 764   }
 765
 766   @Override
 767   public void keyReleased(KeyEvent evt)
 768   {
 769   }
 770
 771   @Override
 772   public void keyTyped(KeyEvent evt)
 773   {
 774   }
 775
 776   @Override
 777   public void itemStateChanged(ItemEvent evt)
 778   {
 779     final Object source = evt.getSource();
 780     if (source == displayNonconservedMenuItem)
 781     {
 782       displayNonconservedMenuItem_actionPerformed();
 783     }
 784     else if (source == colourTextMenuItem)
 785     {
 786       colourTextMenuItem_actionPerformed();
 787     }
 788     else if (source == wrapMenuItem)
 789     {
 790       wrapMenuItem_actionPerformed();
 791     }
 792     else if (source == scaleAbove)
 793     {
 794       viewport.setScaleAboveWrapped(scaleAbove.getState());
 795     }
 796     else if (source == scaleLeft)
 797     {
 798       viewport.setScaleLeftWrapped(scaleLeft.getState());
 799     }
 800     else if (source == scaleRight)
 801     {
 802       viewport.setScaleRightWrapped(scaleRight.getState());
 803     }
 804     else if (source == seqLimits)
 805     {
 806       seqLimits_itemStateChanged();
 807     }
 808     else if (source == viewBoxesMenuItem)
 809     {
 810       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 811     }
 812     else if (source == viewTextMenuItem)
 813     {
 814       viewport.setShowText(viewTextMenuItem.getState());
 815     }
 816     else if (source == renderGapsMenuItem)
 817     {
 818       viewport.setRenderGaps(renderGapsMenuItem.getState());
 819     }
 820     else if (source == annotationPanelMenuItem)
 821     {
 822       boolean showAnnotations = annotationPanelMenuItem.getState();
 823       showAlignmentAnnotations.setEnabled(showAnnotations);
 824       showSequenceAnnotations.setEnabled(showAnnotations);
 825       viewport.setShowAnnotation(showAnnotations);
 826       alignPanel.setAnnotationVisible(showAnnotations);
 827     }
 828     else if (source == sequenceFeatures)
 829     {
 830       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 831       alignPanel.seqPanel.seqCanvas.repaint();
 832     }
 833     else if (source == showAlignmentAnnotations)
 834     {
 835       setAnnotationsVisibility();
 836     }
 837     else if (source == showSequenceAnnotations)
 838     {
 839       setAnnotationsVisibility();
 840     }
 841     else if (source == sortAnnBySequence)
 842     {
 843       boolean newState = sortAnnBySequence.getState();
 844       sortAnnByLabel.setState(false);
 845       setAnnotationSortOrder(
 846               newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
 847                       : SequenceAnnotationOrder.NONE);
 848       setViewportAnnotationOrder();
 849     }
 850     else if (source == sortAnnByLabel)
 851     {
 852       boolean newState = sortAnnByLabel.getState();
 853       sortAnnBySequence.setState(false);
 854       setAnnotationSortOrder(
 855               newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
 856                       : SequenceAnnotationOrder.NONE);
 857       setViewportAnnotationOrder();
 858     }
 859     else if (source == showAutoFirst)
 860     {
 861       showAutoLast.setState(!showAutoFirst.getState());
 862       setShowAutoCalculatedAbove(showAutoFirst.getState());
 863       setViewportAnnotationOrder();
 864     }
 865     else if (source == showAutoLast)
 866     {
 867       showAutoFirst.setState(!showAutoLast.getState());
 868       setShowAutoCalculatedAbove(showAutoFirst.getState());
 869       setViewportAnnotationOrder();
 870     }
 871     else if (source == conservationMenuItem)
 872     {
 873       conservationMenuItem_actionPerformed();
 874     }
 875     else if (source == abovePIDThreshold)
 876     {
 877       abovePIDThreshold_actionPerformed();
 878     }
 879     else if (source == applyToAllGroups)
 880     {
 881       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 882     }
 883     else if (source == autoCalculate)
 884     {
 885       viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
 886     }
 887     else if (source == sortByTree)
 888     {
 889       viewport.sortByTree = sortByTree.getState();
 890     }
 891     else if (source == this.centreColumnLabelFlag)
 892     {
 893       centreColumnLabelFlag_stateChanged();
 894     }
 895     else if (source == this.followMouseOverFlag)
 896     {
 897       mouseOverFlag_stateChanged();
 898     }
 899     else if (source == showGroupConsensus)
 900     {
 901       showGroupConsensus_actionPerformed();
 902     }
 903     else if (source == showGroupConservation)
 904     {
 905       showGroupConservation_actionPerformed();
 906     }
 907     else if (source == showSequenceLogo)
 908     {
 909       showSequenceLogo_actionPerformed();
 910     }
 911     else if (source == normSequenceLogo)
 912     {
 913       normSequenceLogo_actionPerformed();
 914     }
 915     else if (source == showConsensusHistogram)
 916     {
 917       showConsensusHistogram_actionPerformed();
 918     }
 919     else if (source == applyAutoAnnotationSettings)
 920     {
 921       applyAutoAnnotationSettings_actionPerformed();
 922     }
 923     // TODO: repaint flags set only if warranted
 924     alignPanel.paintAlignment(true, true);
 925   }
 926
 927   /**
 928    * Set the visibility state of sequence-related and/or alignment-related
 929    * annotations depending on checkbox selections, and repaint.
 930    *
 931    * @param visible
 932    */
 933   private void setAnnotationsVisibility()
 934   {
 935     boolean showForAlignment = showAlignmentAnnotations.getState();
 936     boolean showForSequences = showSequenceAnnotations.getState();
 937     if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
 938     {
 939       for (AlignmentAnnotation aa : alignPanel.getAlignment()
 940               .getAlignmentAnnotation())
 941       {
 942         boolean visible = (aa.sequenceRef == null ? showForAlignment
 943                 : showForSequences);
 944         aa.visible = visible;
 945       }
 946     }
 947     alignPanel.validateAnnotationDimensions(true);
 948     validate();
 949     repaint();
 950   }
 951
 952   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
 953   {
 954     this.annotationSortOrder = order;
 955   }
 956
 957   /**
 958    * Set flags on the viewport that control annotation ordering
 959    */
 960   private void setViewportAnnotationOrder()
 961   {
 962     this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
 963     this.alignPanel.av
 964             .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
 965   }
 966
 967   private void setShowAutoCalculatedAbove(boolean showAbove)
 968   {
 969     this.showAutoCalculatedAbove = showAbove;
 970   }
 971
 972   private void mouseOverFlag_stateChanged()
 973   {
 974     viewport.setFollowHighlight(followMouseOverFlag.getState());
 975     // TODO: could kick the scrollTo mechanism to reset view for current
 976     // searchresults.
 977   }
 978
 979   private void centreColumnLabelFlag_stateChanged()
 980   {
 981     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 982     this.alignPanel.annotationPanel.repaint();
 983   }
 984
 985   @Override
 986   public void actionPerformed(ActionEvent evt)
 987   {
 988     viewport.applet.currentAlignFrame = this;
 989
 990     Object source = evt.getSource();
 991
 992     if (source == inputText)
 993     {
 994       inputText_actionPerformed();
 995     }
 996     else if (source == loadTree)
 997     {
 998       loadTree_actionPerformed();
 999     }
1000     else if (source == loadApplication)
1001     {
1002       launchFullApplication();
1003     }
1004     else if (source == loadAnnotations)
1005     {
1006       loadAnnotations();
1007     }
1008     else if (source == outputAnnotations)
1009     {
1010       outputAnnotations(true);
1011     }
1012     else if (source == outputFeatures)
1013     {
1014       outputFeatures(true, "Jalview");
1015     }
1016     else if (source == closeMenuItem)
1017     {
1018       closeMenuItem_actionPerformed();
1019     }
1020     else if (source == copy)
1021     {
1022       copy_actionPerformed();
1023     }
1024     else if (source == undoMenuItem)
1025     {
1026       undoMenuItem_actionPerformed();
1027     }
1028     else if (source == redoMenuItem)
1029     {
1030       redoMenuItem_actionPerformed();
1031     }
1032     else if (source == inputText)
1033     {
1034       inputText_actionPerformed();
1035     }
1036     else if (source == closeMenuItem)
1037     {
1038       closeMenuItem_actionPerformed();
1039     }
1040     else if (source == undoMenuItem)
1041     {
1042       undoMenuItem_actionPerformed();
1043     }
1044     else if (source == redoMenuItem)
1045     {
1046       redoMenuItem_actionPerformed();
1047     }
1048     else if (source == copy)
1049     {
1050       copy_actionPerformed();
1051     }
1052     else if (source == pasteNew)
1053     {
1054       pasteNew_actionPerformed();
1055     }
1056     else if (source == pasteThis)
1057     {
1058       pasteThis_actionPerformed();
1059     }
1060     else if (source == cut)
1061     {
1062       cut_actionPerformed();
1063     }
1064     else if (source == delete)
1065     {
1066       delete_actionPerformed();
1067     }
1068     else if (source == createGroup)
1069     {
1070       createGroup_actionPerformed();
1071     }
1072     else if (source == unGroup)
1073     {
1074       unGroup_actionPerformed();
1075     }
1076     else if (source == grpsFromSelection)
1077     {
1078       makeGrpsFromSelection_actionPerformed();
1079     }
1080     else if (source == deleteGroups)
1081     {
1082       deleteGroups_actionPerformed();
1083     }
1084     else if (source == selectAllSequenceMenuItem)
1085     {
1086       selectAllSequenceMenuItem_actionPerformed();
1087     }
1088     else if (source == deselectAllSequenceMenuItem)
1089     {
1090       deselectAllSequenceMenuItem_actionPerformed();
1091     }
1092     else if (source == invertSequenceMenuItem)
1093     {
1094       invertSequenceMenuItem_actionPerformed();
1095       // uncomment to slave sequence selections in split frame
1096       // viewport.sendSelection();
1097     }
1098     else if (source == invertColSel)
1099     {
1100       viewport.invertColumnSelection();
1101       alignPanel.paintAlignment(false, false);
1102       viewport.sendSelection();
1103     }
1104     else if (source == remove2LeftMenuItem)
1105     {
1106       trimAlignment(true);
1107     }
1108     else if (source == remove2RightMenuItem)
1109     {
1110       trimAlignment(false);
1111     }
1112     else if (source == removeGappedColumnMenuItem)
1113     {
1114       removeGappedColumnMenuItem_actionPerformed();
1115     }
1116     else if (source == removeAllGapsMenuItem)
1117     {
1118       removeAllGapsMenuItem_actionPerformed();
1119     }
1120     else if (source == findMenuItem)
1121     {
1122       findMenuItem_actionPerformed();
1123     }
1124     else if (source == font)
1125     {
1126       new FontChooser(alignPanel);
1127     }
1128     else if (source == newView)
1129     {
1130       newView(null);
1131     }
1132     else if (source == showColumns)
1133     {
1134       viewport.showAllHiddenColumns();
1135       alignPanel.paintAlignment(true, true);
1136       viewport.sendSelection();
1137     }
1138     else if (source == showSeqs)
1139     {
1140       viewport.showAllHiddenSeqs();
1141       alignPanel.paintAlignment(true, true);
1142       // uncomment if we want to slave sequence selections in split frame
1143       // viewport.sendSelection();
1144     }
1145     else if (source == hideColumns)
1146     {
1147       viewport.hideSelectedColumns();
1148       alignPanel.paintAlignment(true, true);
1149       viewport.sendSelection();
1150     }
1151     else if (source == hideSequences
1152             && viewport.getSelectionGroup() != null)
1153     {
1154       viewport.hideAllSelectedSeqs();
1155       alignPanel.paintAlignment(true, true);
1156       // uncomment if we want to slave sequence selections in split frame
1157       // viewport.sendSelection();
1158     }
1159     else if (source == hideAllButSelection)
1160     {
1161       toggleHiddenRegions(false, false);
1162       alignPanel.paintAlignment(true, true);
1163       viewport.sendSelection();
1164     }
1165     else if (source == hideAllSelection)
1166     {
1167       SequenceGroup sg = viewport.getSelectionGroup();
1168       viewport.expandColSelection(sg, false);
1169       viewport.hideAllSelectedSeqs();
1170       viewport.hideSelectedColumns();
1171       alignPanel.paintAlignment(true, true);
1172       viewport.sendSelection();
1173     }
1174     else if (source == showAllHidden)
1175     {
1176       viewport.showAllHiddenColumns();
1177       viewport.showAllHiddenSeqs();
1178       alignPanel.paintAlignment(true, true);
1179       viewport.sendSelection();
1180     }
1181     else if (source == showGroupConsensus)
1182     {
1183       showGroupConsensus_actionPerformed();
1184     }
1185     else if (source == showGroupConservation)
1186     {
1187       showGroupConservation_actionPerformed();
1188     }
1189     else if (source == showSequenceLogo)
1190     {
1191       showSequenceLogo_actionPerformed();
1192     }
1193     else if (source == normSequenceLogo)
1194     {
1195       normSequenceLogo_actionPerformed();
1196     }
1197     else if (source == showConsensusHistogram)
1198     {
1199       showConsensusHistogram_actionPerformed();
1200     }
1201     else if (source == applyAutoAnnotationSettings)
1202     {
1203       applyAutoAnnotationSettings_actionPerformed();
1204     }
1205     else if (source == featureSettings)
1206     {
1207       showFeatureSettingsUI();
1208     }
1209     else if (source == alProperties)
1210     {
1211       StringBuffer contents = new jalview.io.AlignmentProperties(
1212               viewport.getAlignment()).formatAsString();
1213       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214       cap.setText(contents.toString());
1215       Frame frame = new Frame();
1216       frame.add(cap);
1217       jalview.bin.JalviewLite.addFrame(frame, MessageManager
1218               .formatMessage("label.alignment_properties", new String[]
1219               { getTitle() }), 400, 250);
1220     }
1221     else if (source == overviewMenuItem)
1222     {
1223       overviewMenuItem_actionPerformed();
1224     }
1225     else if (source == noColourmenuItem)
1226     {
1227       changeColour(null);
1228     }
1229     else if (source == clustalColour)
1230     {
1231       abovePIDThreshold.setState(false);
1232       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1233     }
1234     else if (source == zappoColour)
1235     {
1236       changeColour(new ZappoColourScheme());
