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.FeatureRenderer;
  27 import jalview.api.SequenceStructureBinding;
  28 import jalview.bin.JalviewLite;
  29 import jalview.commands.CommandI;
  30 import jalview.commands.EditCommand;
  31 import jalview.commands.EditCommand.Action;
  32 import jalview.commands.OrderCommand;
  33 import jalview.commands.RemoveGapColCommand;
  34 import jalview.commands.RemoveGapsCommand;
  35 import jalview.commands.SlideSequencesCommand;
  36 import jalview.commands.TrimRegionCommand;
  37 import jalview.datamodel.Alignment;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.ColumnSelection;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceGroup;
  44 import jalview.datamodel.SequenceI;
  45 import jalview.io.AnnotationFile;
  46 import jalview.io.AppletFormatAdapter;
  47 import jalview.io.FeaturesFile;
  48 import jalview.io.TCoffeeScoreFile;
  49 import jalview.schemes.Blosum62ColourScheme;
  50 import jalview.schemes.BuriedColourScheme;
  51 import jalview.schemes.ClustalxColourScheme;
  52 import jalview.schemes.ColourSchemeI;
  53 import jalview.schemes.HelixColourScheme;
  54 import jalview.schemes.HydrophobicColourScheme;
  55 import jalview.schemes.NucleotideColourScheme;
  56 import jalview.schemes.PIDColourScheme;
  57 import jalview.schemes.PurinePyrimidineColourScheme;
  58 import jalview.schemes.RNAHelicesColourChooser;
  59 import jalview.schemes.RNAInteractionColourScheme;
  60 import jalview.schemes.StrandColourScheme;
  61 import jalview.schemes.TCoffeeColourScheme;
  62 import jalview.schemes.TaylorColourScheme;
  63 import jalview.schemes.TurnColourScheme;
  64 import jalview.schemes.ZappoColourScheme;
  65 import jalview.structure.StructureSelectionManager;
  66 import jalview.util.MessageManager;
  67
  68 import java.awt.BorderLayout;
  69 import java.awt.Canvas;
  70 import java.awt.CheckboxMenuItem;
  71 import java.awt.Color;
  72 import java.awt.Font;
  73 import java.awt.FontMetrics;
  74 import java.awt.Frame;
  75 import java.awt.Graphics;
  76 import java.awt.Label;
  77 import java.awt.Menu;
  78 import java.awt.MenuBar;
  79 import java.awt.MenuItem;
  80 import java.awt.event.ActionEvent;
  81 import java.awt.event.ActionListener;
  82 import java.awt.event.FocusEvent;
  83 import java.awt.event.FocusListener;
  84 import java.awt.event.ItemEvent;
  85 import java.awt.event.ItemListener;
  86 import java.awt.event.KeyEvent;
  87 import java.awt.event.KeyListener;
  88 import java.awt.event.WindowAdapter;
  89 import java.awt.event.WindowEvent;
  90 import java.io.IOException;
  91 import java.net.URL;
  92 import java.net.URLEncoder;
  93 import java.util.Arrays;
  94 import java.util.Hashtable;
  95 import java.util.List;
  96 import java.util.Map;
  97 import java.util.StringTokenizer;
  98 import java.util.Vector;
  99
 100 public class AlignFrame extends EmbmenuFrame implements ActionListener,
 101         ItemListener, KeyListener, AlignViewControllerGuiI
 102 {
 103   public AlignViewControllerI avc;
 104
 105   public AlignmentPanel alignPanel;
 106
 107   public AlignViewport viewport;
 108
 109   int DEFAULT_WIDTH = 700;
 110
 111   int DEFAULT_HEIGHT = 500;
 112
 113   String jalviewServletURL;
 114
 115   public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
 116           String title, boolean embedded)
 117   {
 118     if (applet != null)
 119     {
 120       jalviewServletURL = applet.getParameter("APPLICATION_URL");
 121     }
 122
 123     try
 124     {
 125       jbInit();
 126     } catch (Exception ex)
 127     {
 128       ex.printStackTrace();
 129     }
 130     // need to get window geometry before we calculate alignment layout
 131     if (applet != null)
 132     {
 133       String param;
 134       try
 135       {
 136         param = applet.getParameter("windowWidth");
 137         if (param != null)
 138         {
 139           int width = Integer.parseInt(param);
 140           DEFAULT_WIDTH = width;
 141         }
 142         param = applet.getParameter("windowHeight");
 143         if (param != null)
 144         {
 145           int height = Integer.parseInt(param);
 146           DEFAULT_HEIGHT = height;
 147         }
 148       } catch (Exception ex)
 149       {
 150       }
 151     }
 152     viewport = new AlignViewport(al, applet);
 153     alignPanel = new AlignmentPanel(this, viewport);
 154     avc = new jalview.controller.AlignViewController(this, viewport,
 155             alignPanel);
 156     viewport.updateConservation(alignPanel);
 157     viewport.updateConsensus(alignPanel);
 158
 159     annotationPanelMenuItem.setState(viewport.showAnnotation);
 160     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
 161     followMouseOverFlag.setState(viewport.getFollowHighlight());
 162     showGroupConsensus.setState(viewport.isShowGroupConsensus());
 163     showGroupConservation.setState(viewport.isShowGroupConservation());
 164     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
 165     showSequenceLogo.setState(viewport.isShowSequenceLogo());
 166     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
 167     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
 168
 169     seqLimits.setState(viewport.showJVSuffix);
 170
 171     if (applet != null)
 172     {
 173       String param = applet.getParameter("sortBy");
 174       if (param != null)
 175       {
 176         if (param.equalsIgnoreCase("Id"))
 177         {
 178           sortIDMenuItem_actionPerformed();
 179         }
 180         else if (param.equalsIgnoreCase("Pairwise Identity"))
 181         {
 182           sortPairwiseMenuItem_actionPerformed();
 183         }
 184         else if (param.equalsIgnoreCase("Length"))
 185         {
 186           sortLengthMenuItem_actionPerformed();
 187         }
 188       }
 189
 190       param = applet.getParameter("wrap");
 191       if (param != null)
 192       {
 193         if (param.equalsIgnoreCase("true"))
 194         {
 195           wrapMenuItem.setState(true);
 196           wrapMenuItem_actionPerformed();
 197         }
 198       }
 199       param = applet.getParameter("centrecolumnlabels");
 200       if (param != null)
 201       {
 202         centreColumnLabelFlag.setState(true);
 203         centreColumnLabelFlag_stateChanged();
 204       }
 205
 206     }
 207     if (viewport.getAlignment().isNucleotide())
 208     {
 209       viewport.updateStrucConsensus(alignPanel);
 210       if (viewport.getAlignment().hasRNAStructure())
 211       {
 212         RNAHelixColour.setEnabled(true);
 213       }
 214       else
 215       {
 216         RNAHelixColour.setEnabled(false);
 217       }
 218     }
 219     else
 220     {
 221       RNAHelixColour.setEnabled(false);
 222       purinePyrimidineColour.setEnabled(false);
 223     }
 224     // Some JVMS send keyevents to Top frame or lowest panel,
 225     // Havent worked out why yet. So add to both this frame and seqCanvas for
 226     // now
 227     this.addKeyListener(this);
 228     alignPanel.seqPanel.seqCanvas.addKeyListener(this);
 229     alignPanel.idPanel.idCanvas.addKeyListener(this);
 230     alignPanel.scalePanel.addKeyListener(this);
 231     alignPanel.annotationPanel.addKeyListener(this);
 232     alignPanel.annotationPanelHolder.addKeyListener(this);
 233     alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
 234     alignPanel.alabels.addKeyListener(this);
 235     createAlignFrameWindow(embedded, title);
 236
 237     validate();
 238     alignPanel.adjustAnnotationHeight();
 239     alignPanel.paintAlignment(true);
 240   }
 241
 242   public AlignViewport getAlignViewport()
 243   {
 244     return viewport;
 245   }
 246
 247   public SeqCanvas getSeqcanvas()
 248   {
 249     return alignPanel.seqPanel.seqCanvas;
 250   }
 251
 252   /**
 253    * Load a features file onto the alignment
 254    *
 255    * @param file
 256    *          file URL, content, or other resolvable path
 257    * @param type
 258    *          is protocol for accessing data referred to by file
 259    */
 260
 261   public boolean parseFeaturesFile(String file, String type)
 262   {
 263     return parseFeaturesFile(file, type, true);
 264   }
 265
 266   /**
 267    * Load a features file onto the alignment
 268    *
 269    * @param file
 270    *          file URL, content, or other resolvable path
 271    * @param type
 272    *          is protocol for accessing data referred to by file
 273    * @param autoenabledisplay
 274    *          when true, display features flag will be automatically enabled if
 275    *          features are loaded
 276    * @return true if data parsed as a features file
 277    */
 278   public boolean parseFeaturesFile(String file, String type,
 279           boolean autoenabledisplay)
 280   {
 281     // TODO: test if importing a features file onto an alignment which already
 282     // has features with links overwrites the original links.
 283
 284     Hashtable featureLinks = new Hashtable();
 285     boolean featuresFile = false;
 286     try
 287     {
 288       featuresFile = new jalview.io.FeaturesFile(file, type)
 289               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
 290                       .getFeatureRenderer().getFeatureColours(), featureLinks,
 291                       true, viewport.applet.getDefaultParameter(
 292                               "relaxedidmatch", false));
 293     } catch (Exception ex)
 294     {
 295       ex.printStackTrace();
 296     }
 297
 298     if (featuresFile)
 299     {
 300       if (featureLinks.size() > 0)
 301       {
 302         alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
 303       }
 304       if (autoenabledisplay)
 305       {
 306         viewport.setShowSequenceFeatures(true);
 307         sequenceFeatures.setState(true);
 308       }
 309       if (alignPanel.seqPanel.seqCanvas.fr != null)
 310       {
 311         // update the min/max ranges where necessary
 312         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
 313       }
 314       if (viewport.featureSettings != null)
 315       {
 316         viewport.featureSettings.refreshTable();
 317       }
 318       alignPanel.paintAlignment(true);
 319       statusBar.setText(MessageManager
 320               .getString("label.successfully_added_features_alignment"));
 321     }
 322     return featuresFile;
 323   }
 324
 325   @Override
 326   public void keyPressed(KeyEvent evt)
 327   {
 328     if (viewport.cursorMode
 329             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 330                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 331                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 332             && Character.isDigit(evt.getKeyChar()))
 333     {
 334       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 335     }
 336
 337     switch (evt.getKeyCode())
 338     {
 339     case 27: // escape key
 340       deselectAllSequenceMenuItem_actionPerformed();
 341
 342       alignPanel.alabels.cancelDrag();
 343       break;
 344     case KeyEvent.VK_X:
 345       if (evt.isControlDown() || evt.isMetaDown())
 346       {
 347         cut_actionPerformed();
 348       }
 349       break;
 350     case KeyEvent.VK_C:
 351       if (viewport.cursorMode && !evt.isControlDown())
 352       {
 353         alignPanel.seqPanel.setCursorColumn();
 354       }
 355       if (evt.isControlDown() || evt.isMetaDown())
 356       {
 357         copy_actionPerformed();
 358       }
 359       break;
 360     case KeyEvent.VK_V:
 361       if (evt.isControlDown())
 362       {
 363         paste(evt.isShiftDown());
 364       }
 365       break;
 366     case KeyEvent.VK_A:
 367       if (evt.isControlDown() || evt.isMetaDown())
 368       {
 369         selectAllSequenceMenuItem_actionPerformed();
 370       }
 371       break;
 372     case KeyEvent.VK_DOWN:
 373       if (viewport.cursorMode)
 374       {
 375         alignPanel.seqPanel.moveCursor(0, 1);
 376       }
 377       else
 378       {
 379         moveSelectedSequences(false);
 380       }
 381       break;
 382
 383     case KeyEvent.VK_UP:
 384       if (viewport.cursorMode)
 385       {
 386         alignPanel.seqPanel.moveCursor(0, -1);
 387       }
 388       else
 389       {
 390         moveSelectedSequences(true);
 391       }
 392       break;
 393
 394     case KeyEvent.VK_LEFT:
 395       if (evt.isAltDown() || !viewport.cursorMode)
 396       {
 397         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 398       }
 399       else
 400       {
 401         alignPanel.seqPanel.moveCursor(-1, 0);
 402       }
 403       break;
 404
 405     case KeyEvent.VK_RIGHT:
 406       if (evt.isAltDown() || !viewport.cursorMode)
 407       {
 408         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 409       }
 410       else
 411       {
 412         alignPanel.seqPanel.moveCursor(1, 0);
 413       }
 414       break;
 415
 416     case KeyEvent.VK_SPACE:
 417       if (viewport.cursorMode)
 418       {
 419         alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 420                 || evt.isShiftDown() || evt.isAltDown());
 421       }
 422       break;
 423
 424     case KeyEvent.VK_DELETE:
 425     case KeyEvent.VK_BACK_SPACE:
 426       if (viewport.cursorMode)
 427       {
 428         alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 429                 || evt.isShiftDown() || evt.isAltDown());
 430       }
 431       else
 432       {
 433         cut_actionPerformed();
 434         alignPanel.seqPanel.seqCanvas.repaint();
 435       }
 436       break;
 437
 438     case KeyEvent.VK_S:
 439       if (viewport.cursorMode)
 440       {
 441         alignPanel.seqPanel.setCursorRow();
 442       }
 443       break;
 444     case KeyEvent.VK_P:
 445       if (viewport.cursorMode)
 446       {
 447         alignPanel.seqPanel.setCursorPosition();
 448       }
 449       break;
 450
 451     case KeyEvent.VK_ENTER:
 452     case KeyEvent.VK_COMMA:
 453       if (viewport.cursorMode)
 454       {
 455         alignPanel.seqPanel.setCursorRowAndColumn();
 456       }
 457       break;
 458
 459     case KeyEvent.VK_Q:
 460       if (viewport.cursorMode)
 461       {
 462         alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 463       }
 464       break;
 465     case KeyEvent.VK_M:
 466       if (viewport.cursorMode)
 467       {
 468         alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 469       }
 470       break;
 471
 472     case KeyEvent.VK_F2:
 473       viewport.cursorMode = !viewport.cursorMode;
 474       statusBar.setText(MessageManager.formatMessage(
 475               "label.keyboard_editing_mode", new String[]
 476               { (viewport.cursorMode ? "on" : "off") }));
 477       if (viewport.cursorMode)
 478       {
 479         alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 480         alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 481       }
 482       break;
 483
 484     case KeyEvent.VK_F:
 485       if (evt.isControlDown())
 486       {
 487         findMenuItem_actionPerformed();
 488       }
 489       break;
 490
 491     case KeyEvent.VK_H:
 492     {
 493       boolean toggleSeqs = !evt.isControlDown();
 494       boolean toggleCols = !evt.isShiftDown();
 495       toggleHiddenRegions(toggleSeqs, toggleCols);
 496       break;
 497     }
 498
 499     case KeyEvent.VK_PAGE_UP:
 500       if (viewport.wrapAlignment)
 501       {
 502         alignPanel.scrollUp(true);
 503       }
 504       else
 505       {
 506         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 507                 - viewport.endSeq + viewport.startSeq);
 508       }
 509       break;
 510
 511     case KeyEvent.VK_PAGE_DOWN:
 512       if (viewport.wrapAlignment)
 513       {
 514         alignPanel.scrollUp(false);
 515       }
 516       else
 517       {
 518         alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 519                 + viewport.endSeq - viewport.startSeq);
 520       }
 521       break;
 522
 523     case KeyEvent.VK_Z:
 524       if (evt.isControlDown())
 525       {
 526         undoMenuItem_actionPerformed();
 527       }
 528       break;
 529
 530     case KeyEvent.VK_Y:
 531       if (evt.isControlDown())
 532       {
 533         redoMenuItem_actionPerformed();
 534       }
 535       break;
 536
 537     case KeyEvent.VK_L:
 538       if (evt.isControlDown())
 539       {
 540         trimAlignment(true);
 541       }
 542       break;
 543
 544     case KeyEvent.VK_R:
 545       if (evt.isControlDown())
 546       {
 547         trimAlignment(false);
 548       }
 549       break;
 550
 551     case KeyEvent.VK_E:
 552       if (evt.isControlDown())
 553       {
 554         if (evt.isShiftDown())
 555         {
 556           this.removeAllGapsMenuItem_actionPerformed();
 557         }
 558         else
 559         {
 560           removeGappedColumnMenuItem_actionPerformed();
 561         }
 562       }
 563       break;
 564     case KeyEvent.VK_I:
 565       if (evt.isControlDown())
 566       {
 567         if (evt.isAltDown())
 568         {
 569           invertColSel_actionPerformed();
 570         }
 571         else
 572         {
 573           invertSequenceMenuItem_actionPerformed();
 574         }
 575       }
 576       break;
 577
 578     case KeyEvent.VK_G:
 579       if (evt.isControlDown())
 580       {
 581         if (evt.isShiftDown())
 582         {
 583           this.unGroup_actionPerformed();
 584         }
 585         else
 586         {
 587           this.createGroup_actionPerformed();
 588         }
 589       }
 590       break;
 591
 592     case KeyEvent.VK_U:
 593       if (evt.isControlDown())
 594       {
 595         this.deleteGroups_actionPerformed();
 596       }
 597       break;
 598
 599     case KeyEvent.VK_T:
 600       if (evt.isControlDown())
 601       {
 602         newView(null);
 603       }
 604       break;
 605
 606     }
 607     alignPanel.paintAlignment(true);
 608   }
 609
 610   /**
 611    * called by key handler and the hide all/show all menu items
 612    *
 613    * @param toggleSeqs
 614    * @param toggleCols
 615    */
 616   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
 617   {
 618     boolean hide = false;
 619     SequenceGroup sg = viewport.getSelectionGroup();
 620     if (!toggleSeqs && !toggleCols)
 621     {
 622       // Hide everything by the current selection - this is a hack - we do the
 623       // invert and then hide
 624       // first check that there will be visible columns after the invert.
