src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import jalview.analysis.AAFrequency;
  21 import jalview.analysis.AlignmentSorter;
  22 import jalview.analysis.Conservation;
  23 import jalview.analysis.CrossRef;
  24 import jalview.analysis.NJTree;
  25 import jalview.analysis.ParseProperties;
  26 import jalview.analysis.SequenceIdMatcher;
  27 import jalview.bin.Cache;
  28 import jalview.commands.CommandI;
  29 import jalview.commands.EditCommand;
  30 import jalview.commands.OrderCommand;
  31 import jalview.commands.RemoveGapColCommand;
  32 import jalview.commands.RemoveGapsCommand;
  33 import jalview.commands.SlideSequencesCommand;
  34 import jalview.commands.TrimRegionCommand;
  35 import jalview.datamodel.AlignedCodonFrame;
  36 import jalview.datamodel.Alignment;
  37 import jalview.datamodel.AlignmentAnnotation;
  38 import jalview.datamodel.AlignmentI;
  39 import jalview.datamodel.AlignmentOrder;
  40 import jalview.datamodel.AlignmentView;
  41 import jalview.datamodel.ColumnSelection;
  42 import jalview.datamodel.PDBEntry;
  43 import jalview.datamodel.SeqCigar;
  44 import jalview.datamodel.Sequence;
  45 import jalview.datamodel.SequenceGroup;
  46 import jalview.datamodel.SequenceI;
  47 import jalview.io.AlignmentProperties;
  48 import jalview.io.AnnotationFile;
  49 import jalview.io.FeaturesFile;
  50 import jalview.io.FileLoader;
  51 import jalview.io.FormatAdapter;
  52 import jalview.io.HTMLOutput;
  53 import jalview.io.IdentifyFile;
  54 import jalview.io.JalviewFileChooser;
  55 import jalview.io.JalviewFileView;
  56 import jalview.io.JnetAnnotationMaker;
  57 import jalview.io.NewickFile;
  58 import jalview.io.TCoffeeScoreFile;
  59 import jalview.jbgui.GAlignFrame;
  60 import jalview.schemes.Blosum62ColourScheme;
  61 import jalview.schemes.BuriedColourScheme;
  62 import jalview.schemes.ClustalxColourScheme;
  63 import jalview.schemes.ColourSchemeI;
  64 import jalview.schemes.ColourSchemeProperty;
  65 import jalview.schemes.HelixColourScheme;
  66 import jalview.schemes.HydrophobicColourScheme;
  67 import jalview.schemes.NucleotideColourScheme;
  68 import jalview.schemes.PIDColourScheme;
  69 import jalview.schemes.PurinePyrimidineColourScheme;
  70 import jalview.schemes.RNAHelicesColourChooser;
  71 import jalview.schemes.ResidueProperties;
  72 import jalview.schemes.StrandColourScheme;
  73 import jalview.schemes.TCoffeeColourScheme;
  74 import jalview.schemes.TaylorColourScheme;
  75 import jalview.schemes.TurnColourScheme;
  76 import jalview.schemes.UserColourScheme;
  77 import jalview.schemes.ZappoColourScheme;
  78 import jalview.ws.jws1.Discoverer;
  79 import jalview.ws.jws2.Jws2Discoverer;
  80 import jalview.ws.seqfetcher.DbSourceProxy;
  81
  82 import java.awt.BorderLayout;
  83 import java.awt.Color;
  84 import java.awt.Component;
  85 import java.awt.GridLayout;
  86 import java.awt.Rectangle;
  87 import java.awt.Toolkit;
  88 import java.awt.datatransfer.Clipboard;
  89 import java.awt.datatransfer.DataFlavor;
  90 import java.awt.datatransfer.StringSelection;
  91 import java.awt.datatransfer.Transferable;
  92 import java.awt.dnd.DnDConstants;
  93 import java.awt.dnd.DropTargetDragEvent;
  94 import java.awt.dnd.DropTargetDropEvent;
  95 import java.awt.dnd.DropTargetEvent;
  96 import java.awt.dnd.DropTargetListener;
  97 import java.awt.event.ActionEvent;
  98 import java.awt.event.ActionListener;
  99 import java.awt.event.KeyAdapter;
 100 import java.awt.event.KeyEvent;
 101 import java.awt.event.MouseAdapter;
 102 import java.awt.event.MouseEvent;
 103 import java.awt.print.PageFormat;
 104 import java.awt.print.PrinterJob;
 105 import java.beans.PropertyChangeEvent;
 106 import java.io.File;
 107 import java.net.URL;
 108 import java.util.ArrayList;
 109 import java.util.Enumeration;
 110 import java.util.Hashtable;
 111 import java.util.List;
 112 import java.util.Vector;
 113
 114 import javax.swing.JButton;
 115 import javax.swing.JEditorPane;
 116 import javax.swing.JInternalFrame;
 117 import javax.swing.JLabel;
 118 import javax.swing.JLayeredPane;
 119 import javax.swing.JMenu;
 120 import javax.swing.JMenuItem;
 121 import javax.swing.JOptionPane;
 122 import javax.swing.JPanel;
 123 import javax.swing.JProgressBar;
 124 import javax.swing.JRadioButtonMenuItem;
 125 import javax.swing.JScrollPane;
 126 import javax.swing.SwingUtilities;
 127
 128 /**
 129  * DOCUMENT ME!
 130  *
 131  * @author $author$
 132  * @version $Revision$
 133  */
 134 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 135         IProgressIndicator
 136 {
 137
 138   /** DOCUMENT ME!! */
 139   public static final int DEFAULT_WIDTH = 700;
 140
 141   /** DOCUMENT ME!! */
 142   public static final int DEFAULT_HEIGHT = 500;
 143
 144   public AlignmentPanel alignPanel;
 145
 146   AlignViewport viewport;
 147
 148   Vector alignPanels = new Vector();
 149
 150   /**
 151    * Last format used to load or save alignments in this window
 152    */
 153   String currentFileFormat = null;
 154
 155   /**
 156    * Current filename for this alignment
 157    */
 158   String fileName = null;
 159
 160   /**
 161    * Creates a new AlignFrame object with specific width and height.
 162    *
 163    * @param al
 164    * @param width
 165    * @param height
 166    */
 167   public AlignFrame(AlignmentI al, int width, int height)
 168   {
 169     this(al, null, width, height);
 170   }
 171
 172   /**
 173    * Creates a new AlignFrame object with specific width, height and
 174    * sequenceSetId
 175    *
 176    * @param al
 177    * @param width
 178    * @param height
 179    * @param sequenceSetId
 180    */
 181   public AlignFrame(AlignmentI al, int width, int height,
 182           String sequenceSetId)
 183   {
 184     this(al, null, width, height, sequenceSetId);
 185   }
 186
 187   /**
 188    * Creates a new AlignFrame object with specific width, height and
 189    * sequenceSetId
 190    *
 191    * @param al
 192    * @param width
 193    * @param height
 194    * @param sequenceSetId
 195    * @param viewId
 196    */
 197   public AlignFrame(AlignmentI al, int width, int height,
 198           String sequenceSetId, String viewId)
 199   {
 200     this(al, null, width, height, sequenceSetId, viewId);
 201   }
 202
 203   /**
 204    * new alignment window with hidden columns
 205    *
 206    * @param al
 207    *          AlignmentI
 208    * @param hiddenColumns
 209    *          ColumnSelection or null
 210    * @param width
 211    *          Width of alignment frame
 212    * @param height
 213    *          height of frame.