1237     }
1238     else if (source == taylorColour)
1239     {
1240       changeColour(new TaylorColourScheme());
1241     }
1242     else if (source == hydrophobicityColour)
1243     {
1244       changeColour(new HydrophobicColourScheme());
1245     }
1246     else if (source == helixColour)
1247     {
1248       changeColour(new HelixColourScheme());
1249     }
1250     else if (source == strandColour)
1251     {
1252       changeColour(new StrandColourScheme());
1253     }
1254     else if (source == turnColour)
1255     {
1256       changeColour(new TurnColourScheme());
1257     }
1258     else if (source == buriedColour)
1259     {
1260       changeColour(new BuriedColourScheme());
1261     }
1262     else if (source == nucleotideColour)
1263     {
1264       changeColour(new NucleotideColourScheme());
1265     }
1266     else if (source == purinePyrimidineColour)
1267     {
1268       changeColour(new PurinePyrimidineColourScheme());
1269     }
1270     // else if (source == RNAInteractionColour)
1271     // {
1272     // changeColour(new RNAInteractionColourScheme());
1273     // }
1274     else if (source == RNAHelixColour)
1275     {
1276       changeColour(new RNAHelicesColour(viewport.getAlignment()));
1277       // new RNAHelicesColourChooser(viewport, alignPanel);
1278     }
1279     else if (source == modifyPID)
1280     {
1281       modifyPID_actionPerformed();
1282     }
1283     else if (source == modifyConservation)
1284     {
1285       modifyConservation_actionPerformed();
1286     }
1287     else if (source == userDefinedColour)
1288     {
1289       new UserDefinedColours(alignPanel, null);
1290     }
1291     else if (source == PIDColour)
1292     {
1293       changeColour(new PIDColourScheme());
1294     }
1295     else if (source == BLOSUM62Colour)
1296     {
1297       changeColour(new Blosum62ColourScheme());
1298     }
1299     else if (source == tcoffeeColour)
1300     {
1301       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1302     }
1303     else if (source == annotationColour)
1304     {
1305       new AnnotationColourChooser(viewport, alignPanel);
1306     }
1307     else if (source == annotationColumnSelection)
1308     {
1309       new AnnotationColumnChooser(viewport, alignPanel);
1310     }
1311     else if (source == sortPairwiseMenuItem)
1312     {
1313       sortPairwiseMenuItem_actionPerformed();
1314     }
1315     else if (source == sortIDMenuItem)
1316     {
1317       sortIDMenuItem_actionPerformed();
1318     }
1319     else if (source == sortLengthMenuItem)
1320     {
1321       sortLengthMenuItem_actionPerformed();
1322     }
1323     else if (source == sortGroupMenuItem)
1324     {
1325       sortGroupMenuItem_actionPerformed();
1326     }
1327     else if (source == removeRedundancyMenuItem)
1328     {
1329       removeRedundancyMenuItem_actionPerformed();
1330     }
1331     else if (source == pairwiseAlignmentMenuItem)
1332     {
1333       pairwiseAlignmentMenuItem_actionPerformed();
1334     }
1335     else if (source == PCAMenuItem)
1336     {
1337       PCAMenuItem_actionPerformed();
1338     }
1339     else if (source == averageDistanceTreeMenuItem)
1340     {
1341       averageDistanceTreeMenuItem_actionPerformed();
1342     }
1343     else if (source == neighbourTreeMenuItem)
1344     {
1345       neighbourTreeMenuItem_actionPerformed();
1346     }
1347     else if (source == njTreeBlosumMenuItem)
1348     {
1349       njTreeBlosumMenuItem_actionPerformed();
1350     }
1351     else if (source == avDistanceTreeBlosumMenuItem)
1352     {
1353       avTreeBlosumMenuItem_actionPerformed();
1354     }
1355     else if (source == documentation)
1356     {
1357       documentation_actionPerformed();
1358     }
1359     else if (source == about)
1360     {
1361       about_actionPerformed();
1362     }
1363
1364   }
1365
1366   public void inputText_actionPerformed()
1367   {
1368     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1369     Frame frame = new Frame();
1370     frame.add(cap);
1371     jalview.bin.JalviewLite.addFrame(frame,
1372             MessageManager.getString("label.input_cut_paste"), 500, 500);
1373   }
1374
1375   protected void outputText_actionPerformed(ActionEvent e)
1376   {
1377     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1378     Frame frame = new Frame();
1379     frame.add(cap);
1380     JalviewLite.addFrame(frame, MessageManager
1381             .formatMessage("label.alignment_output_command", new Object[]
1382             { e.getActionCommand() }), 600, 500);
1383
1384     FileFormatI fileFormat = FileFormats.getInstance()
1385             .forName(e.getActionCommand());
1386     cap.setText(
1387             new AppletFormatAdapter(alignPanel).formatSequences(fileFormat,
1388                     viewport.getAlignment(), viewport.getShowJVSuffix()));
1389   }
1390
1391   public void loadAnnotations()
1392   {
1393     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1394     cap.setText(MessageManager
1395             .getString("label.paste_features_annotations_Tcoffee_here"));
1396     cap.setAnnotationImport();
1397     Frame frame = new Frame();
1398     frame.add(cap);
1399     jalview.bin.JalviewLite.addFrame(frame,
1400             MessageManager.getString("action.paste_annotations"), 400, 300);
1401
1402   }
1403
1404   public String outputAnnotations(boolean displayTextbox)
1405   {
1406     String annotation = new AnnotationFile()
1407             .printAnnotationsForView(viewport);
1408
1409     if (displayTextbox)
1410     {
1411       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1412       Frame frame = new Frame();
1413       frame.add(cap);
1414       jalview.bin.JalviewLite.addFrame(frame,
1415               MessageManager.getString("label.annotations"), 600, 500);
1416       cap.setText(annotation);
1417     }
1418
1419     return annotation;
1420   }
1421
1422   private Map<String, FeatureColourI> getDisplayedFeatureCols()
1423   {
1424     if (alignPanel.getFeatureRenderer() != null
1425             && viewport.getFeaturesDisplayed() != null)
1426     {
1427       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1428
1429     }
1430     return null;
1431   }
1432
1433   private List<String> getDisplayedFeatureGroups()
1434   {
1435     if (alignPanel.getFeatureRenderer() != null
1436             && viewport.getFeaturesDisplayed() != null)
1437     {
1438       return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
1439
1440     }
1441     return null;
1442   }
1443
1444   public String outputFeatures(boolean displayTextbox, String format)
1445   {
1446     String features;
1447     FeaturesFile formatter = new FeaturesFile();
1448     if (format.equalsIgnoreCase("Jalview"))
1449     {
1450       features = formatter.printJalviewFormat(
1451               viewport.getAlignment().getSequencesArray(),
1452               alignPanel.getFeatureRenderer(), true, false);
1453     }
1454     else
1455     {
1456       features = formatter.printGffFormat(viewport.getAlignment()
1457               .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
1458               false);
1459     }
1460
1461     if (displayTextbox)
1462     {
1463       boolean frimport = false;
1464       if (features == null || features.equals("No Features Visible"))
1465       {
1466         features = "# No features visible - paste some and import them here.";
1467         frimport = true;
1468       }
1469
1470       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1471       if (frimport)
1472       {
1473         cap.setAnnotationImport();
1474       }
1475       Frame frame = new Frame();
1476       frame.add(cap);
1477       jalview.bin.JalviewLite.addFrame(frame,
1478               MessageManager.getString("label.features"), 600, 500);
1479       cap.setText(features);
1480     }
1481     else
1482     {
1483       if (features == null)
1484       {
1485         features = "";
1486       }
1487     }
1488
1489     return features;
1490   }
1491
1492   void launchFullApplication()
1493   {
1494     StringBuffer url = new StringBuffer(jalviewServletURL);
1495
1496     // allow servlet parameters to be passed in applet parameter
1497     String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1498             : "?";
1499     url.append(firstSep);
1500
1501     url.append(
1502             "open=" + appendProtocol(viewport.applet.getParameter("file")));
1503
1504     if (viewport.applet.getParameter("features") != null)
1505     {
1506       url.append("&features=");
1507       url.append(appendProtocol(viewport.applet.getParameter("features")));
1508     }
1509
1510     if (viewport.applet.getParameter("annotations") != null)
1511     {
1512       url.append("&annotations=");
1513       url.append(
1514               appendProtocol(viewport.applet.getParameter("annotations")));
1515     }
1516
1517     if (viewport.applet.getParameter("jnetfile") != null
1518             || viewport.applet.getParameter("jpredfile") != null)
1519     {
1520       url.append("&annotations=");
1521       url.append(appendProtocol(
1522               viewport.applet.getParameter("jnetfile") != null
1523                       ? viewport.applet.getParameter("jnetfile")
1524                       : viewport.applet.getParameter("jpredfile")));
1525     }
1526
1527     if (viewport.applet.getParameter("defaultColour") != null)
1528     {
1529       url.append("&colour=" + removeWhiteSpace(
1530               viewport.applet.getParameter("defaultColour")));
1531     }
1532
1533     if (viewport.applet.getParameter("userDefinedColour") != null)
1534     {
1535       url.append("&colour=" + removeWhiteSpace(
1536               viewport.applet.getParameter("userDefinedColour")));
1537     }
1538     if (viewport.applet.getParameter("tree") != null)
1539     {
1540       url.append("&tree="
1541               + appendProtocol(viewport.applet.getParameter("tree")));
1542     }
1543     if (viewport.applet.getParameter("treeFile") != null)
1544     {
1545       url.append("&tree="
1546               + appendProtocol(viewport.applet.getParameter("treeFile")));
1547     }
1548
1549     showURL(url.toString(), "FULL_APP");
1550   }
1551
1552   String removeWhiteSpace(String colour)
1553   {
1554     StringBuffer sb = new StringBuffer();
1555     for (int i = 0; i < colour.length(); i++)
1556     {
1557       if (Character.isWhitespace(colour.charAt(i)))
1558       {
1559         sb.append("%20");
1560       }
1561       else
1562       {
1563         sb.append(colour.charAt(i));
1564       }
1565     }
1566
1567     return sb.toString();
1568   }
1569
1570   String appendProtocol(String url)
1571   {
1572     try
1573     {
1574       new URL(url);
1575       url = URLEncoder.encode(url, "UTF-8");
1576     }
1577     /*
1578      * When we finally deprecate 1.1 compatibility, we can start to use
1579      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1580      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1581      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1582      * ex.printStackTrace(); }
1583      */
1584     catch (java.net.MalformedURLException ex)
1585     {
1586       url = viewport.applet.getCodeBase() + url;
1587     }
1588     catch (UnsupportedEncodingException ex)
1589     {
1590       System.err.println(
1591               "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
1592                       + url);
1593       ex.printStackTrace();
1594     }
1595     return url;
1596   }
1597
1598   public void closeMenuItem_actionPerformed()
1599   {
1600     PaintRefresher.RemoveComponent(alignPanel);
1601     if (alignPanel.seqPanel != null
1602             && alignPanel.seqPanel.seqCanvas != null)
1603     {
1604       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1605     }
1606     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1607     {
1608       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1609     }
1610
1611     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1612     {
1613       System.exit(0);
1614     }
1615
1616     viewport = null;
1617     if (alignPanel != null && alignPanel.overviewPanel != null)
1618     {
1619       alignPanel.overviewPanel.dispose();
1620     }
1621     alignPanel = null;
1622     this.dispose();
1623   }
1624
1625   /**
1626    * TODO: JAL-1104
1627    */
1628   void updateEditMenuBar()
1629   {
1630
1631     if (viewport.getHistoryList().size() > 0)
1632     {
1633       undoMenuItem.setEnabled(true);
1634       CommandI command = viewport.getHistoryList().peek();
1635       undoMenuItem.setLabel(MessageManager
1636               .formatMessage("label.undo_command", new Object[]
1637               { command.getDescription() }));
1638     }
1639     else
1640     {
1641       undoMenuItem.setEnabled(false);
1642       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1643     }
1644
1645     if (viewport.getRedoList().size() > 0)
1646     {
1647       redoMenuItem.setEnabled(true);
1648
1649       CommandI command = viewport.getRedoList().peek();
1650       redoMenuItem.setLabel(MessageManager
1651               .formatMessage("label.redo_command", new Object[]
1652               { command.getDescription() }));
1653     }
1654     else
1655     {
1656       redoMenuItem.setEnabled(false);
1657       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1658     }
1659   }
1660
1661   /**
1662    * TODO: JAL-1104
1663    */
1664   @Override
1665   public void addHistoryItem(CommandI command)
1666   {
1667     if (command.getSize() > 0)
1668     {
1669       viewport.addToHistoryList(command);
1670       viewport.clearRedoList();
1671       updateEditMenuBar();
1672       viewport.updateHiddenColumns();
1673     }
1674   }
1675
1676   /**
1677    * TODO: JAL-1104 DOCUMENT ME!
1678    *
1679    * @param e
1680    *          DOCUMENT ME!
1681    */
1682   protected void undoMenuItem_actionPerformed()
1683   {
1684     if (viewport.getHistoryList().isEmpty())
1685     {
1686       return;
1687     }
1688
1689     CommandI command = viewport.getHistoryList().pop();
1690     viewport.addToRedoList(command);
1691     command.undoCommand(null);
1692
1693     AlignmentViewport originalSource = getOriginatingSource(command);
1694     // JBPNote Test
1695     if (originalSource != viewport)
1696     {
1697       System.err
1698               .println("Warning: Viewport object mismatch whilst undoing");
1699     }
1700     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1701                                           // viewport.getColumnSelection().getHiddenColumns()
1702                                           // != null;
1703     updateEditMenuBar();
1704     originalSource.notifyAlignment();
1705   }
1706
1707   /**
1708    * TODO: JAL-1104 DOCUMENT ME!
1709    *
1710    * @param e
1711    *          DOCUMENT ME!
