src/jalview/appletgui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.Conservation;
  25 import jalview.api.AlignViewControllerGuiI;
  26 import jalview.api.AlignViewControllerI;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.OrderCommand;
  32 import jalview.commands.RemoveGapColCommand;
  33 import jalview.commands.RemoveGapsCommand;
  34 import jalview.commands.SlideSequencesCommand;
  35 import jalview.commands.TrimRegionCommand;
  36 import jalview.datamodel.Alignment;
  37 import jalview.datamodel.AlignmentI;
  38 import jalview.datamodel.AlignmentOrder;
  39 import jalview.datamodel.ColumnSelection;
  40 import jalview.datamodel.PDBEntry;
  41 import jalview.datamodel.Sequence;
  42 import jalview.datamodel.SequenceGroup;
  43 import jalview.datamodel.SequenceI;
  44 import jalview.io.AnnotationFile;
  45 import jalview.io.AppletFormatAdapter;
  46 import jalview.io.FeaturesFile;
  47 import jalview.io.TCoffeeScoreFile;
  48 import jalview.schemes.Blosum62ColourScheme;
  49 import jalview.schemes.BuriedColourScheme;
  50 import jalview.schemes.ClustalxColourScheme;
  51 import jalview.schemes.ColourSchemeI;
  52 import jalview.schemes.HelixColourScheme;
  53 import jalview.schemes.HydrophobicColourScheme;
  54 import jalview.schemes.NucleotideColourScheme;
  55 import jalview.schemes.PIDColourScheme;
  56 import jalview.schemes.PurinePyrimidineColourScheme;
  57 import jalview.schemes.RNAHelicesColourChooser;
  58 import jalview.schemes.RNAInteractionColourScheme;
  59 import jalview.schemes.ResidueProperties;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.util.MessageManager;
  67
  68 import java.awt.BorderLayout;
  69 import java.awt.Canvas;
  70 import java.awt.CheckboxMenuItem;
  71 import java.awt.Color;
  72 import java.awt.Font;
  73 import java.awt.FontMetrics;
  74 import java.awt.Frame;
  75 import java.awt.Graphics;
  76 import java.awt.Label;
  77 import java.awt.Menu;
  78 import java.awt.MenuBar;
  79 import java.awt.MenuItem;
  80 import java.awt.event.ActionEvent;
  81 import java.awt.event.ActionListener;
  82 import java.awt.event.FocusEvent;
  83 import java.awt.event.FocusListener;
  84 import java.awt.event.ItemEvent;
  85 import java.awt.event.ItemListener;
  86 import java.awt.event.KeyEvent;
  87 import java.awt.event.KeyListener;
  88 import java.awt.event.WindowAdapter;
  89 import java.awt.event.WindowEvent;
  90 import java.io.IOException;
  91 import java.net.URL;
  92 import java.net.URLEncoder;
  93 import java.util.Enumeration;
  94 import java.util.Hashtable;
  95 import java.util.List;
  96 import java.util.StringTokenizer;
  97 import java.util.Vector;
  98
  99 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 100         ItemListener, KeyListener, AlignViewControllerGuiI
 101 {
 102   public AlignViewControllerI avc;
 103
 104   public AlignmentPanel alignPanel;
 105
 106   public AlignViewport viewport;
 107
 108   int DEFAULT_WIDTH = 700;
 109
 110   int DEFAULT_HEIGHT = 500;
 111
 112   String jalviewServletURL;
 113
 114   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 115           String title, boolean embedded)
 116   {
 117     if (applet != null)
 118     {
 119       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 120     }
 121
 122     try
 123     {
 124       jbInit();
 125     } catch (Exception ex)
 126     {
 127       ex.printStackTrace();
 128     }
 129     // need to get window geometry before we calculate alignment layout
 130     if (applet != null)
 131     {
 132       String param;
 133       try
 134       {
 135         param = applet.getParameter("windowWidth");
 136         if (param != null)
 137         {
 138           int width = Integer.parseInt(param);
 139           DEFAULT_WIDTH = width;
 140         }
 141         param = applet.getParameter("windowHeight");
 142         if (param != null)
 143         {
 144           int height = Integer.parseInt(param);
 145           DEFAULT_HEIGHT = height;
 146         }
 147       } catch (Exception ex)
 148       {
 149       }
 150     }
 151     viewport = new AlignViewport(al, applet);
 152     alignPanel = new AlignmentPanel(this, viewport);
 153     avc = new jalview.controller.AlignViewController(this, viewport,
 154             alignPanel);
 155     viewport.updateConservation(alignPanel);
 156     viewport.updateConsensus(alignPanel);
 157
 158     annotationPanelMenuItem.setState(viewport.showAnnotation);
 159     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 160     followMouseOverFlag.setState(viewport.getFollowHighlight());
 161     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 162     showGroupConservation.setState(viewport.isShowGroupConservation());
 163     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 164     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 165     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 166     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 167
 168     seqLimits.setState(viewport.showJVSuffix);
 169
 170     if (applet != null)
 171     {
 172       String param = applet.getParameter("sortBy");
 173       if (param != null)
 174       {
 175         if (param.equalsIgnoreCase("Id"))
 176         {
 177           sortIDMenuItem_actionPerformed();
 178         }
 179         else if (param.equalsIgnoreCase("Pairwise Identity"))
 180         {
 181           sortPairwiseMenuItem_actionPerformed();
 182         }
 183         else if (param.equalsIgnoreCase("Length"))
 184         {
 185           sortLengthMenuItem_actionPerformed();
 186         }
 187       }
 188
 189       param = applet.getParameter("wrap");
 190       if (param != null)
 191       {
 192         if (param.equalsIgnoreCase("true"))
 193         {
 194           wrapMenuItem.setState(true);
 195           wrapMenuItem_actionPerformed();
 196         }
 197       }
 198       param = applet.getParameter("centrecolumnlabels");
 199       if (param != null)
 200       {
 201         centreColumnLabelFlag.setState(true);
 202         centreColumnLabelFlag_stateChanged();
 203       }
 204
 205     }
 206     if (viewport.getAlignment().isNucleotide())
 207     {
 208       viewport.updateStrucConsensus(alignPanel);
 209       if (viewport.getAlignment().hasRNAStructure())
 210       {
 211         RNAHelixColour.setEnabled(true);
 212       }
 213       else
 214       {
 215         RNAHelixColour.setEnabled(false);
 216       }
 217     }
 218     else
 219     {
 220       RNAHelixColour.setEnabled(false);
 221       purinePyrimidineColour.setEnabled(false);
 222     }
 223     // Some JVMS send keyevents to Top frame or lowest panel,
 224     // Havent worked out why yet. So add to both this frame and seqCanvas for
 225     // now
 226     this.addKeyListener(this);
 227     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 228     alignPanel.idPanel.idCanvas.addKeyListener(this);
 229     alignPanel.scalePanel.addKeyListener(this);
 230     alignPanel.annotationPanel.addKeyListener(this);
 231     alignPanel.annotationPanelHolder.addKeyListener(this);
 232     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 233     alignPanel.alabels.addKeyListener(this);
 234     createAlignFrameWindow(embedded, title);
 235
 236     validate();
 237     alignPanel.adjustAnnotationHeight();
 238     alignPanel.paintAlignment(true);
 239   }
 240
 241   public AlignViewport getAlignViewport()
 242   {
 243     return viewport;
 244   }
 245
 246   public SeqCanvas getSeqcanvas()
 247   {
 248     return alignPanel.seqPanel.seqCanvas;
 249   }
 250
 251   /**
 252    * Load a features file onto the alignment
 253    *
 254    * @param file
 255    *          file URL, content, or other resolvable path
 256    * @param type
 257    *          is protocol for accessing data referred to by file
 258    */
 259
 260   public boolean parseFeaturesFile(String file, String type)
 261   {
 262     return parseFeaturesFile(file, type, true);
 263   }
 264
 265   /**
 266    * Load a features file onto the alignment
 267    *
 268    * @param file
 269    *          file URL, content, or other resolvable path
 270    * @param type
 271    *          is protocol for accessing data referred to by file
 272    * @param autoenabledisplay
 273    *          when true, display features flag will be automatically enabled if
 274    *          features are loaded
 275    * @return true if data parsed as a features file
 276    */
 277   public boolean parseFeaturesFile(String file, String type,
 278           boolean autoenabledisplay)
 279   {
 280     // TODO: test if importing a features file onto an alignment which already
 281     // has features with links overwrites the original links.
 282
 283     Hashtable featureLinks = new Hashtable();
 284     boolean featuresFile = false;
 285     try
 286     {
 287       featuresFile = new jalview.io.FeaturesFile(file, type)
 288               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 289                       .getFeatureRenderer().featureColours, featureLinks,
 290                       true, viewport.applet.getDefaultParameter(
 291                               "relaxedidmatch", false));
 292     } catch (Exception ex)
 293     {
 294       ex.printStackTrace();
 295     }
 296
 297     if (featuresFile)
 298     {
 299       if (featureLinks.size() > 0)
 300       {
 301         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 302       }
 303       if (autoenabledisplay)
 304       {
 305         viewport.showSequenceFeatures = true;
 306         sequenceFeatures.setState(true);
 307       }
 308       if (viewport.featureSettings != null)
 309       {
 310         viewport.featureSettings.refreshTable();
 311       }
 312       alignPanel.paintAlignment(true);
 313       statusBar.setText(MessageManager
 314               .getString("label.successfully_added_features_alignment"));
 315     }
 316     return featuresFile;
 317   }
 318
 319   @Override
 320   public void keyPressed(KeyEvent evt)
 321   {
 322     if (viewport.cursorMode
 323             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 324                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 325                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 326             && Character.isDigit(evt.getKeyChar()))
 327       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 328
 329     switch (evt.getKeyCode())
 330     {
 331     case 27: // escape key
 332       deselectAllSequenceMenuItem_actionPerformed();
 333
 334       alignPanel.alabels.cancelDrag();
 335       break;
 336     case KeyEvent.VK_X:
 337       if (evt.isControlDown() || evt.isMetaDown())
 338       {
 339         cut_actionPerformed();
 340       }
 341       break;
 342     case KeyEvent.VK_C:
 343       if (viewport.cursorMode && !evt.isControlDown())
 344       {
 345         alignPanel.seqPanel.setCursorColumn();
 346       }
 347       if (evt.isControlDown() || evt.isMetaDown())
 348       {
 349         copy_actionPerformed();
 350       }
 351       break;
 352     case KeyEvent.VK_V:
 353       if (evt.isControlDown())
 354       {
 355         paste(evt.isShiftDown());
 356       }
 357       break;
 358     case KeyEvent.VK_A:
 359       if (evt.isControlDown() || evt.isMetaDown())
 360       {
 361         selectAllSequenceMenuItem_actionPerformed();
 362       }
 363       break;
 364     case KeyEvent.VK_DOWN:
 365       if (viewport.cursorMode)
 366       {
 367         alignPanel.seqPanel.moveCursor(0, 1);
 368       }
 369       else
 370       {
 371         moveSelectedSequences(false);
 372       }
 373       break;
 374
 375     case KeyEvent.VK_UP:
 376       if (viewport.cursorMode)
 377       {
 378         alignPanel.seqPanel.moveCursor(0, -1);
 379       }
 380       else
 381       {
 382         moveSelectedSequences(true);
 383       }
 384       break;
 385
 386     case KeyEvent.VK_LEFT:
 387       if (evt.isAltDown() || !viewport.cursorMode)
 388         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 389       else
 390         alignPanel.seqPanel.moveCursor(-1, 0);
 391       break;
 392
 393     case KeyEvent.VK_RIGHT:
 394       if (evt.isAltDown() || !viewport.cursorMode)
 395         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 396       else
 397         alignPanel.seqPanel.moveCursor(1, 0);
 398       break;
 399
 400     case KeyEvent.VK_SPACE:
 401       if (viewport.cursorMode)
 402       {
 403         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 404                 || evt.isShiftDown() || evt.isAltDown());
 405       }
 406       break;
 407
 408     case KeyEvent.VK_DELETE:
 409     case KeyEvent.VK_BACK_SPACE:
 410       if (viewport.cursorMode)
 411       {
 412         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 413                 || evt.isShiftDown() || evt.isAltDown());
 414       }
 415       else
 416       {
 417         cut_actionPerformed();
 418         alignPanel.seqPanel.seqCanvas.repaint();
 419       }
 420       break;
 421
 422     case KeyEvent.VK_S:
 423       if (viewport.cursorMode)
 424       {
 425         alignPanel.seqPanel.setCursorRow();
 426       }
 427       break;
 428     case KeyEvent.VK_P:
 429       if (viewport.cursorMode)
 430       {
 431         alignPanel.seqPanel.setCursorPosition();
 432       }
 433       break;
 434
 435     case KeyEvent.VK_ENTER:
 436     case KeyEvent.VK_COMMA:
 437       if (viewport.cursorMode)
 438       {
 439         alignPanel.seqPanel.setCursorRowAndColumn();
 440       }
 441       break;
 442
 443     case KeyEvent.VK_Q:
 444       if (viewport.cursorMode)
 445       {
 446         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 447       }
 448       break;
 449     case KeyEvent.VK_M:
 450       if (viewport.cursorMode)
 451       {
 452         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 453       }
 454       break;
 455
 456     case KeyEvent.VK_F2:
 457       viewport.cursorMode = !viewport.cursorMode;
 458       statusBar.setText(MessageManager.formatMessage(
 459               "label.keyboard_editing_mode", new String[]
 460               { (viewport.cursorMode ? "on" : "off") }));
 461       if (viewport.cursorMode)
 462       {
 463         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 464         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 465       }
 466       break;
 467
 468     case KeyEvent.VK_F:
 469       if (evt.isControlDown())
 470       {
 471         findMenuItem_actionPerformed();
 472       }
 473       break;
 474
 475     case KeyEvent.VK_H:
 476     {
 477       boolean toggleSeqs = !evt.isControlDown();
 478       boolean toggleCols = !evt.isShiftDown();
 479       toggleHiddenRegions(toggleSeqs, toggleCols);
 480       break;
 481     }
 482
 483     case KeyEvent.VK_PAGE_UP:
 484       if (viewport.wrapAlignment)
 485       {
 486         alignPanel.scrollUp(true);
 487       }
 488       else
 489       {
 490         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 491                 - viewport.endSeq + viewport.startSeq);
 492       }
 493       break;
 494
 495     case KeyEvent.VK_PAGE_DOWN:
 496       if (viewport.wrapAlignment)
 497       {
 498         alignPanel.scrollUp(false);
 499       }
 500       else
 501       {
 502         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 503                 + viewport.endSeq - viewport.startSeq);
 504       }
 505       break;
 506
 507     case KeyEvent.VK_Z:
 508       if (evt.isControlDown())
 509       {
 510         undoMenuItem_actionPerformed();
 511       }
 512       break;
 513
 514     case KeyEvent.VK_Y:
 515       if (evt.isControlDown())
 516       {
 517         redoMenuItem_actionPerformed();
 518       }
 519       break;
 520
 521     case KeyEvent.VK_L:
 522       if (evt.isControlDown())
 523       {
 524         trimAlignment(true);
 525       }
 526       break;
 527
 528     case KeyEvent.VK_R:
 529       if (evt.isControlDown())
 530       {
 531         trimAlignment(false);
 532       }
 533       break;
 534
 535     case KeyEvent.VK_E:
 536       if (evt.isControlDown())
 537       {
 538         if (evt.isShiftDown())
 539         {
 540           this.removeAllGapsMenuItem_actionPerformed();
 541         }
 542         else
 543         {
 544           removeGappedColumnMenuItem_actionPerformed();
 545         }
 546       }
 547       break;
 548     case KeyEvent.VK_I:
 549       if (evt.isControlDown())
 550       {
 551         if (evt.isAltDown())
 552         {
 553           invertColSel_actionPerformed();
 554         }
 555         else
 556         {
 557           invertSequenceMenuItem_actionPerformed();
 558         }
 559       }
 560       break;
 561
 562     case KeyEvent.VK_G:
 563       if (evt.isControlDown())
 564       {
 565         if (evt.isShiftDown())
 566         {
 567           this.unGroup_actionPerformed();
 568         }
 569         else
 570         {
 571           this.createGroup_actionPerformed();
 572         }
 573       }
 574       break;
 575
 576     case KeyEvent.VK_U:
 577       if (evt.isControlDown())
 578       {
 579         this.deleteGroups_actionPerformed();
 580       }
 581       break;
 582
 583     case KeyEvent.VK_T:
 584       if (evt.isControlDown())
 585       {
 586         newView(null);
 587       }
 588       break;
 589
 590     }
 591     alignPanel.paintAlignment(true);
 592   }
 593
 594   /**
 595    * called by key handler and the hide all/show all menu items
 596    *
 597    * @param toggleSeqs
 598    * @param toggleCols
 599    */
 600   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 601   {
 602     boolean hide = false;
 603     SequenceGroup sg = viewport.getSelectionGroup();
 604     if (!toggleSeqs && !toggleCols)
 605     {
 606       // Hide everything by the current selection - this is a hack - we do the
 607       // invert and then hide
 608       // first check that there will be visible columns after the invert.