 625       if ((viewport.getColumnSelection() != null
 626               && viewport.getColumnSelection().getSelected() != null && viewport
 627               .getColumnSelection().getSelected().size() > 0)
 628               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
 629                       .getEndRes()))
 630       {
 631         // now invert the sequence set, if required - empty selection implies
 632         // that no hiding is required.
 633         if (sg != null)
 634         {
 635           invertSequenceMenuItem_actionPerformed();
 636           sg = viewport.getSelectionGroup();
 637           toggleSeqs = true;
 638
 639         }
 640         viewport.expandColSelection(sg, true);
 641         // finally invert the column selection and get the new sequence
 642         // selection and indicate it should be hidden.
 643         invertColSel_actionPerformed();
 644         toggleCols = true;
 645       }
 646     }
 647
 648     if (toggleSeqs)
 649     {
 650       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
 651       {
 652         hide = true;
 653         viewport.hideAllSelectedSeqs();
 654       }
 655       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
 656               .size() > 0))
 657       {
 658         viewport.showAllHiddenSeqs();
 659       }
 660     }
 661
 662     if (toggleCols)
 663     {
 664       if (viewport.getColumnSelection().getSelected().size() > 0)
 665       {
 666         viewport.hideSelectedColumns();
 667         if (!toggleSeqs)
 668         {
 669           viewport.setSelectionGroup(sg);
 670         }
 671       }
 672       else if (!hide)
 673       {
 674         viewport.showAllHiddenColumns();
 675       }
 676     }
 677   }
 678
 679   @Override
 680   public void keyReleased(KeyEvent evt)
 681   {
 682   }
 683
 684   @Override
 685   public void keyTyped(KeyEvent evt)
 686   {
 687   }
 688
 689   @Override
 690   public void itemStateChanged(ItemEvent evt)
 691   {
 692     if (evt.getSource() == displayNonconservedMenuItem)
 693     {
 694       displayNonconservedMenuItem_actionPerformed();
 695     }
 696     else if (evt.getSource() == colourTextMenuItem)
 697     {
 698       colourTextMenuItem_actionPerformed();
 699     }
 700     else if (evt.getSource() == wrapMenuItem)
 701     {
 702       wrapMenuItem_actionPerformed();
 703     }
 704     else if (evt.getSource() == scaleAbove)
 705     {
 706       viewport.setScaleAboveWrapped(scaleAbove.getState());
 707     }
 708     else if (evt.getSource() == scaleLeft)
 709     {
 710       viewport.setScaleLeftWrapped(scaleLeft.getState());
 711     }
 712     else if (evt.getSource() == scaleRight)
 713     {
 714       viewport.setScaleRightWrapped(scaleRight.getState());
 715     }
 716     else if (evt.getSource() == seqLimits)
 717     {
 718       seqLimits_itemStateChanged();
 719     }
 720     else if (evt.getSource() == viewBoxesMenuItem)
 721     {
 722       viewport.setShowBoxes(viewBoxesMenuItem.getState());
 723     }
 724     else if (evt.getSource() == viewTextMenuItem)
 725     {
 726       viewport.setShowText(viewTextMenuItem.getState());
 727     }
 728     else if (evt.getSource() == renderGapsMenuItem)
 729     {
 730       viewport.setRenderGaps(renderGapsMenuItem.getState());
 731     }
 732     else if (evt.getSource() == annotationPanelMenuItem)
 733     {
 734       viewport.setShowAnnotation(annotationPanelMenuItem.getState());
 735       alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
 736     }
 737     else if (evt.getSource() == sequenceFeatures)
 738     {
 739       viewport.setShowSequenceFeatures(sequenceFeatures.getState());
 740       alignPanel.seqPanel.seqCanvas.repaint();
 741     }
 742     else if (evt.getSource() == conservationMenuItem)
 743     {
 744       conservationMenuItem_actionPerformed();
 745     }
 746     else if (evt.getSource() == abovePIDThreshold)
 747     {
 748       abovePIDThreshold_actionPerformed();
 749     }
 750     else if (evt.getSource() == applyToAllGroups)
 751     {
 752       viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
 753     }
 754     else if (evt.getSource() == autoCalculate)
 755     {
 756       viewport.autoCalculateConsensus = autoCalculate.getState();
 757     }
 758     else if (evt.getSource() == sortByTree)
 759     {
 760       viewport.sortByTree = sortByTree.getState();
 761     }
 762     else if (evt.getSource() == this.centreColumnLabelFlag)
 763     {
 764       centreColumnLabelFlag_stateChanged();
 765     }
 766     else if (evt.getSource() == this.followMouseOverFlag)
 767     {
 768       mouseOverFlag_stateChanged();
 769     }
 770     else if (evt.getSource() == showGroupConsensus)
 771     {
 772       showGroupConsensus_actionPerformed();
 773     }
 774     else if (evt.getSource() == showGroupConservation)
 775     {
 776       showGroupConservation_actionPerformed();
 777     }
 778     else if (evt.getSource() == showSequenceLogo)
 779     {
 780       showSequenceLogo_actionPerformed();
 781     }
 782     else if (evt.getSource() == normSequenceLogo)
 783     {
 784       normSequenceLogo_actionPerformed();
 785     }
 786     else if (evt.getSource() == showConsensusHistogram)
 787     {
 788       showConsensusHistogram_actionPerformed();
 789     }
 790     else if (evt.getSource() == applyAutoAnnotationSettings)
 791     {
 792       applyAutoAnnotationSettings_actionPerformed();
 793     }
 794     alignPanel.paintAlignment(true);
 795   }
 796
 797   private void mouseOverFlag_stateChanged()
 798   {
 799     viewport.followHighlight = followMouseOverFlag.getState();
 800     // TODO: could kick the scrollTo mechanism to reset view for current
 801     // searchresults.
 802   }
 803
 804   private void centreColumnLabelFlag_stateChanged()
 805   {
 806     viewport.centreColumnLabels = centreColumnLabelFlag.getState();
 807     this.alignPanel.annotationPanel.repaint();
 808   }
 809
 810   @Override
 811   public void actionPerformed(ActionEvent evt)
 812   {
 813     Object source = evt.getSource();
 814
 815     if (source == inputText)
 816     {
 817       inputText_actionPerformed();
 818     }
 819     else if (source == loadTree)
 820     {
 821       loadTree_actionPerformed();
 822     }
 823     else if (source == loadApplication)
 824     {
 825       launchFullApplication();
 826     }
 827     else if (source == loadAnnotations)
 828     {
 829       loadAnnotations();
 830     }
 831     else if (source == outputAnnotations)
 832     {
 833       outputAnnotations(true);
 834     }
 835     else if (source == outputFeatures)
 836     {
 837       outputFeatures(true, "Jalview");
 838     }
 839     else if (source == closeMenuItem)
 840     {
 841       closeMenuItem_actionPerformed();
 842     }
 843     else if (source == copy)
 844     {
 845       copy_actionPerformed();
 846     }
 847     else if (source == undoMenuItem)
 848     {
 849       undoMenuItem_actionPerformed();
 850     }
 851     else if (source == redoMenuItem)
 852     {
 853       redoMenuItem_actionPerformed();
 854     }
 855     else if (source == inputText)
 856     {
 857       inputText_actionPerformed();
 858     }
 859     else if (source == closeMenuItem)
 860     {
 861       closeMenuItem_actionPerformed();
 862     }
 863     else if (source == undoMenuItem)
 864     {
 865       undoMenuItem_actionPerformed();
 866     }
 867     else if (source == redoMenuItem)
 868     {
 869       redoMenuItem_actionPerformed();
 870     }
 871     else if (source == copy)
 872     {
 873       copy_actionPerformed();
 874     }
 875     else if (source == pasteNew)
 876     {
 877       pasteNew_actionPerformed();
 878     }
 879     else if (source == pasteThis)
 880     {
 881       pasteThis_actionPerformed();
 882     }
 883     else if (source == cut)
 884     {
 885       cut_actionPerformed();
 886     }
 887     else if (source == delete)
 888     {
 889       delete_actionPerformed();
 890     }
 891     else if (source == grpsFromSelection)
 892     {
 893       makeGrpsFromSelection_actionPerformed();
 894     }
 895     else if (source == deleteGroups)
 896     {
 897       deleteGroups_actionPerformed();
 898     }
 899     else if (source == selectAllSequenceMenuItem)
 900     {
 901       selectAllSequenceMenuItem_actionPerformed();
 902     }
 903     else if (source == deselectAllSequenceMenuItem)
 904     {
 905       deselectAllSequenceMenuItem_actionPerformed();
 906     }
 907     else if (source == invertSequenceMenuItem)
 908     {
 909       invertSequenceMenuItem_actionPerformed();
 910     }
 911     else if (source == invertColSel)
 912     {
 913       viewport.invertColumnSelection();
 914       alignPanel.paintAlignment(true);
 915     }
 916     else if (source == remove2LeftMenuItem)
 917     {
 918       trimAlignment(true);
 919     }
 920     else if (source == remove2RightMenuItem)
 921     {
 922       trimAlignment(false);
 923     }
 924     else if (source == removeGappedColumnMenuItem)
 925     {
 926       removeGappedColumnMenuItem_actionPerformed();
 927     }
 928     else if (source == removeAllGapsMenuItem)
 929     {
 930       removeAllGapsMenuItem_actionPerformed();
 931     }
 932     else if (source == findMenuItem)
 933     {
 934       findMenuItem_actionPerformed();
 935     }
 936     else if (source == font)
 937     {
 938       new FontChooser(alignPanel);
 939     }
 940     else if (source == newView)
 941     {
 942       newView(null);
 943     }
 944     else if (source == showColumns)
 945     {
 946       viewport.showAllHiddenColumns();
 947       alignPanel.paintAlignment(true);
 948     }
 949     else if (source == showSeqs)
 950     {
 951       viewport.showAllHiddenSeqs();
 952       alignPanel.paintAlignment(true);
 953     }
 954     else if (source == hideColumns)
 955     {
 956       viewport.hideSelectedColumns();
 957       alignPanel.paintAlignment(true);
 958     }
 959     else if (source == hideSequences
 960             && viewport.getSelectionGroup() != null)
 961     {
 962       viewport.hideAllSelectedSeqs();
 963       alignPanel.paintAlignment(true);
 964     }
 965     else if (source == hideAllButSelection)
 966     {
 967       toggleHiddenRegions(false, false);
 968       alignPanel.paintAlignment(true);
 969     }
 970     else if (source == hideAllSelection)
 971     {
 972       SequenceGroup sg = viewport.getSelectionGroup();
 973       viewport.expandColSelection(sg, false);
 974       viewport.hideAllSelectedSeqs();
 975       viewport.hideSelectedColumns();
 976       alignPanel.paintAlignment(true);
 977     }
 978     else if (source == showAllHidden)
 979     {
 980       viewport.showAllHiddenColumns();
 981       viewport.showAllHiddenSeqs();
 982       alignPanel.paintAlignment(true);
 983     }
 984     else if (source == showGroupConsensus)
 985     {
 986       showGroupConsensus_actionPerformed();
 987     }
 988     else if (source == showGroupConservation)
 989     {
 990       showGroupConservation_actionPerformed();
 991     }
 992     else if (source == showSequenceLogo)
 993     {
 994       showSequenceLogo_actionPerformed();
 995     }
 996     else if (source == normSequenceLogo)
 997     {
 998       normSequenceLogo_actionPerformed();
 999     }
1000     else if (source == showConsensusHistogram)
1001     {
1002       showConsensusHistogram_actionPerformed();
1003     }
1004     else if (source == applyAutoAnnotationSettings)
1005     {
1006       applyAutoAnnotationSettings_actionPerformed();
1007     }
1008     else if (source == featureSettings)
1009     {
1010       new FeatureSettings(alignPanel);
1011     }
1012     else if (source == alProperties)
1013     {
1014       StringBuffer contents = new jalview.io.AlignmentProperties(
1015               viewport.getAlignment()).formatAsString();
1016       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1017       cap.setText(contents.toString());
1018       Frame frame = new Frame();
1019       frame.add(cap);
1020       jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1021               "label.alignment_properties", new String[]
1022               { getTitle() }), 400, 250);
1023     }
1024     else if (source == overviewMenuItem)
1025     {
1026       overviewMenuItem_actionPerformed();
1027     }
1028     else if (source == noColourmenuItem)
1029     {
1030       changeColour(null);
1031     }
1032     else if (source == clustalColour)
1033     {
1034       abovePIDThreshold.setState(false);
1035       changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1036     }
1037     else if (source == zappoColour)
1038     {
1039       changeColour(new ZappoColourScheme());
1040     }
1041     else if (source == taylorColour)
1042     {
1043       changeColour(new TaylorColourScheme());
1044     }
1045     else if (source == hydrophobicityColour)
1046     {
1047       changeColour(new HydrophobicColourScheme());
1048     }
1049     else if (source == helixColour)
1050     {
1051       changeColour(new HelixColourScheme());
1052     }
1053     else if (source == strandColour)
1054     {
1055       changeColour(new StrandColourScheme());
1056     }
1057     else if (source == turnColour)