1712    */
1713   protected void redoMenuItem_actionPerformed()
1714   {
1715     if (viewport.getRedoList().isEmpty())
1716     {
1717       return;
1718     }
1719
1720     CommandI command = viewport.getRedoList().pop();
1721     viewport.addToHistoryList(command);
1722     command.doCommand(null);
1723
1724     AlignmentViewport originalSource = getOriginatingSource(command);
1725     // JBPNote Test
1726     if (originalSource != viewport)
1727     {
1728       System.err
1729               .println("Warning: Viewport object mismatch whilst re-doing");
1730     }
1731     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1732                                           // viewport.getColumnSelection().getHiddenColumns()
1733                                           // != null;
1734
1735     updateEditMenuBar();
1736     originalSource.notifyAlignment();
1737   }
1738
1739   AlignmentViewport getOriginatingSource(CommandI command)
1740   {
1741     AlignmentViewport originalSource = null;
1742     // For sequence removal and addition, we need to fire
1743     // the property change event FROM the viewport where the
1744     // original alignment was altered
1745     AlignmentI al = null;
1746     if (command instanceof EditCommand)
1747     {
1748       EditCommand editCommand = (EditCommand) command;
1749       al = editCommand.getAlignment();
1750       Vector comps = PaintRefresher.components
1751               .get(viewport.getSequenceSetId());
1752       for (int i = 0; i < comps.size(); i++)
1753       {
1754         if (comps.elementAt(i) instanceof AlignmentPanel)
1755         {
1756           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1757           {
1758             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1759             break;
1760           }
1761         }
1762       }
1763     }
1764
1765     if (originalSource == null)
1766     {
1767       // The original view is closed, we must validate
1768       // the current view against the closed view first
1769       if (al != null)
1770       {
1771         PaintRefresher.validateSequences(al, viewport.getAlignment());
1772       }
1773
1774       originalSource = viewport;
1775     }
1776
1777     return originalSource;
1778   }
1779
1780   /**
1781    * Move the currently selected sequences up or down one position in the
1782    * alignment
1783    *
1784    * @param up
1785    */
1786   public void moveSelectedSequences(boolean up)
1787   {
1788     SequenceGroup sg = viewport.getSelectionGroup();
1789     if (sg == null)
1790     {
1791       return;
1792     }
1793     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1794             up ? null : viewport.getHiddenRepSequences(), up);
1795     alignPanel.paintAlignment(true, false);
1796
1797     /*
1798      * Also move cDNA/protein complement sequences
1799      */
1800     AlignViewportI complement = viewport.getCodingComplement();
1801     if (complement != null)
1802     {
1803       SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1804               viewport, complement);
1805       complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1806               up ? null : complement.getHiddenRepSequences(), up);
1807       getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
1808               false);
1809     }
1810   }
1811
1812   synchronized void slideSequences(boolean right, int size)
1813   {
1814     List<SequenceI> sg = new Vector<>();
1815     if (viewport.cursorMode)
1816     {
1817       sg.add(viewport.getAlignment()
1818               .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));
1819     }
1820     else if (viewport.getSelectionGroup() != null
1821             && viewport.getSelectionGroup().getSize() != viewport
1822                     .getAlignment().getHeight())
1823     {
1824       sg = viewport.getSelectionGroup()
1825               .getSequences(viewport.getHiddenRepSequences());
1826     }
1827
1828     if (sg.size() < 1)
1829     {
1830       return;
1831     }
1832
1833     Vector<SequenceI> invertGroup = new Vector();
1834
1835     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1836     {
1837       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1838       {
1839         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1840       }
1841     }
1842
1843     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1844
1845     SequenceI[] seqs2 = invertGroup
1846             .toArray(new SequenceI[invertGroup.size()]);
1847     for (int i = 0; i < invertGroup.size(); i++)
1848     {
1849       seqs2[i] = invertGroup.elementAt(i);
1850     }
1851
1852     SlideSequencesCommand ssc;
1853     if (right)
1854     {
1855       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1856               viewport.getGapCharacter());
1857     }
1858     else
1859     {
1860       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1861               viewport.getGapCharacter());
1862     }
1863
1864     int groupAdjustment = 0;
1865     if (ssc.getGapsInsertedBegin() && right)
1866     {
1867       if (viewport.cursorMode)
1868       {
1869         alignPanel.seqPanel.moveCursor(size, 0);
1870       }
1871       else
1872       {
1873         groupAdjustment = size;
1874       }
1875     }
1876     else if (!ssc.getGapsInsertedBegin() && !right)
1877     {
1878       if (viewport.cursorMode)
1879       {
1880         alignPanel.seqPanel.moveCursor(-size, 0);
1881       }
1882       else
1883       {
1884         groupAdjustment = -size;
1885       }
1886     }
1887
1888     if (groupAdjustment != 0)
1889     {
1890       viewport.getSelectionGroup().setStartRes(
1891               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1892       viewport.getSelectionGroup().setEndRes(
1893               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1894     }
1895
1896     boolean appendHistoryItem = false;
1897     Deque<CommandI> historyList = viewport.getHistoryList();
1898     if (historyList != null && historyList.size() > 0
1899             && historyList.peek() instanceof SlideSequencesCommand)
1900     {
1901       appendHistoryItem = ssc.appendSlideCommand(
1902               (SlideSequencesCommand) historyList.peek());
1903     }
1904
1905     if (!appendHistoryItem)
1906     {
1907       addHistoryItem(ssc);
1908     }
1909
1910     repaint();
1911   }
1912
1913   static StringBuffer copiedSequences;
1914
1915   static HiddenColumns copiedHiddenColumns;
1916
1917   protected void copy_actionPerformed()
1918   {
1919     if (viewport.getSelectionGroup() == null)
1920     {
1921       return;
1922     }
1923
1924     SequenceGroup sg = viewport.getSelectionGroup();
1925     copiedSequences = new StringBuffer();
1926     Map<Integer, SequenceI> orderedSeqs = new HashMap<>();
1927     for (int i = 0; i < sg.getSize(); i++)
1928     {
1929       SequenceI seq = sg.getSequenceAt(i);
1930       int index = viewport.getAlignment().findIndex(seq);
1931       orderedSeqs.put(index, seq);
1932     }
1933
1934     int index = 0, startRes, endRes;
1935     char ch;
1936
1937     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1938     {
1939       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1940       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1941
1942       // create new HiddenColumns object with copy of hidden regions
1943       // between startRes and endRes, offset by startRes
1944       copiedHiddenColumns = new HiddenColumns(
1945               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1946               hiddenCutoff, hiddenOffset);
1947     }
1948     else
1949     {
1950       copiedHiddenColumns = null;
1951     }
1952
1953     for (int i = 0; i < sg.getSize(); i++)
1954     {
1955       SequenceI seq = null;
1956
1957       while (seq == null)
1958       {
1959         if (orderedSeqs.containsKey(index))
1960         {
1961           seq = orderedSeqs.get(index);
1962           index++;
1963           break;
1964         }
1965         else
1966         {
1967           index++;
1968         }
1969       }
1970
1971       // FIND START RES
1972       // Returns residue following index if gap
1973       startRes = seq.findPosition(sg.getStartRes());
1974
1975       // FIND END RES
1976       // Need to find the residue preceeding index if gap
1977       endRes = 0;
1978
1979       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1980       {
1981         ch = seq.getCharAt(j);
1982         if (!jalview.util.Comparison.isGap((ch)))
1983         {
1984           endRes++;
1985         }
1986       }
1987
1988       if (endRes > 0)
1989       {
1990         endRes += seq.getStart() - 1;
1991       }
1992
1993       copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes
1994               + "\t" + seq.getSequenceAsString(sg.getStartRes(),
1995                       sg.getEndRes() + 1)
1996               + "\n");
1997     }
1998
1999   }
2000
2001   protected void pasteNew_actionPerformed()
2002   {
2003     paste(true);
2004   }
2005
2006   protected void pasteThis_actionPerformed()
2007   {
2008     paste(false);
2009   }
2010
2011   void paste(boolean newAlignment)
2012   {
2013     try
2014     {
2015       if (copiedSequences == null)
2016       {
2017         return;
2018       }
2019
2020       StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
2021               "\t");
2022       Vector seqs = new Vector();
2023       while (st.hasMoreElements())
2024       {
2025         String name = st.nextToken();
2026         int start = Integer.parseInt(st.nextToken());
2027         int end = Integer.parseInt(st.nextToken());
2028         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2029       }
2030       SequenceI[] newSeqs = new SequenceI[seqs.size()];
2031       for (int i = 0; i < seqs.size(); i++)
2032       {
2033         newSeqs[i] = (SequenceI) seqs.elementAt(i);
2034       }
2035
2036       if (newAlignment)
2037       {
2038         String newtitle = MessageManager
2039                 .getString("label.copied_sequences");
2040         if (getTitle().startsWith(
2041                 MessageManager.getString("label.copied_sequences")))
2042         {
2043           newtitle = getTitle();
2044         }
2045         else
2046         {
2047           newtitle = newtitle.concat(MessageManager
2048                   .formatMessage("label.from_msname", new String[]
2049                   { getTitle() }));
2050         }
2051         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2052                 viewport.applet, newtitle, false);
2053         af.viewport.setHiddenColumns(copiedHiddenColumns);
2054
2055         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2056                 frameHeight);
2057       }
2058       else
2059       {
2060         addSequences(newSeqs);
2061       }
2062
2063     } catch (Exception ex)
2064     {
2065     } // could be anything being pasted in here
2066
2067   }
2068
2069   void addSequences(SequenceI[] seqs)
2070   {
2071     for (int i = 0; i < seqs.length; i++)
2072     {
2073       viewport.getAlignment().addSequence(seqs[i]);
2074     }
2075
2076     // !newAlignment
2077     addHistoryItem(new EditCommand(
2078             MessageManager.getString("label.add_sequences"), Action.PASTE,
2079             seqs, 0, viewport.getAlignment().getWidth(),
2080             viewport.getAlignment()));
2081
2082     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
2083                                                                              // 2019.04.18
2084     viewport.getAlignment().getWidth();
2085     viewport.notifyAlignment();
2086
2087   }
2088
2089   protected void cut_actionPerformed()
2090   {
2091     copy_actionPerformed();
2092     delete_actionPerformed();
2093   }
2094
2095   protected void delete_actionPerformed()
2096   {
2097
2098     SequenceGroup sg = viewport.getSelectionGroup();
2099     if (sg == null)
2100     {
2101       return;
2102     }
2103
2104     Vector seqs = new Vector();
2105     SequenceI seq;
2106     for (int i = 0; i < sg.getSize(); i++)
2107     {
2108       seq = sg.getSequenceAt(i);
2109       seqs.addElement(seq);
2110     }
2111
2112     /*
2113      * If the cut affects all sequences, warn, remove highlighted columns
2114      */
2115     if (sg.getSize() == viewport.getAlignment().getHeight())
2116     {
2117       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2118               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2119       if (isEntireAlignWidth)
2120       {
2121         String title = MessageManager.getString("label.delete_all");
2122         Panel infoPanel = new Panel();
2123         infoPanel.setLayout(new FlowLayout());
2124         infoPanel.add(
2125                 new Label(MessageManager.getString("warn.delete_all")));
2126
2127         final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2128         dialog.setMainPanel(infoPanel);
2129         dialog.ok.setLabel(MessageManager.getString("action.ok"));
2130         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2131         dialog.setVisible(true);
2132
2133         if (!dialog.accept)
2134         {
2135           return;
2136         }
2137       }
2138       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2139               sg.getEndRes() + 1);
2140     }
2141
2142     SequenceI[] cut = new SequenceI[seqs.size()];
2143     for (int i = 0; i < seqs.size(); i++)
2144     {
2145       cut[i] = (SequenceI) seqs.elementAt(i);
2146     }
2147
2148     /*
2149      * //ADD HISTORY ITEM
2150      */
2151     addHistoryItem(new EditCommand(
2152             MessageManager.getString("label.cut_sequences"), Action.CUT,
2153             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2154             viewport.getAlignment()));
2155
2156     viewport.setSelectionGroup(null);
2157     viewport.getAlignment().deleteGroup(sg);
2158
2159     viewport.notifyAlignment();
2160
2161     if (viewport.getAlignment().getHeight() < 1)
2162     {
2163       this.setVisible(false);
2164     }
2165     viewport.sendSelection();
2166   }
2167
2168   /**
2169    * group consensus toggled
2170    *
2171    */
2172   protected void showGroupConsensus_actionPerformed()
2173   {
2174     viewport.setShowGroupConsensus(showGroupConsensus.getState());
2175     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2176
2177   }
2178
2179   /**
2180    * group conservation toggled.
2181    */
2182   protected void showGroupConservation_actionPerformed()
2183   {
2184     viewport.setShowGroupConservation(showGroupConservation.getState());
2185     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2186   }
2187
2188   /*
2189    * (non-Javadoc)
2190    *
2191    * @see
2192    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2193    * .event.ActionEvent)
2194    */
2195   protected void showConsensusHistogram_actionPerformed()
2196   {
2197     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2198     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199   }
2200
2201   /*
2202    * (non-Javadoc)
2203    *
2204    * @see
2205    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2206    * .event.ActionEvent)
2207    */
2208   protected void showSequenceLogo_actionPerformed()
2209   {
2210     viewport.setShowSequenceLogo(showSequenceLogo.getState());
2211     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212   }
2213
2214   protected void normSequenceLogo_actionPerformed()
2215   {
2216     showSequenceLogo.setState(true);
2217     viewport.setShowSequenceLogo(true);
2218     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2219     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2220   }
2221
2222   protected void applyAutoAnnotationSettings_actionPerformed()
2223   {
2224     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2225   }
2226
2227   protected void makeGrpsFromSelection_actionPerformed()
2228   {
2229     if (avc.makeGroupsFromSelection())
2230     {
2231       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2232       alignPanel.updateAnnotation();
2233       alignPanel.paintAlignment(true, true);
2234     }
2235   }
2236
2237   protected void createGroup_actionPerformed()
2238   {
2239     avc.createGroup();
2240   }
2241
2242   protected void unGroup_actionPerformed()
2243   {
2244     if (avc.unGroup())
2245     {
2246       alignPanel.alignmentChanged();
2247     }
2248   }
2249
2250   protected void deleteGroups_actionPerformed()
2251   {
2252     if (avc.deleteGroups())
2253     {
2254       alignPanel.alignmentChanged();
2255     }
2256   }
2257
2258   public void selectAllSequenceMenuItem_actionPerformed()
2259   {
2260     SequenceGroup sg = new SequenceGroup();
2261     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2262     {
2263       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2264     }
2265     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2266     viewport.setSelectionGroup(sg);
2267     // JAL-2034 - should delegate to
2268     // alignPanel to decide if overview needs
2269     // updating.