 214    */
 215   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 216           int width, int height)
 217   {
 218     this(al, hiddenColumns, width, height, null);
 219   }
 220
 221   /**
 222    * Create alignment frame for al with hiddenColumns, a specific width and
 223    * height, and specific sequenceId
 224    *
 225    * @param al
 226    * @param hiddenColumns
 227    * @param width
 228    * @param height
 229    * @param sequenceSetId
 230    *          (may be null)
 231    */
 232   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 233           int width, int height, String sequenceSetId)
 234   {
 235     this(al, hiddenColumns, width, height, sequenceSetId, null);
 236   }
 237
 238   /**
 239    * Create alignment frame for al with hiddenColumns, a specific width and
 240    * height, and specific sequenceId
 241    *
 242    * @param al
 243    * @param hiddenColumns
 244    * @param width
 245    * @param height
 246    * @param sequenceSetId
 247    *          (may be null)
 248    * @param viewId
 249    *          (may be null)
 250    */
 251   public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns,
 252           int width, int height, String sequenceSetId, String viewId)
 253   {
 254     setSize(width, height);
 255     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 256
 257     alignPanel = new AlignmentPanel(this, viewport);
 258
 259     if (al.getDataset() == null)
 260     {
 261       al.setDataset(null);
 262     }
 263
 264     addAlignmentPanel(alignPanel, true);
 265     init();
 266   }
 267
 268   /**
 269    * Make a new AlignFrame from exisiting alignmentPanels
 270    *
 271    * @param ap
 272    *          AlignmentPanel
 273    * @param av
 274    *          AlignViewport
 275    */
 276   public AlignFrame(AlignmentPanel ap)
 277   {
 278     viewport = ap.av;
 279     alignPanel = ap;
 280     addAlignmentPanel(ap, false);
 281     init();
 282   }
 283
 284   /**
 285    * initalise the alignframe from the underlying viewport data and the
 286    * configurations
 287    */
 288   void init()
 289   {
 290     if (viewport.getAlignmentConservationAnnotation() == null)
 291     {
 292       BLOSUM62Colour.setEnabled(false);
 293       conservationMenuItem.setEnabled(false);
 294       modifyConservation.setEnabled(false);
 295       // PIDColour.setEnabled(false);
 296       // abovePIDThreshold.setEnabled(false);
 297       // modifyPID.setEnabled(false);
 298     }
 299
 300     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 301             "No sort");
 302
 303     if (sortby.equals("Id"))
 304     {
 305       sortIDMenuItem_actionPerformed(null);
 306     }
 307     else if (sortby.equals("Pairwise Identity"))
 308     {
 309       sortPairwiseMenuItem_actionPerformed(null);
 310     }
 311
 312     if (Desktop.desktop != null)
 313     {
 314       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 315       addServiceListeners();
 316       setGUINucleotide(viewport.getAlignment().isNucleotide());
 317     }
 318
 319     setMenusFromViewport(viewport);
 320     buildSortByAnnotationScoresMenu();
 321     if (viewport.wrapAlignment)
 322     {
 323       wrapMenuItem_actionPerformed(null);
 324     }
 325
 326     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 327     {
 328       this.overviewMenuItem_actionPerformed(null);
 329     }
 330
 331     addKeyListener();
 332
 333   }
 334
 335   /**
 336    * Change the filename and format for the alignment, and enable the 'reload'
 337    * button functionality.
 338    *
 339    * @param file
 340    *          valid filename
 341    * @param format
 342    *          format of file
 343    */
 344   public void setFileName(String file, String format)
 345   {
 346     fileName = file;
 347     currentFileFormat = format;
 348     reload.setEnabled(true);
 349   }
 350
 351   void addKeyListener()
 352   {
 353     addKeyListener(new KeyAdapter()
 354     {
 355       @Override
 356       public void keyPressed(KeyEvent evt)
 357       {
 358         if (viewport.cursorMode
 359                 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
 360                         .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
 361                         .getKeyCode() <= KeyEvent.VK_NUMPAD9))
 362                 && Character.isDigit(evt.getKeyChar()))
 363           alignPanel.seqPanel.numberPressed(evt.getKeyChar());
 364
 365         switch (evt.getKeyCode())
 366         {
 367
 368         case 27: // escape key
 369           deselectAllSequenceMenuItem_actionPerformed(null);
 370
 371           break;
 372
 373         case KeyEvent.VK_DOWN:
 374           if (evt.isAltDown() || !viewport.cursorMode)
 375             moveSelectedSequences(false);
 376           if (viewport.cursorMode)
 377             alignPanel.seqPanel.moveCursor(0, 1);
 378           break;
 379
 380         case KeyEvent.VK_UP:
 381           if (evt.isAltDown() || !viewport.cursorMode)
 382             moveSelectedSequences(true);
 383           if (viewport.cursorMode)
 384             alignPanel.seqPanel.moveCursor(0, -1);
 385
 386           break;
 387
 388         case KeyEvent.VK_LEFT:
 389           if (evt.isAltDown() || !viewport.cursorMode)
 390             slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
 391           else
 392             alignPanel.seqPanel.moveCursor(-1, 0);
 393
 394           break;
 395
 396         case KeyEvent.VK_RIGHT:
 397           if (evt.isAltDown() || !viewport.cursorMode)
 398             slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
 399           else
 400             alignPanel.seqPanel.moveCursor(1, 0);
 401           break;
 402
 403         case KeyEvent.VK_SPACE:
 404           if (viewport.cursorMode)
 405           {
 406             alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
 407                     || evt.isShiftDown() || evt.isAltDown());
 408           }
 409           break;
 410
 411         // case KeyEvent.VK_A:
 412         // if (viewport.cursorMode)
 413         // {
 414         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 415         // //System.out.println("A");
 416         // }
 417         // break;
 418         /*
 419          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 420          * System.out.println("closing bracket"); } break;
 421          */
 422         case KeyEvent.VK_DELETE:
 423         case KeyEvent.VK_BACK_SPACE:
 424           if (!viewport.cursorMode)
 425           {
 426             cut_actionPerformed(null);
 427           }
 428           else
 429           {
 430             alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
 431                     || evt.isShiftDown() || evt.isAltDown());
 432           }
 433
 434           break;
 435
 436         case KeyEvent.VK_S:
 437           if (viewport.cursorMode)
 438           {
 439             alignPanel.seqPanel.setCursorRow();
 440           }
 441           break;
 442         case KeyEvent.VK_C:
 443           if (viewport.cursorMode && !evt.isControlDown())
 444           {
 445             alignPanel.seqPanel.setCursorColumn();
 446           }
 447           break;
 448         case KeyEvent.VK_P:
 449           if (viewport.cursorMode)
 450           {
 451             alignPanel.seqPanel.setCursorPosition();
 452           }
 453           break;
 454
 455         case KeyEvent.VK_ENTER:
 456         case KeyEvent.VK_COMMA:
 457           if (viewport.cursorMode)
 458           {
 459             alignPanel.seqPanel.setCursorRowAndColumn();
 460           }
 461           break;
 462
 463         case KeyEvent.VK_Q:
 464           if (viewport.cursorMode)
 465           {
 466             alignPanel.seqPanel.setSelectionAreaAtCursor(true);
 467           }
 468           break;
 469         case KeyEvent.VK_M:
 470           if (viewport.cursorMode)
 471           {
 472             alignPanel.seqPanel.setSelectionAreaAtCursor(false);
 473           }
 474           break;
 475
 476         case KeyEvent.VK_F2:
 477           viewport.cursorMode = !viewport.cursorMode;
 478           statusBar.setText("Keyboard editing mode is "
 479                   + (viewport.cursorMode ? "on" : "off"));
 480           if (viewport.cursorMode)
 481           {
 482             alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
 483             alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
 484           }
 485           alignPanel.seqPanel.seqCanvas.repaint();
 486           break;
 487
 488         case KeyEvent.VK_F1:
 489           try
 490           {
 491             ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();
 492             java.net.URL url = javax.help.HelpSet.findHelpSet(cl,
 493                     "help/help");
 494             javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);
 495
 496             javax.help.HelpBroker hb = hs.createHelpBroker();
 497             hb.setCurrentID("home");
 498             hb.setDisplayed(true);
 499           } catch (Exception ex)
 500           {
 501             ex.printStackTrace();
 502           }
 503           break;
 504         case KeyEvent.VK_H:
 505         {
 506           boolean toggleSeqs = !evt.isControlDown();