 609       if ((viewport.getColumnSelection() != null
 610               && viewport.getColumnSelection().getSelected() != null && viewport
 611               .getColumnSelection().getSelected().size() > 0)
 612               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 613                       .getEndRes()))
 614       {
 615         // now invert the sequence set, if required - empty selection implies
 616         // that no hiding is required.
 617         if (sg != null)
 618         {
 619           invertSequenceMenuItem_actionPerformed();
 620           sg = viewport.getSelectionGroup();
 621           toggleSeqs = true;
 622
 623         }
 624         viewport.expandColSelection(sg, true);
 625         // finally invert the column selection and get the new sequence
 626         // selection and indicate it should be hidden.
 627         invertColSel_actionPerformed();
 628         toggleCols = true;
 629       }
 630     }
 631
 632     if (toggleSeqs)
 633     {
 634       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 635       {
 636         hide = true;
 637         viewport.hideAllSelectedSeqs();
 638       }
 639       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 640               .size() > 0))
 641       {
 642         viewport.showAllHiddenSeqs();
 643       }
 644     }
 645
 646     if (toggleCols)
 647     {
 648       if (viewport.getColumnSelection().getSelected().size() > 0)
 649       {
 650         viewport.hideSelectedColumns();
 651         if (!toggleSeqs)
 652         {
 653           viewport.setSelectionGroup(sg);
 654         }
 655       }
 656       else if (!hide)
 657       {
 658         viewport.showAllHiddenColumns();
 659       }
 660     }
 661   }
 662
 663   @Override
 664   public void keyReleased(KeyEvent evt)
 665   {
 666   }
 667
 668   @Override
 669   public void keyTyped(KeyEvent evt)
 670   {
 671   }
 672
 673   @Override
 674   public void itemStateChanged(ItemEvent evt)
 675   {
 676     if (evt.getSource() == displayNonconservedMenuItem)
 677     {
 678       displayNonconservedMenuItem_actionPerformed();
 679     }
 680     else if (evt.getSource() == colourTextMenuItem)
 681     {
 682       colourTextMenuItem_actionPerformed();
 683     }
 684     else if (evt.getSource() == wrapMenuItem)
 685     {
 686       wrapMenuItem_actionPerformed();
 687     }
 688     else if (evt.getSource() == scaleAbove)
 689     {
 690       viewport.setScaleAboveWrapped(scaleAbove.getState());
 691     }
 692     else if (evt.getSource() == scaleLeft)
 693     {
 694       viewport.setScaleLeftWrapped(scaleLeft.getState());
 695     }
 696     else if (evt.getSource() == scaleRight)
 697     {
 698       viewport.setScaleRightWrapped(scaleRight.getState());
 699     }
 700     else if (evt.getSource() == seqLimits)
 701     {
 702       seqLimits_itemStateChanged();
 703     }
 704     else if (evt.getSource() == viewBoxesMenuItem)
 705     {
 706       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 707     }
 708     else if (evt.getSource() == viewTextMenuItem)
 709     {
 710       viewport.setShowText(viewTextMenuItem.getState());
 711     }
 712     else if (evt.getSource() == renderGapsMenuItem)
 713     {
 714       viewport.setRenderGaps(renderGapsMenuItem.getState());
 715     }
 716     else if (evt.getSource() == annotationPanelMenuItem)
 717     {
 718       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 719       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 720     }
 721     else if (evt.getSource() == sequenceFeatures)
 722     {
 723       viewport.showSequenceFeatures(sequenceFeatures.getState());
 724       alignPanel.seqPanel.seqCanvas.repaint();
 725     }
 726     else if (evt.getSource() == conservationMenuItem)
 727     {
 728       conservationMenuItem_actionPerformed();
 729     }
 730     else if (evt.getSource() == abovePIDThreshold)
 731     {
 732       abovePIDThreshold_actionPerformed();
 733     }
 734     else if (evt.getSource() == applyToAllGroups)
 735     {
 736       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 737     }
 738     else if (evt.getSource() == autoCalculate)
 739     {
 740       viewport.autoCalculateConsensus = autoCalculate.getState();
 741     }
 742     else if (evt.getSource() == sortByTree)
 743     {
 744       viewport.sortByTree = sortByTree.getState();
 745     }
 746     else if (evt.getSource() == this.centreColumnLabelFlag)
 747     {
 748       centreColumnLabelFlag_stateChanged();
 749     }
 750     else if (evt.getSource() == this.followMouseOverFlag)
 751     {
 752       mouseOverFlag_stateChanged();
 753     }
 754     else if (evt.getSource() == showGroupConsensus)
 755     {
 756       showGroupConsensus_actionPerformed();
 757     }
 758     else if (evt.getSource() == showGroupConservation)
 759     {
 760       showGroupConservation_actionPerformed();
 761     }
 762     else if (evt.getSource() == showSequenceLogo)
 763     {
 764       showSequenceLogo_actionPerformed();
 765     }
 766     else if (evt.getSource() == normSequenceLogo)
 767     {
 768       normSequenceLogo_actionPerformed();
 769     }
 770     else if (evt.getSource() == showConsensusHistogram)
 771     {
 772       showConsensusHistogram_actionPerformed();
 773     }
 774     else if (evt.getSource() == applyAutoAnnotationSettings)
 775     {
 776       applyAutoAnnotationSettings_actionPerformed();
 777     }
 778     alignPanel.paintAlignment(true);
 779   }
 780
 781   private void mouseOverFlag_stateChanged()
 782   {
 783     viewport.followHighlight = followMouseOverFlag.getState();
 784     // TODO: could kick the scrollTo mechanism to reset view for current
 785     // searchresults.
 786   }
 787
 788   private void centreColumnLabelFlag_stateChanged()
 789   {
 790     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 791     this.alignPanel.annotationPanel.repaint();
 792   }
 793
 794   @Override
 795   public void actionPerformed(ActionEvent evt)
 796   {
 797     Object source = evt.getSource();
 798
 799     if (source == inputText)
 800     {
 801       inputText_actionPerformed();
 802     }
 803     else if (source == loadTree)
 804     {
 805       loadTree_actionPerformed();
 806     }
 807     else if (source == loadApplication)
 808     {
 809       launchFullApplication();
 810     }
 811     else if (source == loadAnnotations)
 812     {
 813       loadAnnotations();
 814     }
 815     else if (source == outputAnnotations)
 816     {
 817       outputAnnotations(true);
 818     }
 819     else if (source == outputFeatures)
 820     {
 821       outputFeatures(true, "Jalview");
 822     }
 823     else if (source == closeMenuItem)
 824     {
 825       closeMenuItem_actionPerformed();
 826     }
 827     else if (source == copy)
 828     {
 829       copy_actionPerformed();
 830     }
 831     else if (source == undoMenuItem)
 832     {
 833       undoMenuItem_actionPerformed();
 834     }
 835     else if (source == redoMenuItem)
 836     {
 837       redoMenuItem_actionPerformed();
 838     }
 839     else if (source == inputText)
 840     {
 841       inputText_actionPerformed();
 842     }
 843     else if (source == closeMenuItem)
 844     {
 845       closeMenuItem_actionPerformed();
 846     }
 847     else if (source == undoMenuItem)
 848     {
 849       undoMenuItem_actionPerformed();
 850     }
 851     else if (source == redoMenuItem)
 852     {
 853       redoMenuItem_actionPerformed();
 854     }
 855     else if (source == copy)
 856     {
 857       copy_actionPerformed();
 858     }
 859     else if (source == pasteNew)
 860     {
 861       pasteNew_actionPerformed();
 862     }
 863     else if (source == pasteThis)
 864     {
 865       pasteThis_actionPerformed();
 866     }
 867     else if (source == cut)
 868     {
 869       cut_actionPerformed();
 870     }
 871     else if (source == delete)
 872     {
 873       delete_actionPerformed();
 874     }
 875     else if (source == grpsFromSelection)
 876     {
 877       makeGrpsFromSelection_actionPerformed();
 878     }
 879     else if (source == deleteGroups)
 880     {
 881       deleteGroups_actionPerformed();
 882     }
 883     else if (source == selectAllSequenceMenuItem)
 884     {
 885       selectAllSequenceMenuItem_actionPerformed();
 886     }
 887     else if (source == deselectAllSequenceMenuItem)
 888     {
 889       deselectAllSequenceMenuItem_actionPerformed();
 890     }
 891     else if (source == invertSequenceMenuItem)
 892     {
 893       invertSequenceMenuItem_actionPerformed();
 894     }
 895     else if (source == invertColSel)
 896     {
 897       viewport.invertColumnSelection();
 898       alignPanel.paintAlignment(true);
 899     }
 900     else if (source == remove2LeftMenuItem)
 901     {
 902       trimAlignment(true);
 903     }
 904     else if (source == remove2RightMenuItem)
 905     {
 906       trimAlignment(false);
 907     }
 908     else if (source == removeGappedColumnMenuItem)
 909     {
 910       removeGappedColumnMenuItem_actionPerformed();
 911     }
 912     else if (source == removeAllGapsMenuItem)
 913     {
 914       removeAllGapsMenuItem_actionPerformed();
 915     }
 916     else if (source == findMenuItem)
 917     {
 918       findMenuItem_actionPerformed();
 919     }
 920     else if (source == font)
 921     {
 922       new FontChooser(alignPanel);
 923     }
 924     else if (source == newView)
 925     {
 926       newView(null);
 927     }
 928     else if (source == showColumns)
 929     {
 930       viewport.showAllHiddenColumns();
 931       alignPanel.paintAlignment(true);
 932     }
 933     else if (source == showSeqs)
 934     {
 935       viewport.showAllHiddenSeqs();
 936       alignPanel.paintAlignment(true);
 937     }
 938     else if (source == hideColumns)
 939     {
 940       viewport.hideSelectedColumns();
 941       alignPanel.paintAlignment(true);
 942     }
 943     else if (source == hideSequences
 944             && viewport.getSelectionGroup() != null)
 945     {
 946       viewport.hideAllSelectedSeqs();
 947       alignPanel.paintAlignment(true);
 948     }
 949     else if (source == hideAllButSelection)
 950     {
 951       toggleHiddenRegions(false, false);
 952       alignPanel.paintAlignment(true);
 953     }
 954     else if (source == hideAllSelection)
 955     {
 956       SequenceGroup sg = viewport.getSelectionGroup();
 957       viewport.expandColSelection(sg, false);
 958       viewport.hideAllSelectedSeqs();
 959       viewport.hideSelectedColumns();
 960       alignPanel.paintAlignment(true);
 961     }
 962     else if (source == showAllHidden)
 963     {
 964       viewport.showAllHiddenColumns();
 965       viewport.showAllHiddenSeqs();
 966       alignPanel.paintAlignment(true);
 967     }
 968     else if (source == showGroupConsensus)
 969     {
 970       showGroupConsensus_actionPerformed();
 971     }
 972     else if (source == showGroupConservation)
 973     {
 974       showGroupConservation_actionPerformed();
 975     }
 976     else if (source == showSequenceLogo)
 977     {
 978       showSequenceLogo_actionPerformed();
 979     }
 980     else if (source == normSequenceLogo)
 981     {
 982       normSequenceLogo_actionPerformed();
 983     }
 984     else if (source == showConsensusHistogram)
 985     {
 986       showConsensusHistogram_actionPerformed();
 987     }
 988     else if (source == applyAutoAnnotationSettings)
 989     {
 990       applyAutoAnnotationSettings_actionPerformed();
 991     }
 992     else if (source == featureSettings)
 993     {
 994       new FeatureSettings(alignPanel);
 995     }
 996     else if (source == alProperties)
 997     {
 998       StringBuffer contents = new jalview.io.AlignmentProperties(
 999               viewport.getAlignment()).formatAsString();
1000       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1001       cap.setText(contents.toString());
1002       Frame frame = new Frame();
1003       frame.add(cap);
1004       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1005               "label.alignment_properties", new String[]
1006               { getTitle() }), 400, 250);
1007     }
1008     else if (source == overviewMenuItem)
1009     {
1010       overviewMenuItem_actionPerformed();
1011     }
1012     else if (source == noColourmenuItem)
1013     {
1014       changeColour(null);
1015     }
1016     else if (source == clustalColour)
1017     {
1018       abovePIDThreshold.setState(false);
1019       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1020     }
1021     else if (source == zappoColour)
1022     {
1023       changeColour(new ZappoColourScheme());
1024     }
1025     else if (source == taylorColour)
1026     {
1027       changeColour(new TaylorColourScheme());
1028     }
1029     else if (source == hydrophobicityColour)
1030     {
1031       changeColour(new HydrophobicColourScheme());
1032     }
1033     else if (source == helixColour)
1034     {
1035       changeColour(new HelixColourScheme());
1036     }
1037     else if (source == strandColour)
1038     {
1039       changeColour(new StrandColourScheme());
1040     }
1041     else if (source == turnColour)
1042     {
1043       changeColour(new TurnColourScheme());