1058     {
1059       changeColour(new TurnColourScheme());
1060     }
1061     else if (source == buriedColour)
1062     {
1063       changeColour(new BuriedColourScheme());
1064     }
1065     else if (source == nucleotideColour)
1066     {
1067       changeColour(new NucleotideColourScheme());
1068     }
1069     else if (source == purinePyrimidineColour)
1070     {
1071       changeColour(new PurinePyrimidineColourScheme());
1072     }
1073     else if (source == RNAInteractionColour)
1074     {
1075       changeColour(new RNAInteractionColourScheme());
1076     }
1077     else if (source == RNAHelixColour)
1078     {
1079       new RNAHelicesColourChooser(viewport, alignPanel);
1080     }
1081     else if (source == modifyPID)
1082     {
1083       modifyPID_actionPerformed();
1084     }
1085     else if (source == modifyConservation)
1086     {
1087       modifyConservation_actionPerformed();
1088     }
1089     else if (source == userDefinedColour)
1090     {
1091       new UserDefinedColours(alignPanel, null);
1092     }
1093     else if (source == PIDColour)
1094     {
1095       changeColour(new PIDColourScheme());
1096     }
1097     else if (source == BLOSUM62Colour)
1098     {
1099       changeColour(new Blosum62ColourScheme());
1100     }
1101     else if (source == tcoffeeColour)
1102     {
1103       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1104     }
1105     else if (source == annotationColour)
1106     {
1107       new AnnotationColourChooser(viewport, alignPanel);
1108     }
1109     else if (source == annotationColumnSelection)
1110     {
1111       new AnnotationColumnChooser(viewport, alignPanel);
1112     }
1113     else if (source == sortPairwiseMenuItem)
1114     {
1115       sortPairwiseMenuItem_actionPerformed();
1116     }
1117     else if (source == sortIDMenuItem)
1118     {
1119       sortIDMenuItem_actionPerformed();
1120     }
1121     else if (source == sortLengthMenuItem)
1122     {
1123       sortLengthMenuItem_actionPerformed();
1124     }
1125     else if (source == sortGroupMenuItem)
1126     {
1127       sortGroupMenuItem_actionPerformed();
1128     }
1129     else if (source == removeRedundancyMenuItem)
1130     {
1131       removeRedundancyMenuItem_actionPerformed();
1132     }
1133     else if (source == pairwiseAlignmentMenuItem)
1134     {
1135       pairwiseAlignmentMenuItem_actionPerformed();
1136     }
1137     else if (source == PCAMenuItem)
1138     {
1139       PCAMenuItem_actionPerformed();
1140     }
1141     else if (source == averageDistanceTreeMenuItem)
1142     {
1143       averageDistanceTreeMenuItem_actionPerformed();
1144     }
1145     else if (source == neighbourTreeMenuItem)
1146     {
1147       neighbourTreeMenuItem_actionPerformed();
1148     }
1149     else if (source == njTreeBlosumMenuItem)
1150     {
1151       njTreeBlosumMenuItem_actionPerformed();
1152     }
1153     else if (source == avDistanceTreeBlosumMenuItem)
1154     {
1155       avTreeBlosumMenuItem_actionPerformed();
1156     }
1157     else if (source == documentation)
1158     {
1159       documentation_actionPerformed();
1160     }
1161     else if (source == about)
1162     {
1163       about_actionPerformed();
1164     }
1165
1166   }
1167
1168   public void inputText_actionPerformed()
1169   {
1170     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1171     Frame frame = new Frame();
1172     frame.add(cap);
1173     jalview.bin.JalviewLite.addFrame(frame,
1174             MessageManager.getString("label.input_cut_paste"), 500, 500);
1175   }
1176
1177   protected void outputText_actionPerformed(ActionEvent e)
1178   {
1179     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1180     Frame frame = new Frame();
1181     frame.add(cap);
1182     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1183             "label.alignment_output_command", new String[]
1184             { e.getActionCommand() }), 600, 500);
1185     cap.setText(new AppletFormatAdapter().formatSequences(
1186             e.getActionCommand(), viewport.getAlignment(),
1187             viewport.showJVSuffix));
1188   }
1189
1190   public void loadAnnotations()
1191   {
1192     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1193     cap.setText(MessageManager
1194             .getString("label.paste_features_annotations_Tcoffee_here"));
1195     cap.setAnnotationImport();
1196     Frame frame = new Frame();
1197     frame.add(cap);
1198     jalview.bin.JalviewLite.addFrame(frame,
1199             MessageManager.getString("action.paste_annotations"), 400, 300);
1200
1201   }
1202
1203   public String outputAnnotations(boolean displayTextbox)
1204   {
1205     String annotation = new AnnotationFile().printAnnotations(
1206             viewport.showAnnotation ? viewport.getAlignment()
1207                     .getAlignmentAnnotation() : null, viewport
1208                     .getAlignment().getGroups(), ((Alignment) viewport
1209                     .getAlignment()).alignmentProperties);
1210
1211     if (displayTextbox)
1212     {
1213       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214       Frame frame = new Frame();
1215       frame.add(cap);
1216       jalview.bin.JalviewLite.addFrame(frame,
1217               MessageManager.getString("label.annotations"), 600, 500);
1218       cap.setText(annotation);
1219     }
1220
1221     return annotation;
1222   }
1223
1224   private Map<String,Object> getDisplayedFeatureCols()
1225   {
1226     if (alignPanel.getFeatureRenderer() != null
1227             && viewport.getFeaturesDisplayed()!= null)
1228     {
1229       return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1230
1231     }
1232     return null;
1233   }
1234
1235   public String outputFeatures(boolean displayTextbox, String format)
1236   {
1237     String features;
1238     if (format.equalsIgnoreCase("Jalview"))
1239     {
1240       features = new FeaturesFile().printJalviewFormat(viewport
1241               .getAlignment().getSequencesArray(),
1242               getDisplayedFeatureCols());
1243     }
1244     else
1245     {
1246       features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1247               .getSequencesArray(), getDisplayedFeatureCols());
1248     }
1249
1250     if (displayTextbox)
1251     {
1252       boolean frimport = false;
1253       if (features == null || features.equals("No Features Visible"))
1254       {
1255         features = "# No features visible - paste some and import them here.";
1256         frimport = true;
1257       }
1258
1259       CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1260       if (frimport)
1261       {
1262         cap.setAnnotationImport();
1263       }
1264       Frame frame = new Frame();
1265       frame.add(cap);
1266       jalview.bin.JalviewLite.addFrame(frame,
1267               MessageManager.getString("label.features"), 600, 500);
1268       cap.setText(features);
1269     }
1270     else
1271     {
1272       if (features == null)
1273       {
1274         features = "";
1275       }
1276     }
1277
1278     return features;
1279   }
1280
1281   void launchFullApplication()
1282   {
1283     StringBuffer url = new StringBuffer(jalviewServletURL);
1284
1285     url.append("?open="
1286             + appendProtocol(viewport.applet.getParameter("file")));
1287
1288     if (viewport.applet.getParameter("features") != null)
1289     {
1290       url.append("&features=");
1291       url.append(appendProtocol(viewport.applet.getParameter("features")));
1292     }
1293
1294     if (viewport.applet.getParameter("annotations") != null)
1295     {
1296       url.append("&annotations=");
1297       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1298     }
1299
1300     if (viewport.applet.getParameter("jnetfile") != null)
1301     {
1302       url.append("&annotations=");
1303       url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1304     }
1305
1306     if (viewport.applet.getParameter("defaultColour") != null)
1307     {
1308       url.append("&colour="
1309               + removeWhiteSpace(viewport.applet
1310                       .getParameter("defaultColour")));
1311     }
1312
1313     if (viewport.applet.getParameter("userDefinedColour") != null)
1314     {
1315       url.append("&colour="
1316               + removeWhiteSpace(viewport.applet
1317                       .getParameter("userDefinedColour")));
1318     }
1319     if (viewport.applet.getParameter("tree") != null)
1320     {
1321       url.append("&tree="
1322               + appendProtocol(viewport.applet.getParameter("tree")));
1323     }
1324     if (viewport.applet.getParameter("treeFile") != null)
1325     {
1326       url.append("&tree="
1327               + appendProtocol(viewport.applet.getParameter("treeFile")));
1328     }
1329
1330     showURL(url.toString(), "FULL_APP");
1331   }
1332
1333   String removeWhiteSpace(String colour)
1334   {
1335     StringBuffer sb = new StringBuffer();
1336     for (int i = 0; i < colour.length(); i++)
1337     {
1338       if (Character.isWhitespace(colour.charAt(i)))
1339       {
1340         sb.append("%20");
1341       }
1342       else
1343       {
1344         sb.append(colour.charAt(i));
1345       }
1346     }
1347
1348     return sb.toString();
1349   }
1350
1351   String appendProtocol(String url)
1352   {
1353     try
1354     {
1355       new URL(url);
1356       url = URLEncoder.encode(url);
1357     }
1358     /*
1359      * When we finally deprecate 1.1 compatibility, we can start to use
1360      * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1361      * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1362      * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1363      * ex.printStackTrace(); }
1364      */
1365     catch (java.net.MalformedURLException ex)
1366     {
1367       url = viewport.applet.getCodeBase() + url;
1368     }
1369     return url;
1370   }
1371
1372   public void closeMenuItem_actionPerformed()
1373   {
1374     PaintRefresher.RemoveComponent(alignPanel);
1375     if (alignPanel.seqPanel != null
1376             && alignPanel.seqPanel.seqCanvas != null)
1377     {
1378       PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1379     }
1380     if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1381     {
1382       PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1383     }
1384
1385     if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1386     {
1387       System.exit(0);
1388     }
1389     else
1390     {
1391     }
1392     viewport = null;
1393     alignPanel = null;
1394     this.dispose();
1395   }
1396
1397   /**
1398    * TODO: JAL-1104
1399    */
1400   void updateEditMenuBar()
1401   {
1402
1403     if (viewport.historyList.size() > 0)
1404     {
1405       undoMenuItem.setEnabled(true);
1406       CommandI command = (CommandI) viewport.historyList.peek();
1407       undoMenuItem.setLabel(MessageManager.formatMessage(
1408               "label.undo_command", new String[]
1409               { command.getDescription() }));
1410     }
1411     else
1412     {
1413       undoMenuItem.setEnabled(false);
1414       undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1415     }
1416
1417     if (viewport.redoList.size() > 0)
1418     {
1419       redoMenuItem.setEnabled(true);
1420
1421       CommandI command = (CommandI) viewport.redoList.peek();
1422       redoMenuItem.setLabel(MessageManager.formatMessage(
1423               "label.redo_command", new String[]
1424               { command.getDescription() }));
1425     }
1426     else
1427     {
1428       redoMenuItem.setEnabled(false);
1429       redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1430     }
1431   }
1432
1433   /**
1434    * TODO: JAL-1104
1435    */
1436   @Override
1437   public void addHistoryItem(CommandI command)
1438   {
1439     if (command.getSize() > 0)
1440     {
1441       viewport.historyList.push(command);
1442       viewport.redoList.removeAllElements();
1443       updateEditMenuBar();
1444       viewport.updateHiddenColumns();
1445     }
1446   }
1447
1448   /**
1449    * TODO: JAL-1104 DOCUMENT ME!
1450    *
1451    * @param e
1452    *          DOCUMENT ME!
1453    */
1454   protected void undoMenuItem_actionPerformed()
1455   {
1456     if (viewport.historyList.size() < 1)
1457     {
1458       return;
1459     }
1460
1461     CommandI command = (CommandI) viewport.historyList.pop();
1462     viewport.redoList.push(command);
1463     command.undoCommand(null);
1464
1465     AlignViewport originalSource = getOriginatingSource(command);
1466     // JBPNote Test
1467     if (originalSource != viewport)
1468     {
1469       System.err
1470               .println("Warning: Viewport object mismatch whilst undoing");
1471     }
1472     originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1473                                           // viewport.getColumnSelection().getHiddenColumns()
1474                                           // != null;
1475     updateEditMenuBar();
1476     originalSource.firePropertyChange("alignment", null, originalSource
1477             .getAlignment().getSequences());
1478   }
1479
1480   /**
1481    * TODO: JAL-1104 DOCUMENT ME!
1482    *
1483    * @param e
1484    *          DOCUMENT ME!