 507           boolean toggleCols = !evt.isShiftDown();
 508           toggleHiddenRegions(toggleSeqs, toggleCols);
 509           break;
 510         }
 511         case KeyEvent.VK_PAGE_UP:
 512           if (viewport.wrapAlignment)
 513           {
 514             alignPanel.scrollUp(true);
 515           }
 516           else
 517           {
 518             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 519                     - viewport.endSeq + viewport.startSeq);
 520           }
 521           break;
 522         case KeyEvent.VK_PAGE_DOWN:
 523           if (viewport.wrapAlignment)
 524           {
 525             alignPanel.scrollUp(false);
 526           }
 527           else
 528           {
 529             alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
 530                     + viewport.endSeq - viewport.startSeq);
 531           }
 532           break;
 533         }
 534       }
 535
 536       @Override
 537       public void keyReleased(KeyEvent evt)
 538       {
 539         switch (evt.getKeyCode())
 540         {
 541         case KeyEvent.VK_LEFT:
 542           if (evt.isAltDown() || !viewport.cursorMode)
 543             viewport.firePropertyChange("alignment", null, viewport
 544                     .getAlignment().getSequences());
 545           break;
 546
 547         case KeyEvent.VK_RIGHT:
 548           if (evt.isAltDown() || !viewport.cursorMode)
 549             viewport.firePropertyChange("alignment", null, viewport
 550                     .getAlignment().getSequences());
 551           break;
 552         }
 553       }
 554     });
 555   }
 556
 557   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 558   {
 559     ap.alignFrame = this;
 560
 561     alignPanels.addElement(ap);
 562
 563     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 564
 565     int aSize = alignPanels.size();
 566
 567     tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
 568
 569     if (aSize == 1 && ap.av.viewName == null)
 570     {
 571       this.getContentPane().add(ap, BorderLayout.CENTER);
 572     }
 573     else
 574     {
 575       if (aSize == 2)
 576       {
 577         setInitialTabVisible();
 578       }
 579
 580       expandViews.setEnabled(true);
 581       gatherViews.setEnabled(true);
 582       tabbedPane.addTab(ap.av.viewName, ap);
 583
 584       ap.setVisible(false);
 585     }
 586
 587     if (newPanel)
 588     {
 589       if (ap.av.isPadGaps())
 590       {
 591         ap.av.getAlignment().padGaps();
 592       }
 593       ap.av.updateConservation(ap);
 594       ap.av.updateConsensus(ap);
 595       ap.av.updateStrucConsensus(ap);
 596     }
 597   }
 598
 599   public void setInitialTabVisible()
 600   {
 601     expandViews.setEnabled(true);
 602     gatherViews.setEnabled(true);
 603     tabbedPane.setVisible(true);
 604     AlignmentPanel first = (AlignmentPanel) alignPanels.firstElement();
 605     tabbedPane.addTab(first.av.viewName, first);
 606     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 607   }
 608
 609   public AlignViewport getViewport()
 610   {
 611     return viewport;
 612   }
 613
 614   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 615   private void addServiceListeners()
 616   {
 617     final java.beans.PropertyChangeListener thisListener;
 618     Desktop.instance.addJalviewPropertyChangeListener("services",
 619             thisListener = new java.beans.PropertyChangeListener()
 620             {
 621               @Override
 622               public void propertyChange(PropertyChangeEvent evt)
 623               {
 624                 // // System.out.println("Discoverer property change.");
 625                 // if (evt.getPropertyName().equals("services"))
 626                 {
 627                   SwingUtilities.invokeLater(new Runnable()
 628                   {
 629
 630                     @Override
 631                     public void run()
 632                     {
 633                       System.err
 634                               .println("Rebuild WS Menu for service change");
 635                       BuildWebServiceMenu();
 636                     }
 637
 638                   });
 639                 }
 640               }
 641             });
 642     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 643     {
 644       @Override
 645       public void internalFrameClosed(
 646               javax.swing.event.InternalFrameEvent evt)
 647       {
 648         System.out.println("deregistering discoverer listener");
 649         Desktop.instance.removeJalviewPropertyChangeListener("services",
 650                 thisListener);
 651         closeMenuItem_actionPerformed(true);
 652       };
 653     });
 654     // Finally, build the menu once to get current service state
 655     new Thread(new Runnable()
 656     {
 657       @Override
 658       public void run()
 659       {
 660         BuildWebServiceMenu();
 661       }
 662     }).start();
 663   }
 664
 665   public void setGUINucleotide(boolean nucleotide)
 666   {
 667     showTranslation.setVisible(nucleotide);
 668     conservationMenuItem.setEnabled(!nucleotide);
 669     modifyConservation.setEnabled(!nucleotide);
 670     showGroupConservation.setEnabled(!nucleotide);
 671     rnahelicesColour.setEnabled(nucleotide);
 672     purinePyrimidineColour.setEnabled(nucleotide);
 673     // Remember AlignFrame always starts as protein
 674     // if (!nucleotide)
 675     // {
 676     // showTr
 677     // calculateMenu.remove(calculateMenu.getItemCount() - 2);
 678     // }
 679   }
 680
 681   /**
 682    * set up menus for the currently viewport. This may be called after any
 683    * operation that affects the data in the current view (selection changed,
 684    * etc) to update the menus to reflect the new state.
 685    */
 686   public void setMenusForViewport()
 687   {
 688     setMenusFromViewport(viewport);
 689   }
 690
 691   /**
 692    * Need to call this method when tabs are selected for multiple views, or when
 693    * loading from Jalview2XML.java
 694    *
 695    * @param av
 696    *          AlignViewport
 697    */
 698   void setMenusFromViewport(AlignViewport av)
 699   {
 700     padGapsMenuitem.setSelected(av.isPadGaps());
 701     colourTextMenuItem.setSelected(av.showColourText);
 702     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 703     conservationMenuItem.setSelected(av.getConservationSelected());
 704     seqLimits.setSelected(av.getShowJVSuffix());
 705     idRightAlign.setSelected(av.rightAlignIds);
 706     centreColumnLabelsMenuItem.setState(av.centreColumnLabels);
 707     renderGapsMenuItem.setSelected(av.renderGaps);
 708     wrapMenuItem.setSelected(av.wrapAlignment);
 709     scaleAbove.setVisible(av.wrapAlignment);
 710     scaleLeft.setVisible(av.wrapAlignment);
 711     scaleRight.setVisible(av.wrapAlignment);
 712     annotationPanelMenuItem.setState(av.showAnnotation);
 713     viewBoxesMenuItem.setSelected(av.showBoxes);
 714     viewTextMenuItem.setSelected(av.showText);
 715     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 716     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 717     showGroupConservation.setSelected(av.isShowGroupConservation());
 718     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 719     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 720     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 721
 722     setColourSelected(ColourSchemeProperty.getColourName(av
 723             .getGlobalColourScheme()));
 724
 725     showSeqFeatures.setSelected(av.showSequenceFeatures);
 726     hiddenMarkers.setState(av.showHiddenMarkers);
 727     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 728     showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
 729     showDbRefsMenuitem.setSelected(av.isShowDbRefs());
 730     autoCalculate.setSelected(av.autoCalculateConsensus);
 731     sortByTree.setSelected(av.sortByTree);
 732     listenToViewSelections.setSelected(av.followSelection);
 733     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
 734     rnahelicesColour
 735             .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
 736     setShowProductsEnabled();
 737
 738     updateEditMenuBar();
 739   }
 740   // methods for implementing IProgressIndicator
 741   // need to refactor to a reusable stub class
 742   Hashtable progressBars, progressBarHandlers;
 743
 744   /*
 745    * (non-Javadoc)
 746    *
 747    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 748    */
 749   @Override
 750   public void setProgressBar(String message, long id)
 751   {
 752     if (progressBars == null)
 753     {
 754       progressBars = new Hashtable();
 755       progressBarHandlers = new Hashtable();
 756     }
 757
 758     JPanel progressPanel;
 759     Long lId = new Long(id);
 760     GridLayout layout = (GridLayout) statusPanel.getLayout();
 761     if (progressBars.get(lId) != null)
 762     {
 763       progressPanel = (JPanel) progressBars.get(new Long(id));
 764       statusPanel.remove(progressPanel);
 765       progressBars.remove(lId);
 766       progressPanel = null;
 767       if (message != null)
 768       {
 769         statusBar.setText(message);
