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.api.AlignViewControllerGuiI;
  25 import jalview.api.AlignViewControllerI;
  26 import jalview.api.SequenceStructureBinding;
  27 import jalview.api.FeatureRenderer;
  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.StrandColourScheme;
  60 import jalview.schemes.TCoffeeColourScheme;
  61 import jalview.schemes.TaylorColourScheme;
  62 import jalview.schemes.TurnColourScheme;
  63 import jalview.schemes.ZappoColourScheme;
  64 import jalview.structure.StructureSelectionManager;
  65 import jalview.util.MessageManager;
  66
  67 import java.awt.BorderLayout;
  68 import java.awt.Canvas;
  69 import java.awt.CheckboxMenuItem;
  70 import java.awt.Color;
  71 import java.awt.Font;
  72 import java.awt.FontMetrics;
  73 import java.awt.Frame;
  74 import java.awt.Graphics;
  75 import java.awt.Label;
  76 import java.awt.Menu;
  77 import java.awt.MenuBar;
  78 import java.awt.MenuItem;
  79 import java.awt.event.ActionEvent;
  80 import java.awt.event.ActionListener;
  81 import java.awt.event.FocusEvent;
  82 import java.awt.event.FocusListener;
  83 import java.awt.event.ItemEvent;
  84 import java.awt.event.ItemListener;
  85 import java.awt.event.KeyEvent;
  86 import java.awt.event.KeyListener;
  87 import java.awt.event.WindowAdapter;
  88 import java.awt.event.WindowEvent;
  89 import java.io.IOException;
  90 import java.net.URL;
  91 import java.net.URLEncoder;
  92 import java.util.Arrays;
  93 import java.util.Enumeration;
  94 import java.util.Hashtable;
  95 import java.util.Iterator;
  96 import java.util.List;
  97 import java.util.Map;
  98 import java.util.StringTokenizer;
  99 import java.util.Vector;
 100
 101 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 102         ItemListener, KeyListener, AlignViewControllerGuiI
 103 {
 104   public AlignViewControllerI avc;
 105
 106   public AlignmentPanel alignPanel;
 107
 108   public AlignViewport viewport;
 109
 110   int DEFAULT_WIDTH = 700;
 111
 112   int DEFAULT_HEIGHT = 500;
 113
 114   String jalviewServletURL;
 115
 116   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 117           String title, boolean embedded)
 118   {
 119     if (applet != null)
 120     {
 121       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 122     }
 123
 124     try
 125     {
 126       jbInit();
 127     } catch (Exception ex)
 128     {
 129       ex.printStackTrace();
 130     }
 131     // need to get window geometry before we calculate alignment layout
 132     if (applet != null)
 133     {
 134       String param;
 135       try
 136       {
 137         param = applet.getParameter("windowWidth");
 138         if (param != null)
 139         {
 140           int width = Integer.parseInt(param);
 141           DEFAULT_WIDTH = width;
 142         }
 143         param = applet.getParameter("windowHeight");
 144         if (param != null)
 145         {
 146           int height = Integer.parseInt(param);
 147           DEFAULT_HEIGHT = height;
 148         }
 149       } catch (Exception ex)
 150       {
 151       }
 152     }
 153     viewport = new AlignViewport(al, applet);
 154     alignPanel = new AlignmentPanel(this, viewport);
 155     avc = new jalview.controller.AlignViewController(this, viewport,
 156             alignPanel);
 157     viewport.updateConservation(alignPanel);
 158     viewport.updateConsensus(alignPanel);
 159
 160     annotationPanelMenuItem.setState(viewport.showAnnotation);
 161     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 162     followMouseOverFlag.setState(viewport.getFollowHighlight());
 163     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 164     showGroupConservation.setState(viewport.isShowGroupConservation());
 165     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 166     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 167     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 168     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 169
 170     seqLimits.setState(viewport.showJVSuffix);
 171
 172     if (applet != null)
 173     {
 174       String param = applet.getParameter("sortBy");
 175       if (param != null)
 176       {
 177         if (param.equalsIgnoreCase("Id"))
 178         {
 179           sortIDMenuItem_actionPerformed();
 180         }
 181         else if (param.equalsIgnoreCase("Pairwise Identity"))
 182         {
 183           sortPairwiseMenuItem_actionPerformed();
 184         }
 185         else if (param.equalsIgnoreCase("Length"))
 186         {
 187           sortLengthMenuItem_actionPerformed();
 188         }
 189       }
 190
 191       param = applet.getParameter("wrap");
 192       if (param != null)
 193       {
 194         if (param.equalsIgnoreCase("true"))
 195         {
 196           wrapMenuItem.setState(true);
 197           wrapMenuItem_actionPerformed();
 198         }
 199       }
 200       param = applet.getParameter("centrecolumnlabels");
 201       if (param != null)
 202       {
 203         centreColumnLabelFlag.setState(true);
 204         centreColumnLabelFlag_stateChanged();
 205       }
 206
 207     }
 208     if (viewport.getAlignment().isNucleotide())
 209     {
 210       viewport.updateStrucConsensus(alignPanel);
 211       if (viewport.getAlignment().hasRNAStructure())
 212       {
 213         RNAHelixColour.setEnabled(true);
 214       }
 215       else
 216       {
 217         RNAHelixColour.setEnabled(false);
 218       }
 219     }
 220     else
 221     {
 222       RNAHelixColour.setEnabled(false);
 223       purinePyrimidineColour.setEnabled(false);
 224     }
 225     // Some JVMS send keyevents to Top frame or lowest panel,
 226     // Havent worked out why yet. So add to both this frame and seqCanvas for
 227     // now
 228     this.addKeyListener(this);
 229     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 230     alignPanel.idPanel.idCanvas.addKeyListener(this);
 231     alignPanel.scalePanel.addKeyListener(this);
 232     alignPanel.annotationPanel.addKeyListener(this);
 233     alignPanel.annotationPanelHolder.addKeyListener(this);
 234     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 235     alignPanel.alabels.addKeyListener(this);
 236     createAlignFrameWindow(embedded, title);
 237
 238     validate();
 239     alignPanel.adjustAnnotationHeight();
 240     alignPanel.paintAlignment(true);
 241   }
 242
 243   public AlignViewport getAlignViewport()
 244   {
 245     return viewport;
 246   }
 247
 248   public SeqCanvas getSeqcanvas()
 249   {
 250     return alignPanel.seqPanel.seqCanvas;
 251   }
 252
 253   /**
 254    * Load a features file onto the alignment
 255    *
 256    * @param file
 257    *          file URL, content, or other resolvable path
 258    * @param type
 259    *          is protocol for accessing data referred to by file
 260    */
 261
 262   public boolean parseFeaturesFile(String file, String type)
 263   {
 264     return parseFeaturesFile(file, type, true);
 265   }
 266
 267   /**
 268    * Load a features file onto the alignment
 269    *
 270    * @param file
 271    *          file URL, content, or other resolvable path
 272    * @param type
 273    *          is protocol for accessing data referred to by file
 274    * @param autoenabledisplay
 275    *          when true, display features flag will be automatically enabled if
 276    *          features are loaded
 277    * @return true if data parsed as a features file
 278    */
 279   public boolean parseFeaturesFile(String file, String type,
 280           boolean autoenabledisplay)
 281   {
 282     // TODO: test if importing a features file onto an alignment which already
 283     // has features with links overwrites the original links.
 284
 285     Hashtable featureLinks = new Hashtable();
 286     boolean featuresFile = false;
 287     try
 288     {
 289       featuresFile = new jalview.io.FeaturesFile(file, type)
 290               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 291                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 292                       true, viewport.applet.getDefaultParameter(
 293                               "relaxedidmatch", false));
 294     } catch (Exception ex)
 295     {
 296       ex.printStackTrace();
 297     }
 298
 299     if (featuresFile)
 300     {
 301       if (featureLinks.size() > 0)
 302       {
 303         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 304       }
 305       if (autoenabledisplay)
 306       {
 307         viewport.setShowSequenceFeatures(true);
 308         sequenceFeatures.setState(true);
 309       }
 310       if (alignPanel.seqPanel.seqCanvas.fr != null)
 311       {
 312         // update the min/max ranges where necessary
 313         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 314       }
 315       if (viewport.featureSettings != null)
 316       {
 317         viewport.featureSettings.refreshTable();
 318       }
 319       alignPanel.paintAlignment(true);
 320       statusBar.setText(MessageManager
 321               .getString("label.successfully_added_features_alignment"));
 322     }
 323     return featuresFile;
 324   }
 325
 326   @Override
 327   public void keyPressed(KeyEvent evt)
 328   {
 329     if (viewport.cursorMode
 330             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 331                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 332                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 333             && Character.isDigit(evt.getKeyChar()))
 334     {
 335       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 336     }
 337
 338     switch (evt.getKeyCode())
 339     {
 340     case 27: // escape key
 341       deselectAllSequenceMenuItem_actionPerformed();
 342
 343       alignPanel.alabels.cancelDrag();
 344       break;
 345     case KeyEvent.VK_X:
 346       if (evt.isControlDown() || evt.isMetaDown())
 347       {
 348         cut_actionPerformed();
 349       }
 350       break;
 351     case KeyEvent.VK_C:
 352       if (viewport.cursorMode && !evt.isControlDown())
 353       {
 354         alignPanel.seqPanel.setCursorColumn();
 355       }
 356       if (evt.isControlDown() || evt.isMetaDown())
 357       {
 358         copy_actionPerformed();
 359       }
 360       break;
 361     case KeyEvent.VK_V:
 362       if (evt.isControlDown())
 363       {
 364         paste(evt.isShiftDown());
 365       }
 366       break;
 367     case KeyEvent.VK_A:
 368       if (evt.isControlDown() || evt.isMetaDown())
 369       {
 370         selectAllSequenceMenuItem_actionPerformed();
 371       }
 372       break;
 373     case KeyEvent.VK_DOWN:
 374       if (viewport.cursorMode)
 375       {
 376         alignPanel.seqPanel.moveCursor(0, 1);
 377       }
 378       else
 379       {
 380         moveSelectedSequences(false);
 381       }
 382       break;
 383
 384     case KeyEvent.VK_UP:
 385       if (viewport.cursorMode)
 386       {
 387         alignPanel.seqPanel.moveCursor(0, -1);
 388       }
 389       else
 390       {
 391         moveSelectedSequences(true);
 392       }
 393       break;
 394
 395     case KeyEvent.VK_LEFT:
 396       if (evt.isAltDown() || !viewport.cursorMode)
 397       {
 398         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 399       }
 400       else
 401       {
 402         alignPanel.seqPanel.moveCursor(-1, 0);
 403       }
 404       break;
 405
 406     case KeyEvent.VK_RIGHT:
 407       if (evt.isAltDown() || !viewport.cursorMode)
 408       {
 409         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 410       }
 411       else
 412       {
 413         alignPanel.seqPanel.moveCursor(1, 0);
 414       }
 415       break;
 416
 417     case KeyEvent.VK_SPACE:
 418       if (viewport.cursorMode)
 419       {
 420         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 421                 || evt.isShiftDown() || evt.isAltDown());
 422       }
 423       break;
 424
 425     case KeyEvent.VK_DELETE:
 426     case KeyEvent.VK_BACK_SPACE:
 427       if (viewport.cursorMode)
 428       {
 429         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 430                 || evt.isShiftDown() || evt.isAltDown());
 431       }
 432       else
 433       {
 434         cut_actionPerformed();
 435         alignPanel.seqPanel.seqCanvas.repaint();
 436       }
 437       break;
 438
 439     case KeyEvent.VK_S:
 440       if (viewport.cursorMode)
 441       {
 442         alignPanel.seqPanel.setCursorRow();
 443       }
 444       break;
 445     case KeyEvent.VK_P:
 446       if (viewport.cursorMode)
 447       {
 448         alignPanel.seqPanel.setCursorPosition();
 449       }
 450       break;
 451
 452     case KeyEvent.VK_ENTER:
 453     case KeyEvent.VK_COMMA:
 454       if (viewport.cursorMode)
 455       {
 456         alignPanel.seqPanel.setCursorRowAndColumn();
 457       }
 458       break;
 459
 460     case KeyEvent.VK_Q:
 461       if (viewport.cursorMode)
 462       {
 463         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 464       }
 465       break;
 466     case KeyEvent.VK_M:
 467       if (viewport.cursorMode)
 468       {
 469         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 470       }
 471       break;
 472
 473     case KeyEvent.VK_F2:
 474       viewport.cursorMode = !viewport.cursorMode;
 475       statusBar.setText(MessageManager.formatMessage(
 476               "label.keyboard_editing_mode", new String[]
 477               { (viewport.cursorMode ? "on" : "off") }));
 478       if (viewport.cursorMode)
 479       {
 480         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 481         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 482       }
 483       break;
 484
 485     case KeyEvent.VK_F:
 486       if (evt.isControlDown())
 487       {
 488         findMenuItem_actionPerformed();
 489       }
 490       break;
 491
 492     case KeyEvent.VK_H:
 493     {
 494       boolean toggleSeqs = !evt.isControlDown();
 495       boolean toggleCols = !evt.isShiftDown();
 496       toggleHiddenRegions(toggleSeqs, toggleCols);
 497       break;
 498     }
 499
 500     case KeyEvent.VK_PAGE_UP:
 501       if (viewport.wrapAlignment)
 502       {
 503         alignPanel.scrollUp(true);
 504       }
 505       else
 506       {
 507         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 508                 - viewport.endSeq + viewport.startSeq);
 509       }
 510       break;
 511
 512     case KeyEvent.VK_PAGE_DOWN:
 513       if (viewport.wrapAlignment)
 514       {
 515         alignPanel.scrollUp(false);
 516       }
 517       else
 518       {
 519         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 520                 + viewport.endSeq - viewport.startSeq);
 521       }
 522       break;
 523
 524     case KeyEvent.VK_Z:
 525       if (evt.isControlDown())
 526       {
 527         undoMenuItem_actionPerformed();
 528       }
 529       break;
 530
 531     case KeyEvent.VK_Y:
 532       if (evt.isControlDown())
 533       {
 534         redoMenuItem_actionPerformed();
 535       }
 536       break;
 537
 538     case KeyEvent.VK_L:
 539       if (evt.isControlDown())
 540       {
 541         trimAlignment(true);
 542       }
 543       break;
 544
 545     case KeyEvent.VK_R:
 546       if (evt.isControlDown())
 547       {
 548         trimAlignment(false);
 549       }
 550       break;
 551
 552     case KeyEvent.VK_E:
 553       if (evt.isControlDown())
 554       {
 555         if (evt.isShiftDown())
 556         {
 557           this.removeAllGapsMenuItem_actionPerformed();
 558         }
 559         else
 560         {
 561           removeGappedColumnMenuItem_actionPerformed();
 562         }
 563       }
 564       break;
 565     case KeyEvent.VK_I:
 566       if (evt.isControlDown())
 567       {
 568         if (evt.isAltDown())
 569         {
 570           invertColSel_actionPerformed();
 571         }
 572         else
 573         {
 574           invertSequenceMenuItem_actionPerformed();
 575         }
 576       }
 577       break;
 578
 579     case KeyEvent.VK_G:
 580       if (evt.isControlDown())
 581       {
 582         if (evt.isShiftDown())
 583         {
 584           this.unGroup_actionPerformed();
 585         }
 586         else
 587         {
 588           this.createGroup_actionPerformed();
 589         }
 590       }
 591       break;
 592
 593     case KeyEvent.VK_U:
 594       if (evt.isControlDown())
 595       {
 596         this.deleteGroups_actionPerformed();
 597       }
 598       break;
 599
 600     case KeyEvent.VK_T:
 601       if (evt.isControlDown())
 602       {
 603         newView(null);
 604       }
 605       break;
 606
 607     }
 608     alignPanel.paintAlignment(true);
 609   }
 610
 611   /**
 612    * called by key handler and the hide all/show all menu items
 613    *
 614    * @param toggleSeqs
 615    * @param toggleCols
 616    */
 617   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 618   {
 619     boolean hide = false;
 620     SequenceGroup sg = viewport.getSelectionGroup();
 621     if (!toggleSeqs && !toggleCols)
 622     {
 623       // Hide everything by the current selection - this is a hack - we do the
 624       // invert and then hide
 625       // first check that there will be visible columns after the invert.