1485    */
1486   protected void redoMenuItem_actionPerformed()
1487   {
1488     if (viewport.redoList.size() < 1)
1489     {
1490       return;
1491     }
1492
1493     CommandI command = (CommandI) viewport.redoList.pop();
1494     viewport.historyList.push(command);
1495     command.doCommand(null);
1496
1497     AlignViewport originalSource = getOriginatingSource(command);
1498     // JBPNote Test
1499     if (originalSource != viewport)
1500     {
1501       System.err
1502               .println("Warning: Viewport object mismatch whilst re-doing");
1503     }
1504     originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1505                                           // viewport.getColumnSelection().getHiddenColumns()
1506                                           // != null;
1507
1508     updateEditMenuBar();
1509     originalSource.firePropertyChange("alignment", null, originalSource
1510             .getAlignment().getSequences());
1511   }
1512
1513   AlignViewport getOriginatingSource(CommandI command)
1514   {
1515     AlignViewport originalSource = null;
1516     // For sequence removal and addition, we need to fire
1517     // the property change event FROM the viewport where the
1518     // original alignment was altered
1519     AlignmentI al = null;
1520     if (command instanceof EditCommand)
1521     {
1522       EditCommand editCommand = (EditCommand) command;
1523       al = editCommand.getAlignment();
1524       Vector comps = (Vector) PaintRefresher.components.get(viewport
1525               .getSequenceSetId());
1526       for (int i = 0; i < comps.size(); i++)
1527       {
1528         if (comps.elementAt(i) instanceof AlignmentPanel)
1529         {
1530           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1531           {
1532             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1533             break;
1534           }
1535         }
1536       }
1537     }
1538
1539     if (originalSource == null)
1540     {
1541       // The original view is closed, we must validate
1542       // the current view against the closed view first
1543       if (al != null)
1544       {
1545         PaintRefresher.validateSequences(al, viewport.getAlignment());
1546       }
1547
1548       originalSource = viewport;
1549     }
1550
1551     return originalSource;
1552   }
1553
1554   public void moveSelectedSequences(boolean up)
1555   {
1556     SequenceGroup sg = viewport.getSelectionGroup();
1557     if (sg == null)
1558     {
1559       return;
1560     }
1561     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1562             up ? null : viewport.getHiddenRepSequences(), up);
1563     alignPanel.paintAlignment(true);
1564   }
1565
1566   synchronized void slideSequences(boolean right, int size)
1567   {
1568     List<SequenceI> sg = new Vector<SequenceI>();
1569     if (viewport.cursorMode)
1570     {
1571       sg.add(viewport.getAlignment().getSequenceAt(
1572               alignPanel.seqPanel.seqCanvas.cursorY));
1573     }
1574     else if (viewport.getSelectionGroup() != null
1575             && viewport.getSelectionGroup().getSize() != viewport
1576                     .getAlignment().getHeight())
1577     {
1578       sg = viewport.getSelectionGroup().getSequences(
1579               viewport.getHiddenRepSequences());
1580     }
1581
1582     if (sg.size() < 1)
1583     {
1584       return;
1585     }
1586
1587     Vector<SequenceI> invertGroup = new Vector();
1588
1589     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1590     {
1591       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1592       {
1593         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1594       }
1595     }
1596
1597     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1598
1599     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1600             .size()]);
1601     for (int i = 0; i < invertGroup.size(); i++)
1602     {
1603       seqs2[i] = invertGroup.elementAt(i);
1604     }
1605
1606     SlideSequencesCommand ssc;
1607     if (right)
1608     {
1609       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1610               size, viewport.getGapCharacter());
1611     }
1612     else
1613     {
1614       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1615               size, viewport.getGapCharacter());
1616     }
1617
1618     int groupAdjustment = 0;
1619     if (ssc.getGapsInsertedBegin() && right)
1620     {
1621       if (viewport.cursorMode)
1622       {
1623         alignPanel.seqPanel.moveCursor(size, 0);
1624       }
1625       else
1626       {
1627         groupAdjustment = size;
1628       }
1629     }
1630     else if (!ssc.getGapsInsertedBegin() && !right)
1631     {
1632       if (viewport.cursorMode)
1633       {
1634         alignPanel.seqPanel.moveCursor(-size, 0);
1635       }
1636       else
1637       {
1638         groupAdjustment = -size;
1639       }
1640     }
1641
1642     if (groupAdjustment != 0)
1643     {
1644       viewport.getSelectionGroup().setStartRes(
1645               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1646       viewport.getSelectionGroup().setEndRes(
1647               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1648     }
1649
1650     boolean appendHistoryItem = false;
1651     if (viewport.historyList != null && viewport.historyList.size() > 0
1652             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1653     {
1654       appendHistoryItem = ssc
1655               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1656                       .peek());
1657     }
1658
1659     if (!appendHistoryItem)
1660     {
1661       addHistoryItem(ssc);
1662     }
1663
1664     repaint();
1665   }
1666
1667   static StringBuffer copiedSequences;
1668
1669   static Vector copiedHiddenColumns;
1670
1671   protected void copy_actionPerformed()
1672   {
1673     if (viewport.getSelectionGroup() == null)
1674     {
1675       return;
1676     }
1677
1678     SequenceGroup sg = viewport.getSelectionGroup();
1679     copiedSequences = new StringBuffer();
1680     Hashtable orderedSeqs = new Hashtable();
1681     for (int i = 0; i < sg.getSize(); i++)
1682     {
1683       SequenceI seq = sg.getSequenceAt(i);
1684       int index = viewport.getAlignment().findIndex(seq);
1685       orderedSeqs.put(index + "", seq);
1686     }
1687
1688     int index = 0, startRes, endRes;
1689     char ch;
1690
1691     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1692     {
1693       copiedHiddenColumns = new Vector();
1694       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1695       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1696               .size(); i++)
1697       {
1698         int[] region = (int[]) viewport.getColumnSelection()
1699                 .getHiddenColumns().elementAt(i);
1700
1701         copiedHiddenColumns.addElement(new int[]
1702         { region[0] - hiddenOffset, region[1] - hiddenOffset });
1703       }
1704     }
1705     else
1706     {
1707       copiedHiddenColumns = null;
1708     }
1709
1710     for (int i = 0; i < sg.getSize(); i++)
1711     {
1712       SequenceI seq = null;
1713
1714       while (seq == null)
1715       {
1716         if (orderedSeqs.containsKey(index + ""))
1717         {
1718           seq = (SequenceI) orderedSeqs.get(index + "");
1719           index++;
1720
1721           break;
1722         }
1723         else
1724         {
1725           index++;
1726         }
1727       }
1728
1729       // FIND START RES
1730       // Returns residue following index if gap
1731       startRes = seq.findPosition(sg.getStartRes());
1732
1733       // FIND END RES
1734       // Need to find the residue preceeding index if gap
1735       endRes = 0;
1736
1737       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1738       {
1739         ch = seq.getCharAt(j);
1740         if (!jalview.util.Comparison.isGap((ch)))
1741         {
1742           endRes++;
1743         }
1744       }
1745
1746       if (endRes > 0)
1747       {
1748         endRes += seq.getStart() - 1;
1749       }
1750
1751       copiedSequences.append(seq.getName()
1752               + "\t"
1753               + startRes
1754               + "\t"
1755               + endRes
1756               + "\t"
1757               + seq.getSequenceAsString(sg.getStartRes(),
1758                       sg.getEndRes() + 1) + "\n");
1759     }
1760
1761   }
1762
1763   protected void pasteNew_actionPerformed()
1764   {
1765     paste(true);
1766   }
1767
1768   protected void pasteThis_actionPerformed()
1769   {
1770     paste(false);
1771   }
1772
1773   void paste(boolean newAlignment)
1774   {
1775     try
1776     {
1777
1778       if (copiedSequences == null)
1779       {
1780         return;
1781       }
1782
1783       StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1784       Vector seqs = new Vector();
1785       while (st.hasMoreElements())
1786       {
1787         String name = st.nextToken();
1788         int start = Integer.parseInt(st.nextToken());
1789         int end = Integer.parseInt(st.nextToken());
1790         seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1791       }
1792       SequenceI[] newSeqs = new SequenceI[seqs.size()];
1793       for (int i = 0; i < seqs.size(); i++)
1794       {
1795         newSeqs[i] = (SequenceI) seqs.elementAt(i);
1796       }
1797
1798       if (newAlignment)
1799       {
1800         String newtitle = MessageManager.getString("label.copied_sequences");
1801         if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1802         {
1803           newtitle = getTitle();
1804         }
1805         else
1806         {
1807           newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1808         }
1809         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1810                 viewport.applet, newtitle, false);
1811         if (copiedHiddenColumns != null)
1812         {
1813           for (int i = 0; i < copiedHiddenColumns.size(); i++)
1814           {
1815             int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1816             af.viewport.hideColumns(region[0], region[1]);
1817           }
1818         }
1819
1820         jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1821                 DEFAULT_HEIGHT);
1822       }
1823       else
1824       {
1825         addSequences(newSeqs);
1826       }
1827
1828     } catch (Exception ex)
1829     {
1830     } // could be anything being pasted in here
1831
1832   }
1833
1834   void addSequences(SequenceI[] seqs)
1835   {
1836     for (int i = 0; i < seqs.length; i++)
1837     {
1838       viewport.getAlignment().addSequence(seqs[i]);
1839     }
1840
1841     // !newAlignment
1842     addHistoryItem(new EditCommand(
1843             MessageManager.getString("label.add_sequences"), Action.PASTE,
1844             seqs, 0, viewport.getAlignment().getWidth(),
1845             viewport.getAlignment()));
1846
1847     viewport.setEndSeq(viewport.getAlignment().getHeight());
1848     viewport.getAlignment().getWidth();
1849     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1850             .getSequences());
1851
1852   }
1853
1854   protected void cut_actionPerformed()
1855   {
1856     copy_actionPerformed();
1857     delete_actionPerformed();
1858   }
1859
1860   protected void delete_actionPerformed()
1861   {
1862
1863     SequenceGroup sg = viewport.getSelectionGroup();
1864     if (sg == null)
1865     {
1866       return;
1867     }
1868
1869     Vector seqs = new Vector();
1870     SequenceI seq;
1871     for (int i = 0; i < sg.getSize(); i++)
1872     {
1873       seq = sg.getSequenceAt(i);
1874       seqs.addElement(seq);
1875     }
1876
1877     // If the cut affects all sequences, remove highlighted columns
1878     if (sg.getSize() == viewport.getAlignment().getHeight())
1879     {
1880       viewport.getColumnSelection().removeElements(sg.getStartRes(),
1881               sg.getEndRes() + 1);
1882     }
1883
1884     SequenceI[] cut = new SequenceI[seqs.size()];
1885     for (int i = 0; i < seqs.size(); i++)
1886     {
1887       cut[i] = (SequenceI) seqs.elementAt(i);
1888     }
1889
1890     /*
1891      * //ADD HISTORY ITEM
1892      */
1893     addHistoryItem(new EditCommand(
1894             MessageManager.getString("label.cut_sequences"), Action.CUT,
1895             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1896             viewport.getAlignment()));
1897
1898     viewport.setSelectionGroup(null);
1899     viewport.getAlignment().deleteGroup(sg);
1900
1901     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1902             .getSequences());
1903
1904     if (viewport.getAlignment().getHeight() < 1)
1905     {
1906       this.setVisible(false);
1907     }
1908     viewport.sendSelection();
1909   }
1910
1911   /**
1912    * group consensus toggled
1913    *
1914    */
1915   protected void showGroupConsensus_actionPerformed()
1916   {
1917     viewport.setShowGroupConsensus(showGroupConsensus.getState());
1918     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1919
1920   }
1921
1922   /**
1923    * group conservation toggled.
1924    */
1925   protected void showGroupConservation_actionPerformed()
1926   {
1927     viewport.setShowGroupConservation(showGroupConservation.getState());
1928     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1929   }
1930
1931   /*
1932    * (non-Javadoc)
1933    *
1934    * @see
1935    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1936    * .event.ActionEvent)
1937    */
1938   protected void showConsensusHistogram_actionPerformed()
1939   {
1940     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1941     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1942   }
1943
1944   /*
1945    * (non-Javadoc)
1946    *
1947    * @see
1948    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1949    * .event.ActionEvent)
1950    */
1951   protected void showSequenceLogo_actionPerformed()
1952   {
1953     viewport.setShowSequenceLogo(showSequenceLogo.getState());
1954     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1955   }
1956
1957   protected void normSequenceLogo_actionPerformed()
1958   {
1959     showSequenceLogo.setState(true);
1960     viewport.setShowSequenceLogo(true);
1961     viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1962     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1963   }
1964
1965   protected void applyAutoAnnotationSettings_actionPerformed()
1966   {
1967     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1968   }
1969
1970   protected void makeGrpsFromSelection_actionPerformed()
1971   {
1972     if (avc.makeGroupsFromSelection())
1973     {
1974       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1975       alignPanel.updateAnnotation();
1976       alignPanel.paintAlignment(true);
1977     }
1978   }
1979
1980   protected void createGroup_actionPerformed()
1981   {
1982     avc.createGroup();
1983   }
1984
1985   protected void unGroup_actionPerformed()
1986   {
1987     if (avc.unGroup())
1988     {
1989       alignPanel.alignmentChanged();
1990     }
1991   }
1992
1993   protected void deleteGroups_actionPerformed()
1994   {
1995     if (avc.deleteGroups())
1996     {
1997       alignPanel.alignmentChanged();
1998     }
1999   }
2000
2001   public void selectAllSequenceMenuItem_actionPerformed()
2002   {
2003     SequenceGroup sg = new SequenceGroup();
2004     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2005     {
2006       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2007     }
2008     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2009     viewport.setSelectionGroup(sg);
2010     alignPanel.paintAlignment(true);
2011     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2012     viewport.sendSelection();
2013   }
2014
2015   public void deselectAllSequenceMenuItem_actionPerformed()
2016   {
2017     if (viewport.cursorMode)
2018     {
2019       alignPanel.seqPanel.keyboardNo1 = null;
2020       alignPanel.seqPanel.keyboardNo2 = null;
2021     }
2022     viewport.setSelectionGroup(null);
2023     viewport.getColumnSelection().clear();
2024     viewport.setSelectionGroup(null);
2025     alignPanel.idPanel.idCanvas.searchResults = null;
2026     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2027     alignPanel.paintAlignment(true);
2028     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2029     viewport.sendSelection();
2030   }
2031
2032   public void invertSequenceMenuItem_actionPerformed()
2033   {
2034     SequenceGroup sg = viewport.getSelectionGroup();
2035     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2036     {
2037       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2038     }
2039
2040     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2041     viewport.sendSelection();
2042   }
2043
2044   public void invertColSel_actionPerformed()
2045   {
2046     viewport.invertColumnSelection();
2047     alignPanel.paintAlignment(true);
2048     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2049     viewport.sendSelection();
2050   }
2051
2052   void trimAlignment(boolean trimLeft)
2053   {
2054     ColumnSelection colSel = viewport.getColumnSelection();
2055     int column;
2056
2057     if (colSel.size() > 0)
2058     {
2059       if (trimLeft)
2060       {
2061         column = colSel.getMin();
2062       }
2063       else
2064       {
2065         column = colSel.getMax();