2270     alignPanel.paintAlignment(false, false);
2271     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2272     viewport.sendSelection();
2273   }
2274
2275   public void deselectAllSequenceMenuItem_actionPerformed()
2276   {
2277     if (viewport.cursorMode)
2278     {
2279       alignPanel.seqPanel.keyboardNo1 = null;
2280       alignPanel.seqPanel.keyboardNo2 = null;
2281     }
2282     viewport.setSelectionGroup(null);
2283     viewport.getColumnSelection().clear();
2284     viewport.setSelectionGroup(null);
2285     alignPanel.idPanel.idCanvas.searchResults = null;
2286     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2287     // JAL-2034 - should delegate to
2288     // alignPanel to decide if overview needs
2289     // updating.
2290     alignPanel.paintAlignment(false, false);
2291     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2292     viewport.sendSelection();
2293   }
2294
2295   public void invertSequenceMenuItem_actionPerformed()
2296   {
2297     SequenceGroup sg = viewport.getSelectionGroup();
2298     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2299     {
2300       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2301     }
2302
2303     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2304     viewport.sendSelection();
2305   }
2306
2307   public void invertColSel_actionPerformed()
2308   {
2309     viewport.invertColumnSelection();
2310     alignPanel.paintAlignment(true, false);
2311     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2312     viewport.sendSelection();
2313   }
2314
2315   void trimAlignment(boolean trimLeft)
2316   {
2317     AlignmentI al = viewport.getAlignment();
2318     ViewportRanges ranges = viewport.getRanges();
2319     ColumnSelection colSel = viewport.getColumnSelection();
2320     int column;
2321
2322     if (!colSel.isEmpty())
2323     {
2324       if (trimLeft)
2325       {
2326         column = colSel.getMin();
2327       }
2328       else
2329       {
2330         column = colSel.getMax();
2331       }
2332
2333       SequenceI[] seqs;
2334       if (viewport.getSelectionGroup() != null)
2335       {
2336         seqs = viewport.getSelectionGroup()
2337                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2338       }
2339       else
2340       {
2341         seqs = al.getSequencesArray();
2342       }
2343
2344       TrimRegionCommand trimRegion;
2345       if (trimLeft)
2346       {
2347         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2348                 column, al);
2349         ranges.setStartRes(0);
2350       }
2351       else
2352       {
2353         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2354                 column, al);
2355       }
2356
2357       setStatus(MessageManager
2358               .formatMessage("label.removed_columns", new String[]
2359               { Integer.valueOf(trimRegion.getSize()).toString() }));
2360       addHistoryItem(trimRegion);
2361
2362       for (SequenceGroup sg : al.getGroups())
2363       {
2364         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2365                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2366         {
2367           al.deleteGroup(sg);
2368         }
2369       }
2370
2371       viewport.notifyAlignment();
2372     }
2373   }
2374
2375   public void removeGappedColumnMenuItem_actionPerformed()
2376   {
2377     AlignmentI al = viewport.getAlignment();
2378     ViewportRanges ranges = viewport.getRanges();
2379     int start = 0;
2380     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2381
2382     SequenceI[] seqs;
2383     if (viewport.getSelectionGroup() != null)
2384     {
2385       seqs = viewport.getSelectionGroup()
2386               .getSequencesAsArray(viewport.getHiddenRepSequences());
2387       start = viewport.getSelectionGroup().getStartRes();
2388       end = viewport.getSelectionGroup().getEndRes();
2389     }
2390     else
2391     {
2392       seqs = viewport.getAlignment().getSequencesArray();
2393     }
2394
2395     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2396             "Remove Gapped Columns", seqs, start, end,
2397             viewport.getAlignment());
2398
2399     addHistoryItem(removeGapCols);
2400
2401     setStatus(MessageManager
2402             .formatMessage("label.removed_empty_columns", new String[]
2403             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2404
2405     // This is to maintain viewport position on first residue
2406     // of first sequence
2407     SequenceI seq = al.getSequenceAt(0);
2408     int startRes = seq.findPosition(ranges.getStartRes());
2409     // ShiftList shifts;
2410     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2411     // edit.alColumnChanges=shifts.getInverse();
2412     // if (viewport.hasHiddenColumns)
2413     // viewport.getColumnSelection().compensateForEdits(shifts);
2414     ranges.setStartRes(seq.findIndex(startRes) - 1);
2415     viewport.notifyAlignment();
2416
2417   }
2418
2419   public void removeAllGapsMenuItem_actionPerformed()
2420   {
2421     AlignmentI al = viewport.getAlignment();
2422     ViewportRanges ranges = viewport.getRanges();
2423     int start = 0;
2424     int end = ranges.getAbsoluteAlignmentWidth() - 1;
2425
2426     SequenceI[] seqs;
2427     if (viewport.getSelectionGroup() != null)
2428     {
2429       seqs = viewport.getSelectionGroup()
2430               .getSequencesAsArray(viewport.getHiddenRepSequences());
2431       start = viewport.getSelectionGroup().getStartRes();
2432       end = viewport.getSelectionGroup().getEndRes();
2433     }
2434     else
2435     {
2436       seqs = viewport.getAlignment().getSequencesArray();
2437     }
2438
2439     // This is to maintain viewport position on first residue
2440     // of first sequence
2441     SequenceI seq = al.getSequenceAt(0);
2442     int startRes = seq.findPosition(ranges.getStartRes());
2443
2444     addHistoryItem(
2445             new RemoveGapsCommand("Remove Gaps", seqs, start, end, al));
2446
2447     ranges.setStartRes(seq.findIndex(startRes) - 1);
2448
2449     viewport.notifyAlignment();
2450
2451   }
2452
2453   public void findMenuItem_actionPerformed()
2454   {
2455     new Finder(alignPanel);
2456   }
2457
2458   /**
2459    * create a new view derived from the current view
2460    *
2461    * @param viewtitle
2462    * @return frame for the new view
2463    */
2464   public AlignFrame newView(String viewtitle)
2465   {
2466     AlignmentI newal;
2467     if (viewport.hasHiddenRows())
2468     {
2469       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2470               .getFullAlignment().getSequencesArray());
2471     }
2472     else
2473     {
2474       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2475     }
2476
2477     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2478     {
2479       for (int i = 0; i < viewport.getAlignment()
2480               .getAlignmentAnnotation().length; i++)
2481       {
2482         if (!viewport.getAlignment()
2483                 .getAlignmentAnnotation()[i].autoCalculated)
2484         {
2485           newal.addAnnotation(
2486                   viewport.getAlignment().getAlignmentAnnotation()[i]);
2487         }
2488       }
2489     }
2490
2491     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2492
2493     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2494     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2495     PaintRefresher.Register(newaf.alignPanel,
2496             newaf.alignPanel.av.getSequenceSetId());
2497
2498     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2499             newaf.alignPanel.av.getSequenceSetId());
2500     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2501             newaf.alignPanel.av.getSequenceSetId());
2502
2503     Vector comps = PaintRefresher.components
2504             .get(viewport.getSequenceSetId());
2505     int viewSize = -1;
2506     for (int i = 0; i < comps.size(); i++)
2507     {
2508       if (comps.elementAt(i) instanceof AlignmentPanel)
2509       {
2510         viewSize++;
2511       }
2512     }
2513
2514     String title = new String(this.getTitle());
2515     if (viewtitle != null)
2516     {
2517       title = viewtitle + " ( " + title + ")";
2518     }
2519     else
2520     {
2521       if (title.indexOf("(View") > -1)
2522       {
2523         title = title.substring(0, title.indexOf("(View"));
2524       }
2525       title += "(View " + viewSize + ")";
2526     }
2527
2528     newaf.setTitle(title.toString());
2529
2530     newaf.viewport.setHistoryList(viewport.getHistoryList());
2531     newaf.viewport.setRedoList(viewport.getRedoList());
2532     return newaf;
2533   }
2534
2535   /**
2536    *
2537    * @return list of feature groups on the view
2538    */
2539   public String[] getFeatureGroups()
2540   {
2541     FeatureRenderer fr = null;
2542     if (alignPanel != null
2543             && (fr = alignPanel.getFeatureRenderer()) != null)
2544     {
2545       List<String> gps = fr.getFeatureGroups();
2546       String[] _gps = gps.toArray(new String[gps.size()]);
2547       return _gps;
2548     }
2549     return null;
2550   }
2551
2552   /**
2553    * get sequence feature groups that are hidden or shown
2554    *
2555    * @param visible
2556    *          true is visible
2557    * @return list
2558    */
2559   public String[] getFeatureGroupsOfState(boolean visible)
2560   {
2561     FeatureRenderer fr = null;
2562     if (alignPanel != null
2563             && (fr = alignPanel.getFeatureRenderer()) != null)
2564     {
2565       List<String> gps = fr.getGroups(visible);
2566       String[] _gps = gps.toArray(new String[gps.size()]);
2567       return _gps;
2568     }
2569     return null;
2570   }
2571
2572   /**
2573    * Change the display state for the given feature groups
2574    *
2575    * @param groups
2576    *          list of group strings
2577    * @param state
2578    *          visible or invisible
2579    */
2580   public void setFeatureGroupState(String[] groups, boolean state)
2581   {
2582     FeatureRenderer fr = null;
2583     this.sequenceFeatures.setState(true);
2584     viewport.setShowSequenceFeatures(true);
2585     if (alignPanel != null
2586             && (fr = alignPanel.getFeatureRenderer()) != null)
2587     {
2588
2589       fr.setGroupVisibility(Arrays.asList(groups), state);
2590       alignPanel.seqPanel.seqCanvas.repaint();
2591       if (alignPanel.overviewPanel != null)
2592       {
2593         alignPanel.overviewPanel.updateOverviewImage();
2594       }
2595     }
2596   }
2597
2598   public void seqLimits_itemStateChanged()
2599   {
2600     viewport.setShowJVSuffix(seqLimits.getState());
2601     alignPanel.fontChanged();
2602     alignPanel.paintAlignment(true, false);
2603   }
2604
2605   protected void colourTextMenuItem_actionPerformed()
2606   {
2607     viewport.setColourText(colourTextMenuItem.getState());
2608     alignPanel.paintAlignment(false, false);
2609   }
2610
2611   protected void displayNonconservedMenuItem_actionPerformed()
2612   {
2613     viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2614     alignPanel.paintAlignment(false, false);
2615   }
2616
2617   protected void wrapMenuItem_actionPerformed()
2618   {
2619     viewport.setWrapAlignment(wrapMenuItem.getState());
2620     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2621     scaleAbove.setEnabled(wrapMenuItem.getState());
2622     scaleLeft.setEnabled(wrapMenuItem.getState());
2623     scaleRight.setEnabled(wrapMenuItem.getState());
2624     alignPanel.paintAlignment(true, false);
2625   }
2626
2627   public void overviewMenuItem_actionPerformed()
2628   {
2629     if (alignPanel.overviewPanel != null)
2630     {
2631       return;
2632     }
2633
2634     Frame frame = new Frame();
2635     final OverviewPanel overview = new OverviewPanel(alignPanel);
2636     frame.add(overview);
2637     // +50 must allow for applet frame window
2638     jalview.bin.JalviewLite.addFrame(frame, MessageManager
2639             .formatMessage("label.overview_params", new String[]
2640             { this.getTitle() }), overview.getPreferredSize().width,
2641             overview.getPreferredSize().height + 50);
2642
2643     frame.pack();
2644     final AlignmentPanel ap = alignPanel;
2645     frame.addWindowListener(new WindowAdapter()
2646     {
2647       @Override
2648       public void windowClosing(WindowEvent e)
2649       {
2650         overview.dispose();
2651         if (ap != null)
2652         {
2653           ap.setOverviewPanel(null);
2654         }
2655       };
2656     });
2657
2658     alignPanel.setOverviewPanel(overview);
2659
2660   }
2661
2662   @Override
2663   public void changeColour(ColourSchemeI cs)
2664   {
2665     viewport.setGlobalColourScheme(cs);
2666
2667     alignPanel.paintAlignment(true, true);
2668   }
2669
2670   protected void modifyPID_actionPerformed()
2671   {
2672     if (viewport.getAbovePIDThreshold()
2673             && viewport.getGlobalColourScheme() != null)
2674     {
2675       SliderPanel.setPIDSliderSource(alignPanel,
2676               viewport.getResidueShading(), alignPanel.getViewName());
2677       SliderPanel.showPIDSlider();
2678     }
2679   }
2680
2681   protected void modifyConservation_actionPerformed()
2682   {
2683     if (viewport.getConservationSelected()
2684             && viewport.getGlobalColourScheme() != null)
2685     {
2686       SliderPanel.setConservationSlider(alignPanel,
2687               viewport.getResidueShading(), alignPanel.getViewName());
2688       SliderPanel.showConservationSlider();
2689     }
2690   }
2691
2692   protected void conservationMenuItem_actionPerformed()
2693   {
2694     boolean selected = conservationMenuItem.getState();
2695     modifyConservation.setEnabled(selected);
2696     viewport.setConservationSelected(selected);
2697     viewport.getResidueShading().setConservationApplied(selected);
2698
2699     changeColour(viewport.getGlobalColourScheme());
2700
2701     if (selected)
2702     {
2703       modifyConservation_actionPerformed();
2704     }
2705     else
2706     {
2707       SliderPanel.hideConservationSlider();
2708     }
2709   }
2710
2711   public void abovePIDThreshold_actionPerformed()
2712   {
2713     boolean selected = abovePIDThreshold.getState();
2714     modifyPID.setEnabled(selected);
2715     viewport.setAbovePIDThreshold(selected);
2716     if (!selected)
2717     {
2718       viewport.getResidueShading().setThreshold(0,
2719               viewport.isIgnoreGapsConsensus());
2720     }
2721
2722     changeColour(viewport.getGlobalColourScheme());
2723
2724     if (selected)
2725     {
2726       modifyPID_actionPerformed();
2727     }
2728     else
2729     {
2730       SliderPanel.hidePIDSlider();
2731     }
2732   }
2733
2734   public void sortPairwiseMenuItem_actionPerformed()
2735   {
2736     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737     AlignmentSorter.sortByPID(viewport.getAlignment(),
2738             viewport.getAlignment().getSequenceAt(0));
2739
2740     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2741             viewport.getAlignment()));
2742     alignPanel.paintAlignment(true, false);
2743   }
2744
2745   public void sortIDMenuItem_actionPerformed()
2746   {
2747     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2748     AlignmentSorter.sortByID(viewport.getAlignment());
2749     addHistoryItem(
2750             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
2751     alignPanel.paintAlignment(true, false);
2752   }
2753
2754   public void sortLengthMenuItem_actionPerformed()
2755   {
2756     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2757     AlignmentSorter.sortByLength(viewport.getAlignment());
2758     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2759             viewport.getAlignment()));
2760     alignPanel.paintAlignment(true, false);
2761   }
2762
2763   public void sortGroupMenuItem_actionPerformed()
2764   {
2765     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2766     AlignmentSorter.sortByGroup(viewport.getAlignment());
2767     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2768             viewport.getAlignment()));
2769     alignPanel.paintAlignment(true, false);
2770
2771   }
2772
2773   public void removeRedundancyMenuItem_actionPerformed()
2774   {
2775     new RedundancyPanel(alignPanel);
2776   }
2777
2778   public void pairwiseAlignmentMenuItem_actionPerformed()
2779   {
2780     if (viewport.getSelectionGroup() != null
2781             && viewport.getSelectionGroup().getSize() > 1)
2782     {
2783       Frame frame = new Frame();
2784       frame.add(new PairwiseAlignPanel(alignPanel));
2785       jalview.bin.JalviewLite.addFrame(frame,
2786               MessageManager.getString("action.pairwise_alignment"), 600,
2787               500);
2788     }
2789   }
2790
2791   public void PCAMenuItem_actionPerformed()
2792   {
2793     // are the sequences aligned?