 626       if ((viewport.getColumnSelection() != null
 627               && viewport.getColumnSelection().getSelected() != null && viewport
 628               .getColumnSelection().getSelected().size() > 0)
 629               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 630                       .getEndRes()))
 631       {
 632         // now invert the sequence set, if required - empty selection implies
 633         // that no hiding is required.
 634         if (sg != null)
 635         {
 636           invertSequenceMenuItem_actionPerformed();
 637           sg = viewport.getSelectionGroup();
 638           toggleSeqs = true;
 639
 640         }
 641         viewport.expandColSelection(sg, true);
 642         // finally invert the column selection and get the new sequence
 643         // selection and indicate it should be hidden.
 644         invertColSel_actionPerformed();
 645         toggleCols = true;
 646       }
 647     }
 648
 649     if (toggleSeqs)
 650     {
 651       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 652       {
 653         hide = true;
 654         viewport.hideAllSelectedSeqs();
 655       }
 656       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 657               .size() > 0))
 658       {
 659         viewport.showAllHiddenSeqs();
 660       }
 661     }
 662
 663     if (toggleCols)
 664     {
 665       if (viewport.getColumnSelection().getSelected().size() > 0)
 666       {
 667         viewport.hideSelectedColumns();
 668         if (!toggleSeqs)
 669         {
 670           viewport.setSelectionGroup(sg);
 671         }
 672       }
 673       else if (!hide)
 674       {
 675         viewport.showAllHiddenColumns();
 676       }
 677     }
 678   }
 679
 680   @Override
 681   public void keyReleased(KeyEvent evt)
 682   {
 683   }
 684
 685   @Override
 686   public void keyTyped(KeyEvent evt)
 687   {
 688   }
 689
 690   @Override
 691   public void itemStateChanged(ItemEvent evt)
 692   {
 693     if (evt.getSource() == displayNonconservedMenuItem)
 694     {
 695       displayNonconservedMenuItem_actionPerformed();
 696     }
 697     else if (evt.getSource() == colourTextMenuItem)
 698     {
 699       colourTextMenuItem_actionPerformed();
 700     }
 701     else if (evt.getSource() == wrapMenuItem)
 702     {
 703       wrapMenuItem_actionPerformed();
 704     }
 705     else if (evt.getSource() == scaleAbove)
 706     {
 707       viewport.setScaleAboveWrapped(scaleAbove.getState());
 708     }
 709     else if (evt.getSource() == scaleLeft)
 710     {
 711       viewport.setScaleLeftWrapped(scaleLeft.getState());
 712     }
 713     else if (evt.getSource() == scaleRight)
 714     {
 715       viewport.setScaleRightWrapped(scaleRight.getState());
 716     }
 717     else if (evt.getSource() == seqLimits)
 718     {
 719       seqLimits_itemStateChanged();
 720     }
 721     else if (evt.getSource() == viewBoxesMenuItem)
 722     {
 723       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 724     }
 725     else if (evt.getSource() == viewTextMenuItem)
 726     {
 727       viewport.setShowText(viewTextMenuItem.getState());
 728     }
 729     else if (evt.getSource() == renderGapsMenuItem)
 730     {
 731       viewport.setRenderGaps(renderGapsMenuItem.getState());
 732     }
 733     else if (evt.getSource() == annotationPanelMenuItem)
 734     {
 735       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 736       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 737     }
 738     else if (evt.getSource() == sequenceFeatures)
 739     {
 740       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 741       alignPanel.seqPanel.seqCanvas.repaint();
 742     }
 743     else if (evt.getSource() == conservationMenuItem)
 744     {
 745       conservationMenuItem_actionPerformed();
 746     }
 747     else if (evt.getSource() == abovePIDThreshold)
 748     {
 749       abovePIDThreshold_actionPerformed();
 750     }
 751     else if (evt.getSource() == applyToAllGroups)
 752     {
 753       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 754     }
 755     else if (evt.getSource() == autoCalculate)
 756     {
 757       viewport.autoCalculateConsensus = autoCalculate.getState();
 758     }
 759     else if (evt.getSource() == sortByTree)
 760     {
 761       viewport.sortByTree = sortByTree.getState();
 762     }
 763     else if (evt.getSource() == this.centreColumnLabelFlag)
 764     {
 765       centreColumnLabelFlag_stateChanged();
 766     }
 767     else if (evt.getSource() == this.followMouseOverFlag)
 768     {
 769       mouseOverFlag_stateChanged();
 770     }
 771     else if (evt.getSource() == showGroupConsensus)
 772     {
 773       showGroupConsensus_actionPerformed();
 774     }
 775     else if (evt.getSource() == showGroupConservation)
 776     {
 777       showGroupConservation_actionPerformed();
 778     }
 779     else if (evt.getSource() == showSequenceLogo)
 780     {
 781       showSequenceLogo_actionPerformed();
 782     }
 783     else if (evt.getSource() == normSequenceLogo)
 784     {
 785       normSequenceLogo_actionPerformed();
 786     }
 787     else if (evt.getSource() == showConsensusHistogram)
 788     {
 789       showConsensusHistogram_actionPerformed();
 790     }
 791     else if (evt.getSource() == applyAutoAnnotationSettings)
 792     {
 793       applyAutoAnnotationSettings_actionPerformed();
 794     }
 795     alignPanel.paintAlignment(true);
 796   }
 797
 798   private void mouseOverFlag_stateChanged()
 799   {
 800     viewport.followHighlight = followMouseOverFlag.getState();
 801     // TODO: could kick the scrollTo mechanism to reset view for current
 802     // searchresults.
 803   }
 804
 805   private void centreColumnLabelFlag_stateChanged()
 806   {
 807     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 808     this.alignPanel.annotationPanel.repaint();
 809   }
 810
 811   @Override
 812   public void actionPerformed(ActionEvent evt)
 813   {
 814     Object source = evt.getSource();
 815
 816     if (source == inputText)
 817     {
 818       inputText_actionPerformed();
 819     }
 820     else if (source == loadTree)
 821     {
 822       loadTree_actionPerformed();
 823     }
 824     else if (source == loadApplication)
 825     {
 826       launchFullApplication();
 827     }
 828     else if (source == loadAnnotations)
 829     {
 830       loadAnnotations();
 831     }
 832     else if (source == outputAnnotations)
 833     {
 834       outputAnnotations(true);
 835     }
 836     else if (source == outputFeatures)
 837     {
 838       outputFeatures(true, "Jalview");
 839     }
 840     else if (source == closeMenuItem)
 841     {
 842       closeMenuItem_actionPerformed();
 843     }
 844     else if (source == copy)
 845     {
 846       copy_actionPerformed();
 847     }
 848     else if (source == undoMenuItem)
 849     {
 850       undoMenuItem_actionPerformed();
 851     }
 852     else if (source == redoMenuItem)
 853     {
 854       redoMenuItem_actionPerformed();
 855     }
 856     else if (source == inputText)
 857     {
 858       inputText_actionPerformed();
 859     }
 860     else if (source == closeMenuItem)
 861     {
 862       closeMenuItem_actionPerformed();
 863     }
 864     else if (source == undoMenuItem)
 865     {
 866       undoMenuItem_actionPerformed();
 867     }
 868     else if (source == redoMenuItem)
 869     {
 870       redoMenuItem_actionPerformed();
 871     }
 872     else if (source == copy)
 873     {
 874       copy_actionPerformed();
 875     }
 876     else if (source == pasteNew)
 877     {
 878       pasteNew_actionPerformed();
 879     }
 880     else if (source == pasteThis)
 881     {
 882       pasteThis_actionPerformed();
 883     }
 884     else if (source == cut)
 885     {
 886       cut_actionPerformed();
 887     }
 888     else if (source == delete)
 889     {
 890       delete_actionPerformed();
 891     }
 892     else if (source == grpsFromSelection)
 893     {
 894       makeGrpsFromSelection_actionPerformed();
 895     }
 896     else if (source == deleteGroups)
 897     {
 898       deleteGroups_actionPerformed();
 899     }
 900     else if (source == selectAllSequenceMenuItem)
 901     {
 902       selectAllSequenceMenuItem_actionPerformed();
 903     }
 904     else if (source == deselectAllSequenceMenuItem)
 905     {
 906       deselectAllSequenceMenuItem_actionPerformed();
 907     }
 908     else if (source == invertSequenceMenuItem)
 909     {
 910       invertSequenceMenuItem_actionPerformed();
 911     }
 912     else if (source == invertColSel)
 913     {
 914       viewport.invertColumnSelection();
 915       alignPanel.paintAlignment(true);
 916     }
 917     else if (source == remove2LeftMenuItem)
 918     {
 919       trimAlignment(true);
 920     }
 921     else if (source == remove2RightMenuItem)
 922     {
 923       trimAlignment(false);
 924     }
 925     else if (source == removeGappedColumnMenuItem)
 926     {
 927       removeGappedColumnMenuItem_actionPerformed();
 928     }
 929     else if (source == removeAllGapsMenuItem)
 930     {
 931       removeAllGapsMenuItem_actionPerformed();
 932     }
 933     else if (source == findMenuItem)
 934     {
 935       findMenuItem_actionPerformed();
 936     }
 937     else if (source == font)
 938     {
 939       new FontChooser(alignPanel);
 940     }
 941     else if (source == newView)
 942     {
 943       newView(null);
 944     }
 945     else if (source == showColumns)
 946     {
 947       viewport.showAllHiddenColumns();
 948       alignPanel.paintAlignment(true);
 949     }
 950     else if (source == showSeqs)
 951     {
 952       viewport.showAllHiddenSeqs();
 953       alignPanel.paintAlignment(true);
 954     }
 955     else if (source == hideColumns)
 956     {
 957       viewport.hideSelectedColumns();
 958       alignPanel.paintAlignment(true);
 959     }
 960     else if (source == hideSequences
 961             && viewport.getSelectionGroup() != null)
 962     {
 963       viewport.hideAllSelectedSeqs();
 964       alignPanel.paintAlignment(true);
 965     }
 966     else if (source == hideAllButSelection)
 967     {
 968       toggleHiddenRegions(false, false);
 969       alignPanel.paintAlignment(true);
 970     }
 971     else if (source == hideAllSelection)
 972     {
 973       SequenceGroup sg = viewport.getSelectionGroup();
 974       viewport.expandColSelection(sg, false);
 975       viewport.hideAllSelectedSeqs();
 976       viewport.hideSelectedColumns();
 977       alignPanel.paintAlignment(true);
 978     }
 979     else if (source == showAllHidden)
 980     {
 981       viewport.showAllHiddenColumns();
 982       viewport.showAllHiddenSeqs();
 983       alignPanel.paintAlignment(true);
 984     }
 985     else if (source == showGroupConsensus)
 986     {
 987       showGroupConsensus_actionPerformed();
 988     }
 989     else if (source == showGroupConservation)
 990     {
 991       showGroupConservation_actionPerformed();
 992     }
 993     else if (source == showSequenceLogo)
 994     {
 995       showSequenceLogo_actionPerformed();
 996     }
 997     else if (source == normSequenceLogo)
 998     {
 999       normSequenceLogo_actionPerformed();
1000     }
1001     else if (source == showConsensusHistogram)
1002     {
1003       showConsensusHistogram_actionPerformed();
1004     }
1005     else if (source == applyAutoAnnotationSettings)
1006     {
1007       applyAutoAnnotationSettings_actionPerformed();
1008     }
1009     else if (source == featureSettings)
1010     {
1011       new FeatureSettings(alignPanel);
1012     }
1013     else if (source == alProperties)
1014     {
1015       StringBuffer contents = new jalview.io.AlignmentProperties(
1016               viewport.getAlignment()).formatAsString();
1017       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1018       cap.setText(contents.toString());
1019       Frame frame = new Frame();
1020       frame.add(cap);
1021       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1022               "label.alignment_properties", new String[]
1023               { getTitle() }), 400, 250);
1024     }
1025     else if (source == overviewMenuItem)
1026     {
1027       overviewMenuItem_actionPerformed();
1028     }
1029     else if (source == noColourmenuItem)
1030     {
1031       changeColour(null);
1032     }
1033     else if (source == clustalColour)
1034     {
1035       abovePIDThreshold.setState(false);
1036       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1037     }
1038     else if (source == zappoColour)
1039     {
1040       changeColour(new ZappoColourScheme());
1041     }
1042     else if (source == taylorColour)
1043     {
1044       changeColour(new TaylorColourScheme());
1045     }
1046     else if (source == hydrophobicityColour)
1047     {
1048       changeColour(new HydrophobicColourScheme());
1049     }
1050     else if (source == helixColour)
1051     {
1052       changeColour(new HelixColourScheme());
1053     }
1054     else if (source == strandColour)
1055     {
1056       changeColour(new StrandColourScheme());