 770       }
 771       if (progressBarHandlers.contains(lId))
 772       {
 773         progressBarHandlers.remove(lId);
 774       }
 775       layout.setRows(layout.getRows() - 1);
 776     }
 777     else
 778     {
 779       progressPanel = new JPanel(new BorderLayout(10, 5));
 780
 781       JProgressBar progressBar = new JProgressBar();
 782       progressBar.setIndeterminate(true);
 783
 784       progressPanel.add(new JLabel(message), BorderLayout.WEST);
 785       progressPanel.add(progressBar, BorderLayout.CENTER);
 786
 787       layout.setRows(layout.getRows() + 1);
 788       statusPanel.add(progressPanel);
 789
 790       progressBars.put(lId, progressPanel);
 791     }
 792     // update GUI
 793     // setMenusForViewport();
 794     validate();
 795   }
 796
 797   @Override
 798   public void registerHandler(final long id,
 799           final IProgressIndicatorHandler handler)
 800   {
 801     if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
 802     {
 803       throw new Error(
 804               "call setProgressBar before registering the progress bar's handler.");
 805     }
 806     progressBarHandlers.put(new Long(id), handler);
 807     final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
 808     if (handler.canCancel())
 809     {
 810       JButton cancel = new JButton("Cancel");
 811       final IProgressIndicator us = this;
 812       cancel.addActionListener(new ActionListener()
 813       {
 814
 815         @Override
 816         public void actionPerformed(ActionEvent e)
 817         {
 818           handler.cancelActivity(id);
 819           us.setProgressBar(
 820                   "Cancelled "
 821                           + ((JLabel) progressPanel.getComponent(0))
 822                                   .getText(), id);
 823         }
 824       });
 825       progressPanel.add(cancel, BorderLayout.EAST);
 826     }
 827   }
 828
 829   /**
 830    *
 831    * @return true if any progress bars are still active
 832    */
 833   @Override
 834   public boolean operationInProgress()
 835   {
 836     if (progressBars != null && progressBars.size() > 0)
 837     {
 838       return true;
 839     }
 840     return false;
 841   }
 842
 843   /*
 844    * Added so Castor Mapping file can obtain Jalview Version
 845    */
 846   public String getVersion()
 847   {
 848     return jalview.bin.Cache.getProperty("VERSION");
 849   }
 850
 851   public FeatureRenderer getFeatureRenderer()
 852   {
 853     return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();
 854   }
 855
 856   @Override
 857   public void fetchSequence_actionPerformed(ActionEvent e)
 858   {
 859     new SequenceFetcher(this);
 860   }
 861
 862   @Override
 863   public void addFromFile_actionPerformed(ActionEvent e)
 864   {
 865     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
 866   }
 867
 868   @Override
 869   public void reload_actionPerformed(ActionEvent e)
 870   {
 871     if (fileName != null)
 872     {
 873       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
 874       // originating file's format
 875       // TODO: work out how to recover feature settings for correct view(s) when
 876       // file is reloaded.
 877       if (currentFileFormat.equals("Jalview"))
 878       {
 879         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 880         for (int i = 0; i < frames.length; i++)
 881         {
 882           if (frames[i] instanceof AlignFrame && frames[i] != this
 883                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
 884           {
 885             try
 886             {
 887               frames[i].setSelected(true);
 888               Desktop.instance.closeAssociatedWindows();
 889             } catch (java.beans.PropertyVetoException ex)
 890             {
 891             }
 892           }
 893
 894         }
 895         Desktop.instance.closeAssociatedWindows();
 896
 897         FileLoader loader = new FileLoader();
 898         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 899         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
 900       }
 901       else
 902       {
 903         Rectangle bounds = this.getBounds();
 904
 905         FileLoader loader = new FileLoader();
 906         String protocol = fileName.startsWith("http:") ? "URL" : "File";
 907         AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
 908                 protocol, currentFileFormat);
 909
 910         newframe.setBounds(bounds);
 911         if (featureSettings != null && featureSettings.isShowing())
 912         {
 913           final Rectangle fspos = featureSettings.frame.getBounds();
 914           // TODO: need a 'show feature settings' function that takes bounds -
 915           // need to refactor Desktop.addFrame
 916           newframe.featureSettings_actionPerformed(null);
 917           final FeatureSettings nfs = newframe.featureSettings;
 918           SwingUtilities.invokeLater(new Runnable()
 919           {
 920             @Override
 921             public void run()
 922             {
 923               nfs.frame.setBounds(fspos);
 924             }
 925           });
 926           this.featureSettings.close();
 927           this.featureSettings = null;
 928         }
 929         this.closeMenuItem_actionPerformed(true);
 930       }
 931     }
 932   }
 933
 934   @Override
 935   public void addFromText_actionPerformed(ActionEvent e)
 936   {
 937     Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
 938   }
 939
 940   @Override
 941   public void addFromURL_actionPerformed(ActionEvent e)
 942   {
 943     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
 944   }
 945
 946   @Override
 947   public void save_actionPerformed(ActionEvent e)
 948   {
 949     if (fileName == null
 950             || (currentFileFormat == null || !jalview.io.FormatAdapter
 951                     .isValidIOFormat(currentFileFormat, true))
 952             || fileName.startsWith("http"))
 953     {
 954       saveAs_actionPerformed(null);
 955     }
 956     else
 957     {
 958       saveAlignment(fileName, currentFileFormat);
 959     }
 960   }
 961
 962   /**
 963    * DOCUMENT ME!
 964    *
 965    * @param e
 966    *          DOCUMENT ME!
 967    */
 968   @Override
 969   public void saveAs_actionPerformed(ActionEvent e)
 970   {
 971     JalviewFileChooser chooser = new JalviewFileChooser(
 972             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 973             jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
 974             jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
 975             currentFileFormat, false);
 976
 977     chooser.setFileView(new JalviewFileView());
 978     chooser.setDialogTitle("Save Alignment to file");
 979     chooser.setToolTipText("Save");
 980
 981     int value = chooser.showSaveDialog(this);
 982
 983     if (value == JalviewFileChooser.APPROVE_OPTION)
 984     {
 985       currentFileFormat = chooser.getSelectedFormat();
 986       if (currentFileFormat == null)
 987       {
 988         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 989                 "You must select a file format before saving!",
 990                 "File format not specified", JOptionPane.WARNING_MESSAGE);
 991         value = chooser.showSaveDialog(this);
 992         return;
 993       }
 994
 995       fileName = chooser.getSelectedFile().getPath();
 996
 997       jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
 998               currentFileFormat);
 999
1000       jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
1001       if (currentFileFormat.indexOf(" ") > -1)
1002       {
1003         currentFileFormat = currentFileFormat.substring(0,
1004                 currentFileFormat.indexOf(" "));
1005       }
1006       saveAlignment(fileName, currentFileFormat);
1007     }
1008   }
1009
1010   public boolean saveAlignment(String file, String format)
1011   {
1012     boolean success = true;
1013
1014     if (format.equalsIgnoreCase("Jalview"))
1015     {
1016       String shortName = title;
1017
1018       if (shortName.indexOf(java.io.File.separatorChar) > -1)
1019       {
1020         shortName = shortName.substring(shortName
1021                 .lastIndexOf(java.io.File.separatorChar) + 1);
1022       }
1023
1024       success = new Jalview2XML().SaveAlignment(this, file, shortName);
1025
1026       statusBar.setText("Successfully saved to file: " + fileName + " in "
1027               + format + " format.");
1028
1029     }
1030     else
1031     {
1032       if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
1033       {
1034         warningMessage("Cannot save file " + fileName + " using format "
1035                 + format, "Alignment output format not supported");
1036         saveAs_actionPerformed(null);
1037         // JBPNote need to have a raise_gui flag here
1038         return false;
1039       }
1040
1041       String[] omitHidden = null;
1042
1043       if (viewport.hasHiddenColumns())
1044       {
1045         int reply = JOptionPane
1046                 .showInternalConfirmDialog(
1047                         Desktop.desktop,
1048                         "The Alignment contains hidden columns."