1044     }
1045     else if (source == buriedColour)
1046     {
1047       changeColour(new BuriedColourScheme());
1048     }
1049     else if (source == nucleotideColour)
1050     {
1051       changeColour(new NucleotideColourScheme());
1052     }
1053     else if (source == purinePyrimidineColour)
1054     {
1055       changeColour(new PurinePyrimidineColourScheme());
1056     }
1057     else if (source == RNAInteractionColour)
1058     {
1059       changeColour(new RNAInteractionColourScheme());
1060     }
1061     else if (source == RNAHelixColour)
1062     {
1063       new RNAHelicesColourChooser(viewport, alignPanel);
1064     }
1065     else if (source == modifyPID)
1066     {
1067       modifyPID_actionPerformed();
1068     }
1069     else if (source == modifyConservation)
1070     {
1071       modifyConservation_actionPerformed();
1072     }
1073     else if (source == userDefinedColour)
1074     {
1075       new UserDefinedColours(alignPanel, null);
1076     }
1077     else if (source == PIDColour)
1078     {
1079       changeColour(new PIDColourScheme());
1080     }
1081     else if (source == BLOSUM62Colour)
1082     {
1083       changeColour(new Blosum62ColourScheme());
1084     }
1085     else if (source == tcoffeeColour)
1086     {
1087       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1088     }
1089     else if (source == annotationColour)
1090     {
1091       new AnnotationColourChooser(viewport, alignPanel);
1092     }
1093     else if (source == sortPairwiseMenuItem)
1094     {
1095       sortPairwiseMenuItem_actionPerformed();
1096     }
1097     else if (source == sortIDMenuItem)
1098     {
1099       sortIDMenuItem_actionPerformed();
1100     }
1101     else if (source == sortLengthMenuItem)
1102     {
1103       sortLengthMenuItem_actionPerformed();
1104     }
1105     else if (source == sortGroupMenuItem)
1106     {
1107       sortGroupMenuItem_actionPerformed();
1108     }
1109     else if (source == removeRedundancyMenuItem)
1110     {
1111       removeRedundancyMenuItem_actionPerformed();
1112     }
1113     else if (source == pairwiseAlignmentMenuItem)
1114     {
1115       pairwiseAlignmentMenuItem_actionPerformed();
1116     }
1117     else if (source == PCAMenuItem)
1118     {
1119       PCAMenuItem_actionPerformed();
1120     }
1121     else if (source == averageDistanceTreeMenuItem)
1122     {
1123       averageDistanceTreeMenuItem_actionPerformed();
1124     }
1125     else if (source == neighbourTreeMenuItem)
1126     {
1127       neighbourTreeMenuItem_actionPerformed();
1128     }
1129     else if (source == njTreeBlosumMenuItem)
1130     {
1131       njTreeBlosumMenuItem_actionPerformed();
1132     }
1133     else if (source == avDistanceTreeBlosumMenuItem)
1134     {
1135       avTreeBlosumMenuItem_actionPerformed();
1136     }
1137     else if (source == documentation)
1138     {
1139       documentation_actionPerformed();
1140     }
1141     else if (source == about)
1142     {
1143       about_actionPerformed();
1144     }
1145
1146   }
1147
1148   public void inputText_actionPerformed()
1149   {
1150     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1151     Frame frame = new Frame();
1152     frame.add(cap);
1153     jalview.bin.JalviewLite.addFrame(frame,
1154             MessageManager.getString("label.input_cut_paste"), 500, 500);
1155   }
1156
1157   protected void outputText_actionPerformed(ActionEvent e)
1158   {
1159     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1160     Frame frame = new Frame();
1161     frame.add(cap);
1162     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1163             "label.alignment_output_command", new String[]
1164             { e.getActionCommand() }), 600, 500);
1165     cap.setText(new AppletFormatAdapter().formatSequences(
1166             e.getActionCommand(), viewport.getAlignment(),
1167             viewport.showJVSuffix));
1168   }
1169
1170   public void loadAnnotations()
1171   {
1172     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1173     cap.setText(MessageManager
1174             .getString("label.paste_features_annotations_Tcoffee_here"));
1175     cap.setAnnotationImport();
1176     Frame frame = new Frame();
1177     frame.add(cap);
1178     jalview.bin.JalviewLite.addFrame(frame,
1179             MessageManager.getString("action.paste_annotations"), 400, 300);
1180
1181   }
1182
1183   public String outputAnnotations(boolean displayTextbox)
1184   {
1185     String annotation = new AnnotationFile().printAnnotations(
1186             viewport.showAnnotation ? viewport.getAlignment()
1187                     .getAlignmentAnnotation() : null, viewport
1188                     .getAlignment().getGroups(), ((Alignment) viewport
1189                     .getAlignment()).alignmentProperties);
1190
1191     if (displayTextbox)
1192     {
1193       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1194       Frame frame = new Frame();
1195       frame.add(cap);
1196       jalview.bin.JalviewLite.addFrame(frame,
1197               MessageManager.getString("label.annotations"), 600, 500);
1198       cap.setText(annotation);
1199     }
1200
1201     return annotation;
1202   }
1203
1204   private Hashtable getDisplayedFeatureCols()
1205   {
1206     if (alignPanel.getFeatureRenderer() != null
1207             && viewport.featuresDisplayed != null)
1208     {
1209       FeatureRenderer fr = alignPanel.getFeatureRenderer();
1210       Hashtable fcols = new Hashtable();
1211       Enumeration en = viewport.featuresDisplayed.keys();
1212       while (en.hasMoreElements())
1213       {
1214         Object col = en.nextElement();
1215         fcols.put(col, fr.featureColours.get(col));
1216       }
1217       return fcols;
1218     }
1219     return null;
1220   }
1221
1222   public String outputFeatures(boolean displayTextbox, String format)
1223   {
1224     String features;
1225     if (format.equalsIgnoreCase("Jalview"))
1226     {
1227       features = new FeaturesFile().printJalviewFormat(viewport
1228               .getAlignment().getSequencesArray(),
1229               getDisplayedFeatureCols());
1230     }
1231     else
1232     {
1233       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1234               .getSequencesArray(), getDisplayedFeatureCols());
1235     }
1236
1237     if (displayTextbox)
1238     {
1239       boolean frimport = false;
1240       if (features == null || features.equals("No Features Visible"))
1241       {
1242         features = "# No features visible - paste some and import them here.";
1243         frimport = true;
1244       }
1245
1246       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1247       if (frimport)
1248       {
1249         cap.setAnnotationImport();
1250       }
1251       Frame frame = new Frame();
1252       frame.add(cap);
1253       jalview.bin.JalviewLite.addFrame(frame,
1254               MessageManager.getString("label.features"), 600, 500);
1255       cap.setText(features);
1256     }
1257     else
1258     {
1259       if (features == null)
1260         features = "";
1261     }
1262
1263     return features;
1264   }
1265
1266   void launchFullApplication()
1267   {
1268     StringBuffer url = new StringBuffer(jalviewServletURL);
1269
1270     url.append("?open="
1271             + appendProtocol(viewport.applet.getParameter("file")));
1272
1273     if (viewport.applet.getParameter("features") != null)
1274     {
1275       url.append("&features=");
1276       url.append(appendProtocol(viewport.applet.getParameter("features")));
1277     }
1278
1279     if (viewport.applet.getParameter("annotations") != null)
1280     {
1281       url.append("&annotations=");
1282       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1283     }
1284
1285     if (viewport.applet.getParameter("jnetfile") != null)
1286     {
1287       url.append("&annotations=");
1288       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1289     }
1290
1291     if (viewport.applet.getParameter("defaultColour") != null)
1292     {
1293       url.append("&colour="
1294               + removeWhiteSpace(viewport.applet
1295                       .getParameter("defaultColour")));
1296     }
1297
1298     if (viewport.applet.getParameter("userDefinedColour") != null)
1299     {
1300       url.append("&colour="
1301               + removeWhiteSpace(viewport.applet
1302                       .getParameter("userDefinedColour")));
1303     }
1304     if (viewport.applet.getParameter("tree") != null)
1305     {
1306       url.append("&tree="
1307               + appendProtocol(viewport.applet.getParameter("tree")));
1308     }
1309     if (viewport.applet.getParameter("treeFile") != null)
1310     {
1311       url.append("&tree="
1312               + appendProtocol(viewport.applet.getParameter("treeFile")));
1313     }
1314
1315     showURL(url.toString(), "FULL_APP");
1316   }
1317
1318   String removeWhiteSpace(String colour)
1319   {
1320     StringBuffer sb = new StringBuffer();
1321     for (int i = 0; i < colour.length(); i++)
1322     {
1323       if (Character.isWhitespace(colour.charAt(i)))
1324       {
1325         sb.append("%20");
1326       }
1327       else
1328       {
1329         sb.append(colour.charAt(i));
1330       }
1331     }
1332
1333     return sb.toString();
1334   }
1335
1336   String appendProtocol(String url)
1337   {
1338     try
1339     {
1340       new URL(url);
1341       url = URLEncoder.encode(url);
1342     }
1343     /*
1344      * When we finally deprecate 1.1 compatibility, we can start to use
1345      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1346      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1347      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1348      * ex.printStackTrace(); }
1349      */
1350     catch (java.net.MalformedURLException ex)
1351     {
1352       url = viewport.applet.getCodeBase() + url;
1353     }
1354     return url;
1355   }
1356
1357   public void closeMenuItem_actionPerformed()
1358   {
1359     PaintRefresher.RemoveComponent(alignPanel);
1360     if (alignPanel.seqPanel != null
1361             && alignPanel.seqPanel.seqCanvas != null)
1362     {
1363       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1364     }
1365     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1366     {
1367       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1368     }
1369
1370     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1371     {
1372       System.exit(0);
1373     }
1374     else
1375     {
1376     }
1377     viewport = null;
1378     alignPanel = null;
1379     this.dispose();
1380   }
1381
1382   /**
1383    * TODO: JAL-1104
1384    */
1385   void updateEditMenuBar()
1386   {
1387
1388     if (viewport.historyList.size() > 0)
1389     {
1390       undoMenuItem.setEnabled(true);
1391       CommandI command = (CommandI) viewport.historyList.peek();
1392       undoMenuItem.setLabel(MessageManager.formatMessage(
1393               "label.undo_command", new String[]
1394               { command.getDescription() }));
1395     }
1396     else
1397     {
1398       undoMenuItem.setEnabled(false);
1399       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1400     }
1401
1402     if (viewport.redoList.size() > 0)
1403     {
1404       redoMenuItem.setEnabled(true);
1405
1406       CommandI command = (CommandI) viewport.redoList.peek();
1407       redoMenuItem.setLabel(MessageManager.formatMessage(
1408               "label.redo_command", new String[]
1409               { command.getDescription() }));
1410     }
1411     else
1412     {
1413       redoMenuItem.setEnabled(false);
1414       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1415     }
1416   }
1417
1418   /**
1419    * TODO: JAL-1104
1420    */
1421   public void addHistoryItem(CommandI command)
1422   {
1423     if (command.getSize() > 0)
1424     {
1425       viewport.historyList.push(command);
1426       viewport.redoList.removeAllElements();
1427       updateEditMenuBar();
1428       viewport.updateHiddenColumns();
1429     }
1430   }
1431
1432   /**
1433    * TODO: JAL-1104 DOCUMENT ME!
1434    *
1435    * @param e
1436    *          DOCUMENT ME!
1437    */
1438   protected void undoMenuItem_actionPerformed()
1439   {
1440     if (viewport.historyList.size() < 1)
1441     {
1442       return;
1443     }
1444
1445     CommandI command = (CommandI) viewport.historyList.pop();
1446     viewport.redoList.push(command);
1447     command.undoCommand(null);
1448
1449     AlignViewport originalSource = getOriginatingSource(command);
1450     // JBPNote Test
1451     if (originalSource != viewport)
1452     {
1453       System.err
1454               .println("Warning: Viewport object mismatch whilst undoing");
1455     }
1456     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1457                                           // viewport.getColumnSelection().getHiddenColumns()
1458                                           // != null;
1459     updateEditMenuBar();
1460     originalSource.firePropertyChange("alignment", null, originalSource
1461             .getAlignment().getSequences());
1462   }
1463
1464   /**
1465    * TODO: JAL-1104 DOCUMENT ME!
1466    *
1467    * @param e
1468    *          DOCUMENT ME!