1057     }
1058     else if (source == turnColour)
1059     {
1060       changeColour(new TurnColourScheme());
1061     }
1062     else if (source == buriedColour)
1063     {
1064       changeColour(new BuriedColourScheme());
1065     }
1066     else if (source == nucleotideColour)
1067     {
1068       changeColour(new NucleotideColourScheme());
1069     }
1070     else if (source == purinePyrimidineColour)
1071     {
1072       changeColour(new PurinePyrimidineColourScheme());
1073     }
1074     else if (source == RNAInteractionColour)
1075     {
1076       changeColour(new RNAInteractionColourScheme());
1077     }
1078     else if (source == RNAHelixColour)
1079     {
1080       new RNAHelicesColourChooser(viewport, alignPanel);
1081     }
1082     else if (source == modifyPID)
1083     {
1084       modifyPID_actionPerformed();
1085     }
1086     else if (source == modifyConservation)
1087     {
1088       modifyConservation_actionPerformed();
1089     }
1090     else if (source == userDefinedColour)
1091     {
1092       new UserDefinedColours(alignPanel, null);
1093     }
1094     else if (source == PIDColour)
1095     {
1096       changeColour(new PIDColourScheme());
1097     }
1098     else if (source == BLOSUM62Colour)
1099     {
1100       changeColour(new Blosum62ColourScheme());
1101     }
1102     else if (source == tcoffeeColour)
1103     {
1104       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1105     }
1106     else if (source == annotationColour)
1107     {
1108       new AnnotationColourChooser(viewport, alignPanel);
1109     }
1110     else if (source == sortPairwiseMenuItem)
1111     {
1112       sortPairwiseMenuItem_actionPerformed();
1113     }
1114     else if (source == sortIDMenuItem)
1115     {
1116       sortIDMenuItem_actionPerformed();
1117     }
1118     else if (source == sortLengthMenuItem)
1119     {
1120       sortLengthMenuItem_actionPerformed();
1121     }
1122     else if (source == sortGroupMenuItem)
1123     {
1124       sortGroupMenuItem_actionPerformed();
1125     }
1126     else if (source == removeRedundancyMenuItem)
1127     {
1128       removeRedundancyMenuItem_actionPerformed();
1129     }
1130     else if (source == pairwiseAlignmentMenuItem)
1131     {
1132       pairwiseAlignmentMenuItem_actionPerformed();
1133     }
1134     else if (source == PCAMenuItem)
1135     {
1136       PCAMenuItem_actionPerformed();
1137     }
1138     else if (source == averageDistanceTreeMenuItem)
1139     {
1140       averageDistanceTreeMenuItem_actionPerformed();
1141     }
1142     else if (source == neighbourTreeMenuItem)
1143     {
1144       neighbourTreeMenuItem_actionPerformed();
1145     }
1146     else if (source == njTreeBlosumMenuItem)
1147     {
1148       njTreeBlosumMenuItem_actionPerformed();
1149     }
1150     else if (source == avDistanceTreeBlosumMenuItem)
1151     {
1152       avTreeBlosumMenuItem_actionPerformed();
1153     }
1154     else if (source == documentation)
1155     {
1156       documentation_actionPerformed();
1157     }
1158     else if (source == about)
1159     {
1160       about_actionPerformed();
1161     }
1162
1163   }
1164
1165   public void inputText_actionPerformed()
1166   {
1167     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1168     Frame frame = new Frame();
1169     frame.add(cap);
1170     jalview.bin.JalviewLite.addFrame(frame,
1171             MessageManager.getString("label.input_cut_paste"), 500, 500);
1172   }
1173
1174   protected void outputText_actionPerformed(ActionEvent e)
1175   {
1176     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1177     Frame frame = new Frame();
1178     frame.add(cap);
1179     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1180             "label.alignment_output_command", new String[]
1181             { e.getActionCommand() }), 600, 500);
1182     cap.setText(new AppletFormatAdapter().formatSequences(
1183             e.getActionCommand(), viewport.getAlignment(),
1184             viewport.showJVSuffix));
1185   }
1186
1187   public void loadAnnotations()
1188   {
1189     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1190     cap.setText(MessageManager
1191             .getString("label.paste_features_annotations_Tcoffee_here"));
1192     cap.setAnnotationImport();
1193     Frame frame = new Frame();
1194     frame.add(cap);
1195     jalview.bin.JalviewLite.addFrame(frame,
1196             MessageManager.getString("action.paste_annotations"), 400, 300);
1197
1198   }
1199
1200   public String outputAnnotations(boolean displayTextbox)
1201   {
1202     String annotation = new AnnotationFile().printAnnotations(
1203             viewport.showAnnotation ? viewport.getAlignment()
1204                     .getAlignmentAnnotation() : null, viewport
1205                     .getAlignment().getGroups(), ((Alignment) viewport
1206                     .getAlignment()).alignmentProperties);
1207
1208     if (displayTextbox)
1209     {
1210       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1211       Frame frame = new Frame();
1212       frame.add(cap);
1213       jalview.bin.JalviewLite.addFrame(frame,
1214               MessageManager.getString("label.annotations"), 600, 500);
1215       cap.setText(annotation);
1216     }
1217
1218     return annotation;
1219   }
1220
1221   private Map<String,Object> getDisplayedFeatureCols()
1222   {
1223     if (alignPanel.getFeatureRenderer() != null
1224             && viewport.getFeaturesDisplayed()!= null)
1225     {
1226       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1227
1228     }
1229     return null;
1230   }
1231
1232   public String outputFeatures(boolean displayTextbox, String format)
1233   {
1234     String features;
1235     if (format.equalsIgnoreCase("Jalview"))
1236     {
1237       features = new FeaturesFile().printJalviewFormat(viewport
1238               .getAlignment().getSequencesArray(),
1239               getDisplayedFeatureCols());
1240     }
1241     else
1242     {
1243       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1244               .getSequencesArray(), getDisplayedFeatureCols());
1245     }
1246
1247     if (displayTextbox)
1248     {
1249       boolean frimport = false;
1250       if (features == null || features.equals("No Features Visible"))
1251       {
1252         features = "# No features visible - paste some and import them here.";
1253         frimport = true;
1254       }
1255
1256       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1257       if (frimport)
1258       {
1259         cap.setAnnotationImport();
1260       }
1261       Frame frame = new Frame();
1262       frame.add(cap);
1263       jalview.bin.JalviewLite.addFrame(frame,
1264               MessageManager.getString("label.features"), 600, 500);
1265       cap.setText(features);
1266     }
1267     else
1268     {
1269       if (features == null)
1270       {
1271         features = "";
1272       }
1273     }
1274
1275     return features;
1276   }
1277
1278   void launchFullApplication()
1279   {
1280     StringBuffer url = new StringBuffer(jalviewServletURL);
1281
1282     url.append("?open="
1283             + appendProtocol(viewport.applet.getParameter("file")));
1284
1285     if (viewport.applet.getParameter("features") != null)
1286     {
1287       url.append("&features=");
1288       url.append(appendProtocol(viewport.applet.getParameter("features")));
1289     }
1290
1291     if (viewport.applet.getParameter("annotations") != null)
1292     {
1293       url.append("&annotations=");
1294       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1295     }
1296
1297     if (viewport.applet.getParameter("jnetfile") != null)
1298     {
1299       url.append("&annotations=");
1300       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1301     }
1302
1303     if (viewport.applet.getParameter("defaultColour") != null)
1304     {
1305       url.append("&colour="
1306               + removeWhiteSpace(viewport.applet
1307                       .getParameter("defaultColour")));
1308     }
1309
1310     if (viewport.applet.getParameter("userDefinedColour") != null)
1311     {
1312       url.append("&colour="
1313               + removeWhiteSpace(viewport.applet
1314                       .getParameter("userDefinedColour")));
1315     }
1316     if (viewport.applet.getParameter("tree") != null)
1317     {
1318       url.append("&tree="
1319               + appendProtocol(viewport.applet.getParameter("tree")));
1320     }
1321     if (viewport.applet.getParameter("treeFile") != null)
1322     {
1323       url.append("&tree="
1324               + appendProtocol(viewport.applet.getParameter("treeFile")));
1325     }
1326
1327     showURL(url.toString(), "FULL_APP");
1328   }
1329
1330   String removeWhiteSpace(String colour)
1331   {
1332     StringBuffer sb = new StringBuffer();
1333     for (int i = 0; i < colour.length(); i++)
1334     {
1335       if (Character.isWhitespace(colour.charAt(i)))
1336       {
1337         sb.append("%20");
1338       }
1339       else
1340       {
1341         sb.append(colour.charAt(i));
1342       }
1343     }
1344
1345     return sb.toString();
1346   }
1347
1348   String appendProtocol(String url)
1349   {
1350     try
1351     {
1352       new URL(url);
1353       url = URLEncoder.encode(url);
1354     }
1355     /*
1356      * When we finally deprecate 1.1 compatibility, we can start to use
1357      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1358      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1359      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1360      * ex.printStackTrace(); }
1361      */
1362     catch (java.net.MalformedURLException ex)
1363     {
1364       url = viewport.applet.getCodeBase() + url;
1365     }
1366     return url;
1367   }
1368
1369   public void closeMenuItem_actionPerformed()
1370   {
1371     PaintRefresher.RemoveComponent(alignPanel);
1372     if (alignPanel.seqPanel != null
1373             && alignPanel.seqPanel.seqCanvas != null)
1374     {
1375       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1376     }
1377     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1378     {
1379       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1380     }
1381
1382     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1383     {
1384       System.exit(0);
1385     }
1386     else
1387     {
1388     }
1389     viewport = null;
1390     alignPanel = null;
1391     this.dispose();
1392   }
1393
1394   /**
1395    * TODO: JAL-1104
1396    */
1397   void updateEditMenuBar()
1398   {
1399
1400     if (viewport.historyList.size() > 0)
1401     {
1402       undoMenuItem.setEnabled(true);
1403       CommandI command = (CommandI) viewport.historyList.peek();
1404       undoMenuItem.setLabel(MessageManager.formatMessage(
1405               "label.undo_command", new String[]
1406               { command.getDescription() }));
1407     }
1408     else
1409     {
1410       undoMenuItem.setEnabled(false);
1411       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1412     }
1413
1414     if (viewport.redoList.size() > 0)
1415     {
1416       redoMenuItem.setEnabled(true);
1417
1418       CommandI command = (CommandI) viewport.redoList.peek();
1419       redoMenuItem.setLabel(MessageManager.formatMessage(
1420               "label.redo_command", new String[]
1421               { command.getDescription() }));
1422     }
1423     else
1424     {
1425       redoMenuItem.setEnabled(false);
1426       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1427     }
1428   }
1429
1430   /**
1431    * TODO: JAL-1104
1432    */
1433   @Override
1434   public void addHistoryItem(CommandI command)
1435   {
1436     if (command.getSize() > 0)
1437     {
1438       viewport.historyList.push(command);
1439       viewport.redoList.removeAllElements();
1440       updateEditMenuBar();
1441       viewport.updateHiddenColumns();
1442     }
1443   }
1444
1445   /**
1446    * TODO: JAL-1104 DOCUMENT ME!
1447    *
1448    * @param e
1449    *          DOCUMENT ME!
1450    */
1451   protected void undoMenuItem_actionPerformed()
1452   {
1453     if (viewport.historyList.size() < 1)
1454     {
1455       return;
1456     }
1457
1458     CommandI command = (CommandI) viewport.historyList.pop();
1459     viewport.redoList.push(command);
1460     command.undoCommand(null);
1461
1462     AlignViewport originalSource = getOriginatingSource(command);
1463     // JBPNote Test
1464     if (originalSource != viewport)
1465     {
1466       System.err
1467               .println("Warning: Viewport object mismatch whilst undoing");
1468     }
1469     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1470                                           // viewport.getColumnSelection().getHiddenColumns()
1471                                           // != null;
1472     updateEditMenuBar();
1473     originalSource.firePropertyChange("alignment", null, originalSource
1474             .getAlignment().getSequences());
1475   }
1476
1477   /**
1478    * TODO: JAL-1104 DOCUMENT ME!
1479    *
1480    * @param e
1481    *          DOCUMENT ME!