1049                                 + "\nDo you want to save only the visible alignment?",
1050                         "Save / Omit Hidden Columns",
1051                         JOptionPane.YES_NO_OPTION,
1052                         JOptionPane.QUESTION_MESSAGE);
1053
1054         if (reply == JOptionPane.YES_OPTION)
1055         {
1056           omitHidden = viewport.getViewAsString(false);
1057         }
1058       }
1059       FormatAdapter f = new FormatAdapter();
1060       String output = f.formatSequences(
1061               format,
1062               viewport.getAlignment(), // class cast exceptions will
1063               // occur in the distant future
1064               omitHidden, f.getCacheSuffixDefault(format),
1065               viewport.getColumnSelection());
1066
1067       if (output == null)
1068       {
1069         success = false;
1070       }
1071       else
1072       {
1073         try
1074         {
1075           java.io.PrintWriter out = new java.io.PrintWriter(
1076                   new java.io.FileWriter(file));
1077
1078           out.print(output);
1079           out.close();
1080           this.setTitle(file);
1081           statusBar.setText("Successfully saved to file: " + fileName
1082                   + " in " + format + " format.");
1083         } catch (Exception ex)
1084         {
1085           success = false;
1086           ex.printStackTrace();
1087         }
1088       }
1089     }
1090
1091     if (!success)
1092     {
1093       JOptionPane.showInternalMessageDialog(this, "Couldn't save file: "
1094               + fileName, "Error Saving File", JOptionPane.WARNING_MESSAGE);
1095     }
1096
1097     return success;
1098   }
1099
1100   private void warningMessage(String warning, String title)
1101   {
1102     if (new jalview.util.Platform().isHeadless())
1103     {
1104       System.err.println("Warning: " + title + "\nWarning: " + warning);
1105
1106     }
1107     else
1108     {
1109       JOptionPane.showInternalMessageDialog(this, warning, title,
1110               JOptionPane.WARNING_MESSAGE);
1111     }
1112     return;
1113   }
1114
1115   /**
1116    * DOCUMENT ME!
1117    *
1118    * @param e
1119    *          DOCUMENT ME!
1120    */
1121   @Override
1122   protected void outputText_actionPerformed(ActionEvent e)
1123   {
1124     String[] omitHidden = null;
1125
1126     if (viewport.hasHiddenColumns())
1127     {
1128       int reply = JOptionPane
1129               .showInternalConfirmDialog(
1130                       Desktop.desktop,
1131                       "The Alignment contains hidden columns."
1132                               + "\nDo you want to output only the visible alignment?",
1133                       "Save / Omit Hidden Columns",
1134                       JOptionPane.YES_NO_OPTION,
1135                       JOptionPane.QUESTION_MESSAGE);
1136
1137       if (reply == JOptionPane.YES_OPTION)
1138       {
1139         omitHidden = viewport.getViewAsString(false);
1140       }
1141     }
1142
1143     CutAndPasteTransfer cap = new CutAndPasteTransfer();
1144     cap.setForInput(null);
1145
1146     try
1147     {
1148       cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1149               viewport.getAlignment(), omitHidden,
1150               viewport.getColumnSelection()));
1151       Desktop.addInternalFrame(cap,
1152               "Alignment output - " + e.getActionCommand(), 600, 500);
1153     } catch (OutOfMemoryError oom)
1154     {
1155       new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom);
1156       cap.dispose();
1157     }
1158
1159   }
1160
1161   /**
1162    * DOCUMENT ME!
1163    *
1164    * @param e
1165    *          DOCUMENT ME!
1166    */
1167   @Override
1168   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1169   {
1170     new HTMLOutput(alignPanel,
1171             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
1172             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1173   }
1174
1175   public void createImageMap(File file, String image)
1176   {
1177     alignPanel.makePNGImageMap(file, image);
1178   }
1179
1180   /**
1181    * DOCUMENT ME!
1182    *
1183    * @param e
1184    *          DOCUMENT ME!
1185    */
1186   @Override
1187   public void createPNG(File f)
1188   {
1189     alignPanel.makePNG(f);
1190   }
1191
1192   /**
1193    * DOCUMENT ME!
1194    *
1195    * @param e
1196    *          DOCUMENT ME!
1197    */
1198   @Override
1199   public void createEPS(File f)
1200   {
1201     alignPanel.makeEPS(f);
1202   }
1203
1204   @Override
1205   public void pageSetup_actionPerformed(ActionEvent e)
1206   {
1207     PrinterJob printJob = PrinterJob.getPrinterJob();
1208     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1209   }
1210
1211   /**
1212    * DOCUMENT ME!
1213    *
1214    * @param e
1215    *          DOCUMENT ME!
1216    */
1217   @Override
1218   public void printMenuItem_actionPerformed(ActionEvent e)
1219   {
1220     // Putting in a thread avoids Swing painting problems
1221     PrintThread thread = new PrintThread(alignPanel);
1222     thread.start();
1223   }
1224
1225   @Override
1226   public void exportFeatures_actionPerformed(ActionEvent e)
1227   {
1228     new AnnotationExporter().exportFeatures(alignPanel);
1229   }
1230
1231   @Override
1232   public void exportAnnotations_actionPerformed(ActionEvent e)
1233   {
1234     new AnnotationExporter().exportAnnotations(alignPanel,
1235             viewport.showAnnotation ? viewport.getAlignment()
1236                     .getAlignmentAnnotation() : null, viewport
1237                     .getAlignment().getGroups(), ((Alignment) viewport
1238                     .getAlignment()).alignmentProperties);
1239   }
1240
1241   @Override
1242   public void associatedData_actionPerformed(ActionEvent e)
1243   {
1244     // Pick the tree file
1245     JalviewFileChooser chooser = new JalviewFileChooser(
1246             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1247     chooser.setFileView(new JalviewFileView());
1248     chooser.setDialogTitle("Load Jalview Annotations or Features File");
1249     chooser.setToolTipText("Load Jalview Annotations / Features file");
1250
1251     int value = chooser.showOpenDialog(null);
1252
1253     if (value == JalviewFileChooser.APPROVE_OPTION)
1254     {
1255       String choice = chooser.getSelectedFile().getPath();
1256       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1257       loadJalviewDataFile(choice, null, null, null);
1258     }
1259
1260   }
1261
1262   /**
1263    * Close the current view or all views in the alignment frame. If the frame
1264    * only contains one view then the alignment will be removed from memory.
1265    *
1266    * @param closeAllTabs
1267    */
1268   @Override
1269   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1270   {
1271     if (alignPanels != null && alignPanels.size() < 2)
1272     {
1273       closeAllTabs = true;
1274     }
1275
1276     try
1277     {
1278       if (alignPanels != null)
1279       {
1280         if (closeAllTabs)
1281         {
1282           if (this.isClosed())
1283           {
1284             // really close all the windows - otherwise wait till
1285             // setClosed(true) is called
1286             for (int i = 0; i < alignPanels.size(); i++)
1287             {
1288               AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i);
1289               ap.closePanel();
1290             }
1291           }
1292         }
1293         else
1294         {
1295           closeView(alignPanel);
1296         }
1297       }
1298
1299       if (closeAllTabs)
1300       {
1301         this.setClosed(true);
1302       }
1303     } catch (Exception ex)
1304     {
1305       ex.printStackTrace();
1306     }
1307   }
1308
1309   /**
1310    * close alignPanel2 and shuffle tabs appropriately.