1469    */
1470   protected void redoMenuItem_actionPerformed()
1471   {
1472     if (viewport.redoList.size() < 1)
1473     {
1474       return;
1475     }
1476
1477     CommandI command = (CommandI) viewport.redoList.pop();
1478     viewport.historyList.push(command);
1479     command.doCommand(null);
1480
1481     AlignViewport originalSource = getOriginatingSource(command);
1482     // JBPNote Test
1483     if (originalSource != viewport)
1484     {
1485       System.err
1486               .println("Warning: Viewport object mismatch whilst re-doing");
1487     }
1488     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1489                                           // viewport.getColumnSelection().getHiddenColumns()
1490                                           // != null;
1491
1492     updateEditMenuBar();
1493     originalSource.firePropertyChange("alignment", null, originalSource
1494             .getAlignment().getSequences());
1495   }
1496
1497   AlignViewport getOriginatingSource(CommandI command)
1498   {
1499     AlignViewport originalSource = null;
1500     // For sequence removal and addition, we need to fire
1501     // the property change event FROM the viewport where the
1502     // original alignment was altered
1503     AlignmentI al = null;
1504     if (command instanceof EditCommand)
1505     {
1506       EditCommand editCommand = (EditCommand) command;
1507       al = editCommand.getAlignment();
1508       Vector comps = (Vector) PaintRefresher.components.get(viewport
1509               .getSequenceSetId());
1510       for (int i = 0; i < comps.size(); i++)
1511       {
1512         if (comps.elementAt(i) instanceof AlignmentPanel)
1513         {
1514           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1515           {
1516             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1517             break;
1518           }
1519         }
1520       }
1521     }
1522
1523     if (originalSource == null)
1524     {
1525       // The original view is closed, we must validate
1526       // the current view against the closed view first
1527       if (al != null)
1528       {
1529         PaintRefresher.validateSequences(al, viewport.getAlignment());
1530       }
1531
1532       originalSource = viewport;
1533     }
1534
1535     return originalSource;
1536   }
1537
1538   public void moveSelectedSequences(boolean up)
1539   {
1540     SequenceGroup sg = viewport.getSelectionGroup();
1541     if (sg == null)
1542     {
1543       return;
1544     }
1545     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1546             up ? null : viewport.getHiddenRepSequences(), up);
1547     alignPanel.paintAlignment(true);
1548   }
1549
1550   synchronized void slideSequences(boolean right, int size)
1551   {
1552     List<SequenceI> sg = new Vector<SequenceI>();
1553     if (viewport.cursorMode)
1554     {
1555       sg.add(viewport.getAlignment().getSequenceAt(
1556               alignPanel.seqPanel.seqCanvas.cursorY));
1557     }
1558     else if (viewport.getSelectionGroup() != null
1559             && viewport.getSelectionGroup().getSize() != viewport
1560                     .getAlignment().getHeight())
1561     {
1562       sg = viewport.getSelectionGroup().getSequences(
1563               viewport.getHiddenRepSequences());
1564     }
1565
1566     if (sg.size() < 1)
1567     {
1568       return;
1569     }
1570
1571     Vector<SequenceI> invertGroup = new Vector();
1572
1573     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1574     {
1575       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1576         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1577     }
1578
1579     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1580
1581     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1582             .size()]);
1583     for (int i = 0; i < invertGroup.size(); i++)
1584       seqs2[i] = invertGroup.elementAt(i);
1585
1586     SlideSequencesCommand ssc;
1587     if (right)
1588       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1589               size, viewport.getGapCharacter());
1590     else
1591       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1592               size, viewport.getGapCharacter());
1593
1594     int groupAdjustment = 0;
1595     if (ssc.getGapsInsertedBegin() && right)
1596     {
1597       if (viewport.cursorMode)
1598         alignPanel.seqPanel.moveCursor(size, 0);
1599       else
1600         groupAdjustment = size;
1601     }
1602     else if (!ssc.getGapsInsertedBegin() && !right)
1603     {
1604       if (viewport.cursorMode)
1605         alignPanel.seqPanel.moveCursor(-size, 0);
1606       else
1607         groupAdjustment = -size;
1608     }
1609
1610     if (groupAdjustment != 0)
1611     {
1612       viewport.getSelectionGroup().setStartRes(
1613               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1614       viewport.getSelectionGroup().setEndRes(
1615               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1616     }
1617
1618     boolean appendHistoryItem = false;
1619     if (viewport.historyList != null && viewport.historyList.size() > 0
1620             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1621     {
1622       appendHistoryItem = ssc
1623               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1624                       .peek());
1625     }
1626
1627     if (!appendHistoryItem)
1628       addHistoryItem(ssc);
1629
1630     repaint();
1631   }
1632
1633   static StringBuffer copiedSequences;
1634
1635   static Vector copiedHiddenColumns;
1636
1637   protected void copy_actionPerformed()
1638   {
1639     if (viewport.getSelectionGroup() == null)
1640     {
1641       return;
1642     }
1643
1644     SequenceGroup sg = viewport.getSelectionGroup();
1645     copiedSequences = new StringBuffer();
1646     Hashtable orderedSeqs = new Hashtable();
1647     for (int i = 0; i < sg.getSize(); i++)
1648     {
1649       SequenceI seq = sg.getSequenceAt(i);
1650       int index = viewport.getAlignment().findIndex(seq);
1651       orderedSeqs.put(index + "", seq);
1652     }
1653
1654     int index = 0, startRes, endRes;
1655     char ch;
1656
1657     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1658     {
1659       copiedHiddenColumns = new Vector();
1660       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1661       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1662               .size(); i++)
1663       {
1664         int[] region = (int[]) viewport.getColumnSelection()
1665                 .getHiddenColumns().elementAt(i);
1666
1667         copiedHiddenColumns.addElement(new int[]
1668         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1669       }
1670     }
1671     else
1672     {
1673       copiedHiddenColumns = null;
1674     }
1675
1676     for (int i = 0; i < sg.getSize(); i++)
1677     {
1678       SequenceI seq = null;
1679
1680       while (seq == null)
1681       {
1682         if (orderedSeqs.containsKey(index + ""))
1683         {
1684           seq = (SequenceI) orderedSeqs.get(index + "");
1685           index++;
1686
1687           break;
1688         }
1689         else
1690         {
1691           index++;
1692         }
1693       }
1694
1695       // FIND START RES
1696       // Returns residue following index if gap
1697       startRes = seq.findPosition(sg.getStartRes());
1698
1699       // FIND END RES
1700       // Need to find the residue preceeding index if gap
1701       endRes = 0;
1702
1703       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1704       {
1705         ch = seq.getCharAt(j);
1706         if (!jalview.util.Comparison.isGap((ch)))
1707         {
1708           endRes++;
1709         }
1710       }
1711
1712       if (endRes > 0)
1713       {
1714         endRes += seq.getStart() - 1;
1715       }
1716
1717       copiedSequences.append(seq.getName()
1718               + "\t"
1719               + startRes
1720               + "\t"
1721               + endRes
1722               + "\t"
1723               + seq.getSequenceAsString(sg.getStartRes(),
1724                       sg.getEndRes() + 1) + "\n");
1725     }
1726
1727   }
1728
1729   protected void pasteNew_actionPerformed()
1730   {
1731     paste(true);
1732   }
1733
1734   protected void pasteThis_actionPerformed()
1735   {
1736     paste(false);
1737   }
1738
1739   void paste(boolean newAlignment)
1740   {
1741     try
1742     {
1743
1744       if (copiedSequences == null)
1745       {
1746         return;
1747       }
1748
1749       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1750       Vector seqs = new Vector();
1751       while (st.hasMoreElements())
1752       {
1753         String name = st.nextToken();
1754         int start = Integer.parseInt(st.nextToken());
1755         int end = Integer.parseInt(st.nextToken());
1756         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1757       }
1758       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1759       for (int i = 0; i < seqs.size(); i++)
1760       {
1761         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1762       }
1763
1764       if (newAlignment)
1765       {
1766         String newtitle = new String("Copied sequences");
1767         if (getTitle().startsWith("Copied sequences"))
1768         {
1769           newtitle = getTitle();
1770         }
1771         else
1772         {
1773           newtitle = newtitle.concat("- from " + getTitle());
1774         }
1775         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1776                 viewport.applet, newtitle, false);
1777         if (copiedHiddenColumns != null)
1778         {
1779           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1780           {
1781             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1782             af.viewport.hideColumns(region[0], region[1]);
1783           }
1784         }
1785
1786         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1787                 DEFAULT_HEIGHT);
1788       }
1789       else
1790       {
1791         addSequences(newSeqs);
1792       }
1793
1794     } catch (Exception ex)
1795     {
1796     } // could be anything being pasted in here
1797
1798   }
1799
1800   void addSequences(SequenceI[] seqs)
1801   {
1802     for (int i = 0; i < seqs.length; i++)
1803     {
1804       viewport.getAlignment().addSequence(seqs[i]);
1805     }
1806
1807     // !newAlignment
1808     addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1809             seqs, 0, viewport.getAlignment().getWidth(),
1810             viewport.getAlignment()));
1811
1812     viewport.setEndSeq(viewport.getAlignment().getHeight());
1813     viewport.getAlignment().getWidth();
1814     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1815             .getSequences());
1816
1817   }
1818
1819   protected void cut_actionPerformed()
1820   {
1821     copy_actionPerformed();
1822     delete_actionPerformed();
1823   }
1824
1825   protected void delete_actionPerformed()
1826   {
1827
1828     SequenceGroup sg = viewport.getSelectionGroup();
1829     if (sg == null)
1830     {
1831       return;
1832     }
1833
1834     Vector seqs = new Vector();
1835     SequenceI seq;
1836     for (int i = 0; i < sg.getSize(); i++)
1837     {
1838       seq = sg.getSequenceAt(i);
1839       seqs.addElement(seq);
1840     }
1841
1842     // If the cut affects all sequences, remove highlighted columns
1843     if (sg.getSize() == viewport.getAlignment().getHeight())
1844     {
1845       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1846               sg.getEndRes() + 1);
1847     }
1848
1849     SequenceI[] cut = new SequenceI[seqs.size()];
1850     for (int i = 0; i < seqs.size(); i++)
1851     {
1852       cut[i] = (SequenceI) seqs.elementAt(i);
1853     }
1854
1855     /*
1856      * //ADD HISTORY ITEM
1857      */
1858     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1859             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1860             viewport.getAlignment()));
1861
1862     viewport.setSelectionGroup(null);
1863     viewport.getAlignment().deleteGroup(sg);
1864
1865     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1866             .getSequences());
1867
1868     if (viewport.getAlignment().getHeight() < 1)
1869     {
1870       this.setVisible(false);
1871     }
1872     viewport.sendSelection();
1873   }
1874
1875   /**
1876    * group consensus toggled
1877    *
1878    */
1879   protected void showGroupConsensus_actionPerformed()
1880   {
1881     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1882     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1883
1884   }
1885
1886   /**
1887    * group conservation toggled.
1888    */
1889   protected void showGroupConservation_actionPerformed()
1890   {
1891     viewport.setShowGroupConservation(showGroupConservation.getState());
1892     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1893   }
1894
1895   /*
1896    * (non-Javadoc)
1897    *
1898    * @see
1899    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1900    * .event.ActionEvent)
1901    */
1902   protected void showConsensusHistogram_actionPerformed()
1903   {
1904     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1905     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1906   }
1907
1908   /*
1909    * (non-Javadoc)
1910    *
1911    * @see
1912    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1913    * .event.ActionEvent)
1914    */
1915   protected void showSequenceLogo_actionPerformed()
1916   {
1917     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1918     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1919   }
1920
1921   protected void normSequenceLogo_actionPerformed()
1922   {
1923     showSequenceLogo.setState(true);
1924     viewport.setShowSequenceLogo(true);
1925     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1926     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1927   }
1928
1929   protected void applyAutoAnnotationSettings_actionPerformed()
1930   {
1931     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1932   }
1933
1934   protected void makeGrpsFromSelection_actionPerformed()
1935   {
1936     if (avc.makeGroupsFromSelection())
1937     {
1938       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1939       alignPanel.updateAnnotation();
1940       alignPanel.paintAlignment(true);
1941     }
1942   }
1943
1944   protected void createGroup_actionPerformed()
1945   {
1946     avc.createGroup();
1947   }
1948
1949   protected void unGroup_actionPerformed()
1950   {
1951     if (avc.unGroup())
1952     {
1953       alignPanel.alignmentChanged();
1954     }
1955   }
1956
1957   protected void deleteGroups_actionPerformed()
1958   {
1959     if (avc.deleteGroups())
1960     {
1961       alignPanel.alignmentChanged();
1962     }
1963   }
1964
1965   public void selectAllSequenceMenuItem_actionPerformed()
1966   {
1967     SequenceGroup sg = new SequenceGroup();
1968     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1969     {
1970       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1971     }
1972     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1973     viewport.setSelectionGroup(sg);
1974     alignPanel.paintAlignment(true);
1975     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1976     viewport.sendSelection();
1977   }
1978
1979   public void deselectAllSequenceMenuItem_actionPerformed()
1980   {
1981     if (viewport.cursorMode)
1982     {
1983       alignPanel.seqPanel.keyboardNo1 = null;
1984       alignPanel.seqPanel.keyboardNo2 = null;
1985     }
1986     viewport.setSelectionGroup(null);
1987     viewport.getColumnSelection().clear();
1988     viewport.setSelectionGroup(null);
1989     alignPanel.idPanel.idCanvas.searchResults = null;
1990     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1991     alignPanel.paintAlignment(true);
1992     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1993     viewport.sendSelection();
1994   }
1995
1996   public void invertSequenceMenuItem_actionPerformed()
1997   {
1998     SequenceGroup sg = viewport.getSelectionGroup();
1999     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2000     {
2001       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2002     }
2003
2004     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2005     viewport.sendSelection();
2006   }
2007
2008   public void invertColSel_actionPerformed()
2009   {
2010     viewport.invertColumnSelection();
2011     alignPanel.paintAlignment(true);
2012     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2013     viewport.sendSelection();
2014   }
2015
2016   void trimAlignment(boolean trimLeft)
2017   {
2018     ColumnSelection colSel = viewport.getColumnSelection();
2019     int column;
2020
2021     if (colSel.size() > 0)
2022     {
2023       if (trimLeft)
2024       {
2025         column = colSel.getMin();
2026       }
2027       else