2794     if (!viewport.getAlignment().isAligned(false))
2795     {
2796       SequenceI current;
2797       int Width = viewport.getAlignment().getWidth();
2798
2799       for (int i = 0; i < viewport.getAlignment().getSequences()
2800               .size(); i++)
2801       {
2802         current = viewport.getAlignment().getSequenceAt(i);
2803
2804         if (current.getLength() < Width)
2805         {
2806           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2807         }
2808       }
2809       alignPanel.paintAlignment(false, false);
2810     }
2811
2812     if ((viewport.getSelectionGroup() != null
2813             && viewport.getSelectionGroup().getSize() < 4
2814             && viewport.getSelectionGroup().getSize() > 0)
2815             || viewport.getAlignment().getHeight() < 4)
2816     {
2817       return;
2818     }
2819
2820     try
2821     {
2822       new PCAPanel(viewport);
2823     } catch (java.lang.OutOfMemoryError ex)
2824     {
2825     }
2826
2827   }
2828
2829   public void averageDistanceTreeMenuItem_actionPerformed()
2830   {
2831     newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2832             "Average distance tree using PID");
2833   }
2834
2835   public void neighbourTreeMenuItem_actionPerformed()
2836   {
2837     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2838             "Neighbour joining tree using PID");
2839   }
2840
2841   protected void njTreeBlosumMenuItem_actionPerformed()
2842   {
2843     newTreePanel(TreeBuilder.NEIGHBOUR_JOINING,
2844             ScoreModels.getInstance().getBlosum62().getName(),
2845             "Neighbour joining tree using BLOSUM62");
2846   }
2847
2848   protected void avTreeBlosumMenuItem_actionPerformed()
2849   {
2850     newTreePanel(TreeBuilder.AVERAGE_DISTANCE,
2851             ScoreModels.getInstance().getBlosum62().getName(),
2852             "Average distance tree using BLOSUM62");
2853   }
2854
2855   void newTreePanel(String type, String pwType, String title)
2856   {
2857     // are the sequences aligned?
2858     if (!viewport.getAlignment().isAligned(false))
2859     {
2860       SequenceI current;
2861       int Width = viewport.getAlignment().getWidth();
2862
2863       for (int i = 0; i < viewport.getAlignment().getSequences()
2864               .size(); i++)
2865       {
2866         current = viewport.getAlignment().getSequenceAt(i);
2867
2868         if (current.getLength() < Width)
2869         {
2870           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2871         }
2872       }
2873       alignPanel.paintAlignment(false, false);
2874
2875     }
2876
2877     if ((viewport.getSelectionGroup() != null
2878             && viewport.getSelectionGroup().getSize() > 1)
2879             || (viewport.getAlignment().getHeight() > 1))
2880     {
2881       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2882
2883       addTreeMenuItem(tp, title);
2884
2885       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2886     }
2887   }
2888
2889   void loadTree_actionPerformed()
2890   {
2891     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2892     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2893     cap.setTreeImport();
2894     Frame frame = new Frame();
2895     frame.add(cap);
2896     jalview.bin.JalviewLite.addFrame(frame,
2897             MessageManager.getString("label.paste_newick_file"), 400, 300);
2898   }
2899
2900   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2901   {
2902     TreePanel tp = new TreePanel(alignPanel, treeFile,
2903             MessageManager.getString("label.load_tree_from_file"), tree);
2904     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2905     addTreeMenuItem(tp, treeFile);
2906   }
2907
2908   /**
2909    * sort the alignment using the given treePanel
2910    *
2911    * @param treePanel
2912    *          tree used to sort view
2913    * @param title
2914    *          string used for undo event name
2915    */
2916   public void sortByTree(TreePanel treePanel, String title)
2917   {
2918     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2919     AlignmentSorter.sortByTree(viewport.getAlignment(),
2920             treePanel.getTree());
2921     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2922     // HistoryItem.SORT));
2923     addHistoryItem(new OrderCommand(MessageManager
2924             .formatMessage("label.order_by_params", new String[]
2925             { title }), oldOrder, viewport.getAlignment()));
2926     alignPanel.paintAlignment(true, false);
2927   }
2928
2929   /**
2930    * Do any automatic reordering of the alignment and add the necessary bits to
2931    * the menu structure for the new tree
2932    *
2933    * @param treePanel
2934    * @param title
2935    */
2936   protected void addTreeMenuItem(final TreePanel treePanel,
2937           final String title)
2938   {
2939     final MenuItem item = new MenuItem(title);
2940     sortByTreeMenu.add(item);
2941     item.addActionListener(new java.awt.event.ActionListener()
2942     {
2943       @Override
2944       public void actionPerformed(ActionEvent evt)
2945       {
2946         sortByTree(treePanel, title); // treePanel.getTitle());
2947       }
2948     });
2949
2950     treePanel.addWindowListener(new WindowAdapter()
2951     {
2952       @Override
2953       public void windowOpened(WindowEvent e)
2954       {
2955         if (viewport.sortByTree)
2956         {
2957           sortByTree(treePanel, title);
2958         }
2959         super.windowOpened(e);
2960       }
2961
2962       @Override
2963       public void windowClosing(WindowEvent e)
2964       {
2965         sortByTreeMenu.remove(item);
2966       };
2967     });
2968   }
2969
2970   public boolean sortBy(AlignmentOrder alorder, String undoname)
2971   {
2972     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2973     if (viewport.applet.debug)
2974     {
2975       System.err.println("Sorting " + alorder.getOrder().size()
2976               + " in alignment '" + getTitle() + "'");
2977     }
2978     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2979     if (undoname != null)
2980     {
2981       addHistoryItem(new OrderCommand(undoname, oldOrder,
2982               viewport.getAlignment()));
2983     }
2984     alignPanel.paintAlignment(true, false);
2985     return true;
2986   }
2987
2988   protected void documentation_actionPerformed()
2989   {
2990     alignPanel.av.applet.openJalviewHelpUrl();
2991   }
2992
2993   protected void about_actionPerformed()
2994   {
2995
2996     class AboutPanel extends Canvas
2997     {
2998       String version;
2999
3000       String builddate;
3001
3002       public AboutPanel(String version, String builddate)
3003       {
3004         this.version = version;
3005         this.builddate = builddate;
3006       }
3007
3008       @Override
3009       public void paint(Graphics g)
3010       {
3011         g.setColor(Color.white);
3012         g.fillRect(0, 0, getSize().width, getSize().height);
3013         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3014         FontMetrics fm = g.getFontMetrics();
3015         int fh = fm.getHeight();
3016         int y = 5, x = 7;
3017         g.setColor(Color.black);
3018         // TODO: update this text for each release or centrally store it for
3019         // lite and application
3020         g.setFont(new Font("Helvetica", Font.BOLD, 14));
3021         g.drawString(MessageManager
3022                 .formatMessage("label.jalviewLite_release", new String[]
3023                 { version }), x, y += fh);
3024         g.setFont(new Font("Helvetica", Font.BOLD, 12));
3025         g.drawString(MessageManager.formatMessage("label.jaview_build_date",
3026                 new String[]
3027                 { builddate }), x, y += fh);
3028         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3029         g.drawString(MessageManager.getString("label.jalview_authors_1"), x,
3030                 y += fh * 1.5);
3031         g.drawString(MessageManager.getString("label.jalview_authors_2"),
3032                 x + 50, y += fh + 8);
3033         g.drawString(MessageManager.getString("label.jalview_dev_managers"),
3034                 x, y += fh);
3035         g.drawString(MessageManager
3036                 .getString("label.jalview_distribution_lists"), x, y += fh);
3037         g.drawString(MessageManager.getString("label.jalview_please_cite"),
3038                 x, y += fh + 8);
3039         g.drawString(
3040                 MessageManager.getString("label.jalview_cite_1_authors"), x,
3041                 y += fh);
3042         g.drawString(MessageManager.getString("label.jalview_cite_1_title"),
3043                 x, y += fh);
3044         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3045                 x, y += fh);
3046       }
3047     }
3048
3049     Frame frame = new Frame();
3050     frame.add(new AboutPanel(JalviewLite.getVersion(),
3051             JalviewLite.getBuildDate()));
3052     jalview.bin.JalviewLite.addFrame(frame,
3053             MessageManager.getString("label.jalview"), 580, 220);
3054
3055   }
3056
3057   public void showURL(String url, String target)
3058   {
3059     if (viewport.applet == null)
3060     {
3061       System.out.println("Not running as applet - no browser available.");
3062     }
3063     else
3064     {
3065       viewport.applet.showURL(url, target);
3066     }
3067   }
3068
3069   // ////////////////////////////////////////////////////////////////////////////////
3070   // JBuilder Graphics here
3071
3072   MenuBar alignFrameMenuBar = new MenuBar();
3073
3074   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3075
3076   MenuItem loadApplication = new MenuItem(
3077           MessageManager.getString("label.view_full_application"));
3078
3079   MenuItem loadTree = new MenuItem(
3080           MessageManager.getString("label.load_associated_tree"));
3081
3082   MenuItem loadAnnotations = new MenuItem(
3083           MessageManager.getString("label.load_features_annotations"));
3084
3085   MenuItem outputFeatures = new MenuItem(
3086           MessageManager.getString("label.export_features"));
3087
3088   MenuItem outputAnnotations = new MenuItem(
3089           MessageManager.getString("label.export_annotations"));
3090
3091   MenuItem closeMenuItem = new MenuItem(
3092           MessageManager.getString("action.close"));
3093
3094   MenuItem selectAllSequenceMenuItem = new MenuItem(
3095           MessageManager.getString("action.select_all"));
3096
3097   MenuItem deselectAllSequenceMenuItem = new MenuItem(
3098           MessageManager.getString("action.deselect_all"));
3099
3100   MenuItem invertSequenceMenuItem = new MenuItem(
3101           MessageManager.getString("action.invert_selection"));
3102
3103   MenuItem remove2LeftMenuItem = new MenuItem();
3104
3105   MenuItem remove2RightMenuItem = new MenuItem();
3106
3107   MenuItem removeGappedColumnMenuItem = new MenuItem();
3108
3109   MenuItem removeAllGapsMenuItem = new MenuItem();
3110
3111   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3112
3113   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3114
3115   MenuItem sortPairwiseMenuItem = new MenuItem();
3116
3117   MenuItem sortIDMenuItem = new MenuItem();
3118
3119   MenuItem sortLengthMenuItem = new MenuItem();
3120
3121   MenuItem sortGroupMenuItem = new MenuItem();
3122
3123   MenuItem removeRedundancyMenuItem = new MenuItem();
3124
3125   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3126
3127   MenuItem PCAMenuItem = new MenuItem();
3128
3129   MenuItem averageDistanceTreeMenuItem = new MenuItem();
3130
3131   MenuItem neighbourTreeMenuItem = new MenuItem();
3132
3133   BorderLayout borderLayout1 = new BorderLayout();
3134
3135   public Label statusBar = new Label();
3136
3137   MenuItem clustalColour = new MenuItem();
3138
3139   MenuItem zappoColour = new MenuItem();
3140
3141   MenuItem taylorColour = new MenuItem();
3142
3143   MenuItem hydrophobicityColour = new MenuItem();
3144
3145   MenuItem helixColour = new MenuItem();
3146
3147   MenuItem strandColour = new MenuItem();
3148
3149   MenuItem turnColour = new MenuItem();
3150
3151   MenuItem buriedColour = new MenuItem();
3152
3153   MenuItem purinePyrimidineColour = new MenuItem();
3154
3155   // MenuItem RNAInteractionColour = new MenuItem();
3156
3157   MenuItem RNAHelixColour = new MenuItem();
3158
3159   MenuItem userDefinedColour = new MenuItem();
3160
3161   MenuItem PIDColour = new MenuItem();
3162
3163   MenuItem BLOSUM62Colour = new MenuItem();
3164
3165   MenuItem tcoffeeColour = new MenuItem();
3166
3167   MenuItem njTreeBlosumMenuItem = new MenuItem();
3168
3169   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3170
3171   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3172
3173   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3174
3175   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3176
3177   MenuItem alProperties = new MenuItem(
3178           MessageManager.getString("label.alignment_props"));
3179
3180   MenuItem overviewMenuItem = new MenuItem();
3181
3182   MenuItem undoMenuItem = new MenuItem();
3183
3184   MenuItem redoMenuItem = new MenuItem();
3185
3186   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3187
3188   MenuItem noColourmenuItem = new MenuItem();
3189
3190   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3191
3192   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3193
3194   MenuItem findMenuItem = new MenuItem();
3195
3196   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3197
3198   MenuItem nucleotideColour = new MenuItem();
3199
3200   MenuItem deleteGroups = new MenuItem();
3201
3202   MenuItem grpsFromSelection = new MenuItem();
3203
3204   MenuItem createGroup = new MenuItem();
3205
3206   MenuItem unGroup = new MenuItem();
3207
3208   MenuItem delete = new MenuItem();
3209
3210   MenuItem copy = new MenuItem();
3211
3212   MenuItem cut = new MenuItem();
3213
3214   Menu pasteMenu = new Menu();
3215
3216   MenuItem pasteNew = new MenuItem();
3217