1482    */
1483   protected void redoMenuItem_actionPerformed()
1484   {
1485     if (viewport.redoList.size() < 1)
1486     {
1487       return;
1488     }
1489
1490     CommandI command = (CommandI) viewport.redoList.pop();
1491     viewport.historyList.push(command);
1492     command.doCommand(null);
1493
1494     AlignViewport originalSource = getOriginatingSource(command);
1495     // JBPNote Test
1496     if (originalSource != viewport)
1497     {
1498       System.err
1499               .println("Warning: Viewport object mismatch whilst re-doing");
1500     }
1501     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1502                                           // viewport.getColumnSelection().getHiddenColumns()
1503                                           // != null;
1504
1505     updateEditMenuBar();
1506     originalSource.firePropertyChange("alignment", null, originalSource
1507             .getAlignment().getSequences());
1508   }
1509
1510   AlignViewport getOriginatingSource(CommandI command)
1511   {
1512     AlignViewport originalSource = null;
1513     // For sequence removal and addition, we need to fire
1514     // the property change event FROM the viewport where the
1515     // original alignment was altered
1516     AlignmentI al = null;
1517     if (command instanceof EditCommand)
1518     {
1519       EditCommand editCommand = (EditCommand) command;
1520       al = editCommand.getAlignment();
1521       Vector comps = (Vector) PaintRefresher.components.get(viewport
1522               .getSequenceSetId());
1523       for (int i = 0; i < comps.size(); i++)
1524       {
1525         if (comps.elementAt(i) instanceof AlignmentPanel)
1526         {
1527           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1528           {
1529             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1530             break;
1531           }
1532         }
1533       }
1534     }
1535
1536     if (originalSource == null)
1537     {
1538       // The original view is closed, we must validate
1539       // the current view against the closed view first
1540       if (al != null)
1541       {
1542         PaintRefresher.validateSequences(al, viewport.getAlignment());
1543       }
1544
1545       originalSource = viewport;
1546     }
1547
1548     return originalSource;
1549   }
1550
1551   public void moveSelectedSequences(boolean up)
1552   {
1553     SequenceGroup sg = viewport.getSelectionGroup();
1554     if (sg == null)
1555     {
1556       return;
1557     }
1558     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1559             up ? null : viewport.getHiddenRepSequences(), up);
1560     alignPanel.paintAlignment(true);
1561   }
1562
1563   synchronized void slideSequences(boolean right, int size)
1564   {
1565     List<SequenceI> sg = new Vector<SequenceI>();
1566     if (viewport.cursorMode)
1567     {
1568       sg.add(viewport.getAlignment().getSequenceAt(
1569               alignPanel.seqPanel.seqCanvas.cursorY));
1570     }
1571     else if (viewport.getSelectionGroup() != null
1572             && viewport.getSelectionGroup().getSize() != viewport
1573                     .getAlignment().getHeight())
1574     {
1575       sg = viewport.getSelectionGroup().getSequences(
1576               viewport.getHiddenRepSequences());
1577     }
1578
1579     if (sg.size() < 1)
1580     {
1581       return;
1582     }
1583
1584     Vector<SequenceI> invertGroup = new Vector();
1585
1586     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1587     {
1588       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1589       {
1590         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1591       }
1592     }
1593
1594     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1595
1596     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1597             .size()]);
1598     for (int i = 0; i < invertGroup.size(); i++)
1599     {
1600       seqs2[i] = invertGroup.elementAt(i);
1601     }
1602
1603     SlideSequencesCommand ssc;
1604     if (right)
1605     {
1606       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1607               size, viewport.getGapCharacter());
1608     }
1609     else
1610     {
1611       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1612               size, viewport.getGapCharacter());
1613     }
1614
1615     int groupAdjustment = 0;
1616     if (ssc.getGapsInsertedBegin() && right)
1617     {
1618       if (viewport.cursorMode)
1619       {
1620         alignPanel.seqPanel.moveCursor(size, 0);
1621       }
1622       else
1623       {
1624         groupAdjustment = size;
1625       }
1626     }
1627     else if (!ssc.getGapsInsertedBegin() && !right)
1628     {
1629       if (viewport.cursorMode)
1630       {
1631         alignPanel.seqPanel.moveCursor(-size, 0);
1632       }
1633       else
1634       {
1635         groupAdjustment = -size;
1636       }
1637     }
1638
1639     if (groupAdjustment != 0)
1640     {
1641       viewport.getSelectionGroup().setStartRes(
1642               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1643       viewport.getSelectionGroup().setEndRes(
1644               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1645     }
1646
1647     boolean appendHistoryItem = false;
1648     if (viewport.historyList != null && viewport.historyList.size() > 0
1649             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1650     {
1651       appendHistoryItem = ssc
1652               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1653                       .peek());
1654     }
1655
1656     if (!appendHistoryItem)
1657     {
1658       addHistoryItem(ssc);
1659     }
1660
1661     repaint();
1662   }
1663
1664   static StringBuffer copiedSequences;
1665
1666   static Vector copiedHiddenColumns;
1667
1668   protected void copy_actionPerformed()
1669   {
1670     if (viewport.getSelectionGroup() == null)
1671     {
1672       return;
1673     }
1674
1675     SequenceGroup sg = viewport.getSelectionGroup();
1676     copiedSequences = new StringBuffer();
1677     Hashtable orderedSeqs = new Hashtable();
1678     for (int i = 0; i < sg.getSize(); i++)
1679     {
1680       SequenceI seq = sg.getSequenceAt(i);
1681       int index = viewport.getAlignment().findIndex(seq);
1682       orderedSeqs.put(index + "", seq);
1683     }
1684
1685     int index = 0, startRes, endRes;
1686     char ch;
1687
1688     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1689     {
1690       copiedHiddenColumns = new Vector();
1691       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1692       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1693               .size(); i++)
1694       {
1695         int[] region = (int[]) viewport.getColumnSelection()
1696                 .getHiddenColumns().elementAt(i);
1697
1698         copiedHiddenColumns.addElement(new int[]
1699         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1700       }
1701     }
1702     else
1703     {
1704       copiedHiddenColumns = null;
1705     }
1706
1707     for (int i = 0; i < sg.getSize(); i++)
1708     {
1709       SequenceI seq = null;
1710
1711       while (seq == null)
1712       {
1713         if (orderedSeqs.containsKey(index + ""))
1714         {
1715           seq = (SequenceI) orderedSeqs.get(index + "");
1716           index++;
1717
1718           break;
1719         }
1720         else
1721         {
1722           index++;
1723         }
1724       }
1725
1726       // FIND START RES
1727       // Returns residue following index if gap
1728       startRes = seq.findPosition(sg.getStartRes());
1729
1730       // FIND END RES
1731       // Need to find the residue preceeding index if gap
1732       endRes = 0;
1733
1734       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1735       {
1736         ch = seq.getCharAt(j);
1737         if (!jalview.util.Comparison.isGap((ch)))
1738         {
1739           endRes++;
1740         }
1741       }
1742
1743       if (endRes > 0)
1744       {
1745         endRes += seq.getStart() - 1;
1746       }
1747
1748       copiedSequences.append(seq.getName()
1749               + "\t"
1750               + startRes
1751               + "\t"
1752               + endRes
1753               + "\t"
1754               + seq.getSequenceAsString(sg.getStartRes(),
1755                       sg.getEndRes() + 1) + "\n");
1756     }
1757
1758   }
1759
1760   protected void pasteNew_actionPerformed()
1761   {
1762     paste(true);
1763   }
1764
1765   protected void pasteThis_actionPerformed()
1766   {
1767     paste(false);
1768   }
1769
1770   void paste(boolean newAlignment)
1771   {
1772     try
1773     {
1774
1775       if (copiedSequences == null)
1776       {
1777         return;
1778       }
1779
1780       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1781       Vector seqs = new Vector();
1782       while (st.hasMoreElements())
1783       {
1784         String name = st.nextToken();
1785         int start = Integer.parseInt(st.nextToken());
1786         int end = Integer.parseInt(st.nextToken());
1787         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1788       }
1789       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1790       for (int i = 0; i < seqs.size(); i++)
1791       {
1792         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1793       }
1794
1795       if (newAlignment)
1796       {
1797         String newtitle = MessageManager.getString("label.copied_sequences");
1798         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1799         {
1800           newtitle = getTitle();
1801         }
1802         else
1803         {
1804           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1805         }
1806         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1807                 viewport.applet, newtitle, false);
1808         if (copiedHiddenColumns != null)
1809         {
1810           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1811           {
1812             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1813             af.viewport.hideColumns(region[0], region[1]);
1814           }
1815         }
1816
1817         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1818                 DEFAULT_HEIGHT);
1819       }
1820       else
1821       {
1822         addSequences(newSeqs);
1823       }
1824
1825     } catch (Exception ex)
1826     {
1827     } // could be anything being pasted in here
1828
1829   }
1830
1831   void addSequences(SequenceI[] seqs)
1832   {
1833     for (int i = 0; i < seqs.length; i++)
1834     {
1835       viewport.getAlignment().addSequence(seqs[i]);
1836     }
1837
1838     // !newAlignment
1839     addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1840             seqs, 0, viewport.getAlignment().getWidth(),
1841             viewport.getAlignment()));
1842
1843     viewport.setEndSeq(viewport.getAlignment().getHeight());
1844     viewport.getAlignment().getWidth();
1845     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1846             .getSequences());
1847
1848   }
1849
1850   protected void cut_actionPerformed()
1851   {
1852     copy_actionPerformed();
1853     delete_actionPerformed();
1854   }
1855
1856   protected void delete_actionPerformed()
1857   {
1858
1859     SequenceGroup sg = viewport.getSelectionGroup();
1860     if (sg == null)
1861     {
1862       return;
1863     }
1864
1865     Vector seqs = new Vector();
1866     SequenceI seq;
1867     for (int i = 0; i < sg.getSize(); i++)
1868     {
1869       seq = sg.getSequenceAt(i);
1870       seqs.addElement(seq);
1871     }
1872
1873     // If the cut affects all sequences, remove highlighted columns
1874     if (sg.getSize() == viewport.getAlignment().getHeight())
1875     {
1876       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1877               sg.getEndRes() + 1);
1878     }
1879
1880     SequenceI[] cut = new SequenceI[seqs.size()];
1881     for (int i = 0; i < seqs.size(); i++)
1882     {
1883       cut[i] = (SequenceI) seqs.elementAt(i);
1884     }
1885
1886     /*
1887      * //ADD HISTORY ITEM
1888      */
1889     addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
1890             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1891             viewport.getAlignment()));
1892
1893     viewport.setSelectionGroup(null);
1894     viewport.getAlignment().deleteGroup(sg);
1895
1896     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1897             .getSequences());
1898
1899     if (viewport.getAlignment().getHeight() < 1)
1900     {
1901       this.setVisible(false);
1902     }
1903     viewport.sendSelection();
1904   }
1905
1906   /**
1907    * group consensus toggled
1908    *
1909    */
1910   protected void showGroupConsensus_actionPerformed()
1911   {
1912     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1913     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1914
1915   }
1916
1917   /**
1918    * group conservation toggled.
1919    */
1920   protected void showGroupConservation_actionPerformed()
1921   {
1922     viewport.setShowGroupConservation(showGroupConservation.getState());
1923     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1924   }
1925
1926   /*
1927    * (non-Javadoc)
1928    *
1929    * @see
1930    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1931    * .event.ActionEvent)
1932    */
1933   protected void showConsensusHistogram_actionPerformed()
1934   {
1935     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1936     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1937   }
1938
1939   /*
1940    * (non-Javadoc)
1941    *
1942    * @see
1943    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1944    * .event.ActionEvent)
1945    */
1946   protected void showSequenceLogo_actionPerformed()
1947   {
1948     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1949     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1950   }
1951
1952   protected void normSequenceLogo_actionPerformed()
1953   {
1954     showSequenceLogo.setState(true);
1955     viewport.setShowSequenceLogo(true);
1956     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1957     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1958   }
1959
1960   protected void applyAutoAnnotationSettings_actionPerformed()
1961   {
1962     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1963   }
1964
1965   protected void makeGrpsFromSelection_actionPerformed()
1966   {
1967     if (avc.makeGroupsFromSelection())
1968     {
1969       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1970       alignPanel.updateAnnotation();
1971       alignPanel.paintAlignment(true);
1972     }
1973   }
1974
1975   protected void createGroup_actionPerformed()
1976   {
1977     avc.createGroup();
1978   }
1979
1980   protected void unGroup_actionPerformed()
1981   {
1982     if (avc.unGroup())
1983     {
1984       alignPanel.alignmentChanged();
1985     }
1986   }
1987
1988   protected void deleteGroups_actionPerformed()
1989   {
1990     if (avc.deleteGroups())
1991     {
1992       alignPanel.alignmentChanged();
1993     }
1994   }
1995
1996   public void selectAllSequenceMenuItem_actionPerformed()
1997   {
1998     SequenceGroup sg = new SequenceGroup();
1999     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2000     {
2001       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2002     }
2003     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2004     viewport.setSelectionGroup(sg);
2005     alignPanel.paintAlignment(true);
2006     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2007     viewport.sendSelection();
2008   }
2009
2010   public void deselectAllSequenceMenuItem_actionPerformed()
2011   {
2012     if (viewport.cursorMode)
2013     {
2014       alignPanel.seqPanel.keyboardNo1 = null;
2015       alignPanel.seqPanel.keyboardNo2 = null;
2016     }
2017     viewport.setSelectionGroup(null);
2018     viewport.getColumnSelection().clear();
2019     viewport.setSelectionGroup(null);
2020     alignPanel.idPanel.idCanvas.searchResults = null;
2021     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2022     alignPanel.paintAlignment(true);
2023     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2024     viewport.sendSelection();
2025   }
2026
2027   public void invertSequenceMenuItem_actionPerformed()
2028   {
2029     SequenceGroup sg = viewport.getSelectionGroup();
2030     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2031     {
2032       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2033     }
2034
2035     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2036     viewport.sendSelection();
2037   }
2038
2039   public void invertColSel_actionPerformed()
2040   {
2041     viewport.invertColumnSelection();
2042     alignPanel.paintAlignment(true);
2043     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2044     viewport.sendSelection();
2045   }
2046
2047   void trimAlignment(boolean trimLeft)
2048   {
2049     ColumnSelection colSel = viewport.getColumnSelection();
2050     int column;
2051
2052     if (colSel.size() > 0)
2053     {
2054       if (trimLeft)
2055       {
2056         column = colSel.getMin();
2057       }
2058       else
2059       {
2060         column = colSel.getMax();
2061       }
2062
2063       SequenceI[] seqs;