1311    *
1312    * @param alignPanel2
1313    */
1314   public void closeView(AlignmentPanel alignPanel2)
1315   {
1316     int index = tabbedPane.getSelectedIndex();
1317     int closedindex = tabbedPane.indexOfComponent(alignPanel2);
1318     alignPanels.removeElement(alignPanel2);
1319     // Unnecessary
1320     // if (viewport == alignPanel2.av)
1321     // {
1322     // viewport = null;
1323     // }
1324     alignPanel2.closePanel();
1325     alignPanel2 = null;
1326
1327     tabbedPane.removeTabAt(closedindex);
1328     tabbedPane.validate();
1329
1330     if (index > closedindex || index == tabbedPane.getTabCount())
1331     {
1332       // modify currently selected tab index if necessary.
1333       index--;
1334     }
1335
1336     this.tabSelectionChanged(index);
1337   }
1338
1339   /**
1340    * DOCUMENT ME!
1341    */
1342   void updateEditMenuBar()
1343   {
1344
1345     if (viewport.historyList.size() > 0)
1346     {
1347       undoMenuItem.setEnabled(true);
1348       CommandI command = (CommandI) viewport.historyList.peek();
1349       undoMenuItem.setText("Undo " + command.getDescription());
1350     }
1351     else
1352     {
1353       undoMenuItem.setEnabled(false);
1354       undoMenuItem.setText("Undo");
1355     }
1356
1357     if (viewport.redoList.size() > 0)
1358     {
1359       redoMenuItem.setEnabled(true);
1360
1361       CommandI command = (CommandI) viewport.redoList.peek();
1362       redoMenuItem.setText("Redo " + command.getDescription());
1363     }
1364     else
1365     {
1366       redoMenuItem.setEnabled(false);
1367       redoMenuItem.setText("Redo");
1368     }
1369   }
1370
1371   public void addHistoryItem(CommandI command)
1372   {
1373     if (command.getSize() > 0)
1374     {
1375       viewport.historyList.push(command);
1376       viewport.redoList.clear();
1377       updateEditMenuBar();
1378       viewport.updateHiddenColumns();
1379       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1380       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1381       // viewport.getColumnSelection()
1382       // .getHiddenColumns().size() > 0);
1383     }
1384   }
1385
1386   /**
1387    *
1388    * @return alignment objects for all views
1389    */
1390   AlignmentI[] getViewAlignments()
1391   {
1392     if (alignPanels != null)
1393     {
1394       Enumeration e = alignPanels.elements();
1395       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1396       for (int i = 0; e.hasMoreElements(); i++)
1397       {
1398         als[i] = ((AlignmentPanel) e.nextElement()).av.getAlignment();
1399       }
1400       return als;
1401     }
1402     if (viewport != null)
1403     {
1404       return new AlignmentI[]
1405       { viewport.getAlignment() };
1406     }
1407     return null;
1408   }
1409
1410   /**
1411    * DOCUMENT ME!
1412    *
1413    * @param e
1414    *          DOCUMENT ME!
1415    */
1416   @Override
1417   protected void undoMenuItem_actionPerformed(ActionEvent e)
1418   {
1419     if (viewport.historyList.empty())
1420       return;
1421     CommandI command = (CommandI) viewport.historyList.pop();
1422     viewport.redoList.push(command);
1423     command.undoCommand(getViewAlignments());
1424
1425     AlignViewport originalSource = getOriginatingSource(command);
1426     updateEditMenuBar();
1427
1428     if (originalSource != null)
1429     {
1430       if (originalSource != viewport)
1431       {
1432         Cache.log
1433                 .warn("Implementation worry: mismatch of viewport origin for undo");
1434       }
1435       originalSource.updateHiddenColumns();
1436       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1437       // null
1438       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1439       // viewport.getColumnSelection()
1440       // .getHiddenColumns().size() > 0);
1441       originalSource.firePropertyChange("alignment", null, originalSource
1442               .getAlignment().getSequences());
1443     }
1444   }
1445
1446   /**
1447    * DOCUMENT ME!
1448    *
1449    * @param e
1450    *          DOCUMENT ME!
1451    */
1452   @Override
1453   protected void redoMenuItem_actionPerformed(ActionEvent e)
1454   {
1455     if (viewport.redoList.size() < 1)
1456     {
1457       return;
1458     }
1459
1460     CommandI command = (CommandI) viewport.redoList.pop();
1461     viewport.historyList.push(command);
1462     command.doCommand(getViewAlignments());
1463
1464     AlignViewport originalSource = getOriginatingSource(command);
1465     updateEditMenuBar();
1466
1467     if (originalSource != null)
1468     {
1469
1470       if (originalSource != viewport)
1471       {
1472         Cache.log
1473                 .warn("Implementation worry: mismatch of viewport origin for redo");
1474       }
1475       originalSource.updateHiddenColumns();
1476       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1477       // null
1478       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1479       // viewport.getColumnSelection()
1480       // .getHiddenColumns().size() > 0);
1481       originalSource.firePropertyChange("alignment", null, originalSource
1482               .getAlignment().getSequences());
1483     }
1484   }
1485
1486   AlignViewport getOriginatingSource(CommandI command)
1487   {
1488     AlignViewport originalSource = null;
1489     // For sequence removal and addition, we need to fire
1490     // the property change event FROM the viewport where the
1491     // original alignment was altered
1492     AlignmentI al = null;
1493     if (command instanceof EditCommand)
1494     {
1495       EditCommand editCommand = (EditCommand) command;
1496       al = editCommand.getAlignment();
1497       Vector comps = (Vector) PaintRefresher.components.get(viewport
1498               .getSequenceSetId());
1499
1500       for (int i = 0; i < comps.size(); i++)
1501       {
1502         if (comps.elementAt(i) instanceof AlignmentPanel)
1503         {
1504           if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1505           {
1506             originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1507             break;
1508           }
1509         }
1510       }
1511     }
1512
1513     if (originalSource == null)
1514     {
1515       // The original view is closed, we must validate
1516       // the current view against the closed view first
1517       if (al != null)
1518       {
1519         PaintRefresher.validateSequences(al, viewport.getAlignment());
1520       }
1521
1522       originalSource = viewport;
1523     }
1524
1525     return originalSource;
1526   }
1527
1528   /**
1529    * DOCUMENT ME!
1530    *
1531    * @param up
1532    *          DOCUMENT ME!