3218   MenuItem pasteThis = new MenuItem();
3219
3220   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3221
3222   MenuItem font = new MenuItem();
3223
3224   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3225
3226   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3227
3228   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3229
3230   MenuItem modifyPID = new MenuItem();
3231
3232   MenuItem modifyConservation = new MenuItem();
3233
3234   CheckboxMenuItem autoCalculate = null;
3235
3236   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3237           "Sort Alignment With New Tree", true);
3238
3239   Menu sortByTreeMenu = new Menu();
3240
3241   MenuItem inputText = new MenuItem();
3242
3243   MenuItem documentation = new MenuItem();
3244
3245   MenuItem about = new MenuItem();
3246
3247   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3248
3249   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3250
3251   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3252
3253   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3254
3255   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3256
3257   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3258
3259   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3260
3261   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3262
3263   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3264
3265   /**
3266    * Initialise menus and other items
3267    *
3268    * @throws Exception
3269    */
3270   private void jbInit() throws Exception
3271   {
3272     setMenuBar(alignFrameMenuBar);
3273
3274     /*
3275      * Configure File menu items and actions
3276      */
3277     inputText
3278             .setLabel(MessageManager.getString("label.input_from_textbox"));
3279     inputText.addActionListener(this);
3280     Menu outputTextboxMenu = new Menu(
3281             MessageManager.getString("label.out_to_textbox"));
3282     for (String ff : FileFormats.getInstance().getWritableFormats(true))
3283     {
3284       MenuItem item = new MenuItem(ff);
3285
3286       item.addActionListener(new java.awt.event.ActionListener()
3287       {
3288         @Override
3289         public void actionPerformed(ActionEvent e)
3290         {
3291           outputText_actionPerformed(e);
3292         }
3293       });
3294
3295       outputTextboxMenu.add(item);
3296     }
3297     closeMenuItem.addActionListener(this);
3298     loadApplication.addActionListener(this);
3299     loadTree.addActionListener(this);
3300     loadAnnotations.addActionListener(this);
3301     outputFeatures.addActionListener(this);
3302     outputAnnotations.addActionListener(this);
3303
3304     /*
3305      * Configure Edit menu items and actions
3306      */
3307     undoMenuItem.setEnabled(false);
3308     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3309     undoMenuItem.addActionListener(this);
3310     redoMenuItem.setEnabled(false);
3311     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3312     redoMenuItem.addActionListener(this);
3313     copy.setLabel(MessageManager.getString("action.copy"));
3314     copy.addActionListener(this);
3315     cut.setLabel(MessageManager.getString("action.cut"));
3316     cut.addActionListener(this);
3317     delete.setLabel(MessageManager.getString("action.delete"));
3318     delete.addActionListener(this);
3319     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3320     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3321     pasteNew.addActionListener(this);
3322     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3323     pasteThis.addActionListener(this);
3324     remove2LeftMenuItem
3325             .setLabel(MessageManager.getString("action.remove_left"));
3326     remove2LeftMenuItem.addActionListener(this);
3327     remove2RightMenuItem
3328             .setLabel(MessageManager.getString("action.remove_right"));
3329     remove2RightMenuItem.addActionListener(this);
3330     removeGappedColumnMenuItem.setLabel(
3331             MessageManager.getString("action.remove_empty_columns"));
3332     removeGappedColumnMenuItem.addActionListener(this);
3333     removeAllGapsMenuItem
3334             .setLabel(MessageManager.getString("action.remove_all_gaps"));
3335     removeAllGapsMenuItem.addActionListener(this);
3336     removeRedundancyMenuItem
3337             .setLabel(MessageManager.getString("action.remove_redundancy"));
3338     removeRedundancyMenuItem.addActionListener(this);
3339
3340     /*
3341      * Configure Select menu items and actions
3342      */
3343     findMenuItem.setLabel(MessageManager.getString("action.find"));
3344     findMenuItem.addActionListener(this);
3345     selectAllSequenceMenuItem.addActionListener(this);
3346     deselectAllSequenceMenuItem.addActionListener(this);
3347     invertSequenceMenuItem.setLabel(
3348             MessageManager.getString("action.invert_sequence_selection"));
3349     invertSequenceMenuItem.addActionListener(this);
3350     invertColSel.setLabel(
3351             MessageManager.getString("action.invert_column_selection"));
3352     invertColSel.addActionListener(this);
3353     deleteGroups
3354             .setLabel(MessageManager.getString("action.undefine_groups"));
3355     deleteGroups.addActionListener(this);
3356     grpsFromSelection.setLabel(
3357             MessageManager.getString("action.make_groups_selection"));
3358     grpsFromSelection.addActionListener(this);
3359     createGroup.setLabel(MessageManager.getString("action.create_group"));
3360     createGroup.addActionListener(this);
3361     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3362     unGroup.addActionListener(this);
3363
3364     annotationColumnSelection.setLabel(
3365             MessageManager.getString("action.select_by_annotation"));
3366     annotationColumnSelection.addActionListener(this);
3367
3368     /*
3369      * Configure View menu items and actions
3370      */
3371     newView.setLabel(MessageManager.getString("action.new_view"));
3372     newView.addActionListener(this);
3373     Menu showMenu = new Menu(MessageManager.getString("action.show"));
3374     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3375     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3376     Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3377     hideColumns
3378             .setLabel(MessageManager.getString("label.selected_columns"));
3379     hideSequences
3380             .setLabel(MessageManager.getString("label.selected_sequences"));
3381     hideAllButSelection.setLabel(
3382             MessageManager.getString("label.all_but_selected_region"));
3383     hideAllSelection
3384             .setLabel(MessageManager.getString("label.selected_region"));
3385     showAllHidden.setLabel(
3386             MessageManager.getString("label.all_sequences_columns"));
3387     showColumns.addActionListener(this);
3388     showSeqs.addActionListener(this);
3389     hideColumns.addActionListener(this);
3390     hideSequences.addActionListener(this);
3391     hideAllButSelection.addActionListener(this);
3392     hideAllSelection.addActionListener(this);
3393     showAllHidden.addActionListener(this);
3394     featureSettings
3395             .setLabel(MessageManager.getString("action.feature_settings"));
3396     featureSettings.addActionListener(this);
3397     sequenceFeatures.setLabel(
3398             MessageManager.getString("label.show_sequence_features"));
3399     sequenceFeatures.addItemListener(this);
3400     sequenceFeatures.setState(false);
3401     followMouseOverFlag.setLabel(
3402             MessageManager.getString("label.automatic_scrolling"));
3403     followMouseOverFlag.addItemListener(this);
3404     alProperties.addActionListener(this);
3405     overviewMenuItem
3406             .setLabel(MessageManager.getString("label.overview_window"));
3407     overviewMenuItem.addActionListener(this);
3408
3409     /*
3410      * Configure Annotations menu items and actions
3411      */
3412     annotationPanelMenuItem
3413             .setLabel(MessageManager.getString("label.show_annotations"));
3414     annotationPanelMenuItem.addItemListener(this);
3415     showGroupConsensus
3416             .setLabel(MessageManager.getString("label.group_consensus"));
3417     showGroupConservation
3418             .setLabel(MessageManager.getString("label.group_conservation"));
3419     showConsensusHistogram.setLabel(
3420             MessageManager.getString("label.show_consensus_histogram"));
3421     showSequenceLogo.setLabel(
3422             MessageManager.getString("label.show_consensus_logo"));
3423     normSequenceLogo.setLabel(
3424             MessageManager.getString("label.norm_consensus_logo"));
3425     applyAutoAnnotationSettings
3426             .setLabel(MessageManager.getString("label.apply_all_groups"));
3427     applyAutoAnnotationSettings.setState(true);
3428     Menu autoAnnMenu = new Menu(
3429             MessageManager.getString("label.autocalculated_annotation"));
3430     showGroupConsensus.addItemListener(this);
3431     showGroupConservation.addItemListener(this);
3432     showConsensusHistogram.addItemListener(this);
3433     showSequenceLogo.addItemListener(this);
3434     normSequenceLogo.addItemListener(this);
3435     applyAutoAnnotationSettings.addItemListener(this);
3436     showAlignmentAnnotations = new CheckboxMenuItem(
3437             MessageManager.getString("label.show_all_al_annotations"));
3438     showSequenceAnnotations = new CheckboxMenuItem(
3439             MessageManager.getString("label.show_all_seq_annotations"));
3440     sortAnnBySequence = new CheckboxMenuItem(
3441             MessageManager.getString("label.sort_annotations_by_sequence"));
3442     sortAnnByLabel = new CheckboxMenuItem(
3443             MessageManager.getString("label.sort_annotations_by_label"));
3444     showAutoFirst = new CheckboxMenuItem(
3445             MessageManager.getString("label.show_first"));
3446     showAutoFirst.setState(false); // pending applet parameter
3447     setShowAutoCalculatedAbove(showAutoFirst.getState());
3448     showAutoLast = new CheckboxMenuItem(
3449             MessageManager.getString("label.show_last"));
3450     showAutoLast.setState(!showAutoFirst.getState());
3451     showAlignmentAnnotations.addItemListener(this);
3452     showSequenceAnnotations.addItemListener(this);
3453     sortAnnBySequence.addItemListener(this);
3454     sortAnnByLabel.addItemListener(this);
3455     showAutoFirst.addItemListener(this);
3456     showAutoLast.addItemListener(this);
3457
3458     /*
3459      * Configure Format menu items and actions
3460      */
3461     font.setLabel(MessageManager.getString("action.font"));
3462     font.addActionListener(this);
3463     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3464     scaleAbove.setState(true);
3465     scaleAbove.setEnabled(false);
3466     scaleAbove.addItemListener(this);
3467     scaleLeft.setEnabled(false);
3468     scaleLeft.setState(true);
3469     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3470     scaleLeft.addItemListener(this);
3471     scaleRight.setEnabled(false);
3472     scaleRight.setState(true);
3473     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3474     scaleRight.addItemListener(this);
3475     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3476     viewBoxesMenuItem.setState(true);
3477     viewBoxesMenuItem.addItemListener(this);
3478     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3479     viewTextMenuItem.setState(true);
3480     viewTextMenuItem.addItemListener(this);
3481     colourTextMenuItem
3482             .setLabel(MessageManager.getString("label.colour_text"));
3483     colourTextMenuItem.addItemListener(this);
3484     displayNonconservedMenuItem
3485             .setLabel(MessageManager.getString("label.show_non_conserved"));
3486     displayNonconservedMenuItem.addItemListener(this);
3487     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3488     wrapMenuItem.addItemListener(this);
3489     renderGapsMenuItem
3490             .setLabel(MessageManager.getString("action.show_gaps"));
3491     renderGapsMenuItem.setState(true);
3492     renderGapsMenuItem.addItemListener(this);
3493     centreColumnLabelFlag.setLabel(
3494             MessageManager.getString("label.centre_column_labels"));
3495     centreColumnLabelFlag.addItemListener(this);
3496     seqLimits.setState(true);
3497     seqLimits.setLabel(
3498             MessageManager.getString("label.show_sequence_limits"));
3499     seqLimits.addItemListener(this);
3500
3501     /*
3502      * Configure Colour menu items and actions
3503      */
3504     applyToAllGroups.setLabel(
3505             MessageManager.getString("label.apply_colour_to_all_groups"));
3506     applyToAllGroups.setState(true);
3507     applyToAllGroups.addItemListener(this);
3508     clustalColour.setLabel(
3509             MessageManager.getString("label.colourScheme_clustal"));
3510     clustalColour.addActionListener(this);
3511     zappoColour
3512             .setLabel(MessageManager.getString("label.colourScheme_zappo"));
3513     zappoColour.addActionListener(this);
3514     taylorColour.setLabel(
3515             MessageManager.getString("label.colourScheme_taylor"));
3516     taylorColour.addActionListener(this);
3517     hydrophobicityColour.setLabel(
3518             MessageManager.getString("label.colourScheme_hydrophobic"));
3519     hydrophobicityColour.addActionListener(this);
3520     helixColour.setLabel(MessageManager
3521             .getString("label.colourScheme_helix_propensity"));
3522     helixColour.addActionListener(this);
3523     strandColour.setLabel(MessageManager
3524             .getString("label.colourScheme_strand_propensity"));
3525     strandColour.addActionListener(this);
3526     turnColour.setLabel(
3527             MessageManager.getString("label.colourScheme_turn_propensity"));
3528     turnColour.addActionListener(this);
3529     buriedColour.setLabel(
3530             MessageManager.getString("label.colourScheme_buried_index"));