2064       if (viewport.getSelectionGroup() != null)
2065       {
2066         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2067                 viewport.getHiddenRepSequences());
2068       }
2069       else
2070       {
2071         seqs = viewport.getAlignment().getSequencesArray();
2072       }
2073
2074       TrimRegionCommand trimRegion;
2075       if (trimLeft)
2076       {
2077         trimRegion = new TrimRegionCommand("Remove Left",
2078                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2079                 viewport.getAlignment(), viewport.getColumnSelection(),
2080                 viewport.getSelectionGroup());
2081         viewport.setStartRes(0);
2082       }
2083       else
2084       {
2085         trimRegion = new TrimRegionCommand("Remove Right",
2086                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2087                 viewport.getAlignment(), viewport.getColumnSelection(),
2088                 viewport.getSelectionGroup());
2089       }
2090
2091       statusBar.setText(MessageManager.formatMessage(
2092               "label.removed_columns", new String[]
2093               { Integer.valueOf(trimRegion.getSize()).toString() }));
2094       addHistoryItem(trimRegion);
2095
2096       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2097       {
2098         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2099                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2100         {
2101           viewport.getAlignment().deleteGroup(sg);
2102         }
2103       }
2104
2105       viewport.firePropertyChange("alignment", null, viewport
2106               .getAlignment().getSequences());
2107     }
2108   }
2109
2110   public void removeGappedColumnMenuItem_actionPerformed()
2111   {
2112     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2113
2114     SequenceI[] seqs;
2115     if (viewport.getSelectionGroup() != null)
2116     {
2117       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2118               viewport.getHiddenRepSequences());
2119       start = viewport.getSelectionGroup().getStartRes();
2120       end = viewport.getSelectionGroup().getEndRes();
2121     }
2122     else
2123     {
2124       seqs = viewport.getAlignment().getSequencesArray();
2125     }
2126
2127     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2128             "Remove Gapped Columns", seqs, start, end,
2129             viewport.getAlignment());
2130
2131     addHistoryItem(removeGapCols);
2132
2133     statusBar.setText(MessageManager.formatMessage(
2134             "label.removed_empty_columns", new String[]
2135             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2136
2137     // This is to maintain viewport position on first residue
2138     // of first sequence
2139     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2140     int startRes = seq.findPosition(viewport.startRes);
2141     // ShiftList shifts;
2142     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2143     // edit.alColumnChanges=shifts.getInverse();
2144     // if (viewport.hasHiddenColumns)
2145     // viewport.getColumnSelection().compensateForEdits(shifts);
2146     viewport.setStartRes(seq.findIndex(startRes) - 1);
2147     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2148             .getSequences());
2149
2150   }
2151
2152   public void removeAllGapsMenuItem_actionPerformed()
2153   {
2154     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2155
2156     SequenceI[] seqs;
2157     if (viewport.getSelectionGroup() != null)
2158     {
2159       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2160               viewport.getHiddenRepSequences());
2161       start = viewport.getSelectionGroup().getStartRes();
2162       end = viewport.getSelectionGroup().getEndRes();
2163     }
2164     else
2165     {
2166       seqs = viewport.getAlignment().getSequencesArray();
2167     }
2168
2169     // This is to maintain viewport position on first residue
2170     // of first sequence
2171     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2172     int startRes = seq.findPosition(viewport.startRes);
2173
2174     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2175             viewport.getAlignment()));
2176
2177     viewport.setStartRes(seq.findIndex(startRes) - 1);
2178
2179     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2180             .getSequences());
2181
2182   }
2183
2184   public void findMenuItem_actionPerformed()
2185   {
2186     new Finder(alignPanel);
2187   }
2188
2189   /**
2190    * create a new view derived from the current view
2191    *
2192    * @param viewtitle
2193    * @return frame for the new view
2194    */
2195   public AlignFrame newView(String viewtitle)
2196   {
2197     AlignmentI newal;
2198     if (viewport.hasHiddenRows())
2199     {
2200       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2201               .getFullAlignment().getSequencesArray());
2202     }
2203     else
2204     {
2205       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2206     }
2207
2208     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2209     {
2210       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2211       {
2212         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2213         {
2214           newal.addAnnotation(viewport.getAlignment()
2215                   .getAlignmentAnnotation()[i]);
2216         }
2217       }
2218     }
2219
2220     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2221
2222     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2223     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2224     PaintRefresher.Register(newaf.alignPanel,
2225             newaf.alignPanel.av.getSequenceSetId());
2226
2227     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2228             newaf.alignPanel.av.getSequenceSetId());
2229     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2230             newaf.alignPanel.av.getSequenceSetId());
2231
2232     Vector comps = (Vector) PaintRefresher.components.get(viewport
2233             .getSequenceSetId());
2234     int viewSize = -1;
2235     for (int i = 0; i < comps.size(); i++)
2236     {
2237       if (comps.elementAt(i) instanceof AlignmentPanel)
2238       {
2239         viewSize++;
2240       }
2241     }
2242
2243     String title = new String(this.getTitle());
2244     if (viewtitle != null)
2245     {
2246       title = viewtitle + " ( " + title + ")";
2247     }
2248     else
2249     {
2250       if (title.indexOf("(View") > -1)
2251       {
2252         title = title.substring(0, title.indexOf("(View"));
2253       }
2254       title += "(View " + viewSize + ")";
2255     }
2256
2257     newaf.setTitle(title.toString());
2258
2259     newaf.viewport.historyList = viewport.historyList;
2260     newaf.viewport.redoList = viewport.redoList;
2261     return newaf;
2262   }
2263
2264   /**
2265    *
2266    * @return list of feature groups on the view
2267    */
2268   public String[] getFeatureGroups()
2269   {
2270     FeatureRenderer fr = null;
2271     if (alignPanel != null
2272             && (fr = alignPanel.getFeatureRenderer()) != null)
2273     {
2274       List gps = fr.getFeatureGroups();
2275       int p=0;
2276       String[] _gps = new String[gps.size()];
2277       for (Object gp:gps)
2278       {
2279         _gps[p++] = gp.toString();
2280       }
2281       return _gps;
2282     }
2283     return null;
2284   }
2285
2286   /**
2287    * get sequence feature groups that are hidden or shown
2288    *
2289    * @param visible
2290    *          true is visible
2291    * @return list
2292    */
2293   public String[] getFeatureGroupsOfState(boolean visible)
2294   {
2295     FeatureRenderer fr = null;
2296     if (alignPanel != null
2297             && (fr = alignPanel.getFeatureRenderer()) != null)
2298     {
2299       List gps = fr.getGroups(visible);
2300       int p=0;
2301       String[] _gps = new String[gps.size()];
2302       for (Object gp:gps)
2303       {
2304         _gps[p++] = gp.toString();
2305       }
2306       return _gps;
2307     }
2308     return null;
2309   }
2310
2311   /**
2312    * Change the display state for the given feature groups
2313    *
2314    * @param groups
2315    *          list of group strings
2316    * @param state
2317    *          visible or invisible
2318    */
2319   public void setFeatureGroupState(String[] groups, boolean state)
2320   {
2321     FeatureRenderer fr = null;
2322     this.sequenceFeatures.setState(true);
2323     viewport.setShowSequenceFeatures(true);
2324     if (alignPanel != null
2325             && (fr = alignPanel.getFeatureRenderer()) != null)
2326     {
2327
2328       fr.setGroupVisibility((List)Arrays.asList(groups), state);
2329       alignPanel.seqPanel.seqCanvas.repaint();
2330       if (alignPanel.overviewPanel != null)
2331       {
2332         alignPanel.overviewPanel.updateOverviewImage();
2333       }
2334     }
2335   }
2336
2337   public void seqLimits_itemStateChanged()
2338   {
2339     viewport.setShowJVSuffix(seqLimits.getState());
2340     alignPanel.fontChanged();
2341     alignPanel.paintAlignment(true);
2342   }
2343
2344   protected void colourTextMenuItem_actionPerformed()
2345   {
2346     viewport.setColourText(colourTextMenuItem.getState());
2347     alignPanel.paintAlignment(true);
2348   }
2349
2350   protected void displayNonconservedMenuItem_actionPerformed()
2351   {
2352     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2353     alignPanel.paintAlignment(true);
2354   }
2355
2356   protected void wrapMenuItem_actionPerformed()
2357   {
2358     viewport.setWrapAlignment(wrapMenuItem.getState());
2359     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2360     scaleAbove.setEnabled(wrapMenuItem.getState());
2361     scaleLeft.setEnabled(wrapMenuItem.getState());
2362     scaleRight.setEnabled(wrapMenuItem.getState());
2363     alignPanel.paintAlignment(true);
2364   }
2365
2366   public void overviewMenuItem_actionPerformed()
2367   {
2368     if (alignPanel.overviewPanel != null)
2369     {
2370       return;
2371     }
2372
2373     Frame frame = new Frame();
2374     OverviewPanel overview = new OverviewPanel(alignPanel);
2375     frame.add(overview);
2376     // +50 must allow for applet frame window
2377     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2378             "label.overview_params", new String[]
2379             { this.getTitle() }), overview.getPreferredSize().width,
2380             overview.getPreferredSize().height + 50);
2381
2382     frame.pack();
2383     final AlignmentPanel ap = alignPanel;
2384     frame.addWindowListener(new WindowAdapter()
2385     {
2386       @Override
2387       public void windowClosing(WindowEvent e)
2388       {
2389         if (ap != null)
2390         {
2391           ap.setOverviewPanel(null);
2392         }
2393       };
2394     });
2395
2396     alignPanel.setOverviewPanel(overview);
2397
2398   }
2399
2400   void changeColour(ColourSchemeI cs)
2401   {
2402     int threshold = 0;
2403
2404     if (cs != null)
2405     {
2406       if (viewport.getAbovePIDThreshold())
2407       {
2408         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2409                 cs, "Background"));
2410       }
2411
2412       if (viewport.getConservationSelected())
2413       {
2414         cs.setConservationApplied(true);
2415         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2416                 cs, "Background"));
2417       }
2418       else
2419       {
2420         cs.setConservationApplied(false);
2421       }
2422     }
2423     viewport.setGlobalColourScheme(cs);
2424
2425     if (alignPanel.getOverviewPanel() != null)
2426     {
2427       alignPanel.getOverviewPanel().updateOverviewImage();
2428     }
2429
2430     jalview.structure.StructureSelectionManager
2431             .getStructureSelectionManager(viewport.applet)
2432             .sequenceColoursChanged(alignPanel);
2433
2434     alignPanel.paintAlignment(true);
2435   }
2436
2437   protected void modifyPID_actionPerformed()
2438   {
2439     if (viewport.getAbovePIDThreshold()
2440             && viewport.getGlobalColourScheme() != null)
2441     {
2442       SliderPanel.setPIDSliderSource(alignPanel,
2443               viewport.getGlobalColourScheme(), "Background");
2444       SliderPanel.showPIDSlider();
2445     }
2446   }
2447
2448   protected void modifyConservation_actionPerformed()
2449   {
2450     if (viewport.getConservationSelected()
2451             && viewport.getGlobalColourScheme() != null)
2452     {
2453       SliderPanel.setConservationSlider(alignPanel,
2454               viewport.getGlobalColourScheme(), "Background");
2455       SliderPanel.showConservationSlider();
2456     }
2457   }
2458
2459   protected void conservationMenuItem_actionPerformed()
2460   {
2461     viewport.setConservationSelected(conservationMenuItem.getState());
2462
2463     viewport.setAbovePIDThreshold(false);
2464     abovePIDThreshold.setState(false);
2465
2466     changeColour(viewport.getGlobalColourScheme());
2467
2468     modifyConservation_actionPerformed();
2469   }
2470
2471   public void abovePIDThreshold_actionPerformed()
2472   {
2473     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2474
2475     conservationMenuItem.setState(false);
2476     viewport.setConservationSelected(false);
2477
2478     changeColour(viewport.getGlobalColourScheme());
2479
2480     modifyPID_actionPerformed();
2481   }
2482
2483   public void sortPairwiseMenuItem_actionPerformed()
2484   {
2485     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2486     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2487             .getAlignment().getSequenceAt(0), null);
2488
2489     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2490             viewport.getAlignment()));
2491     alignPanel.paintAlignment(true);
2492   }
2493
2494   public void sortIDMenuItem_actionPerformed()
2495   {
2496     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2497     AlignmentSorter.sortByID(viewport.getAlignment());
2498     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2499             viewport.getAlignment()));
2500     alignPanel.paintAlignment(true);
2501   }
2502
2503   public void sortLengthMenuItem_actionPerformed()
2504   {
2505     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2506     AlignmentSorter.sortByLength(viewport.getAlignment());
2507     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2508             viewport.getAlignment()));
2509     alignPanel.paintAlignment(true);
2510   }
2511
2512   public void sortGroupMenuItem_actionPerformed()
2513   {
2514     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2515     AlignmentSorter.sortByGroup(viewport.getAlignment());
2516     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2517             viewport.getAlignment()));
2518     alignPanel.paintAlignment(true);
2519
2520   }
2521
2522   public void removeRedundancyMenuItem_actionPerformed()
2523   {
2524     new RedundancyPanel(alignPanel);
2525   }
2526
2527   public void pairwiseAlignmentMenuItem_actionPerformed()
2528   {
2529     if (viewport.getSelectionGroup() != null
2530             && viewport.getSelectionGroup().getSize() > 1)
2531     {
2532       Frame frame = new Frame();
2533       frame.add(new PairwiseAlignPanel(alignPanel));
2534       jalview.bin.JalviewLite.addFrame(frame,
2535               MessageManager.getString("action.pairwise_alignment"), 600,
2536               500);
2537     }
2538   }
2539
2540   public void PCAMenuItem_actionPerformed()
2541   {
2542     // are the sequences aligned?
2543     if (!viewport.getAlignment().isAligned(false))
2544     {
2545       SequenceI current;
2546       int Width = viewport.getAlignment().getWidth();
2547
2548       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2549       {
2550         current = viewport.getAlignment().getSequenceAt(i);
2551
2552         if (current.getLength() < Width)
2553         {
2554           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2555         }
2556       }
2557       alignPanel.paintAlignment(true);
2558     }
2559
2560     if ((viewport.getSelectionGroup() != null
2561             && viewport.getSelectionGroup().getSize() < 4 && viewport
2562             .getSelectionGroup().getSize() > 0)
2563             || viewport.getAlignment().getHeight() < 4)
2564     {
2565       return;
2566     }
2567
2568     try
2569     {
2570       new PCAPanel(viewport);
2571     } catch (java.lang.OutOfMemoryError ex)
2572     {
2573     }
2574
2575   }
2576
2577   public void averageDistanceTreeMenuItem_actionPerformed()
2578   {
2579     NewTreePanel("AV", "PID", "Average distance tree using PID");
2580   }
2581
2582   public void neighbourTreeMenuItem_actionPerformed()
2583   {
2584     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2585   }
2586
2587   protected void njTreeBlosumMenuItem_actionPerformed()
2588   {
2589     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2590   }
2591
2592   protected void avTreeBlosumMenuItem_actionPerformed()
2593   {
2594     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2595   }
2596
2597   void NewTreePanel(String type, String pwType, String title)
2598   {
2599     // are the sequences aligned?