2028       {
2029         column = colSel.getMax();
2030       }
2031
2032       SequenceI[] seqs;
2033       if (viewport.getSelectionGroup() != null)
2034       {
2035         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2036                 viewport.getHiddenRepSequences());
2037       }
2038       else
2039       {
2040         seqs = viewport.getAlignment().getSequencesArray();
2041       }
2042
2043       TrimRegionCommand trimRegion;
2044       if (trimLeft)
2045       {
2046         trimRegion = new TrimRegionCommand("Remove Left",
2047                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2048                 viewport.getAlignment(), viewport.getColumnSelection(),
2049                 viewport.getSelectionGroup());
2050         viewport.setStartRes(0);
2051       }
2052       else
2053       {
2054         trimRegion = new TrimRegionCommand("Remove Right",
2055                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2056                 viewport.getAlignment(), viewport.getColumnSelection(),
2057                 viewport.getSelectionGroup());
2058       }
2059
2060       statusBar.setText(MessageManager.formatMessage(
2061               "label.removed_columns", new String[]
2062               { Integer.valueOf(trimRegion.getSize()).toString() }));
2063       addHistoryItem(trimRegion);
2064
2065       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2066       {
2067         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2068                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2069         {
2070           viewport.getAlignment().deleteGroup(sg);
2071         }
2072       }
2073
2074       viewport.firePropertyChange("alignment", null, viewport
2075               .getAlignment().getSequences());
2076     }
2077   }
2078
2079   public void removeGappedColumnMenuItem_actionPerformed()
2080   {
2081     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2082
2083     SequenceI[] seqs;
2084     if (viewport.getSelectionGroup() != null)
2085     {
2086       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2087               viewport.getHiddenRepSequences());
2088       start = viewport.getSelectionGroup().getStartRes();
2089       end = viewport.getSelectionGroup().getEndRes();
2090     }
2091     else
2092     {
2093       seqs = viewport.getAlignment().getSequencesArray();
2094     }
2095
2096     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2097             "Remove Gapped Columns", seqs, start, end,
2098             viewport.getAlignment());
2099
2100     addHistoryItem(removeGapCols);
2101
2102     statusBar.setText(MessageManager.formatMessage(
2103             "label.removed_empty_columns", new String[]
2104             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2105
2106     // This is to maintain viewport position on first residue
2107     // of first sequence
2108     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2109     int startRes = seq.findPosition(viewport.startRes);
2110     // ShiftList shifts;
2111     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2112     // edit.alColumnChanges=shifts.getInverse();
2113     // if (viewport.hasHiddenColumns)
2114     // viewport.getColumnSelection().compensateForEdits(shifts);
2115     viewport.setStartRes(seq.findIndex(startRes) - 1);
2116     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2117             .getSequences());
2118
2119   }
2120
2121   public void removeAllGapsMenuItem_actionPerformed()
2122   {
2123     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2124
2125     SequenceI[] seqs;
2126     if (viewport.getSelectionGroup() != null)
2127     {
2128       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2129               viewport.getHiddenRepSequences());
2130       start = viewport.getSelectionGroup().getStartRes();
2131       end = viewport.getSelectionGroup().getEndRes();
2132     }
2133     else
2134     {
2135       seqs = viewport.getAlignment().getSequencesArray();
2136     }
2137
2138     // This is to maintain viewport position on first residue
2139     // of first sequence
2140     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2141     int startRes = seq.findPosition(viewport.startRes);
2142
2143     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2144             viewport.getAlignment()));
2145
2146     viewport.setStartRes(seq.findIndex(startRes) - 1);
2147
2148     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2149             .getSequences());
2150
2151   }
2152
2153   public void findMenuItem_actionPerformed()
2154   {
2155     new Finder(alignPanel);
2156   }
2157
2158   /**
2159    * create a new view derived from the current view
2160    *
2161    * @param viewtitle
2162    * @return frame for the new view
2163    */
2164   public AlignFrame newView(String viewtitle)
2165   {
2166     AlignmentI newal;
2167     if (viewport.hasHiddenRows())
2168     {
2169       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2170               .getFullAlignment().getSequencesArray());
2171     }
2172     else
2173     {
2174       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2175     }
2176
2177     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2178     {
2179       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2180       {
2181         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2182         {
2183           newal.addAnnotation(viewport.getAlignment()
2184                   .getAlignmentAnnotation()[i]);
2185         }
2186       }
2187     }
2188
2189     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2190
2191     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2192     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2193     PaintRefresher.Register(newaf.alignPanel,
2194             newaf.alignPanel.av.getSequenceSetId());
2195
2196     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2197             newaf.alignPanel.av.getSequenceSetId());
2198     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2199             newaf.alignPanel.av.getSequenceSetId());
2200
2201     Vector comps = (Vector) PaintRefresher.components.get(viewport
2202             .getSequenceSetId());
2203     int viewSize = -1;
2204     for (int i = 0; i < comps.size(); i++)
2205     {
2206       if (comps.elementAt(i) instanceof AlignmentPanel)
2207       {
2208         viewSize++;
2209       }
2210     }
2211
2212     String title = new String(this.getTitle());
2213     if (viewtitle != null)
2214     {
2215       title = viewtitle + " ( " + title + ")";
2216     }
2217     else
2218     {
2219       if (title.indexOf("(View") > -1)
2220       {
2221         title = title.substring(0, title.indexOf("(View"));
2222       }
2223       title += "(View " + viewSize + ")";
2224     }
2225
2226     newaf.setTitle(title.toString());
2227
2228     newaf.viewport.historyList = viewport.historyList;
2229     newaf.viewport.redoList = viewport.redoList;
2230     return newaf;
2231   }
2232
2233   /**
2234    *
2235    * @return list of feature groups on the view
2236    */
2237   public String[] getFeatureGroups()
2238   {
2239     FeatureRenderer fr = null;
2240     if (alignPanel != null
2241             && (fr = alignPanel.getFeatureRenderer()) != null)
2242     {
2243       return fr.getGroups();
2244     }
2245     return null;
2246   }
2247
2248   /**
2249    * get sequence feature groups that are hidden or shown
2250    *
2251    * @param visible
2252    *          true is visible
2253    * @return list
2254    */
2255   public String[] getFeatureGroupsOfState(boolean visible)
2256   {
2257     FeatureRenderer fr = null;
2258     if (alignPanel != null
2259             && (fr = alignPanel.getFeatureRenderer()) != null)
2260     {
2261       return fr.getGroups(visible);
2262     }
2263     return null;
2264   }
2265
2266   /**
2267    * Change the display state for the given feature groups
2268    *
2269    * @param groups
2270    *          list of group strings
2271    * @param state
2272    *          visible or invisible
2273    */
2274   public void setFeatureGroupState(String[] groups, boolean state)
2275   {
2276     FeatureRenderer fr = null;
2277     this.sequenceFeatures.setState(true);
2278     viewport.showSequenceFeatures(true);
2279     if (alignPanel != null
2280             && (fr = alignPanel.getFeatureRenderer()) != null)
2281     {
2282       fr.setGroupState(groups, state);
2283       alignPanel.seqPanel.seqCanvas.repaint();
2284       if (alignPanel.overviewPanel != null)
2285       {
2286         alignPanel.overviewPanel.updateOverviewImage();
2287       }
2288     }
2289   }
2290
2291   public void seqLimits_itemStateChanged()
2292   {
2293     viewport.setShowJVSuffix(seqLimits.getState());
2294     alignPanel.fontChanged();
2295     alignPanel.paintAlignment(true);
2296   }
2297
2298   protected void colourTextMenuItem_actionPerformed()
2299   {
2300     viewport.setColourText(colourTextMenuItem.getState());
2301     alignPanel.paintAlignment(true);
2302   }
2303
2304   protected void displayNonconservedMenuItem_actionPerformed()
2305   {
2306     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2307     alignPanel.paintAlignment(true);
2308   }
2309
2310   protected void wrapMenuItem_actionPerformed()
2311   {
2312     viewport.setWrapAlignment(wrapMenuItem.getState());
2313     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2314     scaleAbove.setEnabled(wrapMenuItem.getState());
2315     scaleLeft.setEnabled(wrapMenuItem.getState());
2316     scaleRight.setEnabled(wrapMenuItem.getState());
2317     alignPanel.paintAlignment(true);
2318   }
2319
2320   public void overviewMenuItem_actionPerformed()
2321   {
2322     if (alignPanel.overviewPanel != null)
2323     {
2324       return;
2325     }
2326
2327     Frame frame = new Frame();
2328     OverviewPanel overview = new OverviewPanel(alignPanel);
2329     frame.add(overview);
2330     // +50 must allow for applet frame window
2331     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2332             "label.overview_params", new String[]
2333             { this.getTitle() }), overview.getPreferredSize().width,
2334             overview.getPreferredSize().height + 50);
2335
2336     frame.pack();
2337     final AlignmentPanel ap = alignPanel;
2338     frame.addWindowListener(new WindowAdapter()
2339     {
2340       @Override
2341       public void windowClosing(WindowEvent e)
2342       {
2343         if (ap != null)
2344         {
2345           ap.setOverviewPanel(null);
2346         }
2347       };
2348     });
2349
2350     alignPanel.setOverviewPanel(overview);
2351
2352   }
2353
2354   void changeColour(ColourSchemeI cs)
2355   {
2356     int threshold = 0;
2357
2358     if (cs != null)
2359     {
2360       if (viewport.getAbovePIDThreshold())
2361       {
2362         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2363                 cs, "Background"));
2364       }
2365
2366       if (viewport.getConservationSelected())
2367       {
2368         cs.setConservationApplied(true);
2369         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2370                 cs, "Background"));
2371       }
2372       else
2373       {
2374         cs.setConservationApplied(false);
2375       }
2376     }
2377     viewport.setGlobalColourScheme(cs);
2378
2379     if (alignPanel.getOverviewPanel() != null)
2380     {
2381       alignPanel.getOverviewPanel().updateOverviewImage();
2382     }
2383
2384     jalview.structure.StructureSelectionManager
2385             .getStructureSelectionManager(viewport.applet)
2386             .sequenceColoursChanged(alignPanel);
2387
2388     alignPanel.paintAlignment(true);
2389   }
2390
2391   protected void modifyPID_actionPerformed()
2392   {
2393     if (viewport.getAbovePIDThreshold()
2394             && viewport.getGlobalColourScheme() != null)
2395     {
2396       SliderPanel.setPIDSliderSource(alignPanel,
2397               viewport.getGlobalColourScheme(), "Background");
2398       SliderPanel.showPIDSlider();
2399     }
2400   }
2401
2402   protected void modifyConservation_actionPerformed()
2403   {
2404     if (viewport.getConservationSelected()
2405             && viewport.getGlobalColourScheme() != null)
2406     {
2407       SliderPanel.setConservationSlider(alignPanel,
2408               viewport.getGlobalColourScheme(), "Background");
2409       SliderPanel.showConservationSlider();
2410     }
2411   }
2412
2413   protected void conservationMenuItem_actionPerformed()
2414   {
2415     viewport.setConservationSelected(conservationMenuItem.getState());
2416
2417     viewport.setAbovePIDThreshold(false);
2418     abovePIDThreshold.setState(false);
2419
2420     changeColour(viewport.getGlobalColourScheme());
2421
2422     modifyConservation_actionPerformed();
2423   }
2424
2425   public void abovePIDThreshold_actionPerformed()
2426   {
2427     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2428
2429     conservationMenuItem.setState(false);
2430     viewport.setConservationSelected(false);
2431
2432     changeColour(viewport.getGlobalColourScheme());
2433
2434     modifyPID_actionPerformed();
2435   }
2436
2437   public void sortPairwiseMenuItem_actionPerformed()
2438   {
2439     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2440     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2441             .getAlignment().getSequenceAt(0), null);
2442
2443     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2444             viewport.getAlignment()));
2445     alignPanel.paintAlignment(true);
2446   }
2447
2448   public void sortIDMenuItem_actionPerformed()
2449   {
2450     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2451     AlignmentSorter.sortByID(viewport.getAlignment());
2452     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2453             viewport.getAlignment()));
2454     alignPanel.paintAlignment(true);
2455   }
2456
2457   public void sortLengthMenuItem_actionPerformed()
2458   {
2459     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2460     AlignmentSorter.sortByLength(viewport.getAlignment());
2461     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2462             viewport.getAlignment()));
2463     alignPanel.paintAlignment(true);
2464   }
2465
2466   public void sortGroupMenuItem_actionPerformed()
2467   {
2468     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2469     AlignmentSorter.sortByGroup(viewport.getAlignment());
2470     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2471             viewport.getAlignment()));
2472     alignPanel.paintAlignment(true);
2473
2474   }
2475
2476   public void removeRedundancyMenuItem_actionPerformed()
2477   {
2478     new RedundancyPanel(alignPanel);
2479   }
2480
2481   public void pairwiseAlignmentMenuItem_actionPerformed()
2482   {
2483     if (viewport.getSelectionGroup() != null
2484             && viewport.getSelectionGroup().getSize() > 1)
2485     {
2486       Frame frame = new Frame();
2487       frame.add(new PairwiseAlignPanel(alignPanel));
2488       jalview.bin.JalviewLite.addFrame(frame,
2489               MessageManager.getString("action.pairwise_alignment"), 600,
2490               500);
2491     }
2492   }
2493
2494   public void PCAMenuItem_actionPerformed()
2495   {
2496     // are the sequences aligned?
2497     if (!viewport.getAlignment().isAligned(false))
2498     {
2499       SequenceI current;
2500       int Width = viewport.getAlignment().getWidth();
2501
2502       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2503       {
2504         current = viewport.getAlignment().getSequenceAt(i);
2505
2506         if (current.getLength() < Width)
2507         {
2508           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2509         }
2510       }
2511       alignPanel.paintAlignment(true);
2512     }
2513
2514     if ((viewport.getSelectionGroup() != null
2515             && viewport.getSelectionGroup().getSize() < 4 && viewport
2516             .getSelectionGroup().getSize() > 0)
2517             || viewport.getAlignment().getHeight() < 4)
2518     {
2519       return;
2520     }
2521
2522     try
2523     {
2524       new PCAPanel(viewport);
2525     } catch (java.lang.OutOfMemoryError ex)
2526     {
2527     }
2528
2529   }
2530
2531   public void averageDistanceTreeMenuItem_actionPerformed()
2532   {
2533     NewTreePanel("AV", "PID", "Average distance tree using PID");
2534   }
2535
2536   public void neighbourTreeMenuItem_actionPerformed()
2537   {
2538     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2539   }
2540
2541   protected void njTreeBlosumMenuItem_actionPerformed()
2542   {
2543     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2544   }
2545
2546   protected void avTreeBlosumMenuItem_actionPerformed()
2547   {
2548     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2549   }
2550
2551   void NewTreePanel(String type, String pwType, String title)
2552   {
2553     // are the sequences aligned?