3531     buriedColour.addActionListener(this);
3532     purinePyrimidineColour.setLabel(MessageManager
3533             .getString("label.colourScheme_purine/pyrimidine"));
3534     purinePyrimidineColour.addActionListener(this);
3535     // RNAInteractionColour.setLabel(MessageManager
3536     // .getString("label.rna_interaction"));
3537     // RNAInteractionColour.addActionListener(this);
3538     RNAHelixColour.setLabel(
3539             MessageManager.getString("label.colourScheme_rna_helices"));
3540     RNAHelixColour.addActionListener(this);
3541     userDefinedColour
3542             .setLabel(MessageManager.getString("action.user_defined"));
3543     userDefinedColour.addActionListener(this);
3544     PIDColour.setLabel(
3545             MessageManager.getString("label.colourScheme_%_identity"));
3546     PIDColour.addActionListener(this);
3547     BLOSUM62Colour.setLabel(
3548             MessageManager.getString("label.colourScheme_blosum62"));
3549     BLOSUM62Colour.addActionListener(this);
3550     tcoffeeColour.setLabel(
3551             MessageManager.getString("label.colourScheme_t-coffee_scores"));
3552     // it will be enabled only if a score file is provided
3553     tcoffeeColour.setEnabled(false);
3554     tcoffeeColour.addActionListener(this);
3555     conservationMenuItem
3556             .setLabel(MessageManager.getString("action.by_conservation"));
3557     conservationMenuItem.addItemListener(this);
3558     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3559     noColourmenuItem.addActionListener(this);
3560     abovePIDThreshold.setLabel(
3561             MessageManager.getString("label.above_identity_threshold"));
3562     abovePIDThreshold.addItemListener(this);
3563     nucleotideColour.setLabel(
3564             MessageManager.getString("label.colourScheme_nucleotide"));
3565     nucleotideColour.addActionListener(this);
3566     modifyPID.setLabel(
3567             MessageManager.getString("label.modify_identity_threshold"));
3568     modifyPID.setEnabled(abovePIDThreshold.getState());
3569     modifyPID.addActionListener(this);
3570     modifyConservation.setLabel(MessageManager
3571             .getString("label.modify_conservation_threshold"));
3572     modifyConservation.setEnabled(conservationMenuItem.getState());
3573     modifyConservation.addActionListener(this);
3574     annotationColour
3575             .setLabel(MessageManager.getString("action.by_annotation"));
3576     annotationColour.addActionListener(this);
3577
3578     /*
3579      * Configure Calculate menu items and actions
3580      */
3581     sortPairwiseMenuItem
3582             .setLabel(MessageManager.getString("action.by_pairwise_id"));
3583     sortPairwiseMenuItem.addActionListener(this);
3584     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3585     sortIDMenuItem.addActionListener(this);
3586     sortLengthMenuItem
3587             .setLabel(MessageManager.getString("action.by_length"));
3588     sortLengthMenuItem.addActionListener(this);
3589     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3590     sortGroupMenuItem.addActionListener(this);
3591     pairwiseAlignmentMenuItem.setLabel(
3592             MessageManager.getString("action.pairwise_alignment"));
3593     pairwiseAlignmentMenuItem.addActionListener(this);
3594     PCAMenuItem.setLabel(
3595             MessageManager.getString("label.principal_component_analysis"));
3596     PCAMenuItem.addActionListener(this);
3597     autoCalculate = new CheckboxMenuItem(
3598             MessageManager.getString("label.autocalculate_consensus"),
3599             true);
3600     averageDistanceTreeMenuItem.setLabel(
3601             MessageManager.getString("label.average_distance_identity"));
3602     averageDistanceTreeMenuItem.addActionListener(this);
3603     neighbourTreeMenuItem.setLabel(
3604             MessageManager.getString("label.neighbour_joining_identity"));
3605     neighbourTreeMenuItem.addActionListener(this);
3606     avDistanceTreeBlosumMenuItem.setLabel(
3607             MessageManager.getString("label.average_distance_blosum62"));
3608     avDistanceTreeBlosumMenuItem.addActionListener(this);
3609     njTreeBlosumMenuItem
3610             .setLabel(MessageManager.getString("label.neighbour_blosum62"));
3611     njTreeBlosumMenuItem.addActionListener(this);
3612     sortByTreeMenu
3613             .setLabel(MessageManager.getString("action.by_tree_order"));
3614     Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3615     Menu calculateTreeMenu = new Menu(
3616             MessageManager.getString("action.calculate_tree"));
3617     autoCalculate.addItemListener(this);
3618     sortByTree.addItemListener(this);
3619
3620     /*
3621      * Configure Help menu items and actions
3622      */
3623     Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3624     documentation.setLabel(MessageManager.getString("label.documentation"));
3625     documentation.addActionListener(this);
3626     about.setLabel(MessageManager.getString("label.about"));
3627     about.addActionListener(this);
3628
3629     /*
3630      * Add top level menus to frame
3631      */
3632     alignFrameMenuBar.add(fileMenu);
3633     Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3634     alignFrameMenuBar.add(editMenu);
3635     Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3636     alignFrameMenuBar.add(selectMenu);
3637     Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3638     alignFrameMenuBar.add(viewMenu);
3639     Menu annotationsMenu = new Menu(
3640             MessageManager.getString("action.annotations"));
3641     alignFrameMenuBar.add(annotationsMenu);
3642     Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3643     alignFrameMenuBar.add(formatMenu);
3644     Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3645     alignFrameMenuBar.add(colourMenu);
3646     Menu calculateMenu = new Menu(
3647             MessageManager.getString("action.calculate"));
3648     alignFrameMenuBar.add(calculateMenu);
3649     alignFrameMenuBar.add(helpMenu);
3650
3651     /*
3652      * File menu
3653      */
3654     fileMenu.add(inputText);
3655     fileMenu.add(loadTree);
3656     fileMenu.add(loadAnnotations);
3657     fileMenu.addSeparator();
3658     fileMenu.add(outputTextboxMenu);
3659     fileMenu.add(outputFeatures);
3660     fileMenu.add(outputAnnotations);
3661     if (jalviewServletURL != null)
3662     {
3663       fileMenu.add(loadApplication);
3664     }
3665     fileMenu.addSeparator();
3666     fileMenu.add(closeMenuItem);
3667
3668     /*
3669      * Edit menu
3670      */
3671     editMenu.add(undoMenuItem);
3672     editMenu.add(redoMenuItem);
3673     editMenu.add(cut);
3674     editMenu.add(copy);
3675     pasteMenu.add(pasteNew);
3676     pasteMenu.add(pasteThis);
3677     editMenu.add(pasteMenu);
3678     editMenu.add(delete);
3679     editMenu.addSeparator();
3680     editMenu.add(remove2LeftMenuItem);
3681     editMenu.add(remove2RightMenuItem);
3682     editMenu.add(removeGappedColumnMenuItem);
3683     editMenu.add(removeAllGapsMenuItem);
3684     editMenu.add(removeRedundancyMenuItem);
3685
3686     /*
3687      * Select menu
3688      */
3689     selectMenu.add(findMenuItem);
3690     selectMenu.addSeparator();
3691     selectMenu.add(selectAllSequenceMenuItem);
3692     selectMenu.add(deselectAllSequenceMenuItem);
3693     selectMenu.add(invertSequenceMenuItem);
3694     selectMenu.add(invertColSel);
3695     selectMenu.add(createGroup);
3696     selectMenu.add(unGroup);
3697     selectMenu.add(grpsFromSelection);
3698     selectMenu.add(deleteGroups);
3699     selectMenu.add(annotationColumnSelection);
3700
3701     /*
3702      * View menu
3703      */
3704     viewMenu.add(newView);
3705     viewMenu.addSeparator();
3706     showMenu.add(showColumns);
3707     showMenu.add(showSeqs);
3708     showMenu.add(showAllHidden);
3709     viewMenu.add(showMenu);
3710     hideMenu.add(hideColumns);
3711     hideMenu.add(hideSequences);
3712     hideMenu.add(hideAllSelection);
3713     hideMenu.add(hideAllButSelection);
3714     viewMenu.add(hideMenu);
3715     viewMenu.addSeparator();
3716     viewMenu.add(followMouseOverFlag);
3717     viewMenu.addSeparator();
3718     viewMenu.add(sequenceFeatures);
3719     viewMenu.add(featureSettings);
3720     viewMenu.addSeparator();
3721     viewMenu.add(alProperties);
3722     viewMenu.addSeparator();
3723     viewMenu.add(overviewMenuItem);
3724
3725     /*
3726      * Annotations menu
3727      */
3728     annotationsMenu.add(annotationPanelMenuItem);
3729     annotationsMenu.addSeparator();
3730     annotationsMenu.add(showAlignmentAnnotations);
3731     annotationsMenu.add(showSequenceAnnotations);
3732     annotationsMenu.add(sortAnnBySequence);
3733     annotationsMenu.add(sortAnnByLabel);
3734     annotationsMenu.addSeparator();
3735     autoAnnMenu.add(showAutoFirst);
3736     autoAnnMenu.add(showAutoLast);
3737     autoAnnMenu.addSeparator();
3738     autoAnnMenu.add(applyAutoAnnotationSettings);
3739     autoAnnMenu.add(showConsensusHistogram);
3740     autoAnnMenu.add(showSequenceLogo);
3741     autoAnnMenu.add(normSequenceLogo);
3742     autoAnnMenu.addSeparator();
3743     autoAnnMenu.add(showGroupConservation);
3744     autoAnnMenu.add(showGroupConsensus);
3745     annotationsMenu.add(autoAnnMenu);
3746
3747     /*
3748      * Format menu
3749      */
3750     formatMenu.add(font);
3751     formatMenu.add(seqLimits);
3752     formatMenu.add(wrapMenuItem);
3753     formatMenu.add(scaleAbove);
3754     formatMenu.add(scaleLeft);
3755     formatMenu.add(scaleRight);
3756     formatMenu.add(viewBoxesMenuItem);
3757     formatMenu.add(viewTextMenuItem);
3758     formatMenu.add(colourTextMenuItem);
3759     formatMenu.add(displayNonconservedMenuItem);
3760     formatMenu.add(renderGapsMenuItem);
3761     formatMenu.add(centreColumnLabelFlag);
3762
3763     /*
3764      * Colour menu
3765      */
3766     colourMenu.add(applyToAllGroups);
3767     colourMenu.addSeparator();
3768     colourMenu.add(noColourmenuItem);
3769     colourMenu.add(clustalColour);
3770     colourMenu.add(BLOSUM62Colour);
3771     colourMenu.add(PIDColour);
3772     colourMenu.add(zappoColour);
3773     colourMenu.add(taylorColour);
3774     colourMenu.add(hydrophobicityColour);
3775     colourMenu.add(helixColour);
3776     colourMenu.add(strandColour);
3777     colourMenu.add(turnColour);
3778     colourMenu.add(buriedColour);
3779     colourMenu.add(nucleotideColour);
3780     colourMenu.add(purinePyrimidineColour);
3781     // colourMenu.add(RNAInteractionColour);
3782     colourMenu.add(tcoffeeColour);
3783     colourMenu.add(userDefinedColour);
3784     colourMenu.addSeparator();
3785     colourMenu.add(conservationMenuItem);
3786     colourMenu.add(modifyConservation);
3787     colourMenu.add(abovePIDThreshold);
3788     colourMenu.add(modifyPID);
3789     colourMenu.add(annotationColour);
3790     colourMenu.add(RNAHelixColour);
3791
3792     /*
3793      * Calculate menu
3794      */
3795     sortMenu.add(sortIDMenuItem);
3796     sortMenu.add(sortLengthMenuItem);
3797     sortMenu.add(sortByTreeMenu);
3798     sortMenu.add(sortGroupMenuItem);
3799     sortMenu.add(sortPairwiseMenuItem);
3800     calculateMenu.add(sortMenu);
3801     calculateTreeMenu.add(averageDistanceTreeMenuItem);
3802     calculateTreeMenu.add(neighbourTreeMenuItem);
3803     calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3804     calculateTreeMenu.add(njTreeBlosumMenuItem);
3805     calculateMenu.add(calculateTreeMenu);
3806     calculateMenu.addSeparator();
3807     calculateMenu.add(pairwiseAlignmentMenuItem);
3808     calculateMenu.add(PCAMenuItem);
3809     calculateMenu.add(autoCalculate);
3810     calculateMenu.add(sortByTree);
3811
3812     /*
3813      * Help menu
3814      */
3815     helpMenu.add(documentation);
3816     helpMenu.add(about);
3817
3818     /*
3819      * Status bar
3820      */
3821     statusBar.setBackground(Color.white);
3822     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3823     setStatus(MessageManager.getString("label.status_bar"));
3824     this.add(statusBar, BorderLayout.SOUTH);
3825   }
3826
3827   @Override
3828   public void setStatus(String string)
3829   {
3830     statusBar.setText(string);
3831   };
3832
3833   MenuItem featureSettings = new MenuItem();
3834
3835   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3836
3837   MenuItem annotationColour = new MenuItem();
3838
3839   MenuItem annotationColumnSelection = new MenuItem();
3840
3841   MenuItem invertColSel = new MenuItem();
3842
3843   MenuItem showColumns = new MenuItem();
3844
3845   MenuItem showSeqs = new MenuItem();
3846
3847   MenuItem hideColumns = new MenuItem();
3848
3849   MenuItem hideSequences = new MenuItem();
3850
3851   MenuItem hideAllButSelection = new MenuItem();
3852
3853   MenuItem hideAllSelection = new MenuItem();
3854
3855   MenuItem showAllHidden = new MenuItem();
3856
3857   MenuItem newView = new MenuItem();
3858
3859   private CheckboxMenuItem showAlignmentAnnotations;
3860
3861   private CheckboxMenuItem showSequenceAnnotations;
3862
3863   private CheckboxMenuItem sortAnnBySequence;
3864
3865   private CheckboxMenuItem sortAnnByLabel;
3866
3867   private CheckboxMenuItem showAutoFirst;
3868
3869   private CheckboxMenuItem showAutoLast;
3870
3871   private SplitFrame splitFrame;
3872
3873   /**
3874    * Attach the alignFrame panels after embedding menus, if necessary. This used
3875    * to be called setEmbedded, but is now creates the dropdown menus in a
3876    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3877    *
3878    * @param reallyEmbedded
3879    *          true to attach the view to the applet area on the page rather than
3880    *          in a new window
3881    */
3882   public void createAlignFrameWindow(boolean reallyEmbedded)
3883   {
3884     if (reallyEmbedded)
3885     {
3886       embedAlignFrameInApplet(viewport.applet);
3887     }
3888     else
3889     {
3890       // //////
3891       // test and embed menu bar if necessary.