1533    */
1534   public void moveSelectedSequences(boolean up)
1535   {
1536     SequenceGroup sg = viewport.getSelectionGroup();
1537
1538     if (sg == null)
1539     {
1540       return;
1541     }
1542     viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up);
1543     alignPanel.paintAlignment(true);
1544   }
1545
1546   synchronized void slideSequences(boolean right, int size)
1547   {
1548     List<SequenceI> sg = new Vector();
1549     if (viewport.cursorMode)
1550     {
1551       sg.add(viewport.getAlignment().getSequenceAt(
1552               alignPanel.seqPanel.seqCanvas.cursorY));
1553     }
1554     else if (viewport.getSelectionGroup() != null
1555             && viewport.getSelectionGroup().getSize() != viewport
1556                     .getAlignment().getHeight())
1557     {
1558       sg = viewport.getSelectionGroup().getSequences(
1559               viewport.getHiddenRepSequences());
1560     }
1561
1562     if (sg.size() < 1)
1563     {
1564       return;
1565     }
1566
1567     Vector invertGroup = new Vector();
1568
1569     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1570     {
1571       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1572         invertGroup.add(viewport.getAlignment().getSequenceAt(i));
1573     }
1574
1575     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1576
1577     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1578     for (int i = 0; i < invertGroup.size(); i++)
1579       seqs2[i] = (SequenceI) invertGroup.elementAt(i);
1580
1581     SlideSequencesCommand ssc;
1582     if (right)
1583       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1584               size, viewport.getGapCharacter());
1585     else
1586       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1587               size, viewport.getGapCharacter());
1588
1589     int groupAdjustment = 0;
1590     if (ssc.getGapsInsertedBegin() && right)
1591     {
1592       if (viewport.cursorMode)
1593         alignPanel.seqPanel.moveCursor(size, 0);
1594       else
1595         groupAdjustment = size;
1596     }
1597     else if (!ssc.getGapsInsertedBegin() && !right)
1598     {
1599       if (viewport.cursorMode)
1600         alignPanel.seqPanel.moveCursor(-size, 0);
1601       else
1602         groupAdjustment = -size;
1603     }
1604
1605     if (groupAdjustment != 0)
1606     {
1607       viewport.getSelectionGroup().setStartRes(
1608               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1609       viewport.getSelectionGroup().setEndRes(
1610               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1611     }
1612
1613     boolean appendHistoryItem = false;
1614     if (viewport.historyList != null && viewport.historyList.size() > 0
1615             && viewport.historyList.peek() instanceof SlideSequencesCommand)
1616     {
1617       appendHistoryItem = ssc
1618               .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1619                       .peek());
1620     }
1621
1622     if (!appendHistoryItem)
1623       addHistoryItem(ssc);
1624
1625     repaint();
1626   }
1627
1628   /**
1629    * DOCUMENT ME!
1630    *
1631    * @param e
1632    *          DOCUMENT ME!
1633    */
1634   @Override
1635   protected void copy_actionPerformed(ActionEvent e)
1636   {
1637     System.gc();
1638     if (viewport.getSelectionGroup() == null)
1639     {
1640       return;
1641     }
1642     // TODO: preserve the ordering of displayed alignment annotation in any
1643     // internal paste (particularly sequence associated annotation)
1644     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1645     String[] omitHidden = null;
1646
1647     if (viewport.hasHiddenColumns())
1648     {
1649       omitHidden = viewport.getViewAsString(true);
1650     }
1651
1652     String output = new FormatAdapter().formatSequences("Fasta", seqs,
1653             omitHidden);
1654
1655     StringSelection ss = new StringSelection(output);
1656
1657     try
1658     {
1659       jalview.gui.Desktop.internalCopy = true;
1660       // Its really worth setting the clipboard contents
1661       // to empty before setting the large StringSelection!!
1662       Toolkit.getDefaultToolkit().getSystemClipboard()
1663               .setContents(new StringSelection(""), null);
1664
1665       Toolkit.getDefaultToolkit().getSystemClipboard()
1666               .setContents(ss, Desktop.instance);
1667     } catch (OutOfMemoryError er)
1668     {
1669       new OOMWarning("copying region", er);
1670       return;
1671     }
1672
1673     Vector hiddenColumns = null;
1674     if (viewport.hasHiddenColumns())
1675     {
1676       hiddenColumns = new Vector();
1677       int hiddenOffset = viewport.getSelectionGroup().getStartRes(), hiddenCutoff = viewport
1678               .getSelectionGroup().getEndRes();
1679       for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1680               .size(); i++)
1681       {
1682         int[] region = (int[]) viewport.getColumnSelection()
1683                 .getHiddenColumns().elementAt(i);
1684         if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
1685         {
1686           hiddenColumns.addElement(new int[]
1687           { region[0] - hiddenOffset, region[1] - hiddenOffset });
1688         }
1689       }
1690     }
1691
1692     Desktop.jalviewClipboard = new Object[]
1693     { seqs, viewport.getAlignment().getDataset(), hiddenColumns };
1694     statusBar.setText("Copied " + seqs.length + " sequences to clipboard.");
1695   }
1696
1697   /**
1698    * DOCUMENT ME!
1699    *
1700    * @param e
1701    *          DOCUMENT ME!
1702    */
1703   @Override
1704   protected void pasteNew_actionPerformed(ActionEvent e)
1705   {
1706     paste(true);
1707   }
1708
1709   /**
1710    * DOCUMENT ME!
1711    *
1712    * @param e
1713    *          DOCUMENT ME!
1714    */
1715   @Override
1716   protected void pasteThis_actionPerformed(ActionEvent e)
1717   {
1718     paste(false);
1719   }
1720
1721   /**
1722    * Paste contents of Jalview clipboard
1723    *
1724    * @param newAlignment
1725    *          true to paste to a new alignment, otherwise add to this.
1726    */
1727   void paste(boolean newAlignment)
1728   {
1729     boolean externalPaste = true;
1730     try
1731     {
1732       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1733       Transferable contents = c.getContents(this);
1734
1735       if (contents == null)
1736       {
1737         return;
1738       }
1739
1740       String str, format;
1741       try
1742       {
1743         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
1744         if (str.length() < 1)
1745         {
1746           return;
1747         }
1748
1749         format = new IdentifyFile().Identify(str, "Paste");
1750
1751       } catch (OutOfMemoryError er)
1752       {
1753         new OOMWarning("Out of memory pasting sequences!!", er);
1754         return;
1755       }
1756
1757       SequenceI[] sequences;
1758       boolean annotationAdded = false;
1759       AlignmentI alignment = null;
1760
1761       if (Desktop.jalviewClipboard != null)
1762       {
1763         // The clipboard was filled from within Jalview, we must use the
1764         // sequences
1765         // And dataset from the copied alignment
1766         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
1767         // be doubly sure that we create *new* sequence objects.
1768         sequences = new SequenceI[newseq.length];
1769         for (int i = 0; i < newseq.length; i++)
1770         {
1771           sequences[i] = new Sequence(newseq[i]);
1772         }
1773         alignment = new Alignment(sequences);
1774         externalPaste = false;
1775       }
1776       else
1777       {
1778         // parse the clipboard as an alignment.
1779         alignment = new FormatAdapter().readFile(str, "Paste", format);
1780         sequences = alignment.getSequencesArray();
1781       }
1782
1783       int alwidth = 0;
1784
1785       if (newAlignment)
1786       {
1787
1788         if (Desktop.jalviewClipboard != null)
1789         {
1790           // dataset is inherited
1791           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
1792         }
1793         else
1794         {
1795           // new dataset is constructed
1796           alignment.setDataset(null);
1797         }
1798         alwidth = alignment.getWidth() + 1;
1799       }
1800       else
1801       {
1802         AlignmentI pastedal = alignment; // preserve pasted alignment object
1803         // Add pasted sequences and dataset into existing alignment.
1804         alignment = viewport.getAlignment();
1805         alwidth = alignment.getWidth() + 1;
1806         // decide if we need to import sequences from an existing dataset
1807         boolean importDs = Desktop.jalviewClipboard != null
1808                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
1809         // importDs==true instructs us to copy over new dataset sequences from
1810         // an existing alignment
1811         Vector newDs = (importDs) ? new Vector() : null; // used to create
1812         // minimum dataset set
1813
1814         for (int i = 0; i < sequences.length; i++)
1815         {
1816           if (importDs)
1817           {
1818             newDs.addElement(null);
1819           }
1820           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
1821           // paste
1822           if (importDs && ds != null)
1823           {
1824             if (!newDs.contains(ds))
1825             {
1826               newDs.setElementAt(ds, i);
1827               ds = new Sequence(ds);
1828               // update with new dataset sequence
1829               sequences[i].setDatasetSequence(ds);
1830             }
1831             else
1832             {
1833               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
1834             }
1835           }
1836           else
1837           {
1838             // copy and derive new dataset sequence
1839             sequences[i] = sequences[i].deriveSequence();
1840             alignment.getDataset().addSequence(
1841                     sequences[i].getDatasetSequence());
1842             // TODO: avoid creation of duplicate dataset sequences with a
1843             // 'contains' method using SequenceI.equals()/SequenceI.contains()
1844           }
1845           alignment.addSequence(sequences[i]); // merges dataset
1846         }
1847         if (newDs != null)
1848         {
1849           newDs.clear(); // tidy up
1850         }
1851         if (pastedal.getAlignmentAnnotation() != null)
1852         {
1853           // Add any annotation attached to alignment.