2600     if (!viewport.getAlignment().isAligned(false))
2601     {
2602       SequenceI current;
2603       int Width = viewport.getAlignment().getWidth();
2604
2605       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2606       {
2607         current = viewport.getAlignment().getSequenceAt(i);
2608
2609         if (current.getLength() < Width)
2610         {
2611           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2612         }
2613       }
2614       alignPanel.paintAlignment(true);
2615
2616     }
2617
2618     if ((viewport.getSelectionGroup() != null && viewport
2619             .getSelectionGroup().getSize() > 1)
2620             || (viewport.getAlignment().getHeight() > 1))
2621     {
2622       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2623
2624       addTreeMenuItem(tp, title);
2625
2626       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2627     }
2628   }
2629
2630   void loadTree_actionPerformed()
2631   {
2632     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2633     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2634     cap.setTreeImport();
2635     Frame frame = new Frame();
2636     frame.add(cap);
2637     jalview.bin.JalviewLite.addFrame(frame,
2638             MessageManager.getString("label.paste_newick_file"), 400, 300);
2639   }
2640
2641   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2642   {
2643     TreePanel tp = new TreePanel(alignPanel, treeFile,
2644             MessageManager.getString("label.load_tree_from_file"), tree);
2645     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2646     addTreeMenuItem(tp, treeFile);
2647   }
2648
2649   /**
2650    * sort the alignment using the given treePanel
2651    *
2652    * @param treePanel
2653    *          tree used to sort view
2654    * @param title
2655    *          string used for undo event name
2656    */
2657   public void sortByTree(TreePanel treePanel, String title)
2658   {
2659     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2660     AlignmentSorter
2661             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2662     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2663     // HistoryItem.SORT));
2664     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2665             "label.order_by_params", new String[]
2666             { title }), oldOrder, viewport.getAlignment()));
2667     alignPanel.paintAlignment(true);
2668   }
2669
2670   /**
2671    * Do any automatic reordering of the alignment and add the necessary bits to
2672    * the menu structure for the new tree
2673    *
2674    * @param treePanel
2675    * @param title
2676    */
2677   protected void addTreeMenuItem(final TreePanel treePanel,
2678           final String title)
2679   {
2680     final MenuItem item = new MenuItem(title);
2681     sortByTreeMenu.add(item);
2682     item.addActionListener(new java.awt.event.ActionListener()
2683     {
2684       @Override
2685       public void actionPerformed(ActionEvent evt)
2686       {
2687         sortByTree(treePanel, title); // treePanel.getTitle());
2688       }
2689     });
2690
2691     treePanel.addWindowListener(new WindowAdapter()
2692     {
2693       @Override
2694       public void windowOpened(WindowEvent e)
2695       {
2696         if (viewport.sortByTree)
2697         {
2698           sortByTree(treePanel, title);
2699         }
2700         super.windowOpened(e);
2701       }
2702
2703       @Override
2704       public void windowClosing(WindowEvent e)
2705       {
2706         sortByTreeMenu.remove(item);
2707       };
2708     });
2709   }
2710
2711   public boolean sortBy(AlignmentOrder alorder, String undoname)
2712   {
2713     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2714     if (viewport.applet.debug)
2715     {
2716       System.err.println("Sorting " + alorder.getOrder().size()
2717               + " in alignment '" + getTitle() + "'");
2718     }
2719     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2720     if (undoname != null)
2721     {
2722       addHistoryItem(new OrderCommand(undoname, oldOrder,
2723               viewport.getAlignment()));
2724     }
2725     alignPanel.paintAlignment(true);
2726     return true;
2727   }
2728
2729   protected void documentation_actionPerformed()
2730   {
2731     alignPanel.av.applet.openJalviewHelpUrl();
2732   }
2733
2734   protected void about_actionPerformed()
2735   {
2736
2737     class AboutPanel extends Canvas
2738     {
2739       String version;
2740
2741       String builddate;
2742
2743       public AboutPanel(String version, String builddate)
2744       {
2745         this.version = version;
2746         this.builddate = builddate;
2747       }
2748
2749       @Override
2750       public void paint(Graphics g)
2751       {
2752         g.setColor(Color.white);
2753         g.fillRect(0, 0, getSize().width, getSize().height);
2754         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2755         FontMetrics fm = g.getFontMetrics();
2756         int fh = fm.getHeight();
2757         int y = 5, x = 7;
2758         g.setColor(Color.black);
2759         // TODO: update this text for each release or centrally store it for
2760         // lite and application
2761         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2762         g.drawString(MessageManager.formatMessage(
2763                 "label.jalviewLite_release", new String[]
2764                 { version }), x, y += fh);
2765         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2766         g.drawString(MessageManager.formatMessage(
2767                 "label.jaview_build_date", new String[]
2768                 { builddate }), x, y += fh);
2769         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2770         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2771                 x, y += fh * 1.5);
2772         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2773                 x + 50, y += fh + 8);
2774         g.drawString(
2775                 MessageManager.getString("label.jalview_dev_managers"), x,
2776                 y += fh);
2777         g.drawString(MessageManager
2778                 .getString("label.jalview_distribution_lists"), x, y += fh);
2779         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2780                 x, y += fh + 8);
2781         g.drawString(
2782                 MessageManager.getString("label.jalview_cite_1_authors"),
2783                 x, y += fh);
2784         g.drawString(
2785                 MessageManager.getString("label.jalview_cite_1_title"), x,
2786                 y += fh);
2787         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2788                 x, y += fh);
2789       }
2790     }
2791
2792     Frame frame = new Frame();
2793     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2794             .getBuildDate()));
2795     jalview.bin.JalviewLite.addFrame(frame,
2796             MessageManager.getString("label.jalview"), 580, 220);
2797
2798   }
2799
2800   public void showURL(String url, String target)
2801   {
2802     if (viewport.applet == null)
2803     {
2804       System.out.println("Not running as applet - no browser available.");
2805     }
2806     else
2807     {
2808       viewport.applet.showURL(url, target);
2809     }
2810   }
2811
2812   // ////////////////////////////////////////////////////////////////////////////////
2813   // JBuilder Graphics here
2814
2815   MenuBar alignFrameMenuBar = new MenuBar();
2816
2817   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2818
2819   MenuItem loadApplication = new MenuItem(
2820           MessageManager.getString("label.view_full_application"));
2821
2822   MenuItem loadTree = new MenuItem(
2823           MessageManager.getString("label.load_associated_tree"));
2824
2825   MenuItem loadAnnotations = new MenuItem(
2826           MessageManager.getString("label.load_features_annotations"));
2827
2828   MenuItem outputFeatures = new MenuItem(
2829           MessageManager.getString("label.export_features").concat("..."));
2830
2831   MenuItem outputAnnotations = new MenuItem(
2832           MessageManager.getString("label.export_annotations").concat("..."));
2833
2834   MenuItem closeMenuItem = new MenuItem(
2835           MessageManager.getString("action.close"));
2836
2837   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2838
2839   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2840
2841   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2842
2843   Menu calculateMenu = new Menu(
2844           MessageManager.getString("action.calculate"));
2845
2846   MenuItem selectAllSequenceMenuItem = new MenuItem(
2847           MessageManager.getString("action.select_all"));
2848
2849   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2850           MessageManager.getString("action.deselect_all"));
2851
2852   MenuItem invertSequenceMenuItem = new MenuItem(
2853           MessageManager.getString("action.invert_selection"));
2854
2855   MenuItem remove2LeftMenuItem = new MenuItem();
2856
2857   MenuItem remove2RightMenuItem = new MenuItem();
2858
2859   MenuItem removeGappedColumnMenuItem = new MenuItem();
2860
2861   MenuItem removeAllGapsMenuItem = new MenuItem();
2862
2863   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2864
2865   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2866
2867   MenuItem sortPairwiseMenuItem = new MenuItem();
2868
2869   MenuItem sortIDMenuItem = new MenuItem();
2870
2871   MenuItem sortLengthMenuItem = new MenuItem();
2872
2873   MenuItem sortGroupMenuItem = new MenuItem();
2874
2875   MenuItem removeRedundancyMenuItem = new MenuItem();
2876
2877   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2878
2879   MenuItem PCAMenuItem = new MenuItem();
2880
2881   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2882
2883   MenuItem neighbourTreeMenuItem = new MenuItem();
2884
2885   BorderLayout borderLayout1 = new BorderLayout();
2886
2887   public Label statusBar = new Label();
2888
2889   Menu outputTextboxMenu = new Menu();
2890
2891   MenuItem clustalColour = new MenuItem();
2892
2893   MenuItem zappoColour = new MenuItem();
2894
2895   MenuItem taylorColour = new MenuItem();
2896
2897   MenuItem hydrophobicityColour = new MenuItem();
2898
2899   MenuItem helixColour = new MenuItem();
2900
2901   MenuItem strandColour = new MenuItem();
2902
2903   MenuItem turnColour = new MenuItem();
2904
2905   MenuItem buriedColour = new MenuItem();
2906
2907   MenuItem purinePyrimidineColour = new MenuItem();
2908
2909   MenuItem RNAInteractionColour = new MenuItem();
2910
2911   MenuItem RNAHelixColour = new MenuItem();
2912
2913   MenuItem userDefinedColour = new MenuItem();
2914
2915   MenuItem PIDColour = new MenuItem();
2916
2917   MenuItem BLOSUM62Colour = new MenuItem();
2918
2919   MenuItem tcoffeeColour = new MenuItem();
2920
2921   MenuItem njTreeBlosumMenuItem = new MenuItem();
2922
2923   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2924
2925   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2926
2927   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2928
2929   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2930
2931   MenuItem alProperties = new MenuItem(
2932           MessageManager.getString("label.alignment_props"));
2933
2934   MenuItem overviewMenuItem = new MenuItem();
2935
2936   MenuItem undoMenuItem = new MenuItem();
2937
2938   MenuItem redoMenuItem = new MenuItem();
2939
2940   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2941
2942   MenuItem noColourmenuItem = new MenuItem();
2943
2944   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2945
2946   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2947
2948   MenuItem findMenuItem = new MenuItem();
2949
2950   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2951
2952   MenuItem nucleotideColour = new MenuItem();
2953
2954   MenuItem deleteGroups = new MenuItem();
2955
2956   MenuItem grpsFromSelection = new MenuItem();
2957
2958   MenuItem createGroup = new MenuItem();
2959
2960   MenuItem unGroup = new MenuItem();
2961
2962   MenuItem delete = new MenuItem();
2963
2964   MenuItem copy = new MenuItem();
2965
2966   MenuItem cut = new MenuItem();
2967
2968   Menu pasteMenu = new Menu();
2969
2970   MenuItem pasteNew = new MenuItem();
2971
2972   MenuItem pasteThis = new MenuItem();
2973
2974   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2975
2976   MenuItem font = new MenuItem();
2977
2978   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2979
2980   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2981
2982   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2983
2984   MenuItem modifyPID = new MenuItem();
2985
2986   MenuItem modifyConservation = new MenuItem();
2987
2988   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2989           "Autocalculate Consensus", true);
2990
2991   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2992           "Sort Alignment With New Tree", true);
2993
2994   Menu sortByTreeMenu = new Menu();
2995
2996   Menu sort = new Menu();
2997
2998   Menu calculate = new Menu();
2999
3000   MenuItem inputText = new MenuItem();
3001
3002   Menu helpMenu = new Menu();
3003
3004   MenuItem documentation = new MenuItem();
3005
3006   MenuItem about = new MenuItem();
3007
3008   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3009
3010   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3011
3012   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3013
3014   Menu autoAnnMenu = new Menu();
3015
3016   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3017
3018   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3019
3020   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3021
3022   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3023
3024   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3025
3026   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3027
3028   private void jbInit() throws Exception
3029   {
3030
3031     setMenuBar(alignFrameMenuBar);
3032
3033     MenuItem item;
3034
3035     // dynamically fill save as menu with available formats
3036     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3037     {
3038
3039       item = new MenuItem(
3040               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3041
3042       item.addActionListener(new java.awt.event.ActionListener()
3043       {
3044         @Override
3045         public void actionPerformed(ActionEvent e)
3046         {
3047           outputText_actionPerformed(e);
3048         }
3049       });
3050
3051       outputTextboxMenu.add(item);
3052     }
3053     closeMenuItem.addActionListener(this);
3054     loadApplication.addActionListener(this);
3055
3056     loadTree.addActionListener(this);
3057     loadAnnotations.addActionListener(this);
3058     outputFeatures.addActionListener(this);
3059     outputAnnotations.addActionListener(this);
3060     selectAllSequenceMenuItem.addActionListener(this);
3061     deselectAllSequenceMenuItem.addActionListener(this);
3062     invertSequenceMenuItem.addActionListener(this);
3063     remove2LeftMenuItem.setLabel(MessageManager
3064             .getString("action.remove_left"));
3065     remove2LeftMenuItem.addActionListener(this);
3066     remove2RightMenuItem.setLabel(MessageManager
3067             .getString("action.remove_right"));
3068     remove2RightMenuItem.addActionListener(this);
3069     removeGappedColumnMenuItem.setLabel(MessageManager
3070             .getString("action.remove_empty_columns"));
3071     removeGappedColumnMenuItem.addActionListener(this);
3072     removeAllGapsMenuItem.setLabel(MessageManager
3073             .getString("action.remove_all_gaps"));
3074     removeAllGapsMenuItem.addActionListener(this);
3075     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3076     viewBoxesMenuItem.setState(true);
3077     viewBoxesMenuItem.addItemListener(this);
3078     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3079     viewTextMenuItem.setState(true);
3080     viewTextMenuItem.addItemListener(this);
3081     sortPairwiseMenuItem.setLabel(MessageManager
3082             .getString("action.by_pairwise_id"));
3083     sortPairwiseMenuItem.addActionListener(this);
3084     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3085     sortIDMenuItem.addActionListener(this);
3086     sortLengthMenuItem.setLabel(MessageManager
3087             .getString("action.by_length"));
3088     sortLengthMenuItem.addActionListener(this);
3089     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3090     sortGroupMenuItem.addActionListener(this);
3091     removeRedundancyMenuItem.setLabel(MessageManager
3092             .getString("action.remove_redundancy").concat("..."));
3093     removeRedundancyMenuItem.addActionListener(this);
3094     pairwiseAlignmentMenuItem.setLabel(MessageManager
3095             .getString("action.pairwise_alignment"));
3096     pairwiseAlignmentMenuItem.addActionListener(this);
3097     PCAMenuItem.setLabel(MessageManager
3098             .getString("label.principal_component_analysis"));
3099     PCAMenuItem.addActionListener(this);
3100     averageDistanceTreeMenuItem.setLabel(MessageManager
3101             .getString("label.average_distance_identity"));
3102     averageDistanceTreeMenuItem.addActionListener(this);
3103     neighbourTreeMenuItem.setLabel(MessageManager
3104             .getString("label.neighbour_joining_identity"));
3105     neighbourTreeMenuItem.addActionListener(this);
3106     statusBar.setBackground(Color.white);
3107     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3108     statusBar.setText(MessageManager.getString("label.status_bar"));
3109     outputTextboxMenu.setLabel(MessageManager
3110             .getString("label.out_to_textbox"));
3111     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3112
3113     clustalColour.addActionListener(this);
3114     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3115     zappoColour.addActionListener(this);
3116     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3117     taylorColour.addActionListener(this);