2066       }
2067
2068       SequenceI[] seqs;
2069       if (viewport.getSelectionGroup() != null)
2070       {
2071         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2072                 viewport.getHiddenRepSequences());
2073       }
2074       else
2075       {
2076         seqs = viewport.getAlignment().getSequencesArray();
2077       }
2078
2079       TrimRegionCommand trimRegion;
2080       if (trimLeft)
2081       {
2082         trimRegion = new TrimRegionCommand("Remove Left",
2083                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2084                 viewport.getAlignment(), viewport.getColumnSelection(),
2085                 viewport.getSelectionGroup());
2086         viewport.setStartRes(0);
2087       }
2088       else
2089       {
2090         trimRegion = new TrimRegionCommand("Remove Right",
2091                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2092                 viewport.getAlignment(), viewport.getColumnSelection(),
2093                 viewport.getSelectionGroup());
2094       }
2095
2096       statusBar.setText(MessageManager.formatMessage(
2097               "label.removed_columns", new String[]
2098               { Integer.valueOf(trimRegion.getSize()).toString() }));
2099       addHistoryItem(trimRegion);
2100
2101       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2102       {
2103         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2104                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2105         {
2106           viewport.getAlignment().deleteGroup(sg);
2107         }
2108       }
2109
2110       viewport.firePropertyChange("alignment", null, viewport
2111               .getAlignment().getSequences());
2112     }
2113   }
2114
2115   public void removeGappedColumnMenuItem_actionPerformed()
2116   {
2117     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2118
2119     SequenceI[] seqs;
2120     if (viewport.getSelectionGroup() != null)
2121     {
2122       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2123               viewport.getHiddenRepSequences());
2124       start = viewport.getSelectionGroup().getStartRes();
2125       end = viewport.getSelectionGroup().getEndRes();
2126     }
2127     else
2128     {
2129       seqs = viewport.getAlignment().getSequencesArray();
2130     }
2131
2132     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2133             "Remove Gapped Columns", seqs, start, end,
2134             viewport.getAlignment());
2135
2136     addHistoryItem(removeGapCols);
2137
2138     statusBar.setText(MessageManager.formatMessage(
2139             "label.removed_empty_columns", new String[]
2140             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2141
2142     // This is to maintain viewport position on first residue
2143     // of first sequence
2144     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2145     int startRes = seq.findPosition(viewport.startRes);
2146     // ShiftList shifts;
2147     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2148     // edit.alColumnChanges=shifts.getInverse();
2149     // if (viewport.hasHiddenColumns)
2150     // viewport.getColumnSelection().compensateForEdits(shifts);
2151     viewport.setStartRes(seq.findIndex(startRes) - 1);
2152     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153             .getSequences());
2154
2155   }
2156
2157   public void removeAllGapsMenuItem_actionPerformed()
2158   {
2159     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2160
2161     SequenceI[] seqs;
2162     if (viewport.getSelectionGroup() != null)
2163     {
2164       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2165               viewport.getHiddenRepSequences());
2166       start = viewport.getSelectionGroup().getStartRes();
2167       end = viewport.getSelectionGroup().getEndRes();
2168     }
2169     else
2170     {
2171       seqs = viewport.getAlignment().getSequencesArray();
2172     }
2173
2174     // This is to maintain viewport position on first residue
2175     // of first sequence
2176     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2177     int startRes = seq.findPosition(viewport.startRes);
2178
2179     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2180             viewport.getAlignment()));
2181
2182     viewport.setStartRes(seq.findIndex(startRes) - 1);
2183
2184     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2185             .getSequences());
2186
2187   }
2188
2189   public void findMenuItem_actionPerformed()
2190   {
2191     new Finder(alignPanel);
2192   }
2193
2194   /**
2195    * create a new view derived from the current view
2196    *
2197    * @param viewtitle
2198    * @return frame for the new view
2199    */
2200   public AlignFrame newView(String viewtitle)
2201   {
2202     AlignmentI newal;
2203     if (viewport.hasHiddenRows())
2204     {
2205       newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2206               .getFullAlignment().getSequencesArray());
2207     }
2208     else
2209     {
2210       newal = new Alignment(viewport.getAlignment().getSequencesArray());
2211     }
2212
2213     if (viewport.getAlignment().getAlignmentAnnotation() != null)
2214     {
2215       for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2216       {
2217         if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2218         {
2219           newal.addAnnotation(viewport.getAlignment()
2220                   .getAlignmentAnnotation()[i]);
2221         }
2222       }
2223     }
2224
2225     AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2226
2227     newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2228     PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2229     PaintRefresher.Register(newaf.alignPanel,
2230             newaf.alignPanel.av.getSequenceSetId());
2231
2232     PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2233             newaf.alignPanel.av.getSequenceSetId());
2234     PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2235             newaf.alignPanel.av.getSequenceSetId());
2236
2237     Vector comps = (Vector) PaintRefresher.components.get(viewport
2238             .getSequenceSetId());
2239     int viewSize = -1;
2240     for (int i = 0; i < comps.size(); i++)
2241     {
2242       if (comps.elementAt(i) instanceof AlignmentPanel)
2243       {
2244         viewSize++;
2245       }
2246     }
2247
2248     String title = new String(this.getTitle());
2249     if (viewtitle != null)
2250     {
2251       title = viewtitle + " ( " + title + ")";
2252     }
2253     else
2254     {
2255       if (title.indexOf("(View") > -1)
2256       {
2257         title = title.substring(0, title.indexOf("(View"));
2258       }
2259       title += "(View " + viewSize + ")";
2260     }
2261
2262     newaf.setTitle(title.toString());
2263
2264     newaf.viewport.historyList = viewport.historyList;
2265     newaf.viewport.redoList = viewport.redoList;
2266     return newaf;
2267   }
2268
2269   /**
2270    *
2271    * @return list of feature groups on the view
2272    */
2273   public String[] getFeatureGroups()
2274   {
2275     FeatureRenderer fr = null;
2276     if (alignPanel != null
2277             && (fr = alignPanel.getFeatureRenderer()) != null)
2278     {
2279       List gps = fr.getFeatureGroups();
2280       int p=0;
2281       String[] _gps = new String[gps.size()];
2282       for (Object gp:gps)
2283       {
2284         _gps[p++] = gp.toString();
2285       }
2286       return _gps;
2287     }
2288     return null;
2289   }
2290
2291   /**
2292    * get sequence feature groups that are hidden or shown
2293    *
2294    * @param visible
2295    *          true is visible
2296    * @return list
2297    */
2298   public String[] getFeatureGroupsOfState(boolean visible)
2299   {
2300     FeatureRenderer fr = null;
2301     if (alignPanel != null
2302             && (fr = alignPanel.getFeatureRenderer()) != null)
2303     {
2304       List gps = fr.getGroups(visible);
2305       int p=0;
2306       String[] _gps = new String[gps.size()];
2307       for (Object gp:gps)
2308       {
2309         _gps[p++] = gp.toString();
2310       }
2311       return _gps;
2312     }
2313     return null;
2314   }
2315
2316   /**
2317    * Change the display state for the given feature groups
2318    *
2319    * @param groups
2320    *          list of group strings
2321    * @param state
2322    *          visible or invisible
2323    */
2324   public void setFeatureGroupState(String[] groups, boolean state)
2325   {
2326     FeatureRenderer fr = null;
2327     this.sequenceFeatures.setState(true);
2328     viewport.setShowSequenceFeatures(true);
2329     if (alignPanel != null
2330             && (fr = alignPanel.getFeatureRenderer()) != null)
2331     {
2332
2333       fr.setGroupVisibility(Arrays.asList(groups), state);
2334       alignPanel.seqPanel.seqCanvas.repaint();
2335       if (alignPanel.overviewPanel != null)
2336       {
2337         alignPanel.overviewPanel.updateOverviewImage();
2338       }
2339     }
2340   }
2341
2342   public void seqLimits_itemStateChanged()
2343   {
2344     viewport.setShowJVSuffix(seqLimits.getState());
2345     alignPanel.fontChanged();
2346     alignPanel.paintAlignment(true);
2347   }
2348
2349   protected void colourTextMenuItem_actionPerformed()
2350   {
2351     viewport.setColourText(colourTextMenuItem.getState());
2352     alignPanel.paintAlignment(true);
2353   }
2354
2355   protected void displayNonconservedMenuItem_actionPerformed()
2356   {
2357     viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2358     alignPanel.paintAlignment(true);
2359   }
2360
2361   protected void wrapMenuItem_actionPerformed()
2362   {
2363     viewport.setWrapAlignment(wrapMenuItem.getState());
2364     alignPanel.setWrapAlignment(wrapMenuItem.getState());
2365     scaleAbove.setEnabled(wrapMenuItem.getState());
2366     scaleLeft.setEnabled(wrapMenuItem.getState());
2367     scaleRight.setEnabled(wrapMenuItem.getState());
2368     alignPanel.paintAlignment(true);
2369   }
2370
2371   public void overviewMenuItem_actionPerformed()
2372   {
2373     if (alignPanel.overviewPanel != null)
2374     {
2375       return;
2376     }
2377
2378     Frame frame = new Frame();
2379     OverviewPanel overview = new OverviewPanel(alignPanel);
2380     frame.add(overview);
2381     // +50 must allow for applet frame window
2382     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2383             "label.overview_params", new String[]
2384             { this.getTitle() }), overview.getPreferredSize().width,
2385             overview.getPreferredSize().height + 50);
2386
2387     frame.pack();
2388     final AlignmentPanel ap = alignPanel;
2389     frame.addWindowListener(new WindowAdapter()
2390     {
2391       @Override
2392       public void windowClosing(WindowEvent e)
2393       {
2394         if (ap != null)
2395         {
2396           ap.setOverviewPanel(null);
2397         }
2398       };
2399     });
2400
2401     alignPanel.setOverviewPanel(overview);
2402
2403   }
2404
2405   void changeColour(ColourSchemeI cs)
2406   {
2407     int threshold = 0;
2408
2409     if (cs != null)
2410     {
2411       if (viewport.getAbovePIDThreshold())
2412       {
2413         viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2414                 cs, "Background"));
2415       }
2416
2417       if (viewport.getConservationSelected())
2418       {
2419         cs.setConservationApplied(true);
2420         viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2421                 cs, "Background"));
2422       }
2423       else
2424       {
2425         cs.setConservationApplied(false);
2426       }
2427     }
2428     viewport.setGlobalColourScheme(cs);
2429
2430     if (alignPanel.getOverviewPanel() != null)
2431     {
2432       alignPanel.getOverviewPanel().updateOverviewImage();
2433     }
2434
2435     jalview.structure.StructureSelectionManager
2436             .getStructureSelectionManager(viewport.applet)
2437             .sequenceColoursChanged(alignPanel);
2438
2439     alignPanel.paintAlignment(true);
2440   }
2441
2442   protected void modifyPID_actionPerformed()
2443   {
2444     if (viewport.getAbovePIDThreshold()
2445             && viewport.getGlobalColourScheme() != null)
2446     {
2447       SliderPanel.setPIDSliderSource(alignPanel,
2448               viewport.getGlobalColourScheme(), "Background");
2449       SliderPanel.showPIDSlider();
2450     }
2451   }
2452
2453   protected void modifyConservation_actionPerformed()
2454   {
2455     if (viewport.getConservationSelected()
2456             && viewport.getGlobalColourScheme() != null)
2457     {
2458       SliderPanel.setConservationSlider(alignPanel,
2459               viewport.getGlobalColourScheme(), "Background");
2460       SliderPanel.showConservationSlider();
2461     }
2462   }
2463
2464   protected void conservationMenuItem_actionPerformed()
2465   {
2466     viewport.setConservationSelected(conservationMenuItem.getState());
2467
2468     viewport.setAbovePIDThreshold(false);
2469     abovePIDThreshold.setState(false);
2470
2471     changeColour(viewport.getGlobalColourScheme());
2472
2473     modifyConservation_actionPerformed();
2474   }
2475
2476   public void abovePIDThreshold_actionPerformed()
2477   {
2478     viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2479
2480     conservationMenuItem.setState(false);
2481     viewport.setConservationSelected(false);
2482
2483     changeColour(viewport.getGlobalColourScheme());
2484
2485     modifyPID_actionPerformed();
2486   }
2487
2488   public void sortPairwiseMenuItem_actionPerformed()
2489   {
2490     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2491     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2492             .getAlignment().getSequenceAt(0), null);
2493
2494     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2495             viewport.getAlignment()));
2496     alignPanel.paintAlignment(true);
2497   }
2498
2499   public void sortIDMenuItem_actionPerformed()
2500   {
2501     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2502     AlignmentSorter.sortByID(viewport.getAlignment());
2503     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2504             viewport.getAlignment()));
2505     alignPanel.paintAlignment(true);
2506   }
2507
2508   public void sortLengthMenuItem_actionPerformed()
2509   {
2510     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2511     AlignmentSorter.sortByLength(viewport.getAlignment());
2512     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2513             viewport.getAlignment()));
2514     alignPanel.paintAlignment(true);
2515   }
2516
2517   public void sortGroupMenuItem_actionPerformed()
2518   {
2519     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2520     AlignmentSorter.sortByGroup(viewport.getAlignment());
2521     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2522             viewport.getAlignment()));
2523     alignPanel.paintAlignment(true);
2524
2525   }
2526
2527   public void removeRedundancyMenuItem_actionPerformed()
2528   {
2529     new RedundancyPanel(alignPanel);
2530   }
2531
2532   public void pairwiseAlignmentMenuItem_actionPerformed()
2533   {
2534     if (viewport.getSelectionGroup() != null
2535             && viewport.getSelectionGroup().getSize() > 1)
2536     {
2537       Frame frame = new Frame();
2538       frame.add(new PairwiseAlignPanel(alignPanel));
2539       jalview.bin.JalviewLite.addFrame(frame,
2540               MessageManager.getString("action.pairwise_alignment"), 600,
2541               500);
2542     }
2543   }
2544
2545   public void PCAMenuItem_actionPerformed()
2546   {
2547     // are the sequences aligned?
2548     if (!viewport.getAlignment().isAligned(false))
2549     {
2550       SequenceI current;
2551       int Width = viewport.getAlignment().getWidth();
2552
2553       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2554       {
2555         current = viewport.getAlignment().getSequenceAt(i);
2556
2557         if (current.getLength() < Width)
2558         {
2559           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2560         }
2561       }
2562       alignPanel.paintAlignment(true);
2563     }
2564
2565     if ((viewport.getSelectionGroup() != null
2566             && viewport.getSelectionGroup().getSize() < 4 && viewport
2567             .getSelectionGroup().getSize() > 0)
2568             || viewport.getAlignment().getHeight() < 4)
2569     {
2570       return;
2571     }
2572
2573     try
2574     {
2575       new PCAPanel(viewport);
2576     } catch (java.lang.OutOfMemoryError ex)
2577     {
2578     }
2579
2580   }
2581
2582   public void averageDistanceTreeMenuItem_actionPerformed()
2583   {
2584     NewTreePanel("AV", "PID", "Average distance tree using PID");
2585   }
2586
2587   public void neighbourTreeMenuItem_actionPerformed()
2588   {
2589     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2590   }
2591
2592   protected void njTreeBlosumMenuItem_actionPerformed()
2593   {
2594     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2595   }
2596
2597   protected void avTreeBlosumMenuItem_actionPerformed()
2598   {
2599     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2600   }
2601
2602   void NewTreePanel(String type, String pwType, String title)
2603   {
2604     // are the sequences aligned?