3892       //
3893       if (embedMenuIfNeeded(alignPanel))
3894       {
3895         /*
3896          * adjust for status bar height too. ? pointless as overridden by layout
3897          * manager
3898          */
3899         alignPanel.setSize(getSize().width,
3900                 getSize().height - statusBar.getHeight());
3901       }
3902       add(statusBar, BorderLayout.SOUTH);
3903       add(alignPanel, BorderLayout.CENTER);
3904       // and register with the applet so it can pass external API calls to us
3905       jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3906               frameHeight);
3907     }
3908   }
3909
3910   /**
3911    * Add the components of this AlignFrame to the applet container.
3912    *
3913    * @param theApplet
3914    */
3915   public void embedAlignFrameInApplet(final JalviewLite theApplet)
3916   {
3917     // ////
3918     // Explicitly build the embedded menu panel for the on-page applet
3919     //
3920     // view cannot be closed if its actually on the page
3921     fileMenu.remove(closeMenuItem);
3922     fileMenu.remove(3); // Remove Separator
3923     // construct embedded menu, using default font
3924     embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3925     // and actually add the components to the applet area
3926     theApplet.setLayout(new BorderLayout());
3927     theApplet.add(embeddedMenu, BorderLayout.NORTH);
3928     theApplet.add(statusBar, BorderLayout.SOUTH);
3929     // TODO should size be left to the layout manager?
3930     alignPanel.setSize(theApplet.getSize().width, theApplet.getSize().height
3931             - embeddedMenu.getHeight() - statusBar.getHeight());
3932     theApplet.add(alignPanel, BorderLayout.CENTER);
3933     final AlignFrame me = this;
3934     theApplet.addFocusListener(new FocusListener()
3935     {
3936
3937       @Override
3938       public void focusLost(FocusEvent e)
3939       {
3940         if (theApplet.currentAlignFrame == me)
3941         {
3942           theApplet.currentAlignFrame = null;
3943         }
3944       }
3945
3946       @Override
3947       public void focusGained(FocusEvent e)
3948       {
3949         theApplet.currentAlignFrame = me;
3950       }
3951     });
3952     theApplet.validate();
3953   }
3954
3955   /**
3956    * create a new binding between structures in an existing jmol viewer instance
3957    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3958    * this does not open a new Jmol window, or modify the display of the
3959    * structures in the original jmol window. Note This method doesn't work
3960    * without an additional javascript library to exchange messages between the
3961    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3962    *
3963    * @param viewer
3964    *          JmolViewer instance
3965    * @param sequenceIds
3966    *          - sequence Ids to search for associations
3967    */
3968   public SequenceStructureBinding addStructureViewInstance(
3969           Object jmolviewer, String[] sequenceIds)
3970   {
3971     Viewer viewer = null;
3972     try
3973     {
3974       viewer = (Viewer) jmolviewer;
3975     } catch (ClassCastException ex)
3976     {
3977       System.err.println(
3978               "Unsupported viewer object :" + jmolviewer.getClass());
3979     }
3980     if (viewer == null)
3981     {
3982       System.err.println("Can't use this object as a structure viewer:"
3983               + jmolviewer.getClass());
3984       return null;
3985     }
3986     SequenceI[] seqs = null;
3987     if (sequenceIds == null || sequenceIds.length == 0)
3988     {
3989       seqs = viewport.getAlignment().getSequencesArray();
3990     }
3991     else
3992     {
3993       Vector sqi = new Vector();
3994       AlignmentI al = viewport.getAlignment();
3995       for (int sid = 0; sid < sequenceIds.length; sid++)
3996       {
3997         SequenceI sq = al.findName(sequenceIds[sid]);
3998         if (sq != null)
3999         {
4000           sqi.addElement(sq);
4001         }
4002       }
4003       if (sqi.size() > 0)
4004       {
4005         seqs = new SequenceI[sqi.size()];
4006         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4007         {
4008           seqs[sid] = (SequenceI) sqi.elementAt(sid);
4009         }
4010       }
4011       else
4012       {
4013         return null;
4014       }
4015     }
4016     AAStructureBindingModel jmv = null;
4017     // TODO: search for a jmv that involves viewer
4018     if (jmv == null)
4019     { // create a new viewer/jalview binding.
4020       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4021     }
4022     return jmv;
4023
4024   }
4025
4026   /**
4027    * bind a pdb file to a sequence in the current view
4028    *
4029    * @param sequenceId
4030    *          - sequenceId within the dataset.
4031    * @param pdbEntryString
4032    *          - the short name for the PDB file
4033    * @param pdbFile
4034    *          - pdb file - either a URL or a valid PDB file.
4035    * @return true if binding was as success TODO: consider making an exception
4036    *         structure for indicating when PDB parsing or sequenceId location
4037    *         fails.
4038    */
4039   public boolean addPdbFile(String sequenceId, String pdbEntryString,
4040           String pdbFile)
4041   {
4042     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4043     boolean needtoadd = false;
4044     if (toaddpdb != null)
4045     {
4046       Vector pdbe = toaddpdb.getAllPDBEntries();
4047       PDBEntry pdbentry = null;
4048       if (pdbe != null && pdbe.size() > 0)
4049       {
4050         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4051         {
4052           pdbentry = (PDBEntry) pdbe.elementAt(pe);
4053           if (!pdbentry.getId().equals(pdbEntryString)
4054                   && !pdbentry.getFile().equals(pdbFile))
4055           {
4056             pdbentry = null;
4057           }
4058           else
4059           {
4060             continue;
4061           }
4062         }
4063       }
4064       if (pdbentry == null)
4065       {
4066         pdbentry = new PDBEntry();
4067         pdbentry.setId(pdbEntryString);
4068         pdbentry.setFile(pdbFile);
4069         needtoadd = true; // add this new entry to sequence.
4070       }
4071       // resolve data source
4072       // TODO: this code should be a refactored to an io package
4073       DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile,
4074               FileFormat.PDB);
4075       if (protocol == null)
4076       {
4077         return false;
4078       }
4079       if (needtoadd)
4080       {
4081         pdbentry.setProperty("protocol", protocol);
4082         toaddpdb.addPDBId(pdbentry);
4083         alignPanel.getStructureSelectionManager()
4084                 .registerPDBEntry(pdbentry);
4085       }
4086     }
4087     return true;
4088   }
4089
4090   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4091   {
4092     if (seqs != null)
4093     {
4094       Vector sequences = new Vector();
4095       for (int i = 0; i < seqs.length; i++)
4096       {
4097         if (seqs[i] != null)
4098         {
4099           sequences
4100                   .addElement(new Object[]
4101                   { seqs[i], (chains != null) ? chains[i] : null });
4102         }
4103       }
4104       seqs = new SequenceI[sequences.size()];
4105       chains = new String[sequences.size()];
4106       for (int i = 0, isize = sequences.size(); i < isize; i++)
4107       {
4108         Object[] oj = (Object[]) sequences.elementAt(i);
4109
4110         seqs[i] = (SequenceI) oj[0];
4111         chains[i] = (String) oj[1];
4112       }
4113     }
4114     return new Object[] { seqs, chains };
4115
4116   }
4117
4118   public void newStructureView(JalviewLite applet, PDBEntry pdb,
4119           SequenceI[] seqs, String[] chains, DataSourceType protocol)
4120   {
4121     // Scrub any null sequences from the array
4122     Object[] sqch = cleanSeqChainArrays(seqs, chains);
4123     seqs = (SequenceI[]) sqch[0];
4124     chains = (String[]) sqch[1];
4125     if (seqs == null || seqs.length == 0)
4126     {
4127       System.err.println(
4128               "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4129     }
4130     if (protocol == null)
4131     {
4132       String sourceType = (String) pdb.getProperty("protocol");
4133       try
4134       {
4135         protocol = DataSourceType.valueOf(sourceType);
4136       } catch (IllegalArgumentException e)
4137       {
4138         // ignore
4139       }
4140       if (protocol == null)
4141       {
4142         System.err.println("Couldn't work out protocol to open structure: "
4143                 + pdb.getId());
4144         return;
4145       }
4146     }
4147     if (applet.useXtrnalSviewer)
4148     {
4149       // register the association(s) and quit, don't create any windows.
4150       if (StructureSelectionManager.getStructureSelectionManager(applet)
4151               .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
4152       {
4153         System.err.println("Failed to map " + pdb.getFile() + " ("
4154                 + protocol + ") to any sequences");
4155       }
4156       return;
4157     }
4158     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4159     {
4160       // can only do alignments with Jmol
4161       // find the last jmol window assigned to this alignment
4162       AppletJmol ajm = null, tajm;
4163       Vector jmols = applet.getAppletWindow(AppletJmol.class);
4164       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4165       {
4166         tajm = (AppletJmol) jmols.elementAt(i);
4167         if (tajm.ap.alignFrame == this)
4168         {
4169           ajm = tajm;
4170           break;
4171         }
4172       }
4173       if (ajm != null)
4174       {
4175         System.err.println(
4176                 "Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4177         // try and add the pdb structure
4178         // ajm.addS
4179         ajm = null;
4180       }
4181     }
4182     // otherwise, create a new window
4183     if (applet.jmolAvailable)
4184     {
4185       new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4186       applet.lastFrameX += 40;
4187       applet.lastFrameY += 40;
4188     }
4189     else
4190     {
4191       new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4192     }
4193
4194   }
4195
4196   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4197           SequenceI[][] seqs, String[][] chains, String[] protocols)
4198   {
4199     // TODO Auto-generated method stub
4200     System.err.println("Aligned Structure View: Not yet implemented.");
4201   }
4202
4203   /**
4204    * modify the current selection, providing the user has not made a selection
4205    * already.
4206    *
4207    * @param sel
4208    *          - sequences from this alignment
4209    * @param csel
4210    *          - columns to be selected on the alignment
4211    */
4212   public void select(SequenceGroup sel, ColumnSelection csel,
4213           HiddenColumns hidden)
4214   {
4215     alignPanel.seqPanel.selection(sel, csel, hidden, null);
4216   }
4217
4218   public void scrollTo(int row, int column)
4219   {
4220     alignPanel.seqPanel.scrollTo(row, column);
4221   }
4222
4223   public void scrollToRow(int row)
4224   {
4225     alignPanel.seqPanel.scrollToRow(row);
4226   }
4227
4228   public void scrollToColumn(int column)
4229   {
4230     alignPanel.seqPanel.scrollToColumn(column);
4231   }
4232
4233   /**
4234    * @return the alignments unique ID.
4235    */
4236   public String getSequenceSetId()
4237   {
4238     return viewport.getSequenceSetId();
4239   }
4240
4241   /**
4242    * Load the (T-Coffee) score file from the specified url
4243    *
4244    * @param source
4245    *          File/URL/T-COFFEE score file contents
4246    * @throws IOException
4247    * @return true if alignment was annotated with data from source
4248    */
4249   public boolean loadScoreFile(String source) throws IOException
4250   {
4251
4252     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4253             AppletFormatAdapter.checkProtocol(source));
4254     if (!file.isValid())
4255     {
4256       // TODO: raise dialog for gui
4257       System.err.println("Problems parsing T-Coffee scores: "
4258               + file.getWarningMessage());
4259       System.err.println("Origin was:\n" + source);
4260       return false;
4261     }
4262
4263     /*
4264      * check that the score matrix matches the alignment dimensions
4265      */
4266     AlignmentI aln;
4267     if ((aln = viewport.getAlignment()) != null
4268             && (aln.getHeight() != file.getHeight()
4269                     || aln.getWidth() != file.getWidth()))
4270     {
4271       // TODO: raise a dialog box here rather than bomb out.
4272       System.err.println(
4273               "The scores matrix does not match the alignment dimensions");
4274
4275     }
4276
4277     // TODO add parameter to indicate if matching should be done
4278     if (file.annotateAlignment(alignPanel.getAlignment(), false))
4279     {
4280       alignPanel.fontChanged();
4281       tcoffeeColour.setEnabled(true);
4282       // switch to this color
4283       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4284       return true;
4285     }
4286     else
4287     {
4288       System.err.println("Problems resolving T-Coffee scores:");
4289       if (file.getWarningMessage() != null)
4290       {
4291         System.err.println(file.getWarningMessage());
4292       }
4293     }
4294     return false;
4295   }
4296
4297   public SplitFrame getSplitFrame()
4298   {
4299     return this.splitFrame;
4300   }
4301
4302   public void setSplitFrame(SplitFrame sf)
4303   {
4304     this.splitFrame = sf;
4305   }
4306
4307   // may not need this
4308   @Override
4309   public void setShowSeqFeatures(boolean b)
4310   {
4311     // showSeqFeatures.setSelected(b);
4312     viewport.setShowSequenceFeatures(b);
4313
4314   }
4315
4316   @Override
4317   public void setMenusForViewport()
4318   {
4319     // setMenusFromViewport(viewport);
4320
4321   }
4322
4323   @Override
4324   public void refreshFeatureUI(boolean enableIfNecessary)
4325   {
4326     if (enableIfNecessary)
4327     {
4328       sequenceFeatures.setState(true);
4329       alignPanel.av.setShowSequenceFeatures(true);
4330     }
4331   }
4332
4333   @Override
4334   public FeatureSettingsControllerI getFeatureSettingsUI()
4335   {
4336     return alignPanel.av.featureSettings;
4337   }
4338
4339   @Override
4340   public FeatureSettingsControllerI showFeatureSettingsUI()
4341   {
4342     return new FeatureSettings(alignPanel);
4343   }
4344
4345   private Rectangle fs_bounds = null;
4346
4347   @Override
4348   public void setFeatureSettingsGeometry(Rectangle bounds)
4349   {
4350     fs_bounds = bounds;
4351   }
4352
4353   @Override
4354   public Rectangle getFeatureSettingsGeometry()
4355   {
4356     return fs_bounds;
4357   }
4358
4359 }