3118     hydrophobicityColour.setLabel(MessageManager
3119             .getString("label.hydrophobicity"));
3120     hydrophobicityColour.addActionListener(this);
3121     helixColour
3122             .setLabel(MessageManager.getString("label.helix_propensity"));
3123     helixColour.addActionListener(this);
3124     strandColour.setLabel(MessageManager
3125             .getString("label.strand_propensity"));
3126     strandColour.addActionListener(this);
3127     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3128     turnColour.addActionListener(this);
3129     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3130     buriedColour.addActionListener(this);
3131     purinePyrimidineColour.setLabel(MessageManager
3132             .getString("label.purine_pyrimidine"));
3133     purinePyrimidineColour.addActionListener(this);
3134     RNAInteractionColour.setLabel(MessageManager
3135             .getString("label.rna_interaction"));
3136     RNAInteractionColour.addActionListener(this);
3137     RNAHelixColour.setLabel(MessageManager
3138             .getString("action.by_rna_helixes"));
3139     RNAHelixColour.addActionListener(this);
3140     userDefinedColour.setLabel(MessageManager
3141             .getString("action.user_defined"));
3142     userDefinedColour.addActionListener(this);
3143     PIDColour.setLabel(MessageManager
3144             .getString("label.percentage_identity"));
3145     PIDColour.addActionListener(this);
3146     BLOSUM62Colour.setLabel(MessageManager
3147             .getString("label.blosum62_score"));
3148     BLOSUM62Colour.addActionListener(this);
3149     tcoffeeColour
3150             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3151     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3152                                      // provided
3153     tcoffeeColour.addActionListener(this);
3154     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3155             .getString("label.average_distance_bloslum62"));
3156     avDistanceTreeBlosumMenuItem.addActionListener(this);
3157     njTreeBlosumMenuItem.setLabel(MessageManager
3158             .getString("label.neighbour_blosum62"));
3159     njTreeBlosumMenuItem.addActionListener(this);
3160     annotationPanelMenuItem.setLabel(MessageManager
3161             .getString("label.show_annotations"));
3162     annotationPanelMenuItem.addItemListener(this);
3163     colourTextMenuItem.setLabel(MessageManager
3164             .getString("label.colour_text"));
3165     colourTextMenuItem.addItemListener(this);
3166     displayNonconservedMenuItem.setLabel(MessageManager
3167             .getString("label.show_non_conversed"));
3168     displayNonconservedMenuItem.addItemListener(this);
3169     alProperties.addActionListener(this);
3170     overviewMenuItem.setLabel(MessageManager
3171             .getString("label.overview_window"));
3172     overviewMenuItem.addActionListener(this);
3173     undoMenuItem.setEnabled(false);
3174     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3175     undoMenuItem.addActionListener(this);
3176     redoMenuItem.setEnabled(false);
3177     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3178     redoMenuItem.addActionListener(this);
3179     conservationMenuItem.setLabel(MessageManager
3180             .getString("action.by_conservation"));
3181     conservationMenuItem.addItemListener(this);
3182     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3183     noColourmenuItem.addActionListener(this);
3184     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3185     wrapMenuItem.addItemListener(this);
3186     renderGapsMenuItem.setLabel(MessageManager
3187             .getString("action.show_gaps"));
3188     renderGapsMenuItem.setState(true);
3189     renderGapsMenuItem.addItemListener(this);
3190     findMenuItem.setLabel(MessageManager.getString("action.find"));
3191     findMenuItem.addActionListener(this);
3192     abovePIDThreshold.setLabel(MessageManager
3193             .getString("label.above_identity_threshold"));
3194     abovePIDThreshold.addItemListener(this);
3195     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3196     nucleotideColour.addActionListener(this);
3197     deleteGroups.setLabel(MessageManager
3198             .getString("action.undefine_groups"));
3199     deleteGroups.addActionListener(this);
3200     grpsFromSelection.setLabel(MessageManager
3201             .getString("action.make_groups_selection"));
3202     grpsFromSelection.addActionListener(this);
3203     createGroup.setLabel(MessageManager.getString("action.create_group"));
3204     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3205     copy.setLabel(MessageManager.getString("action.copy"));
3206     copy.addActionListener(this);
3207     cut.setLabel(MessageManager.getString("action.cut"));
3208     cut.addActionListener(this);
3209     delete.setLabel(MessageManager.getString("action.delete"));
3210     delete.addActionListener(this);
3211     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3212     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3213     pasteNew.addActionListener(this);
3214     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3215     pasteThis.addActionListener(this);
3216     applyToAllGroups.setLabel(MessageManager
3217             .getString("label.apply_colour_to_all_groups"));
3218     applyToAllGroups.setState(true);
3219     applyToAllGroups.addItemListener(this);
3220     font.setLabel(MessageManager.getString("action.font"));
3221     font.addActionListener(this);
3222     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3223     scaleAbove.setState(true);
3224     scaleAbove.setEnabled(false);
3225     scaleAbove.addItemListener(this);
3226     scaleLeft.setEnabled(false);
3227     scaleLeft.setState(true);
3228     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3229     scaleLeft.addItemListener(this);
3230     scaleRight.setEnabled(false);
3231     scaleRight.setState(true);
3232     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3233     scaleRight.addItemListener(this);
3234     modifyPID.setLabel(MessageManager
3235             .getString("label.modify_identity_thereshold"));
3236     modifyPID.addActionListener(this);
3237     modifyConservation.setLabel(MessageManager
3238             .getString("label.modify_conservation_thereshold"));
3239     modifyConservation.addActionListener(this);
3240     sortByTreeMenu.setLabel(MessageManager
3241             .getString("action.by_tree_order"));
3242     sort.setLabel(MessageManager.getString("action.sort"));
3243     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3244     autoCalculate.addItemListener(this);
3245     sortByTree.addItemListener(this);
3246     inputText
3247             .setLabel(MessageManager.getString("label.input_from_textbox"));
3248     inputText.addActionListener(this);
3249     centreColumnLabelFlag.setLabel(MessageManager
3250             .getString("label.centre_column_labels"));
3251     centreColumnLabelFlag.addItemListener(this);
3252     followMouseOverFlag.setLabel(MessageManager
3253             .getString("label.automatic_scrolling"));
3254     followMouseOverFlag.addItemListener(this);
3255     helpMenu.setLabel(MessageManager.getString("action.help"));
3256     documentation.setLabel(MessageManager.getString("label.documentation"));
3257     documentation.addActionListener(this);
3258
3259     about.setLabel(MessageManager.getString("label.about"));
3260     about.addActionListener(this);
3261     seqLimits.setState(true);
3262     seqLimits.setLabel(MessageManager
3263             .getString("label.show_sequence_limits"));
3264     seqLimits.addItemListener(this);
3265     featureSettings.setLabel(MessageManager
3266             .getString("label.feature_settings"));
3267     featureSettings.addActionListener(this);
3268     sequenceFeatures.setLabel(MessageManager
3269             .getString("label.sequence_features"));
3270     sequenceFeatures.addItemListener(this);
3271     sequenceFeatures.setState(false);
3272     annotationColour.setLabel(MessageManager
3273             .getString("action.by_annotation"));
3274     annotationColour.addActionListener(this);
3275     invertSequenceMenuItem.setLabel(MessageManager
3276             .getString("action.invert_sequence_selection"));
3277     invertColSel.setLabel(MessageManager
3278             .getString("action.invert_column_selection"));
3279     menu1.setLabel(MessageManager.getString("action.show"));
3280     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3281     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3282     menu2.setLabel(MessageManager.getString("action.hide"));
3283     hideColumns
3284             .setLabel(MessageManager.getString("label.selected_columns"));
3285     hideSequences.setLabel(MessageManager
3286             .getString("label.selected_sequences"));
3287     hideAllButSelection.setLabel(MessageManager
3288             .getString("label.all_but_selected_region"));
3289     hideAllSelection.setLabel(MessageManager
3290             .getString("label.selected_region"));
3291     showAllHidden.setLabel(MessageManager
3292             .getString("label.all_sequences_columns"));
3293     showGroupConsensus.setLabel(MessageManager
3294             .getString("label.group_consensus"));
3295     showGroupConservation.setLabel(MessageManager
3296             .getString("label.group_conservation"));
3297     showConsensusHistogram.setLabel(MessageManager
3298             .getString("label.show_consensus_histogram"));
3299     showSequenceLogo.setLabel(MessageManager
3300             .getString("label.show_consensus_logo"));
3301     normSequenceLogo.setLabel(MessageManager
3302             .getString("label.norm_consensus_logo"));
3303     applyAutoAnnotationSettings.setLabel(MessageManager
3304             .getString("label.apply_all_groups"));
3305     applyAutoAnnotationSettings.setState(true);
3306     autoAnnMenu.setLabel(MessageManager
3307             .getString("label.autocalculated_annotation"));
3308
3309     invertColSel.addActionListener(this);
3310     showColumns.addActionListener(this);
3311     showSeqs.addActionListener(this);
3312     hideColumns.addActionListener(this);
3313     hideSequences.addActionListener(this);
3314     hideAllButSelection.addActionListener(this);
3315     hideAllSelection.addActionListener(this);
3316     showAllHidden.addActionListener(this);
3317     showGroupConsensus.addItemListener(this);
3318     showGroupConservation.addItemListener(this);
3319     showConsensusHistogram.addItemListener(this);
3320     showSequenceLogo.addItemListener(this);
3321     normSequenceLogo.addItemListener(this);
3322
3323     applyAutoAnnotationSettings.addItemListener(this);
3324     formatMenu.setLabel(MessageManager.getString("action.format"));
3325     selectMenu.setLabel(MessageManager.getString("action.select"));
3326     newView.setLabel(MessageManager.getString("action.new_view"));
3327     newView.addActionListener(this);
3328     alignFrameMenuBar.add(fileMenu);
3329     alignFrameMenuBar.add(editMenu);
3330     alignFrameMenuBar.add(selectMenu);
3331     alignFrameMenuBar.add(viewMenu);
3332     alignFrameMenuBar.add(formatMenu);
3333     alignFrameMenuBar.add(colourMenu);
3334     alignFrameMenuBar.add(calculateMenu);
3335     alignFrameMenuBar.add(helpMenu);
3336
3337     fileMenu.add(inputText);
3338     fileMenu.add(loadTree);
3339     fileMenu.add(loadAnnotations);
3340
3341     fileMenu.addSeparator();
3342     fileMenu.add(outputTextboxMenu);
3343     fileMenu.add(outputFeatures);
3344     fileMenu.add(outputAnnotations);
3345
3346     if (jalviewServletURL != null)
3347     {
3348       fileMenu.add(loadApplication);
3349     }
3350
3351     fileMenu.addSeparator();
3352     fileMenu.add(closeMenuItem);
3353
3354     editMenu.add(undoMenuItem);
3355     editMenu.add(redoMenuItem);
3356     editMenu.add(cut);
3357     editMenu.add(copy);
3358     editMenu.add(pasteMenu);
3359     editMenu.add(delete);
3360     editMenu.addSeparator();
3361     editMenu.add(remove2LeftMenuItem);
3362     editMenu.add(remove2RightMenuItem);
3363     editMenu.add(removeGappedColumnMenuItem);
3364     editMenu.add(removeAllGapsMenuItem);
3365     editMenu.add(removeRedundancyMenuItem);
3366     viewMenu.add(newView);
3367     viewMenu.addSeparator();
3368     viewMenu.add(menu1);
3369     viewMenu.add(menu2);
3370     viewMenu.addSeparator();
3371     viewMenu.add(followMouseOverFlag);
3372     viewMenu.add(annotationPanelMenuItem);
3373     autoAnnMenu.add(applyAutoAnnotationSettings);
3374     autoAnnMenu.add(showConsensusHistogram);
3375     autoAnnMenu.add(showSequenceLogo);
3376     autoAnnMenu.add(normSequenceLogo);
3377     autoAnnMenu.addSeparator();
3378     autoAnnMenu.add(showGroupConservation);
3379     autoAnnMenu.add(showGroupConsensus);
3380     viewMenu.add(autoAnnMenu);
3381     viewMenu.addSeparator();
3382     viewMenu.add(sequenceFeatures);
3383     viewMenu.add(featureSettings);
3384     viewMenu.addSeparator();
3385     viewMenu.add(alProperties);
3386     viewMenu.addSeparator();
3387     viewMenu.add(overviewMenuItem);
3388     colourMenu.add(applyToAllGroups);
3389     colourMenu.addSeparator();
3390     colourMenu.add(noColourmenuItem);
3391     colourMenu.add(clustalColour);
3392     colourMenu.add(BLOSUM62Colour);
3393     colourMenu.add(PIDColour);
3394     colourMenu.add(zappoColour);
3395     colourMenu.add(taylorColour);
3396     colourMenu.add(hydrophobicityColour);
3397     colourMenu.add(helixColour);
3398     colourMenu.add(strandColour);
3399     colourMenu.add(turnColour);
3400     colourMenu.add(buriedColour);
3401     colourMenu.add(nucleotideColour);
3402     colourMenu.add(purinePyrimidineColour);
3403     // colourMenu.add(RNAInteractionColour);
3404     colourMenu.add(tcoffeeColour);
3405     colourMenu.add(userDefinedColour);
3406     colourMenu.addSeparator();
3407     colourMenu.add(conservationMenuItem);
3408     colourMenu.add(modifyConservation);
3409     colourMenu.add(abovePIDThreshold);
3410     colourMenu.add(modifyPID);
3411     colourMenu.add(annotationColour);
3412     colourMenu.add(RNAHelixColour);
3413     calculateMenu.add(sort);
3414     calculateMenu.add(calculate);
3415     calculateMenu.addSeparator();
3416     calculateMenu.add(pairwiseAlignmentMenuItem);
3417     calculateMenu.add(PCAMenuItem);
3418     calculateMenu.add(autoCalculate);
3419     calculateMenu.add(sortByTree);
3420     this.add(statusBar, BorderLayout.SOUTH);
3421     pasteMenu.add(pasteNew);
3422     pasteMenu.add(pasteThis);
3423     sort.add(sortIDMenuItem);
3424     sort.add(sortLengthMenuItem);
3425     sort.add(sortByTreeMenu);
3426     sort.add(sortGroupMenuItem);
3427     sort.add(sortPairwiseMenuItem);
3428     calculate.add(averageDistanceTreeMenuItem);
3429     calculate.add(neighbourTreeMenuItem);
3430     calculate.add(avDistanceTreeBlosumMenuItem);
3431     calculate.add(njTreeBlosumMenuItem);
3432     helpMenu.add(documentation);
3433     helpMenu.add(about);
3434     menu1.add(showColumns);
3435     menu1.add(showSeqs);
3436     menu1.add(showAllHidden);
3437     menu2.add(hideColumns);
3438     menu2.add(hideSequences);
3439     menu2.add(hideAllSelection);
3440     menu2.add(hideAllButSelection);
3441     formatMenu.add(font);
3442     formatMenu.add(seqLimits);
3443     formatMenu.add(wrapMenuItem);
3444     formatMenu.add(scaleAbove);
3445     formatMenu.add(scaleLeft);
3446     formatMenu.add(scaleRight);
3447     formatMenu.add(viewBoxesMenuItem);
3448     formatMenu.add(viewTextMenuItem);
3449     formatMenu.add(colourTextMenuItem);
3450     formatMenu.add(displayNonconservedMenuItem);
3451     formatMenu.add(renderGapsMenuItem);
3452     formatMenu.add(centreColumnLabelFlag);
3453     selectMenu.add(findMenuItem);
3454     selectMenu.addSeparator();
3455     selectMenu.add(selectAllSequenceMenuItem);
3456     selectMenu.add(deselectAllSequenceMenuItem);
3457     selectMenu.add(invertSequenceMenuItem);
3458     selectMenu.add(invertColSel);
3459     selectMenu.add(createGroup);
3460     selectMenu.add(unGroup);
3461     selectMenu.add(grpsFromSelection);
3462     selectMenu.add(deleteGroups);
3463
3464   }
3465
3466   public void setStatus(String string)
3467   {
3468     statusBar.setText(string);
3469   };
3470
3471   MenuItem featureSettings = new MenuItem();
3472
3473   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3474
3475   MenuItem annotationColour = new MenuItem();
3476
3477   MenuItem invertColSel = new MenuItem();
3478
3479   Menu menu1 = new Menu();
3480
3481   MenuItem showColumns = new MenuItem();
3482
3483   MenuItem showSeqs = new MenuItem();
3484
3485   Menu menu2 = new Menu();
3486
3487   MenuItem hideColumns = new MenuItem();
3488
3489   MenuItem hideSequences = new MenuItem();
3490
3491   MenuItem hideAllButSelection = new MenuItem();
3492
3493   MenuItem hideAllSelection = new MenuItem();
3494
3495   MenuItem showAllHidden = new MenuItem();
3496
3497   Menu formatMenu = new Menu();
3498
3499   Menu selectMenu = new Menu();
3500
3501   MenuItem newView = new MenuItem();
3502
3503   /**
3504    * Attach the alignFrame panels after embedding menus, if necessary. This used
3505    * to be called setEmbedded, but is now creates the dropdown menus in a
3506    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3507    *
3508    * @param reallyEmbedded
3509    *          true to attach the view to the applet area on the page rather than
3510    *          in a new window
3511    */
3512   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3513   {
3514     if (reallyEmbedded)
3515     {
3516       // ////
3517       // Explicly build the embedded menu panel for the on-page applet
3518       //
3519       // view cannot be closed if its actually on the page
3520       fileMenu.remove(closeMenuItem);
3521       fileMenu.remove(3); // Remove Seperator
3522       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3523               Font.PLAIN, 11, false); // use our own fonts.