2605     if (!viewport.getAlignment().isAligned(false))
2606     {
2607       SequenceI current;
2608       int Width = viewport.getAlignment().getWidth();
2609
2610       for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2611       {
2612         current = viewport.getAlignment().getSequenceAt(i);
2613
2614         if (current.getLength() < Width)
2615         {
2616           current.insertCharAt(Width - 1, viewport.getGapCharacter());
2617         }
2618       }
2619       alignPanel.paintAlignment(true);
2620
2621     }
2622
2623     if ((viewport.getSelectionGroup() != null && viewport
2624             .getSelectionGroup().getSize() > 1)
2625             || (viewport.getAlignment().getHeight() > 1))
2626     {
2627       final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2628
2629       addTreeMenuItem(tp, title);
2630
2631       jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2632     }
2633   }
2634
2635   void loadTree_actionPerformed()
2636   {
2637     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2638     cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2639     cap.setTreeImport();
2640     Frame frame = new Frame();
2641     frame.add(cap);
2642     jalview.bin.JalviewLite.addFrame(frame,
2643             MessageManager.getString("label.paste_newick_file"), 400, 300);
2644   }
2645
2646   public void loadTree(jalview.io.NewickFile tree, String treeFile)
2647   {
2648     TreePanel tp = new TreePanel(alignPanel, treeFile,
2649             MessageManager.getString("label.load_tree_from_file"), tree);
2650     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2651     addTreeMenuItem(tp, treeFile);
2652   }
2653
2654   /**
2655    * sort the alignment using the given treePanel
2656    *
2657    * @param treePanel
2658    *          tree used to sort view
2659    * @param title
2660    *          string used for undo event name
2661    */
2662   public void sortByTree(TreePanel treePanel, String title)
2663   {
2664     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2665     AlignmentSorter
2666             .sortByTree(viewport.getAlignment(), treePanel.getTree());
2667     // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2668     // HistoryItem.SORT));
2669     addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2670             "label.order_by_params", new String[]
2671             { title }), oldOrder, viewport.getAlignment()));
2672     alignPanel.paintAlignment(true);
2673   }
2674
2675   /**
2676    * Do any automatic reordering of the alignment and add the necessary bits to
2677    * the menu structure for the new tree
2678    *
2679    * @param treePanel
2680    * @param title
2681    */
2682   protected void addTreeMenuItem(final TreePanel treePanel,
2683           final String title)
2684   {
2685     final MenuItem item = new MenuItem(title);
2686     sortByTreeMenu.add(item);
2687     item.addActionListener(new java.awt.event.ActionListener()
2688     {
2689       @Override
2690       public void actionPerformed(ActionEvent evt)
2691       {
2692         sortByTree(treePanel, title); // treePanel.getTitle());
2693       }
2694     });
2695
2696     treePanel.addWindowListener(new WindowAdapter()
2697     {
2698       @Override
2699       public void windowOpened(WindowEvent e)
2700       {
2701         if (viewport.sortByTree)
2702         {
2703           sortByTree(treePanel, title);
2704         }
2705         super.windowOpened(e);
2706       }
2707
2708       @Override
2709       public void windowClosing(WindowEvent e)
2710       {
2711         sortByTreeMenu.remove(item);
2712       };
2713     });
2714   }
2715
2716   public boolean sortBy(AlignmentOrder alorder, String undoname)
2717   {
2718     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2719     if (viewport.applet.debug)
2720     {
2721       System.err.println("Sorting " + alorder.getOrder().size()
2722               + " in alignment '" + getTitle() + "'");
2723     }
2724     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2725     if (undoname != null)
2726     {
2727       addHistoryItem(new OrderCommand(undoname, oldOrder,
2728               viewport.getAlignment()));
2729     }
2730     alignPanel.paintAlignment(true);
2731     return true;
2732   }
2733
2734   protected void documentation_actionPerformed()
2735   {
2736     alignPanel.av.applet.openJalviewHelpUrl();
2737   }
2738
2739   protected void about_actionPerformed()
2740   {
2741
2742     class AboutPanel extends Canvas
2743     {
2744       String version;
2745
2746       String builddate;
2747
2748       public AboutPanel(String version, String builddate)
2749       {
2750         this.version = version;
2751         this.builddate = builddate;
2752       }
2753
2754       @Override
2755       public void paint(Graphics g)
2756       {
2757         g.setColor(Color.white);
2758         g.fillRect(0, 0, getSize().width, getSize().height);
2759         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2760         FontMetrics fm = g.getFontMetrics();
2761         int fh = fm.getHeight();
2762         int y = 5, x = 7;
2763         g.setColor(Color.black);
2764         // TODO: update this text for each release or centrally store it for
2765         // lite and application
2766         g.setFont(new Font("Helvetica", Font.BOLD, 14));
2767         g.drawString(MessageManager.formatMessage(
2768                 "label.jalviewLite_release", new String[]
2769                 { version }), x, y += fh);
2770         g.setFont(new Font("Helvetica", Font.BOLD, 12));
2771         g.drawString(MessageManager.formatMessage(
2772                 "label.jaview_build_date", new String[]
2773                 { builddate }), x, y += fh);
2774         g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2775         g.drawString(MessageManager.getString("label.jalview_authors_1"),
2776                 x, y += fh * 1.5);
2777         g.drawString(MessageManager.getString("label.jalview_authors_2"),
2778                 x + 50, y += fh + 8);
2779         g.drawString(
2780                 MessageManager.getString("label.jalview_dev_managers"), x,
2781                 y += fh);
2782         g.drawString(MessageManager
2783                 .getString("label.jalview_distribution_lists"), x, y += fh);
2784         g.drawString(MessageManager.getString("label.jalview_please_cite"),
2785                 x, y += fh + 8);
2786         g.drawString(
2787                 MessageManager.getString("label.jalview_cite_1_authors"),
2788                 x, y += fh);
2789         g.drawString(
2790                 MessageManager.getString("label.jalview_cite_1_title"), x,
2791                 y += fh);
2792         g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2793                 x, y += fh);
2794       }
2795     }
2796
2797     Frame frame = new Frame();
2798     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2799             .getBuildDate()));
2800     jalview.bin.JalviewLite.addFrame(frame,
2801             MessageManager.getString("label.jalview"), 580, 220);
2802
2803   }
2804
2805   public void showURL(String url, String target)
2806   {
2807     if (viewport.applet == null)
2808     {
2809       System.out.println("Not running as applet - no browser available.");
2810     }
2811     else
2812     {
2813       viewport.applet.showURL(url, target);
2814     }
2815   }
2816
2817   // ////////////////////////////////////////////////////////////////////////////////
2818   // JBuilder Graphics here
2819
2820   MenuBar alignFrameMenuBar = new MenuBar();
2821
2822   Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2823
2824   MenuItem loadApplication = new MenuItem(
2825           MessageManager.getString("label.view_full_application"));
2826
2827   MenuItem loadTree = new MenuItem(
2828           MessageManager.getString("label.load_associated_tree"));
2829
2830   MenuItem loadAnnotations = new MenuItem(
2831           MessageManager.getString("label.load_features_annotations"));
2832
2833   MenuItem outputFeatures = new MenuItem(
2834           MessageManager.getString("label.export_features").concat("..."));
2835
2836   MenuItem outputAnnotations = new MenuItem(
2837           MessageManager.getString("label.export_annotations").concat("..."));
2838
2839   MenuItem closeMenuItem = new MenuItem(
2840           MessageManager.getString("action.close"));
2841
2842   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2843
2844   Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2845
2846   Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2847
2848   Menu calculateMenu = new Menu(
2849           MessageManager.getString("action.calculate"));
2850
2851   MenuItem selectAllSequenceMenuItem = new MenuItem(
2852           MessageManager.getString("action.select_all"));
2853
2854   MenuItem deselectAllSequenceMenuItem = new MenuItem(
2855           MessageManager.getString("action.deselect_all"));
2856
2857   MenuItem invertSequenceMenuItem = new MenuItem(
2858           MessageManager.getString("action.invert_selection"));
2859
2860   MenuItem remove2LeftMenuItem = new MenuItem();
2861
2862   MenuItem remove2RightMenuItem = new MenuItem();
2863
2864   MenuItem removeGappedColumnMenuItem = new MenuItem();
2865
2866   MenuItem removeAllGapsMenuItem = new MenuItem();
2867
2868   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2869
2870   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2871
2872   MenuItem sortPairwiseMenuItem = new MenuItem();
2873
2874   MenuItem sortIDMenuItem = new MenuItem();
2875
2876   MenuItem sortLengthMenuItem = new MenuItem();
2877
2878   MenuItem sortGroupMenuItem = new MenuItem();
2879
2880   MenuItem removeRedundancyMenuItem = new MenuItem();
2881
2882   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2883
2884   MenuItem PCAMenuItem = new MenuItem();
2885
2886   MenuItem averageDistanceTreeMenuItem = new MenuItem();
2887
2888   MenuItem neighbourTreeMenuItem = new MenuItem();
2889
2890   BorderLayout borderLayout1 = new BorderLayout();
2891
2892   public Label statusBar = new Label();
2893
2894   Menu outputTextboxMenu = new Menu();
2895
2896   MenuItem clustalColour = new MenuItem();
2897
2898   MenuItem zappoColour = new MenuItem();
2899
2900   MenuItem taylorColour = new MenuItem();
2901
2902   MenuItem hydrophobicityColour = new MenuItem();
2903
2904   MenuItem helixColour = new MenuItem();
2905
2906   MenuItem strandColour = new MenuItem();
2907
2908   MenuItem turnColour = new MenuItem();
2909
2910   MenuItem buriedColour = new MenuItem();
2911
2912   MenuItem purinePyrimidineColour = new MenuItem();
2913
2914   MenuItem RNAInteractionColour = new MenuItem();
2915
2916   MenuItem RNAHelixColour = new MenuItem();
2917
2918   MenuItem userDefinedColour = new MenuItem();
2919
2920   MenuItem PIDColour = new MenuItem();
2921
2922   MenuItem BLOSUM62Colour = new MenuItem();
2923
2924   MenuItem tcoffeeColour = new MenuItem();
2925
2926   MenuItem njTreeBlosumMenuItem = new MenuItem();
2927
2928   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2929
2930   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2931
2932   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2933
2934   CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2935
2936   MenuItem alProperties = new MenuItem(
2937           MessageManager.getString("label.alignment_props"));
2938
2939   MenuItem overviewMenuItem = new MenuItem();
2940
2941   MenuItem undoMenuItem = new MenuItem();
2942
2943   MenuItem redoMenuItem = new MenuItem();
2944
2945   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2946
2947   MenuItem noColourmenuItem = new MenuItem();
2948
2949   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2950
2951   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2952
2953   MenuItem findMenuItem = new MenuItem();
2954
2955   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2956
2957   MenuItem nucleotideColour = new MenuItem();
2958
2959   MenuItem deleteGroups = new MenuItem();
2960
2961   MenuItem grpsFromSelection = new MenuItem();
2962
2963   MenuItem createGroup = new MenuItem();
2964
2965   MenuItem unGroup = new MenuItem();
2966
2967   MenuItem delete = new MenuItem();
2968
2969   MenuItem copy = new MenuItem();
2970
2971   MenuItem cut = new MenuItem();
2972
2973   Menu pasteMenu = new Menu();
2974
2975   MenuItem pasteNew = new MenuItem();
2976
2977   MenuItem pasteThis = new MenuItem();
2978
2979   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2980
2981   MenuItem font = new MenuItem();
2982
2983   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2984
2985   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2986
2987   CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2988
2989   MenuItem modifyPID = new MenuItem();
2990
2991   MenuItem modifyConservation = new MenuItem();
2992
2993   CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2994           "Autocalculate Consensus", true);
2995
2996   CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2997           "Sort Alignment With New Tree", true);
2998
2999   Menu sortByTreeMenu = new Menu();
3000
3001   Menu sort = new Menu();
3002
3003   Menu calculate = new Menu();
3004
3005   MenuItem inputText = new MenuItem();
3006
3007   Menu helpMenu = new Menu();
3008
3009   MenuItem documentation = new MenuItem();
3010
3011   MenuItem about = new MenuItem();
3012
3013   CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3014
3015   CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3016
3017   CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3018
3019   Menu autoAnnMenu = new Menu();
3020
3021   CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3022
3023   CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3024
3025   CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3026
3027   CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3028
3029   CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3030
3031   CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3032
3033   private void jbInit() throws Exception
3034   {
3035
3036     setMenuBar(alignFrameMenuBar);
3037
3038     MenuItem item;
3039
3040     // dynamically fill save as menu with available formats
3041     for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3042     {
3043
3044       item = new MenuItem(
3045               jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3046
3047       item.addActionListener(new java.awt.event.ActionListener()
3048       {
3049         @Override
3050         public void actionPerformed(ActionEvent e)
3051         {
3052           outputText_actionPerformed(e);
3053         }
3054       });
3055
3056       outputTextboxMenu.add(item);
3057     }
3058     closeMenuItem.addActionListener(this);
3059     loadApplication.addActionListener(this);
3060
3061     loadTree.addActionListener(this);
3062     loadAnnotations.addActionListener(this);
3063     outputFeatures.addActionListener(this);
3064     outputAnnotations.addActionListener(this);
3065     selectAllSequenceMenuItem.addActionListener(this);
3066     deselectAllSequenceMenuItem.addActionListener(this);
3067     invertSequenceMenuItem.addActionListener(this);
3068     remove2LeftMenuItem.setLabel(MessageManager
3069             .getString("action.remove_left"));
3070     remove2LeftMenuItem.addActionListener(this);
3071     remove2RightMenuItem.setLabel(MessageManager
3072             .getString("action.remove_right"));
3073     remove2RightMenuItem.addActionListener(this);
3074     removeGappedColumnMenuItem.setLabel(MessageManager
3075             .getString("action.remove_empty_columns"));
3076     removeGappedColumnMenuItem.addActionListener(this);
3077     removeAllGapsMenuItem.setLabel(MessageManager
3078             .getString("action.remove_all_gaps"));
3079     removeAllGapsMenuItem.addActionListener(this);
3080     viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3081     viewBoxesMenuItem.setState(true);
3082     viewBoxesMenuItem.addItemListener(this);
3083     viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3084     viewTextMenuItem.setState(true);
3085     viewTextMenuItem.addItemListener(this);
3086     sortPairwiseMenuItem.setLabel(MessageManager
3087             .getString("action.by_pairwise_id"));
3088     sortPairwiseMenuItem.addActionListener(this);
3089     sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3090     sortIDMenuItem.addActionListener(this);
3091     sortLengthMenuItem.setLabel(MessageManager
3092             .getString("action.by_length"));
3093     sortLengthMenuItem.addActionListener(this);
3094     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3095     sortGroupMenuItem.addActionListener(this);
3096     removeRedundancyMenuItem.setLabel(MessageManager
3097             .getString("action.remove_redundancy").concat("..."));
3098     removeRedundancyMenuItem.addActionListener(this);
3099     pairwiseAlignmentMenuItem.setLabel(MessageManager
3100             .getString("action.pairwise_alignment"));
3101     pairwiseAlignmentMenuItem.addActionListener(this);
3102     PCAMenuItem.setLabel(MessageManager
3103             .getString("label.principal_component_analysis"));
3104     PCAMenuItem.addActionListener(this);
3105     averageDistanceTreeMenuItem.setLabel(MessageManager
3106             .getString("label.average_distance_identity"));
3107     averageDistanceTreeMenuItem.addActionListener(this);
3108     neighbourTreeMenuItem.setLabel(MessageManager
3109             .getString("label.neighbour_joining_identity"));
3110     neighbourTreeMenuItem.addActionListener(this);
3111     statusBar.setBackground(Color.white);
3112     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3113     statusBar.setText(MessageManager.getString("label.status_bar"));
3114     outputTextboxMenu.setLabel(MessageManager
3115             .getString("label.out_to_textbox"));
3116     clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3117