2554     if (!viewport.getAlignment().isAligned(false))
2555     {
2556       SequenceI current;
2557       int Width = viewport.getAlignment().getWidth();
2558
2559       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2560       {
2561         current = viewport.getAlignment().getSequenceAt(i);
2562
2563         if (current.getLength() < Width)
2564         {
2565           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2566         }
2567       }
2568       alignPanel.paintAlignment(true);
2569
2570     }
2571
2572     if ((viewport.getSelectionGroup() != null && viewport
2573             .getSelectionGroup().getSize() > 1)
2574             || (viewport.getAlignment().getHeight() > 1))
2575     {
2576       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2577
2578       addTreeMenuItem(tp, title);
2579
2580       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2581     }
2582   }
2583
2584   void loadTree_actionPerformed()
2585   {
2586     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2587     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2588     cap.setTreeImport();
2589     Frame frame = new Frame();
2590     frame.add(cap);
2591     jalview.bin.JalviewLite.addFrame(frame,
2592             MessageManager.getString("label.paste_newick_file"), 400, 300);
2593   }
2594
2595   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2596   {
2597     TreePanel tp = new TreePanel(alignPanel, treeFile,
2598             MessageManager.getString("label.load_tree_from_file"), tree);
2599     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2600     addTreeMenuItem(tp, treeFile);
2601   }
2602
2603   /**
2604    * sort the alignment using the given treePanel
2605    *
2606    * @param treePanel
2607    *          tree used to sort view
2608    * @param title
2609    *          string used for undo event name
2610    */
2611   public void sortByTree(TreePanel treePanel, String title)
2612   {
2613     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2614     AlignmentSorter
2615             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2616     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2617     // HistoryItem.SORT));
2618     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2619             "label.order_by_params", new String[]
2620             { title }), oldOrder, viewport.getAlignment()));
2621     alignPanel.paintAlignment(true);
2622   }
2623
2624   /**
2625    * Do any automatic reordering of the alignment and add the necessary bits to
2626    * the menu structure for the new tree
2627    *
2628    * @param treePanel
2629    * @param title
2630    */
2631   protected void addTreeMenuItem(final TreePanel treePanel,
2632           final String title)
2633   {
2634     final MenuItem item = new MenuItem(title);
2635     sortByTreeMenu.add(item);
2636     item.addActionListener(new java.awt.event.ActionListener()
2637     {
2638       @Override
2639       public void actionPerformed(ActionEvent evt)
2640       {
2641         sortByTree(treePanel, title); // treePanel.getTitle());
2642       }
2643     });
2644
2645     treePanel.addWindowListener(new WindowAdapter()
2646     {
2647       @Override
2648       public void windowOpened(WindowEvent e)
2649       {
2650         if (viewport.sortByTree)
2651         {
2652           sortByTree(treePanel, title);
2653         }
2654         super.windowOpened(e);
2655       }
2656
2657       @Override
2658       public void windowClosing(WindowEvent e)
2659       {
2660         sortByTreeMenu.remove(item);
2661       };
2662     });
2663   }
2664
2665   public boolean sortBy(AlignmentOrder alorder, String undoname)
2666   {
2667     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2668     if (viewport.applet.debug)
2669     {
2670       System.err.println("Sorting " + alorder.getOrder().size()
2671               + " in alignment '" + getTitle() + "'");
2672     }
2673     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2674     if (undoname != null)
2675     {
2676       addHistoryItem(new OrderCommand(undoname, oldOrder,
2677               viewport.getAlignment()));
2678     }
2679     alignPanel.paintAlignment(true);
2680     return true;
2681   }
2682
2683   protected void documentation_actionPerformed()
2684   {
2685     alignPanel.av.applet.openJalviewHelpUrl();
2686   }
2687
2688   protected void about_actionPerformed()
2689   {
2690
2691     class AboutPanel extends Canvas
2692     {
2693       String version;
2694
2695       String builddate;
2696
2697       public AboutPanel(String version, String builddate)
2698       {
2699         this.version = version;
2700         this.builddate = builddate;
2701       }
2702
2703       @Override
2704       public void paint(Graphics g)
2705       {
2706         g.setColor(Color.white);
2707         g.fillRect(0, 0, getSize().width, getSize().height);
2708         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2709         FontMetrics fm = g.getFontMetrics();
2710         int fh = fm.getHeight();
2711         int y = 5, x = 7;
2712         g.setColor(Color.black);
2713         // TODO: update this text for each release or centrally store it for
2714         // lite and application
2715         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2716         g.drawString(MessageManager.formatMessage(
2717                 "label.jalviewLite_release", new String[]
2718                 { version }), x, y += fh);
2719         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2720         g.drawString(MessageManager.formatMessage(
2721                 "label.jaview_build_date", new String[]
2722                 { builddate }), x, y += fh);
2723         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2724         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2725                 x, y += fh * 1.5);
2726         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2727                 x + 50, y += fh + 8);
2728         g.drawString(
2729                 MessageManager.getString("label.jalview_dev_managers"), x,
2730                 y += fh);
2731         g.drawString(MessageManager
2732                 .getString("label.jalview_distribution_lists"), x, y += fh);
2733         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2734                 x, y += fh + 8);
2735         g.drawString(
2736                 MessageManager.getString("label.jalview_cite_1_authors"),
2737                 x, y += fh);
2738         g.drawString(
2739                 MessageManager.getString("label.jalview_cite_1_title"), x,
2740                 y += fh);
2741         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2742                 x, y += fh);
2743       }
2744     }
2745
2746     Frame frame = new Frame();
2747     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2748             .getBuildDate()));
2749     jalview.bin.JalviewLite.addFrame(frame,
2750             MessageManager.getString("label.jalview"), 580, 220);
2751
2752   }
2753
2754   public void showURL(String url, String target)
2755   {
2756     if (viewport.applet == null)
2757     {
2758       System.out.println("Not running as applet - no browser available.");
2759     }
2760     else
2761     {
2762       viewport.applet.showURL(url, target);
2763     }
2764   }
2765
2766   // ////////////////////////////////////////////////////////////////////////////////
2767   // JBuilder Graphics here
2768
2769   MenuBar alignFrameMenuBar = new MenuBar();
2770
2771   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2772
2773   MenuItem loadApplication = new MenuItem(
2774           MessageManager.getString("label.view_full_application"));
2775
2776   MenuItem loadTree = new MenuItem(
2777           MessageManager.getString("label.load_associated_tree"));
2778
2779   MenuItem loadAnnotations = new MenuItem(
2780           MessageManager.getString("label.load_features_annotations"));
2781
2782   MenuItem outputFeatures = new MenuItem(
2783           MessageManager.getString("label.export_features"));
2784
2785   MenuItem outputAnnotations = new MenuItem(
2786           MessageManager.getString("label.export_annotations"));
2787
2788   MenuItem closeMenuItem = new MenuItem(
2789           MessageManager.getString("action.close"));
2790
2791   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2792
2793   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2794
2795   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2796
2797   Menu calculateMenu = new Menu(
2798           MessageManager.getString("action.calculate"));
2799
2800   MenuItem selectAllSequenceMenuItem = new MenuItem(
2801           MessageManager.getString("action.select_all"));
2802
2803   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2804           MessageManager.getString("action.deselect_all"));
2805
2806   MenuItem invertSequenceMenuItem = new MenuItem(
2807           MessageManager.getString("action.invert_selection"));
2808
2809   MenuItem remove2LeftMenuItem = new MenuItem();
2810
2811   MenuItem remove2RightMenuItem = new MenuItem();
2812
2813   MenuItem removeGappedColumnMenuItem = new MenuItem();
2814
2815   MenuItem removeAllGapsMenuItem = new MenuItem();
2816
2817   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2818
2819   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2820
2821   MenuItem sortPairwiseMenuItem = new MenuItem();
2822
2823   MenuItem sortIDMenuItem = new MenuItem();
2824
2825   MenuItem sortLengthMenuItem = new MenuItem();
2826
2827   MenuItem sortGroupMenuItem = new MenuItem();
2828
2829   MenuItem removeRedundancyMenuItem = new MenuItem();
2830
2831   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2832
2833   MenuItem PCAMenuItem = new MenuItem();
2834
2835   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2836
2837   MenuItem neighbourTreeMenuItem = new MenuItem();
2838
2839   BorderLayout borderLayout1 = new BorderLayout();
2840
2841   public Label statusBar = new Label();
2842
2843   Menu outputTextboxMenu = new Menu();
2844
2845   MenuItem clustalColour = new MenuItem();
2846
2847   MenuItem zappoColour = new MenuItem();
2848
2849   MenuItem taylorColour = new MenuItem();
2850
2851   MenuItem hydrophobicityColour = new MenuItem();
2852
2853   MenuItem helixColour = new MenuItem();
2854
2855   MenuItem strandColour = new MenuItem();
2856
2857   MenuItem turnColour = new MenuItem();
2858
2859   MenuItem buriedColour = new MenuItem();
2860
2861   MenuItem purinePyrimidineColour = new MenuItem();
2862
2863   MenuItem RNAInteractionColour = new MenuItem();
2864
2865   MenuItem RNAHelixColour = new MenuItem();
2866
2867   MenuItem userDefinedColour = new MenuItem();
2868
2869   MenuItem PIDColour = new MenuItem();
2870
2871   MenuItem BLOSUM62Colour = new MenuItem();
2872
2873   MenuItem tcoffeeColour = new MenuItem();
2874
2875   MenuItem njTreeBlosumMenuItem = new MenuItem();
2876
2877   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2878
2879   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2880
2881   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2882
2883   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2884
2885   MenuItem alProperties = new MenuItem(
2886           MessageManager.getString("label.alignment_props"));
2887
2888   MenuItem overviewMenuItem = new MenuItem();
2889
2890   MenuItem undoMenuItem = new MenuItem();
2891
2892   MenuItem redoMenuItem = new MenuItem();
2893
2894   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2895
2896   MenuItem noColourmenuItem = new MenuItem();
2897
2898   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2899
2900   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2901
2902   MenuItem findMenuItem = new MenuItem();
2903
2904   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2905
2906   MenuItem nucleotideColour = new MenuItem();
2907
2908   MenuItem deleteGroups = new MenuItem();
2909
2910   MenuItem grpsFromSelection = new MenuItem();
2911
2912   MenuItem createGroup = new MenuItem();
2913
2914   MenuItem unGroup = new MenuItem();
2915
2916   MenuItem delete = new MenuItem();
2917
2918   MenuItem copy = new MenuItem();
2919
2920   MenuItem cut = new MenuItem();
2921
2922   Menu pasteMenu = new Menu();
2923
2924   MenuItem pasteNew = new MenuItem();
2925
2926   MenuItem pasteThis = new MenuItem();
2927
2928   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2929
2930   MenuItem font = new MenuItem();
2931
2932   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2933
2934   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2935
2936   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2937
2938   MenuItem modifyPID = new MenuItem();
2939
2940   MenuItem modifyConservation = new MenuItem();
2941
2942   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2943           "Autocalculate Consensus", true);
2944
2945   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2946           "Sort Alignment With New Tree", true);
2947
2948   Menu sortByTreeMenu = new Menu();
2949
2950   Menu sort = new Menu();
2951
2952   Menu calculate = new Menu();
2953
2954   MenuItem inputText = new MenuItem();
2955
2956   Menu helpMenu = new Menu();
2957
2958   MenuItem documentation = new MenuItem();
2959
2960   MenuItem about = new MenuItem();
2961
2962   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2963
2964   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2965
2966   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2967
2968   Menu autoAnnMenu = new Menu();
2969
2970   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2971
2972   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2973
2974   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2975
2976   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2977
2978   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2979
2980   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2981
2982   private void jbInit() throws Exception
2983   {
2984
2985     setMenuBar(alignFrameMenuBar);
2986
2987     MenuItem item;
2988
2989     // dynamically fill save as menu with available formats
2990     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2991     {
2992
2993       item = new MenuItem(
2994               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2995
2996       item.addActionListener(new java.awt.event.ActionListener()
2997       {
2998         @Override
2999         public void actionPerformed(ActionEvent e)
3000         {
3001           outputText_actionPerformed(e);
3002         }
3003       });
3004
3005       outputTextboxMenu.add(item);
3006     }
3007     closeMenuItem.addActionListener(this);
3008     loadApplication.addActionListener(this);
3009
3010     loadTree.addActionListener(this);
3011     loadAnnotations.addActionListener(this);
3012     outputFeatures.addActionListener(this);
3013     outputAnnotations.addActionListener(this);
3014     selectAllSequenceMenuItem.addActionListener(this);
3015     deselectAllSequenceMenuItem.addActionListener(this);
3016     invertSequenceMenuItem.addActionListener(this);
3017     remove2LeftMenuItem.setLabel(MessageManager
3018             .getString("action.remove_left"));
3019     remove2LeftMenuItem.addActionListener(this);
3020     remove2RightMenuItem.setLabel(MessageManager
3021             .getString("action.remove_right"));
3022     remove2RightMenuItem.addActionListener(this);
3023     removeGappedColumnMenuItem.setLabel(MessageManager
3024             .getString("action.remove_empty_columns"));
3025     removeGappedColumnMenuItem.addActionListener(this);
3026     removeAllGapsMenuItem.setLabel(MessageManager
3027             .getString("action.remove_all_gaps"));
3028     removeAllGapsMenuItem.addActionListener(this);
3029     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3030     viewBoxesMenuItem.setState(true);
3031     viewBoxesMenuItem.addItemListener(this);
3032     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3033     viewTextMenuItem.setState(true);
3034     viewTextMenuItem.addItemListener(this);
3035     sortPairwiseMenuItem.setLabel(MessageManager
3036             .getString("action.by_pairwise_id"));
3037     sortPairwiseMenuItem.addActionListener(this);
3038     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3039     sortIDMenuItem.addActionListener(this);
3040     sortLengthMenuItem.setLabel(MessageManager
3041             .getString("action.by_length"));
3042     sortLengthMenuItem.addActionListener(this);
3043     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3044     sortGroupMenuItem.addActionListener(this);
3045     removeRedundancyMenuItem.setLabel(MessageManager
3046             .getString("action.remove_redundancy"));
3047     removeRedundancyMenuItem.addActionListener(this);
3048     pairwiseAlignmentMenuItem.setLabel(MessageManager
3049             .getString("action.pairwise_alignment"));
3050     pairwiseAlignmentMenuItem.addActionListener(this);
3051     PCAMenuItem.setLabel(MessageManager
3052             .getString("label.principal_component_analysis"));
3053     PCAMenuItem.addActionListener(this);
3054     averageDistanceTreeMenuItem.setLabel(MessageManager
3055             .getString("label.average_distance_identity"));
3056     averageDistanceTreeMenuItem.addActionListener(this);
3057     neighbourTreeMenuItem.setLabel(MessageManager
3058             .getString("label.neighbour_joining_identity"));
3059     neighbourTreeMenuItem.addActionListener(this);
3060     statusBar.setBackground(Color.white);
3061     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3062     statusBar.setText(MessageManager.getString("label.status_bar"));
3063     outputTextboxMenu.setLabel(MessageManager
3064             .getString("label.out_to_textbox"));
3065     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3066
3067     clustalColour.addActionListener(this);
3068     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3069     zappoColour.addActionListener(this);
3070     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3071     taylorColour.addActionListener(this);