3524       // and actually add the components to the applet area
3525       viewport.applet.setLayout(new BorderLayout());
3526       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3527       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3528       alignPanel.setSize(viewport.applet.getSize().width,
3529               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3530                       - statusBar.HEIGHT);
3531       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3532       final AlignFrame me = this;
3533       viewport.applet.addFocusListener(new FocusListener()
3534       {
3535
3536         @Override
3537         public void focusLost(FocusEvent e)
3538         {
3539           if (me.viewport.applet.currentAlignFrame == me)
3540           {
3541             me.viewport.applet.currentAlignFrame = null;
3542           }
3543         }
3544
3545         @Override
3546         public void focusGained(FocusEvent e)
3547         {
3548           me.viewport.applet.currentAlignFrame = me;
3549         }
3550       });
3551       viewport.applet.validate();
3552     }
3553     else
3554     {
3555       // //////
3556       // test and embed menu bar if necessary.
3557       //
3558       if (embedMenuIfNeeded(alignPanel))
3559       {
3560         // adjust for status bar height too
3561         alignPanel.setSize(getSize().width, getSize().height
3562                 - statusBar.HEIGHT);
3563       }
3564       add(statusBar, BorderLayout.SOUTH);
3565       add(alignPanel, BorderLayout.CENTER);
3566       // and register with the applet so it can pass external API calls to us
3567       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3568               DEFAULT_HEIGHT);
3569     }
3570   }
3571
3572   /**
3573    * create a new binding between structures in an existing jmol viewer instance
3574    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3575    * this does not open a new Jmol window, or modify the display of the
3576    * structures in the original jmol window. Note This method doesn't work
3577    * without an additional javascript library to exchange messages between the
3578    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3579    *
3580    * @param viewer
3581    *          JmolViewer instance
3582    * @param sequenceIds
3583    *          - sequence Ids to search for associations
3584    */
3585   public SequenceStructureBinding addStructureViewInstance(
3586           Object jmolviewer, String[] sequenceIds)
3587   {
3588     org.jmol.api.JmolViewer viewer = null;
3589     try
3590     {
3591       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3592     } catch (ClassCastException ex)
3593     {
3594       System.err.println("Unsupported viewer object :"
3595               + jmolviewer.getClass());
3596     }
3597     if (viewer == null)
3598     {
3599       System.err.println("Can't use this object as a structure viewer:"
3600               + jmolviewer.getClass());
3601       return null;
3602     }
3603     SequenceI[] seqs = null;
3604     if (sequenceIds == null || sequenceIds.length == 0)
3605     {
3606       seqs = viewport.getAlignment().getSequencesArray();
3607     }
3608     else
3609     {
3610       Vector sqi = new Vector();
3611       AlignmentI al = viewport.getAlignment();
3612       for (int sid = 0; sid < sequenceIds.length; sid++)
3613       {
3614         SequenceI sq = al.findName(sequenceIds[sid]);
3615         if (sq != null)
3616         {
3617           sqi.addElement(sq);
3618         }
3619       }
3620       if (sqi.size() > 0)
3621       {
3622         seqs = new SequenceI[sqi.size()];
3623         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3624         {
3625           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3626         }
3627       }
3628       else
3629       {
3630         return null;
3631       }
3632     }
3633     ExtJmol jmv = null;
3634     // TODO: search for a jmv that involves viewer
3635     if (jmv == null)
3636     { // create a new viewer/jalview binding.
3637       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3638       { seqs });
3639     }
3640     return jmv;
3641
3642   }
3643
3644   /**
3645    * bind a pdb file to a sequence in the current view
3646    *
3647    * @param sequenceId
3648    *          - sequenceId within the dataset.
3649    * @param pdbEntryString
3650    *          - the short name for the PDB file
3651    * @param pdbFile
3652    *          - pdb file - either a URL or a valid PDB file.
3653    * @return true if binding was as success TODO: consider making an exception
3654    *         structure for indicating when PDB parsing or sequenceId location
3655    *         fails.
3656    */
3657   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3658           String pdbFile)
3659   {
3660     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3661     boolean needtoadd = false;
3662     if (toaddpdb != null)
3663     {
3664       Vector pdbe = toaddpdb.getPDBId();
3665       PDBEntry pdbentry = null;
3666       if (pdbe != null && pdbe.size() > 0)
3667       {
3668         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3669         {
3670           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3671           if (!pdbentry.getId().equals(pdbEntryString)
3672                   && !pdbentry.getFile().equals(pdbFile))
3673           {
3674             pdbentry = null;
3675           }
3676           else
3677           {
3678             continue;
3679           }
3680         }
3681       }
3682       if (pdbentry == null)
3683       {
3684         pdbentry = new PDBEntry();
3685         pdbentry.setId(pdbEntryString);
3686         pdbentry.setFile(pdbFile);
3687         needtoadd = true; // add this new entry to sequence.
3688       }
3689       // resolve data source
3690       // TODO: this code should be a refactored to an io package
3691       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3692       if (protocol == null)
3693       {
3694         return false;
3695       }
3696       if (needtoadd)
3697       {
3698         // make a note of the access mode and add
3699         if (pdbentry.getProperty() == null)
3700         {
3701           pdbentry.setProperty(new Hashtable());
3702         }
3703         pdbentry.getProperty().put("protocol", protocol);
3704         toaddpdb.addPDBId(pdbentry);
3705         alignPanel.getStructureSelectionManager()
3706                 .registerPDBEntry(pdbentry);
3707       }
3708     }
3709     return true;
3710   }
3711
3712   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3713   {
3714     if (seqs != null)
3715     {
3716       Vector sequences = new Vector();
3717       for (int i = 0; i < seqs.length; i++)
3718       {
3719         if (seqs[i] != null)
3720         {
3721           sequences.addElement(new Object[]
3722           { seqs[i], (chains != null) ? chains[i] : null });
3723         }
3724       }
3725       seqs = new SequenceI[sequences.size()];
3726       chains = new String[sequences.size()];
3727       for (int i = 0, isize = sequences.size(); i < isize; i++)
3728       {
3729         Object[] oj = (Object[]) sequences.elementAt(i);
3730
3731         seqs[i] = (SequenceI) oj[0];
3732         chains[i] = (String) oj[1];
3733       }
3734     }
3735     return new Object[]
3736     { seqs, chains };
3737
3738   }
3739
3740   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3741           SequenceI[] seqs, String[] chains, String protocol)
3742   {
3743     // Scrub any null sequences from the array
3744     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3745     seqs = (SequenceI[]) sqch[0];
3746     chains = (String[]) sqch[1];
3747     if (seqs == null || seqs.length == 0)
3748     {
3749       System.err
3750               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3751     }
3752     if (protocol == null || protocol.trim().length() == 0
3753             || protocol.equals("null"))
3754     {
3755       protocol = (String) pdb.getProperty().get("protocol");
3756       if (protocol == null)
3757       {
3758         System.err.println("Couldn't work out protocol to open structure: "
3759                 + pdb.getId());
3760         return;
3761       }
3762     }
3763     if (applet.useXtrnalSviewer)
3764     {
3765       // register the association(s) and quit, don't create any windows.
3766       if (StructureSelectionManager.getStructureSelectionManager(applet)
3767               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3768       {
3769         System.err.println("Failed to map " + pdb.getFile() + " ("
3770                 + protocol + ") to any sequences");
3771       }
3772       return;
3773     }
3774     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3775     {
3776       // can only do alignments with Jmol
3777       // find the last jmol window assigned to this alignment
3778       jalview.appletgui.AppletJmol ajm = null, tajm;
3779       Vector jmols = applet
3780               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3781       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3782       {
3783         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3784         if (tajm.ap.alignFrame == this)
3785         {
3786           ajm = tajm;
3787           break;
3788         }
3789       }
3790       if (ajm != null)
3791       {
3792         System.err
3793                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3794         // try and add the pdb structure
3795         // ajm.addS
3796         ajm = null;
3797       }
3798     }
3799     // otherwise, create a new window
3800     if (applet.jmolAvailable)
3801     {
3802       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3803               protocol);
3804       applet.lastFrameX += 40;
3805       applet.lastFrameY += 40;
3806     }
3807     else
3808     {
3809       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3810     }
3811
3812   }
3813
3814   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3815           SequenceI[][] seqs, String[][] chains, String[] protocols)
3816   {
3817     // TODO Auto-generated method stub
3818     System.err.println("Aligned Structure View: Not yet implemented.");
3819   }
3820
3821   /**
3822    * modify the current selection, providing the user has not made a selection
3823    * already.
3824    *
3825    * @param sel
3826    *          - sequences from this alignment
3827    * @param csel
3828    *          - columns to be selected on the alignment
3829    */
3830   public void select(SequenceGroup sel, ColumnSelection csel)
3831   {
3832     alignPanel.seqPanel.selection(sel, csel, null);
3833   }
3834
3835   public void scrollTo(int row, int column)
3836   {
3837     alignPanel.seqPanel.scrollTo(row, column);
3838   }
3839
3840   public void scrollToRow(int row)
3841   {
3842     alignPanel.seqPanel.scrollToRow(row);
3843   }
3844
3845   public void scrollToColumn(int column)
3846   {
3847     alignPanel.seqPanel.scrollToColumn(column);
3848   }
3849
3850   /**
3851    * @return the alignments unique ID.
3852    */
3853   public String getSequenceSetId()
3854   {
3855     return viewport.getSequenceSetId();
3856   }
3857
3858   /**
3859    * Load the (T-Coffee) score file from the specified url
3860    *
3861    * @param source
3862    *          File/URL/T-COFFEE score file contents
3863    * @throws IOException
3864    * @return true if alignment was annotated with data from source
3865    */
3866   public boolean loadScoreFile(String source) throws IOException
3867   {
3868
3869     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3870             AppletFormatAdapter.checkProtocol(source));
3871     if (!file.isValid())
3872     {
3873       // TODO: raise dialog for gui
3874       System.err.println("Problems parsing T-Coffee scores: "
3875               + file.getWarningMessage());
3876       System.err.println("Origin was:\n" + source);
3877       return false;
3878     }
3879
3880     /*
3881      * check that the score matrix matches the alignment dimensions
3882      */
3883     AlignmentI aln;
3884     if ((aln = viewport.getAlignment()) != null
3885             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3886                     .getWidth()))
3887     {
3888       // TODO: raise a dialog box here rather than bomb out.
3889       System.err
3890               .println("The scores matrix does not match the alignment dimensions");
3891
3892     }
3893
3894     // TODO add parameter to indicate if matching should be done
3895     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3896     {
3897       alignPanel.fontChanged();
3898       tcoffeeColour.setEnabled(true);
3899       // switch to this color
3900       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3901       return true;
3902     }
3903     else
3904     {
3905       System.err.println("Problems resolving T-Coffee scores:");
3906       if (file.getWarningMessage() != null)
3907       {
3908         System.err.println(file.getWarningMessage());
3909       }
3910     }
3911     return false;
3912   }
3913
3914 }