3118     clustalColour.addActionListener(this);
3119     zappoColour.setLabel(MessageManager.getString("label.zappo"));
3120     zappoColour.addActionListener(this);
3121     taylorColour.setLabel(MessageManager.getString("label.taylor"));
3122     taylorColour.addActionListener(this);
3123     hydrophobicityColour.setLabel(MessageManager
3124             .getString("label.hydrophobicity"));
3125     hydrophobicityColour.addActionListener(this);
3126     helixColour
3127             .setLabel(MessageManager.getString("label.helix_propensity"));
3128     helixColour.addActionListener(this);
3129     strandColour.setLabel(MessageManager
3130             .getString("label.strand_propensity"));
3131     strandColour.addActionListener(this);
3132     turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3133     turnColour.addActionListener(this);
3134     buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3135     buriedColour.addActionListener(this);
3136     purinePyrimidineColour.setLabel(MessageManager
3137             .getString("label.purine_pyrimidine"));
3138     purinePyrimidineColour.addActionListener(this);
3139     RNAInteractionColour.setLabel(MessageManager
3140             .getString("label.rna_interaction"));
3141     RNAInteractionColour.addActionListener(this);
3142     RNAHelixColour.setLabel(MessageManager
3143             .getString("action.by_rna_helixes"));
3144     RNAHelixColour.addActionListener(this);
3145     userDefinedColour.setLabel(MessageManager
3146             .getString("action.user_defined"));
3147     userDefinedColour.addActionListener(this);
3148     PIDColour.setLabel(MessageManager
3149             .getString("label.percentage_identity"));
3150     PIDColour.addActionListener(this);
3151     BLOSUM62Colour.setLabel(MessageManager
3152             .getString("label.blosum62_score"));
3153     BLOSUM62Colour.addActionListener(this);
3154     tcoffeeColour
3155             .setLabel(MessageManager.getString("label.tcoffee_scores"));
3156     tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3157                                      // provided
3158     tcoffeeColour.addActionListener(this);
3159     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3160             .getString("label.average_distance_bloslum62"));
3161     avDistanceTreeBlosumMenuItem.addActionListener(this);
3162     njTreeBlosumMenuItem.setLabel(MessageManager
3163             .getString("label.neighbour_blosum62"));
3164     njTreeBlosumMenuItem.addActionListener(this);
3165     annotationPanelMenuItem.setLabel(MessageManager
3166             .getString("label.show_annotations"));
3167     annotationPanelMenuItem.addItemListener(this);
3168     colourTextMenuItem.setLabel(MessageManager
3169             .getString("label.colour_text"));
3170     colourTextMenuItem.addItemListener(this);
3171     displayNonconservedMenuItem.setLabel(MessageManager
3172             .getString("label.show_non_conversed"));
3173     displayNonconservedMenuItem.addItemListener(this);
3174     alProperties.addActionListener(this);
3175     overviewMenuItem.setLabel(MessageManager
3176             .getString("label.overview_window"));
3177     overviewMenuItem.addActionListener(this);
3178     undoMenuItem.setEnabled(false);
3179     undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3180     undoMenuItem.addActionListener(this);
3181     redoMenuItem.setEnabled(false);
3182     redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3183     redoMenuItem.addActionListener(this);
3184     conservationMenuItem.setLabel(MessageManager
3185             .getString("action.by_conservation"));
3186     conservationMenuItem.addItemListener(this);
3187     noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3188     noColourmenuItem.addActionListener(this);
3189     wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3190     wrapMenuItem.addItemListener(this);
3191     renderGapsMenuItem.setLabel(MessageManager
3192             .getString("action.show_gaps"));
3193     renderGapsMenuItem.setState(true);
3194     renderGapsMenuItem.addItemListener(this);
3195     findMenuItem.setLabel(MessageManager.getString("action.find"));
3196     findMenuItem.addActionListener(this);
3197     abovePIDThreshold.setLabel(MessageManager
3198             .getString("label.above_identity_threshold"));
3199     abovePIDThreshold.addItemListener(this);
3200     nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3201     nucleotideColour.addActionListener(this);
3202     deleteGroups.setLabel(MessageManager
3203             .getString("action.undefine_groups"));
3204     deleteGroups.addActionListener(this);
3205     grpsFromSelection.setLabel(MessageManager
3206             .getString("action.make_groups_selection"));
3207     grpsFromSelection.addActionListener(this);
3208     createGroup.setLabel(MessageManager.getString("action.create_group"));
3209     unGroup.setLabel(MessageManager.getString("action.remove_group"));
3210     copy.setLabel(MessageManager.getString("action.copy"));
3211     copy.addActionListener(this);
3212     cut.setLabel(MessageManager.getString("action.cut"));
3213     cut.addActionListener(this);
3214     delete.setLabel(MessageManager.getString("action.delete"));
3215     delete.addActionListener(this);
3216     pasteMenu.setLabel(MessageManager.getString("action.paste"));
3217     pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3218     pasteNew.addActionListener(this);
3219     pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3220     pasteThis.addActionListener(this);
3221     applyToAllGroups.setLabel(MessageManager
3222             .getString("label.apply_colour_to_all_groups"));
3223     applyToAllGroups.setState(true);
3224     applyToAllGroups.addItemListener(this);
3225     font.setLabel(MessageManager.getString("action.font"));
3226     font.addActionListener(this);
3227     scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3228     scaleAbove.setState(true);
3229     scaleAbove.setEnabled(false);
3230     scaleAbove.addItemListener(this);
3231     scaleLeft.setEnabled(false);
3232     scaleLeft.setState(true);
3233     scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3234     scaleLeft.addItemListener(this);
3235     scaleRight.setEnabled(false);
3236     scaleRight.setState(true);
3237     scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3238     scaleRight.addItemListener(this);
3239     modifyPID.setLabel(MessageManager
3240             .getString("label.modify_identity_thereshold"));
3241     modifyPID.addActionListener(this);
3242     modifyConservation.setLabel(MessageManager
3243             .getString("label.modify_conservation_thereshold"));
3244     modifyConservation.addActionListener(this);
3245     sortByTreeMenu.setLabel(MessageManager
3246             .getString("action.by_tree_order"));
3247     sort.setLabel(MessageManager.getString("action.sort"));
3248     calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3249     autoCalculate.addItemListener(this);
3250     sortByTree.addItemListener(this);
3251     inputText
3252             .setLabel(MessageManager.getString("label.input_from_textbox"));
3253     inputText.addActionListener(this);
3254     centreColumnLabelFlag.setLabel(MessageManager
3255             .getString("label.centre_column_labels"));
3256     centreColumnLabelFlag.addItemListener(this);
3257     followMouseOverFlag.setLabel(MessageManager
3258             .getString("label.automatic_scrolling"));
3259     followMouseOverFlag.addItemListener(this);
3260     helpMenu.setLabel(MessageManager.getString("action.help"));
3261     documentation.setLabel(MessageManager.getString("label.documentation"));
3262     documentation.addActionListener(this);
3263
3264     about.setLabel(MessageManager.getString("label.about"));
3265     about.addActionListener(this);
3266     seqLimits.setState(true);
3267     seqLimits.setLabel(MessageManager
3268             .getString("label.show_sequence_limits"));
3269     seqLimits.addItemListener(this);
3270     featureSettings.setLabel(MessageManager
3271             .getString("label.feature_settings"));
3272     featureSettings.addActionListener(this);
3273     sequenceFeatures.setLabel(MessageManager
3274             .getString("label.sequence_features"));
3275     sequenceFeatures.addItemListener(this);
3276     sequenceFeatures.setState(false);
3277     annotationColour.setLabel(MessageManager
3278             .getString("action.by_annotation"));
3279     annotationColour.addActionListener(this);
3280
3281     annotationColumnSelection.setLabel("Select by Annotation");
3282     annotationColumnSelection.addActionListener(this);
3283
3284     invertSequenceMenuItem.setLabel(MessageManager
3285             .getString("action.invert_sequence_selection"));
3286     invertColSel.setLabel(MessageManager
3287             .getString("action.invert_column_selection"));
3288     menu1.setLabel(MessageManager.getString("action.show"));
3289     showColumns.setLabel(MessageManager.getString("label.all_columns"));
3290     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3291     menu2.setLabel(MessageManager.getString("action.hide"));
3292     hideColumns
3293             .setLabel(MessageManager.getString("label.selected_columns"));
3294     hideSequences.setLabel(MessageManager
3295             .getString("label.selected_sequences"));
3296     hideAllButSelection.setLabel(MessageManager
3297             .getString("label.all_but_selected_region"));
3298     hideAllSelection.setLabel(MessageManager
3299             .getString("label.selected_region"));
3300     showAllHidden.setLabel(MessageManager
3301             .getString("label.all_sequences_columns"));
3302     showGroupConsensus.setLabel(MessageManager
3303             .getString("label.group_consensus"));
3304     showGroupConservation.setLabel(MessageManager
3305             .getString("label.group_conservation"));
3306     showConsensusHistogram.setLabel(MessageManager
3307             .getString("label.show_consensus_histogram"));
3308     showSequenceLogo.setLabel(MessageManager
3309             .getString("label.show_consensus_logo"));
3310     normSequenceLogo.setLabel(MessageManager
3311             .getString("label.norm_consensus_logo"));
3312     applyAutoAnnotationSettings.setLabel(MessageManager
3313             .getString("label.apply_all_groups"));
3314     applyAutoAnnotationSettings.setState(true);
3315     autoAnnMenu.setLabel(MessageManager
3316             .getString("label.autocalculated_annotation"));
3317
3318     invertColSel.addActionListener(this);
3319     showColumns.addActionListener(this);
3320     showSeqs.addActionListener(this);
3321     hideColumns.addActionListener(this);
3322     hideSequences.addActionListener(this);
3323     hideAllButSelection.addActionListener(this);
3324     hideAllSelection.addActionListener(this);
3325     showAllHidden.addActionListener(this);
3326     showGroupConsensus.addItemListener(this);
3327     showGroupConservation.addItemListener(this);
3328     showConsensusHistogram.addItemListener(this);
3329     showSequenceLogo.addItemListener(this);
3330     normSequenceLogo.addItemListener(this);
3331
3332     applyAutoAnnotationSettings.addItemListener(this);
3333     formatMenu.setLabel(MessageManager.getString("action.format"));
3334     selectMenu.setLabel(MessageManager.getString("action.select"));
3335     newView.setLabel(MessageManager.getString("action.new_view"));
3336     newView.addActionListener(this);
3337     alignFrameMenuBar.add(fileMenu);
3338     alignFrameMenuBar.add(editMenu);
3339     alignFrameMenuBar.add(selectMenu);
3340     alignFrameMenuBar.add(viewMenu);
3341     alignFrameMenuBar.add(formatMenu);
3342     alignFrameMenuBar.add(colourMenu);
3343     alignFrameMenuBar.add(calculateMenu);
3344     alignFrameMenuBar.add(helpMenu);
3345
3346     fileMenu.add(inputText);
3347     fileMenu.add(loadTree);
3348     fileMenu.add(loadAnnotations);
3349
3350     fileMenu.addSeparator();
3351     fileMenu.add(outputTextboxMenu);
3352     fileMenu.add(outputFeatures);
3353     fileMenu.add(outputAnnotations);
3354
3355     if (jalviewServletURL != null)
3356     {
3357       fileMenu.add(loadApplication);
3358     }
3359
3360     fileMenu.addSeparator();
3361     fileMenu.add(closeMenuItem);
3362
3363     editMenu.add(undoMenuItem);
3364     editMenu.add(redoMenuItem);
3365     editMenu.add(cut);
3366     editMenu.add(copy);
3367     editMenu.add(pasteMenu);
3368     editMenu.add(delete);
3369     editMenu.addSeparator();
3370     editMenu.add(remove2LeftMenuItem);
3371     editMenu.add(remove2RightMenuItem);
3372     editMenu.add(removeGappedColumnMenuItem);
3373     editMenu.add(removeAllGapsMenuItem);
3374     editMenu.add(removeRedundancyMenuItem);
3375     viewMenu.add(newView);
3376     viewMenu.addSeparator();
3377     viewMenu.add(menu1);
3378     viewMenu.add(menu2);
3379     viewMenu.addSeparator();
3380     viewMenu.add(followMouseOverFlag);
3381     viewMenu.add(annotationPanelMenuItem);
3382     autoAnnMenu.add(applyAutoAnnotationSettings);
3383     autoAnnMenu.add(showConsensusHistogram);
3384     autoAnnMenu.add(showSequenceLogo);
3385     autoAnnMenu.add(normSequenceLogo);
3386     autoAnnMenu.addSeparator();
3387     autoAnnMenu.add(showGroupConservation);
3388     autoAnnMenu.add(showGroupConsensus);
3389     viewMenu.add(autoAnnMenu);
3390     viewMenu.addSeparator();
3391     viewMenu.add(sequenceFeatures);
3392     viewMenu.add(featureSettings);
3393     viewMenu.addSeparator();
3394     viewMenu.add(alProperties);
3395     viewMenu.addSeparator();
3396     viewMenu.add(overviewMenuItem);
3397     colourMenu.add(applyToAllGroups);
3398     colourMenu.addSeparator();
3399     colourMenu.add(noColourmenuItem);
3400     colourMenu.add(clustalColour);
3401     colourMenu.add(BLOSUM62Colour);
3402     colourMenu.add(PIDColour);
3403     colourMenu.add(zappoColour);
3404     colourMenu.add(taylorColour);
3405     colourMenu.add(hydrophobicityColour);
3406     colourMenu.add(helixColour);
3407     colourMenu.add(strandColour);
3408     colourMenu.add(turnColour);
3409     colourMenu.add(buriedColour);
3410     colourMenu.add(nucleotideColour);
3411     colourMenu.add(purinePyrimidineColour);
3412     // colourMenu.add(RNAInteractionColour);
3413     colourMenu.add(tcoffeeColour);
3414     colourMenu.add(userDefinedColour);
3415     colourMenu.addSeparator();
3416     colourMenu.add(conservationMenuItem);
3417     colourMenu.add(modifyConservation);
3418     colourMenu.add(abovePIDThreshold);
3419     colourMenu.add(modifyPID);
3420     colourMenu.add(annotationColour);
3421     colourMenu.add(RNAHelixColour);
3422     calculateMenu.add(sort);
3423     calculateMenu.add(calculate);
3424     calculateMenu.addSeparator();
3425     calculateMenu.add(pairwiseAlignmentMenuItem);
3426     calculateMenu.add(PCAMenuItem);
3427     calculateMenu.add(autoCalculate);
3428     calculateMenu.add(sortByTree);
3429     this.add(statusBar, BorderLayout.SOUTH);
3430     pasteMenu.add(pasteNew);
3431     pasteMenu.add(pasteThis);
3432     sort.add(sortIDMenuItem);
3433     sort.add(sortLengthMenuItem);
3434     sort.add(sortByTreeMenu);
3435     sort.add(sortGroupMenuItem);
3436     sort.add(sortPairwiseMenuItem);
3437     calculate.add(averageDistanceTreeMenuItem);
3438     calculate.add(neighbourTreeMenuItem);
3439     calculate.add(avDistanceTreeBlosumMenuItem);
3440     calculate.add(njTreeBlosumMenuItem);
3441     helpMenu.add(documentation);
3442     helpMenu.add(about);
3443     menu1.add(showColumns);
3444     menu1.add(showSeqs);
3445     menu1.add(showAllHidden);
3446     menu2.add(hideColumns);
3447     menu2.add(hideSequences);
3448     menu2.add(hideAllSelection);
3449     menu2.add(hideAllButSelection);
3450     formatMenu.add(font);
3451     formatMenu.add(seqLimits);
3452     formatMenu.add(wrapMenuItem);
3453     formatMenu.add(scaleAbove);
3454     formatMenu.add(scaleLeft);
3455     formatMenu.add(scaleRight);
3456     formatMenu.add(viewBoxesMenuItem);
3457     formatMenu.add(viewTextMenuItem);
3458     formatMenu.add(colourTextMenuItem);
3459     formatMenu.add(displayNonconservedMenuItem);
3460     formatMenu.add(renderGapsMenuItem);
3461     formatMenu.add(centreColumnLabelFlag);
3462     selectMenu.add(findMenuItem);
3463     selectMenu.addSeparator();
3464     selectMenu.add(selectAllSequenceMenuItem);
3465     selectMenu.add(deselectAllSequenceMenuItem);
3466     selectMenu.add(invertSequenceMenuItem);
3467     selectMenu.add(invertColSel);
3468     selectMenu.add(createGroup);
3469     selectMenu.add(unGroup);
3470     selectMenu.add(grpsFromSelection);
3471     selectMenu.add(deleteGroups);
3472     selectMenu.add(annotationColumnSelection);
3473
3474   }
3475
3476   public void setStatus(String string)
3477   {
3478     statusBar.setText(string);
3479   };
3480
3481   MenuItem featureSettings = new MenuItem();
3482
3483   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3484
3485   MenuItem annotationColour = new MenuItem();
3486
3487   MenuItem annotationColumnSelection = new MenuItem();
3488
3489   MenuItem invertColSel = new MenuItem();
3490
3491   Menu menu1 = new Menu();
3492
3493   MenuItem showColumns = new MenuItem();
3494
3495   MenuItem showSeqs = new MenuItem();
3496
3497   Menu menu2 = new Menu();
3498
3499   MenuItem hideColumns = new MenuItem();
3500
3501   MenuItem hideSequences = new MenuItem();
3502
3503   MenuItem hideAllButSelection = new MenuItem();
3504
3505   MenuItem hideAllSelection = new MenuItem();
3506
3507   MenuItem showAllHidden = new MenuItem();
3508
3509   Menu formatMenu = new Menu();
3510
3511   Menu selectMenu = new Menu();
3512
3513   MenuItem newView = new MenuItem();
3514
3515   /**
3516    * Attach the alignFrame panels after embedding menus, if necessary. This used
3517    * to be called setEmbedded, but is now creates the dropdown menus in a
3518    * platform independent manner to avoid OSX/Mac menu appendage daftness.