3072     hydrophobicityColour.setLabel(MessageManager
3073             .getString("label.hydrophobicity"));
3074     hydrophobicityColour.addActionListener(this);
3075     helixColour
3076             .setLabel(MessageManager.getString("label.helix_propensity"));
3077     helixColour.addActionListener(this);
3078     strandColour.setLabel(MessageManager
3079             .getString("label.strand_propensity"));
3080     strandColour.addActionListener(this);
3081     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3082     turnColour.addActionListener(this);
3083     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3084     buriedColour.addActionListener(this);
3085     purinePyrimidineColour.setLabel(MessageManager
3086             .getString("label.purine_pyrimidine"));
3087     purinePyrimidineColour.addActionListener(this);
3088     RNAInteractionColour.setLabel(MessageManager
3089             .getString("label.rna_interaction"));
3090     RNAInteractionColour.addActionListener(this);
3091     RNAHelixColour.setLabel(MessageManager
3092             .getString("action.by_rna_helixes"));
3093     RNAHelixColour.addActionListener(this);
3094     userDefinedColour.setLabel(MessageManager
3095             .getString("action.user_defined"));
3096     userDefinedColour.addActionListener(this);
3097     PIDColour.setLabel(MessageManager
3098             .getString("label.percentage_identity"));
3099     PIDColour.addActionListener(this);
3100     BLOSUM62Colour.setLabel(MessageManager
3101             .getString("label.blosum62_score"));
3102     BLOSUM62Colour.addActionListener(this);
3103     tcoffeeColour
3104             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3105     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3106                                      // provided
3107     tcoffeeColour.addActionListener(this);
3108     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3109             .getString("label.average_distance_bloslum62"));
3110     avDistanceTreeBlosumMenuItem.addActionListener(this);
3111     njTreeBlosumMenuItem.setLabel(MessageManager
3112             .getString("label.neighbour_blosum62"));
3113     njTreeBlosumMenuItem.addActionListener(this);
3114     annotationPanelMenuItem.setLabel(MessageManager
3115             .getString("label.show_annotations"));
3116     annotationPanelMenuItem.addItemListener(this);
3117     colourTextMenuItem.setLabel(MessageManager
3118             .getString("label.colour_text"));
3119     colourTextMenuItem.addItemListener(this);
3120     displayNonconservedMenuItem.setLabel(MessageManager
3121             .getString("label.show_non_conversed"));
3122     displayNonconservedMenuItem.addItemListener(this);
3123     alProperties.addActionListener(this);
3124     overviewMenuItem.setLabel(MessageManager
3125             .getString("label.overview_window"));
3126     overviewMenuItem.addActionListener(this);
3127     undoMenuItem.setEnabled(false);
3128     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3129     undoMenuItem.addActionListener(this);
3130     redoMenuItem.setEnabled(false);
3131     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3132     redoMenuItem.addActionListener(this);
3133     conservationMenuItem.setLabel(MessageManager
3134             .getString("action.by_conservation"));
3135     conservationMenuItem.addItemListener(this);
3136     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3137     noColourmenuItem.addActionListener(this);
3138     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3139     wrapMenuItem.addItemListener(this);
3140     renderGapsMenuItem.setLabel(MessageManager
3141             .getString("action.show_gaps"));
3142     renderGapsMenuItem.setState(true);
3143     renderGapsMenuItem.addItemListener(this);
3144     findMenuItem.setLabel(MessageManager.getString("action.find"));
3145     findMenuItem.addActionListener(this);
3146     abovePIDThreshold.setLabel(MessageManager
3147             .getString("label.above_identity_threshold"));
3148     abovePIDThreshold.addItemListener(this);
3149     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3150     nucleotideColour.addActionListener(this);
3151     deleteGroups.setLabel(MessageManager
3152             .getString("action.undefine_groups"));
3153     deleteGroups.addActionListener(this);
3154     grpsFromSelection.setLabel(MessageManager
3155             .getString("action.make_groups_selection"));
3156     grpsFromSelection.addActionListener(this);
3157     createGroup.setLabel(MessageManager.getString("action.create_group"));
3158     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3159     copy.setLabel(MessageManager.getString("action.copy"));
3160     copy.addActionListener(this);
3161     cut.setLabel(MessageManager.getString("action.cut"));
3162     cut.addActionListener(this);
3163     delete.setLabel(MessageManager.getString("action.delete"));
3164     delete.addActionListener(this);
3165     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3166     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3167     pasteNew.addActionListener(this);
3168     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3169     pasteThis.addActionListener(this);
3170     applyToAllGroups.setLabel(MessageManager
3171             .getString("label.apply_colour_to_all_groups"));
3172     applyToAllGroups.setState(true);
3173     applyToAllGroups.addItemListener(this);
3174     font.setLabel(MessageManager.getString("action.font"));
3175     font.addActionListener(this);
3176     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3177     scaleAbove.setState(true);
3178     scaleAbove.setEnabled(false);
3179     scaleAbove.addItemListener(this);
3180     scaleLeft.setEnabled(false);
3181     scaleLeft.setState(true);
3182     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3183     scaleLeft.addItemListener(this);
3184     scaleRight.setEnabled(false);
3185     scaleRight.setState(true);
3186     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3187     scaleRight.addItemListener(this);
3188     modifyPID.setLabel(MessageManager
3189             .getString("label.modify_identity_thereshold"));
3190     modifyPID.addActionListener(this);
3191     modifyConservation.setLabel(MessageManager
3192             .getString("label.modify_conservation_thereshold"));
3193     modifyConservation.addActionListener(this);
3194     sortByTreeMenu.setLabel(MessageManager
3195             .getString("action.by_tree_order"));
3196     sort.setLabel(MessageManager.getString("action.sort"));
3197     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3198     autoCalculate.addItemListener(this);
3199     sortByTree.addItemListener(this);
3200     inputText
3201             .setLabel(MessageManager.getString("label.input_from_textbox"));
3202     inputText.addActionListener(this);
3203     centreColumnLabelFlag.setLabel(MessageManager
3204             .getString("label.centre_column_labels"));
3205     centreColumnLabelFlag.addItemListener(this);
3206     followMouseOverFlag.setLabel(MessageManager
3207             .getString("label.automatic_scrolling"));
3208     followMouseOverFlag.addItemListener(this);
3209     helpMenu.setLabel(MessageManager.getString("action.help"));
3210     documentation.setLabel(MessageManager.getString("label.documentation"));
3211     documentation.addActionListener(this);
3212
3213     about.setLabel(MessageManager.getString("label.about"));
3214     about.addActionListener(this);
3215     seqLimits.setState(true);
3216     seqLimits.setLabel(MessageManager
3217             .getString("label.show_sequence_limits"));
3218     seqLimits.addItemListener(this);
3219     featureSettings.setLabel(MessageManager
3220             .getString("label.feature_settings"));
3221     featureSettings.addActionListener(this);
3222     sequenceFeatures.setLabel(MessageManager
3223             .getString("label.sequence_features"));
3224     sequenceFeatures.addItemListener(this);
3225     sequenceFeatures.setState(false);
3226     annotationColour.setLabel(MessageManager
3227             .getString("action.by_annotation"));
3228     annotationColour.addActionListener(this);
3229     invertSequenceMenuItem.setLabel(MessageManager
3230             .getString("action.invert_sequence_selection"));
3231     invertColSel.setLabel(MessageManager
3232             .getString("action.invert_column_selection"));
3233     menu1.setLabel(MessageManager.getString("action.show"));
3234     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3235     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3236     menu2.setLabel(MessageManager.getString("action.hide"));
3237     hideColumns
3238             .setLabel(MessageManager.getString("label.selected_columns"));
3239     hideSequences.setLabel(MessageManager
3240             .getString("label.selected_sequences"));
3241     hideAllButSelection.setLabel(MessageManager
3242             .getString("label.all_but_selected_region"));
3243     hideAllSelection.setLabel(MessageManager
3244             .getString("label.selected_region"));
3245     showAllHidden.setLabel(MessageManager
3246             .getString("label.all_sequences_columns"));
3247     showGroupConsensus.setLabel(MessageManager
3248             .getString("label.group_consensus"));
3249     showGroupConservation.setLabel(MessageManager
3250             .getString("label.group_conservation"));
3251     showConsensusHistogram.setLabel(MessageManager
3252             .getString("label.show_consensus_histogram"));
3253     showSequenceLogo.setLabel(MessageManager
3254             .getString("label.show_consensus_logo"));
3255     normSequenceLogo.setLabel(MessageManager
3256             .getString("label.norm_consensus_logo"));
3257     applyAutoAnnotationSettings.setLabel(MessageManager
3258             .getString("label.apply_all_groups"));
3259     applyAutoAnnotationSettings.setState(true);
3260     autoAnnMenu.setLabel(MessageManager
3261             .getString("label.autocalculated_annotation"));
3262
3263     invertColSel.addActionListener(this);
3264     showColumns.addActionListener(this);
3265     showSeqs.addActionListener(this);
3266     hideColumns.addActionListener(this);
3267     hideSequences.addActionListener(this);
3268     hideAllButSelection.addActionListener(this);
3269     hideAllSelection.addActionListener(this);
3270     showAllHidden.addActionListener(this);
3271     showGroupConsensus.addItemListener(this);
3272     showGroupConservation.addItemListener(this);
3273     showConsensusHistogram.addItemListener(this);
3274     showSequenceLogo.addItemListener(this);
3275     normSequenceLogo.addItemListener(this);
3276
3277     applyAutoAnnotationSettings.addItemListener(this);
3278     formatMenu.setLabel(MessageManager.getString("action.format"));
3279     selectMenu.setLabel(MessageManager.getString("action.select"));
3280     newView.setLabel(MessageManager.getString("action.new_view"));
3281     newView.addActionListener(this);
3282     alignFrameMenuBar.add(fileMenu);
3283     alignFrameMenuBar.add(editMenu);
3284     alignFrameMenuBar.add(selectMenu);
3285     alignFrameMenuBar.add(viewMenu);
3286     alignFrameMenuBar.add(formatMenu);
3287     alignFrameMenuBar.add(colourMenu);
3288     alignFrameMenuBar.add(calculateMenu);
3289     alignFrameMenuBar.add(helpMenu);
3290
3291     fileMenu.add(inputText);
3292     fileMenu.add(loadTree);
3293     fileMenu.add(loadAnnotations);
3294
3295     fileMenu.addSeparator();
3296     fileMenu.add(outputTextboxMenu);
3297     fileMenu.add(outputFeatures);
3298     fileMenu.add(outputAnnotations);
3299
3300     if (jalviewServletURL != null)
3301     {
3302       fileMenu.add(loadApplication);
3303     }
3304
3305     fileMenu.addSeparator();
3306     fileMenu.add(closeMenuItem);
3307
3308     editMenu.add(undoMenuItem);
3309     editMenu.add(redoMenuItem);
3310     editMenu.add(cut);
3311     editMenu.add(copy);
3312     editMenu.add(pasteMenu);
3313     editMenu.add(delete);
3314     editMenu.addSeparator();
3315     editMenu.add(remove2LeftMenuItem);
3316     editMenu.add(remove2RightMenuItem);
3317     editMenu.add(removeGappedColumnMenuItem);
3318     editMenu.add(removeAllGapsMenuItem);
3319     editMenu.add(removeRedundancyMenuItem);
3320     viewMenu.add(newView);
3321     viewMenu.addSeparator();
3322     viewMenu.add(menu1);
3323     viewMenu.add(menu2);
3324     viewMenu.addSeparator();
3325     viewMenu.add(followMouseOverFlag);
3326     viewMenu.add(annotationPanelMenuItem);
3327     autoAnnMenu.add(applyAutoAnnotationSettings);
3328     autoAnnMenu.add(showConsensusHistogram);
3329     autoAnnMenu.add(showSequenceLogo);
3330     autoAnnMenu.add(normSequenceLogo);
3331     autoAnnMenu.addSeparator();
3332     autoAnnMenu.add(showGroupConservation);
3333     autoAnnMenu.add(showGroupConsensus);
3334     viewMenu.add(autoAnnMenu);
3335     viewMenu.addSeparator();
3336     viewMenu.add(sequenceFeatures);
3337     viewMenu.add(featureSettings);
3338     viewMenu.addSeparator();
3339     viewMenu.add(alProperties);
3340     viewMenu.addSeparator();
3341     viewMenu.add(overviewMenuItem);
3342     colourMenu.add(applyToAllGroups);
3343     colourMenu.addSeparator();
3344     colourMenu.add(noColourmenuItem);
3345     colourMenu.add(clustalColour);
3346     colourMenu.add(BLOSUM62Colour);
3347     colourMenu.add(PIDColour);
3348     colourMenu.add(zappoColour);
3349     colourMenu.add(taylorColour);
3350     colourMenu.add(hydrophobicityColour);
3351     colourMenu.add(helixColour);
3352     colourMenu.add(strandColour);
3353     colourMenu.add(turnColour);
3354     colourMenu.add(buriedColour);
3355     colourMenu.add(nucleotideColour);
3356     colourMenu.add(purinePyrimidineColour);
3357     // colourMenu.add(RNAInteractionColour);
3358     colourMenu.add(tcoffeeColour);
3359     colourMenu.add(userDefinedColour);
3360     colourMenu.addSeparator();
3361     colourMenu.add(conservationMenuItem);
3362     colourMenu.add(modifyConservation);
3363     colourMenu.add(abovePIDThreshold);
3364     colourMenu.add(modifyPID);
3365     colourMenu.add(annotationColour);
3366     colourMenu.add(RNAHelixColour);
3367     calculateMenu.add(sort);
3368     calculateMenu.add(calculate);
3369     calculateMenu.addSeparator();
3370     calculateMenu.add(pairwiseAlignmentMenuItem);
3371     calculateMenu.add(PCAMenuItem);
3372     calculateMenu.add(autoCalculate);
3373     calculateMenu.add(sortByTree);
3374     this.add(statusBar, BorderLayout.SOUTH);
3375     pasteMenu.add(pasteNew);
3376     pasteMenu.add(pasteThis);
3377     sort.add(sortIDMenuItem);
3378     sort.add(sortLengthMenuItem);
3379     sort.add(sortByTreeMenu);
3380     sort.add(sortGroupMenuItem);
3381     sort.add(sortPairwiseMenuItem);
3382     calculate.add(averageDistanceTreeMenuItem);
3383     calculate.add(neighbourTreeMenuItem);
3384     calculate.add(avDistanceTreeBlosumMenuItem);
3385     calculate.add(njTreeBlosumMenuItem);
3386     helpMenu.add(documentation);
3387     helpMenu.add(about);
3388     menu1.add(showColumns);
3389     menu1.add(showSeqs);
3390     menu1.add(showAllHidden);
3391     menu2.add(hideColumns);
3392     menu2.add(hideSequences);
3393     menu2.add(hideAllSelection);
3394     menu2.add(hideAllButSelection);
3395     formatMenu.add(font);
3396     formatMenu.add(seqLimits);
3397     formatMenu.add(wrapMenuItem);
3398     formatMenu.add(scaleAbove);
3399     formatMenu.add(scaleLeft);
3400     formatMenu.add(scaleRight);
3401     formatMenu.add(viewBoxesMenuItem);
3402     formatMenu.add(viewTextMenuItem);
3403     formatMenu.add(colourTextMenuItem);
3404     formatMenu.add(displayNonconservedMenuItem);
3405     formatMenu.add(renderGapsMenuItem);
3406     formatMenu.add(centreColumnLabelFlag);
3407     selectMenu.add(findMenuItem);
3408     selectMenu.addSeparator();
3409     selectMenu.add(selectAllSequenceMenuItem);
3410     selectMenu.add(deselectAllSequenceMenuItem);
3411     selectMenu.add(invertSequenceMenuItem);
3412     selectMenu.add(invertColSel);
3413     selectMenu.add(createGroup);
3414     selectMenu.add(unGroup);
3415     selectMenu.add(grpsFromSelection);
3416     selectMenu.add(deleteGroups);
3417
3418   }
3419
3420   public void setStatus(String string)
3421   {
3422     statusBar.setText(string);
3423   };
3424
3425   MenuItem featureSettings = new MenuItem();
3426
3427   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3428
3429   MenuItem annotationColour = new MenuItem();
3430
3431   MenuItem invertColSel = new MenuItem();
3432
3433   Menu menu1 = new Menu();
3434
3435   MenuItem showColumns = new MenuItem();
3436
3437   MenuItem showSeqs = new MenuItem();
3438
3439   Menu menu2 = new Menu();
3440
3441   MenuItem hideColumns = new MenuItem();
3442
3443   MenuItem hideSequences = new MenuItem();
3444
3445   MenuItem hideAllButSelection = new MenuItem();
3446
3447   MenuItem hideAllSelection = new MenuItem();
3448
3449   MenuItem showAllHidden = new MenuItem();
3450
3451   Menu formatMenu = new Menu();
3452
3453   Menu selectMenu = new Menu();
3454
3455   MenuItem newView = new MenuItem();
3456
3457   /**
3458    * Attach the alignFrame panels after embedding menus, if necessary. This used
3459    * to be called setEmbedded, but is now creates the dropdown menus in a
3460    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3461    *
3462    * @param reallyEmbedded
3463    *          true to attach the view to the applet area on the page rather than
3464    *          in a new window
3465    */
3466   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3467   {
3468     if (reallyEmbedded)
3469     {
3470       // ////
3471       // Explicly build the embedded menu panel for the on-page applet
3472       //
3473       // view cannot be closed if its actually on the page
3474       fileMenu.remove(closeMenuItem);
3475       fileMenu.remove(3); // Remove Seperator
3476       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3477               Font.PLAIN, 11, false); // use our own fonts.
3478       // and actually add the components to the applet area
3479       viewport.applet.setLayout(new BorderLayout());
3480       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3481       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3482       alignPanel.setSize(viewport.applet.getSize().width,
3483               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3484                       - statusBar.HEIGHT);
3485       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3486       final AlignFrame me = this;
3487       viewport.applet.addFocusListener(new FocusListener()
3488       {
3489
3490         @Override
3491         public void focusLost(FocusEvent e)
3492         {
3493           if (me.viewport.applet.currentAlignFrame == me)
3494           {
3495             me.viewport.applet.currentAlignFrame = null;
3496           }
3497         }
3498
3499         @Override
3500         public void focusGained(FocusEvent e)
3501         {
3502           me.viewport.applet.currentAlignFrame = me;
3503         }
3504       });
3505       viewport.applet.validate();
3506     }
3507     else
3508     {
3509       // //////
3510       // test and embed menu bar if necessary.
3511       //
3512       if (embedMenuIfNeeded(alignPanel))
3513       {
3514         // adjust for status bar height too
3515         alignPanel.setSize(getSize().width, getSize().height
3516                 - statusBar.HEIGHT);
3517       }
3518       add(statusBar, BorderLayout.SOUTH);
3519       add(alignPanel, BorderLayout.CENTER);
3520       // and register with the applet so it can pass external API calls to us
3521       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3522               DEFAULT_HEIGHT);
3523     }
3524   }
3525
3526   /**
3527    * create a new binding between structures in an existing jmol viewer instance
3528    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3529    * this does not open a new Jmol window, or modify the display of the
3530    * structures in the original jmol window. Note This method doesn't work
3531    * without an additional javascript library to exchange messages between the
3532    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3533    *
3534    * @param viewer
3535    *          JmolViewer instance
3536    * @param sequenceIds
3537    *          - sequence Ids to search for associations
3538    */
3539   public SequenceStructureBinding addStructureViewInstance(
3540           Object jmolviewer, String[] sequenceIds)
3541   {
3542     org.jmol.api.JmolViewer viewer = null;
3543     try
3544     {
3545       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3546     } catch (ClassCastException ex)
3547     {
3548       System.err.println("Unsupported viewer object :"
3549               + jmolviewer.getClass());
3550     }
3551     if (viewer == null)
3552     {
3553       System.err.println("Can't use this object as a structure viewer:"
3554               + jmolviewer.getClass());
3555       return null;
3556     }
3557     SequenceI[] seqs = null;
3558     if (sequenceIds == null || sequenceIds.length == 0)
3559     {
3560       seqs = viewport.getAlignment().getSequencesArray();
3561     }
3562     else
3563     {
3564       Vector sqi = new Vector();
3565       AlignmentI al = viewport.getAlignment();
3566       for (int sid = 0; sid < sequenceIds.length; sid++)
3567       {
3568         SequenceI sq = al.findName(sequenceIds[sid]);
3569         if (sq != null)
3570         {
3571           sqi.addElement(sq);
3572         }
3573       }
3574       if (sqi.size() > 0)
3575       {
3576         seqs = new SequenceI[sqi.size()];
3577         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3578         {
3579           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3580         }
3581       }
3582       else
3583       {
3584         return null;
3585       }
3586     }
3587     ExtJmol jmv = null;
3588     // TODO: search for a jmv that involves viewer
3589     if (jmv == null)
3590     { // create a new viewer/jalview binding.
3591       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3592       { seqs });
3593     }
3594     return jmv;
3595
3596   }
3597
3598   /**
3599    * bind a pdb file to a sequence in the current view
3600    *
3601    * @param sequenceId
3602    *          - sequenceId within the dataset.
3603    * @param pdbEntryString
3604    *          - the short name for the PDB file
3605    * @param pdbFile
3606    *          - pdb file - either a URL or a valid PDB file.
3607    * @return true if binding was as success TODO: consider making an exception
3608    *         structure for indicating when PDB parsing or sequenceId location
3609    *         fails.
3610    */
3611   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3612           String pdbFile)
3613   {
3614     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3615     boolean needtoadd = false;
3616     if (toaddpdb != null)
3617     {
3618       Vector pdbe = toaddpdb.getPDBId();
3619       PDBEntry pdbentry = null;
3620       if (pdbe != null && pdbe.size() > 0)
3621       {
3622         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3623         {
3624           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3625           if (!pdbentry.getId().equals(pdbEntryString)
3626                   && !pdbentry.getFile().equals(pdbFile))
3627           {
3628             pdbentry = null;
3629           }
3630           else
3631           {
3632             continue;
3633           }
3634         }
3635       }
3636       if (pdbentry == null)
3637       {
3638         pdbentry = new PDBEntry();
3639         pdbentry.setId(pdbEntryString);
3640         pdbentry.setFile(pdbFile);
3641         needtoadd = true; // add this new entry to sequence.
3642       }
3643       // resolve data source
3644       // TODO: this code should be a refactored to an io package
3645       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3646       if (protocol == null)
3647       {
3648         return false;
3649       }
3650       if (needtoadd)
3651       {
3652         // make a note of the access mode and add
3653         if (pdbentry.getProperty() == null)
3654         {
3655           pdbentry.setProperty(new Hashtable());
3656         }
3657         pdbentry.getProperty().put("protocol", protocol);
3658         toaddpdb.addPDBId(pdbentry);
3659       }
3660     }
3661     return true;
3662   }
3663
3664   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3665   {
3666     if (seqs != null)
3667     {
3668       Vector sequences = new Vector();
3669       for (int i = 0; i < seqs.length; i++)
3670       {
3671         if (seqs[i] != null)
3672         {
3673           sequences.addElement(new Object[]
3674           { seqs[i], (chains != null) ? chains[i] : null });
3675         }
3676       }
3677       seqs = new SequenceI[sequences.size()];
3678       chains = new String[sequences.size()];
3679       for (int i = 0, isize = sequences.size(); i < isize; i++)
3680       {
3681         Object[] oj = (Object[]) sequences.elementAt(i);
3682
3683         seqs[i] = (SequenceI) oj[0];
3684         chains[i] = (String) oj[1];
3685       }
3686     }
3687     return new Object[]
3688     { seqs, chains };
3689
3690   }
3691
3692   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3693           SequenceI[] seqs, String[] chains, String protocol)
3694   {
3695     // Scrub any null sequences from the array
3696     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3697     seqs = (SequenceI[]) sqch[0];
3698     chains = (String[]) sqch[1];
3699     if (seqs == null || seqs.length == 0)
3700     {
3701       System.err
3702               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3703     }
3704     if (protocol == null || protocol.trim().length() == 0
3705             || protocol.equals("null"))
3706     {
3707       protocol = (String) pdb.getProperty().get("protocol");
3708       if (protocol == null)
3709       {
3710         System.err.println("Couldn't work out protocol to open structure: "
3711                 + pdb.getId());
3712         return;
3713       }
3714     }
3715     if (applet.useXtrnalSviewer)
3716     {
3717       // register the association(s) and quit, don't create any windows.
3718       if (StructureSelectionManager.getStructureSelectionManager(applet)
3719               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3720       {
3721         System.err.println("Failed to map " + pdb.getFile() + " ("
3722                 + protocol + ") to any sequences");
3723       }
3724       return;
3725     }
3726     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3727     {
3728       // can only do alignments with Jmol
3729       // find the last jmol window assigned to this alignment
3730       jalview.appletgui.AppletJmol ajm = null, tajm;
3731       Vector jmols = applet
3732               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3733       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3734       {
3735         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3736         if (tajm.ap.alignFrame == this)
3737         {
3738           ajm = tajm;
3739           break;
3740         }
3741       }
3742       if (ajm != null)
3743       {
3744         System.err
3745                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3746         // try and add the pdb structure
3747         // ajm.addS
3748         ajm = null;
3749       }
3750     }
3751     // otherwise, create a new window
3752     if (applet.jmolAvailable)
3753     {
3754       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3755               protocol);
3756       applet.lastFrameX += 40;
3757       applet.lastFrameY += 40;
3758     }
3759     else
3760     {
3761       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3762     }
3763
3764   }
3765
3766   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3767           SequenceI[][] seqs, String[][] chains, String[] protocols)
3768   {
3769     // TODO Auto-generated method stub
3770     System.err.println("Aligned Structure View: Not yet implemented.");
3771   }
3772
3773   /**
3774    * modify the current selection, providing the user has not made a selection
3775    * already.
3776    *
3777    * @param sel
3778    *          - sequences from this alignment
3779    * @param csel
3780    *          - columns to be selected on the alignment
3781    */
3782   public void select(SequenceGroup sel, ColumnSelection csel)
3783   {
3784     alignPanel.seqPanel.selection(sel, csel, null);
3785   }
3786
3787   public void scrollTo(int row, int column)
3788   {
3789     alignPanel.seqPanel.scrollTo(row, column);
3790   }
3791
3792   public void scrollToRow(int row)
3793   {
3794     alignPanel.seqPanel.scrollToRow(row);
3795   }
3796
3797   public void scrollToColumn(int column)
3798   {
3799     alignPanel.seqPanel.scrollToColumn(column);
3800   }
3801
3802   /**
3803    * @return the alignments unique ID.
3804    */
3805   public String getSequenceSetId()
3806   {
3807     return viewport.getSequenceSetId();
3808   }
3809
3810   /**
3811    * Load the (T-Coffee) score file from the specified url
3812    *
3813    * @param source
3814    *          File/URL/T-COFFEE score file contents
3815    * @throws IOException
3816    * @return true if alignment was annotated with data from source
3817    */
3818   public boolean loadScoreFile(String source) throws IOException
3819   {
3820
3821     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3822             AppletFormatAdapter.checkProtocol(source));
3823     if (!file.isValid())
3824     {
3825       // TODO: raise dialog for gui
3826       System.err.println("Problems parsing T-Coffee scores: "
3827               + file.getWarningMessage());
3828       System.err.println("Origin was:\n" + source);
3829       return false;
3830     }
3831
3832     /*
3833      * check that the score matrix matches the alignment dimensions
3834      */
3835     AlignmentI aln;
3836     if ((aln = viewport.getAlignment()) != null
3837             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3838                     .getWidth()))
3839     {
3840       // TODO: raise a dialog box here rather than bomb out.
3841       System.err
3842               .println("The scores matrix does not match the alignment dimensions");
3843
3844     }
3845
3846     // TODO add parameter to indicate if matching should be done
3847     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3848     {
3849       alignPanel.fontChanged();
3850       tcoffeeColour.setEnabled(true);
3851       // switch to this color
3852       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3853       return true;
3854     }
3855     else
3856     {
3857       System.err.println("Problems resolving T-Coffee scores:");
3858       if (file.getWarningMessage() != null)
3859       {
3860         System.err.println(file.getWarningMessage());
3861       }
3862     }
3863     return false;
3864   }
3865
3866 }