3519    *
3520    * @param reallyEmbedded
3521    *          true to attach the view to the applet area on the page rather than
3522    *          in a new window
3523    */
3524   public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3525   {
3526     if (reallyEmbedded)
3527     {
3528       // ////
3529       // Explicly build the embedded menu panel for the on-page applet
3530       //
3531       // view cannot be closed if its actually on the page
3532       fileMenu.remove(closeMenuItem);
3533       fileMenu.remove(3); // Remove Seperator
3534       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3535               Font.PLAIN, 11, false); // use our own fonts.
3536       // and actually add the components to the applet area
3537       viewport.applet.setLayout(new BorderLayout());
3538       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3539       viewport.applet.add(statusBar, BorderLayout.SOUTH);
3540       alignPanel.setSize(viewport.applet.getSize().width,
3541               viewport.applet.getSize().height - embeddedMenu.HEIGHT
3542                       - statusBar.HEIGHT);
3543       viewport.applet.add(alignPanel, BorderLayout.CENTER);
3544       final AlignFrame me = this;
3545       viewport.applet.addFocusListener(new FocusListener()
3546       {
3547
3548         @Override
3549         public void focusLost(FocusEvent e)
3550         {
3551           if (me.viewport.applet.currentAlignFrame == me)
3552           {
3553             me.viewport.applet.currentAlignFrame = null;
3554           }
3555         }
3556
3557         @Override
3558         public void focusGained(FocusEvent e)
3559         {
3560           me.viewport.applet.currentAlignFrame = me;
3561         }
3562       });
3563       viewport.applet.validate();
3564     }
3565     else
3566     {
3567       // //////
3568       // test and embed menu bar if necessary.
3569       //
3570       if (embedMenuIfNeeded(alignPanel))
3571       {
3572         // adjust for status bar height too
3573         alignPanel.setSize(getSize().width, getSize().height
3574                 - statusBar.HEIGHT);
3575       }
3576       add(statusBar, BorderLayout.SOUTH);
3577       add(alignPanel, BorderLayout.CENTER);
3578       // and register with the applet so it can pass external API calls to us
3579       jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3580               DEFAULT_HEIGHT);
3581     }
3582   }
3583
3584   /**
3585    * create a new binding between structures in an existing jmol viewer instance
3586    * and an alignpanel with sequences that have existing PDBFile entries. Note,
3587    * this does not open a new Jmol window, or modify the display of the
3588    * structures in the original jmol window. Note This method doesn't work
3589    * without an additional javascript library to exchange messages between the
3590    * distinct applets. See http://issues.jalview.org/browse/JAL-621
3591    *
3592    * @param viewer
3593    *          JmolViewer instance
3594    * @param sequenceIds
3595    *          - sequence Ids to search for associations
3596    */
3597   public SequenceStructureBinding addStructureViewInstance(
3598           Object jmolviewer, String[] sequenceIds)
3599   {
3600     org.jmol.api.JmolViewer viewer = null;
3601     try
3602     {
3603       viewer = (org.jmol.api.JmolViewer) jmolviewer;
3604     } catch (ClassCastException ex)
3605     {
3606       System.err.println("Unsupported viewer object :"
3607               + jmolviewer.getClass());
3608     }
3609     if (viewer == null)
3610     {
3611       System.err.println("Can't use this object as a structure viewer:"
3612               + jmolviewer.getClass());
3613       return null;
3614     }
3615     SequenceI[] seqs = null;
3616     if (sequenceIds == null || sequenceIds.length == 0)
3617     {
3618       seqs = viewport.getAlignment().getSequencesArray();
3619     }
3620     else
3621     {
3622       Vector sqi = new Vector();
3623       AlignmentI al = viewport.getAlignment();
3624       for (int sid = 0; sid < sequenceIds.length; sid++)
3625       {
3626         SequenceI sq = al.findName(sequenceIds[sid]);
3627         if (sq != null)
3628         {
3629           sqi.addElement(sq);
3630         }
3631       }
3632       if (sqi.size() > 0)
3633       {
3634         seqs = new SequenceI[sqi.size()];
3635         for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3636         {
3637           seqs[sid] = (SequenceI) sqi.elementAt(sid);
3638         }
3639       }
3640       else
3641       {
3642         return null;
3643       }
3644     }
3645     ExtJmol jmv = null;
3646     // TODO: search for a jmv that involves viewer
3647     if (jmv == null)
3648     { // create a new viewer/jalview binding.
3649       jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3650       { seqs });
3651     }
3652     return jmv;
3653
3654   }
3655
3656   /**
3657    * bind a pdb file to a sequence in the current view
3658    *
3659    * @param sequenceId
3660    *          - sequenceId within the dataset.
3661    * @param pdbEntryString
3662    *          - the short name for the PDB file
3663    * @param pdbFile
3664    *          - pdb file - either a URL or a valid PDB file.
3665    * @return true if binding was as success TODO: consider making an exception
3666    *         structure for indicating when PDB parsing or sequenceId location
3667    *         fails.
3668    */
3669   public boolean addPdbFile(String sequenceId, String pdbEntryString,
3670           String pdbFile)
3671   {
3672     SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3673     boolean needtoadd = false;
3674     if (toaddpdb != null)
3675     {
3676       Vector pdbe = toaddpdb.getPDBId();
3677       PDBEntry pdbentry = null;
3678       if (pdbe != null && pdbe.size() > 0)
3679       {
3680         for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3681         {
3682           pdbentry = (PDBEntry) pdbe.elementAt(pe);
3683           if (!pdbentry.getId().equals(pdbEntryString)
3684                   && !pdbentry.getFile().equals(pdbFile))
3685           {
3686             pdbentry = null;
3687           }
3688           else
3689           {
3690             continue;
3691           }
3692         }
3693       }
3694       if (pdbentry == null)
3695       {
3696         pdbentry = new PDBEntry();
3697         pdbentry.setId(pdbEntryString);
3698         pdbentry.setFile(pdbFile);
3699         needtoadd = true; // add this new entry to sequence.
3700       }
3701       // resolve data source
3702       // TODO: this code should be a refactored to an io package
3703       String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3704       if (protocol == null)
3705       {
3706         return false;
3707       }
3708       if (needtoadd)
3709       {
3710         // make a note of the access mode and add
3711         if (pdbentry.getProperty() == null)
3712         {
3713           pdbentry.setProperty(new Hashtable());
3714         }
3715         pdbentry.getProperty().put("protocol", protocol);
3716         toaddpdb.addPDBId(pdbentry);
3717         alignPanel.getStructureSelectionManager()
3718                 .registerPDBEntry(pdbentry);
3719       }
3720     }
3721     return true;
3722   }
3723
3724   private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3725   {
3726     if (seqs != null)
3727     {
3728       Vector sequences = new Vector();
3729       for (int i = 0; i < seqs.length; i++)
3730       {
3731         if (seqs[i] != null)
3732         {
3733           sequences.addElement(new Object[]
3734           { seqs[i], (chains != null) ? chains[i] : null });
3735         }
3736       }
3737       seqs = new SequenceI[sequences.size()];
3738       chains = new String[sequences.size()];
3739       for (int i = 0, isize = sequences.size(); i < isize; i++)
3740       {
3741         Object[] oj = (Object[]) sequences.elementAt(i);
3742
3743         seqs[i] = (SequenceI) oj[0];
3744         chains[i] = (String) oj[1];
3745       }
3746     }
3747     return new Object[]
3748     { seqs, chains };
3749
3750   }
3751
3752   public void newStructureView(JalviewLite applet, PDBEntry pdb,
3753           SequenceI[] seqs, String[] chains, String protocol)
3754   {
3755     // Scrub any null sequences from the array
3756     Object[] sqch = cleanSeqChainArrays(seqs, chains);
3757     seqs = (SequenceI[]) sqch[0];
3758     chains = (String[]) sqch[1];
3759     if (seqs == null || seqs.length == 0)
3760     {
3761       System.err
3762               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3763     }
3764     if (protocol == null || protocol.trim().length() == 0
3765             || protocol.equals("null"))
3766     {
3767       protocol = (String) pdb.getProperty().get("protocol");
3768       if (protocol == null)
3769       {
3770         System.err.println("Couldn't work out protocol to open structure: "
3771                 + pdb.getId());
3772         return;
3773       }
3774     }
3775     if (applet.useXtrnalSviewer)
3776     {
3777       // register the association(s) and quit, don't create any windows.
3778       if (StructureSelectionManager.getStructureSelectionManager(applet)
3779               .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3780       {
3781         System.err.println("Failed to map " + pdb.getFile() + " ("
3782                 + protocol + ") to any sequences");
3783       }
3784       return;
3785     }
3786     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3787     {
3788       // can only do alignments with Jmol
3789       // find the last jmol window assigned to this alignment
3790       jalview.appletgui.AppletJmol ajm = null, tajm;
3791       Vector jmols = applet
3792               .getAppletWindow(jalview.appletgui.AppletJmol.class);
3793       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3794       {
3795         tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3796         if (tajm.ap.alignFrame == this)
3797         {
3798           ajm = tajm;
3799           break;
3800         }
3801       }
3802       if (ajm != null)
3803       {
3804         System.err
3805                 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3806         // try and add the pdb structure
3807         // ajm.addS
3808         ajm = null;
3809       }
3810     }
3811     // otherwise, create a new window
3812     if (applet.jmolAvailable)
3813     {
3814       new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3815               protocol);
3816       applet.lastFrameX += 40;
3817       applet.lastFrameY += 40;
3818     }
3819     else
3820     {
3821       new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3822     }
3823
3824   }
3825
3826   public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3827           SequenceI[][] seqs, String[][] chains, String[] protocols)
3828   {
3829     // TODO Auto-generated method stub
3830     System.err.println("Aligned Structure View: Not yet implemented.");
3831   }
3832
3833   /**
3834    * modify the current selection, providing the user has not made a selection
3835    * already.
3836    *
3837    * @param sel
3838    *          - sequences from this alignment
3839    * @param csel
3840    *          - columns to be selected on the alignment
3841    */
3842   public void select(SequenceGroup sel, ColumnSelection csel)
3843   {
3844     alignPanel.seqPanel.selection(sel, csel, null);
3845   }
3846
3847   public void scrollTo(int row, int column)
3848   {
3849     alignPanel.seqPanel.scrollTo(row, column);
3850   }
3851
3852   public void scrollToRow(int row)
3853   {
3854     alignPanel.seqPanel.scrollToRow(row);
3855   }
3856
3857   public void scrollToColumn(int column)
3858   {
3859     alignPanel.seqPanel.scrollToColumn(column);
3860   }
3861
3862   /**
3863    * @return the alignments unique ID.
3864    */
3865   public String getSequenceSetId()
3866   {
3867     return viewport.getSequenceSetId();
3868   }
3869
3870   /**
3871    * Load the (T-Coffee) score file from the specified url
3872    *
3873    * @param source
3874    *          File/URL/T-COFFEE score file contents
3875    * @throws IOException
3876    * @return true if alignment was annotated with data from source
3877    */
3878   public boolean loadScoreFile(String source) throws IOException
3879   {
3880
3881     TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3882             AppletFormatAdapter.checkProtocol(source));
3883     if (!file.isValid())
3884     {
3885       // TODO: raise dialog for gui
3886       System.err.println("Problems parsing T-Coffee scores: "
3887               + file.getWarningMessage());
3888       System.err.println("Origin was:\n" + source);
3889       return false;
3890     }
3891
3892     /*
3893      * check that the score matrix matches the alignment dimensions
3894      */
3895     AlignmentI aln;
3896     if ((aln = viewport.getAlignment()) != null
3897             && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3898                     .getWidth()))
3899     {
3900       // TODO: raise a dialog box here rather than bomb out.
3901       System.err
3902               .println("The scores matrix does not match the alignment dimensions");
3903
3904     }
3905
3906     // TODO add parameter to indicate if matching should be done
3907     if (file.annotateAlignment(alignPanel.getAlignment(), false))
3908     {
3909       alignPanel.fontChanged();
3910       tcoffeeColour.setEnabled(true);
3911       // switch to this color
3912       changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3913       return true;
3914     }
3915     else
3916     {
3917       System.err.println("Problems resolving T-Coffee scores:");
3918       if (file.getWarningMessage() != null)
3919       {
3920         System.err.println(file.getWarningMessage());
3921       }
3922     }
3923     return false;
3924   }
3925
3926 }