1854           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
1855           for (int i = 0; i < alann.length; i++)
1856           {
1857             annotationAdded = true;
1858             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
1859             {
1860               AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]);
1861               newann.padAnnotation(alwidth);
1862               alignment.addAnnotation(newann);
1863             }
1864           }
1865         }
1866       }
1867       if (!newAlignment)
1868       {
1869         // /////
1870         // ADD HISTORY ITEM
1871         //
1872         addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1873                 sequences, 0, alignment.getWidth(), alignment));
1874       }
1875       // Add any annotations attached to sequences
1876       for (int i = 0; i < sequences.length; i++)
1877       {
1878         if (sequences[i].getAnnotation() != null)
1879         {
1880           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
1881           {
1882             annotationAdded = true;
1883             sequences[i].getAnnotation()[a].adjustForAlignment();
1884             sequences[i].getAnnotation()[a].padAnnotation(alwidth);
1885             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
1886             // was
1887             // duplicated
1888             // earlier
1889             alignment
1890                     .setAnnotationIndex(sequences[i].getAnnotation()[a], a);
1891           }
1892         }
1893       }
1894       if (!newAlignment)
1895       {
1896
1897         // propagate alignment changed.
1898         viewport.setEndSeq(alignment.getHeight());
1899         if (annotationAdded)
1900         {
1901           // Duplicate sequence annotation in all views.
1902           AlignmentI[] alview = this.getViewAlignments();
1903           for (int i = 0; i < sequences.length; i++)
1904           {
1905             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
1906             if (sann == null)
1907               continue;
1908             for (int avnum = 0; avnum < alview.length; avnum++)
1909             {
1910               if (alview[avnum] != alignment)
1911               {
1912                 // duplicate in a view other than the one with input focus
1913                 int avwidth = alview[avnum].getWidth() + 1;
1914                 // this relies on sann being preserved after we
1915                 // modify the sequence's annotation array for each duplication
1916                 for (int a = 0; a < sann.length; a++)
1917                 {
1918                   AlignmentAnnotation newann = new AlignmentAnnotation(
1919                           sann[a]);
1920                   sequences[i].addAlignmentAnnotation(newann);
1921                   newann.padAnnotation(avwidth);
1922                   alview[avnum].addAnnotation(newann); // annotation was
1923                   // duplicated earlier
1924                   alview[avnum].setAnnotationIndex(newann, a);
1925                 }
1926               }
1927             }
1928           }
1929           buildSortByAnnotationScoresMenu();
1930         }
1931         viewport.firePropertyChange("alignment", null,
1932                 alignment.getSequences());
1933
1934       }
1935       else
1936       {
1937         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
1938                 DEFAULT_HEIGHT);
1939         String newtitle = new String("Copied sequences");
1940
1941         if (Desktop.jalviewClipboard != null
1942                 && Desktop.jalviewClipboard[2] != null)
1943         {
1944           Vector hc = (Vector) Desktop.jalviewClipboard[2];
1945           for (int i = 0; i < hc.size(); i++)
1946           {
1947             int[] region = (int[]) hc.elementAt(i);
1948             af.viewport.hideColumns(region[0], region[1]);
1949           }
1950         }
1951
1952         // >>>This is a fix for the moment, until a better solution is
1953         // found!!<<<
1954         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer()
1955                 .transferSettings(
1956                         alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
1957
1958         // TODO: maintain provenance of an alignment, rather than just make the
1959         // title a concatenation of operations.
1960         if (!externalPaste)
1961         {
1962           if (title.startsWith("Copied sequences"))
1963           {
1964             newtitle = title;
1965           }
1966           else
1967           {
1968             newtitle = newtitle.concat("- from " + title);
1969           }
1970         }
1971         else
1972         {
1973           newtitle = new String("Pasted sequences");
1974         }
1975
1976         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
1977                 DEFAULT_HEIGHT);
1978
1979       }
1980
1981     } catch (Exception ex)
1982     {
1983       ex.printStackTrace();
1984       System.out.println("Exception whilst pasting: " + ex);
1985       // could be anything being pasted in here
1986     }
1987
1988   }
1989
1990   /**
1991    * DOCUMENT ME!
1992    *
1993    * @param e
1994    *          DOCUMENT ME!
1995    */
1996   @Override
1997   protected void cut_actionPerformed(ActionEvent e)
1998   {
1999     copy_actionPerformed(null);
2000     delete_actionPerformed(null);
2001   }
2002
2003   /**
2004    * DOCUMENT ME!
2005    *
2006    * @param e
2007    *          DOCUMENT ME!
2008    */
2009   @Override
2010   protected void delete_actionPerformed(ActionEvent evt)
2011   {
2012
2013     SequenceGroup sg = viewport.getSelectionGroup();
2014     if (sg == null)
2015     {
2016       return;
2017     }
2018
2019     Vector seqs = new Vector();
2020     SequenceI seq;
2021     for (int i = 0; i < sg.getSize(); i++)
2022     {
2023       seq = sg.getSequenceAt(i);
2024       seqs.addElement(seq);
2025     }
2026
2027     // If the cut affects all sequences, remove highlighted columns
2028     if (sg.getSize() == viewport.getAlignment().getHeight())
2029     {
2030       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2031               sg.getEndRes() + 1);
2032     }
2033
2034     SequenceI[] cut = new SequenceI[seqs.size()];
2035     for (int i = 0; i < seqs.size(); i++)
2036     {
2037       cut[i] = (SequenceI) seqs.elementAt(i);
2038     }
2039
2040     /*
2041      * //ADD HISTORY ITEM
2042      */
2043     addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
2044             sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2045             viewport.getAlignment()));
2046
2047     viewport.setSelectionGroup(null);
2048     viewport.sendSelection();
2049     viewport.getAlignment().deleteGroup(sg);
2050
2051     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2052             .getSequences());
2053     if (viewport.getAlignment().getHeight() < 1)
2054     {
2055       try
2056       {
2057         this.setClosed(true);
2058       } catch (Exception ex)
2059       {
2060       }
2061     }
2062   }
2063
2064   /**
2065    * DOCUMENT ME!
2066    *
2067    * @param e
2068    *          DOCUMENT ME!
2069    */
2070   @Override
2071   protected void deleteGroups_actionPerformed(ActionEvent e)
2072   {
2073     viewport.getAlignment().deleteAllGroups();
2074     viewport.sequenceColours = null;
2075     viewport.setSelectionGroup(null);
2076     PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2077     alignPanel.updateAnnotation();
2078     alignPanel.paintAlignment(true);
2079   }
2080
2081   /**
2082    * DOCUMENT ME!
2083    *
2084    * @param e
2085    *          DOCUMENT ME!
2086    */
2087   @Override
2088   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2089   {
2090     SequenceGroup sg = new SequenceGroup();
2091
2092     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2093     {
2094       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2095     }
2096
2097     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2098     viewport.setSelectionGroup(sg);
2099     viewport.sendSelection();
2100     alignPanel.paintAlignment(true);
2101     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2102   }
2103
2104   /**
2105    * DOCUMENT ME!
2106    *
2107    * @param e
2108    *          DOCUMENT ME!
2109    */
2110   @Override
2111   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2112   {
2113     if (viewport.cursorMode)
2114     {
2115       alignPanel.seqPanel.keyboardNo1 = null;
2116       alignPanel.seqPanel.keyboardNo2 = null;
2117     }
2118     viewport.setSelectionGroup(null);
2119     viewport.getColumnSelection().clear();
2120     viewport.setSelectionGroup(null);
2121     alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2122     alignPanel.idPanel.idCanvas.searchResults = null;
2123     alignPanel.paintAlignment(true);
2124     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2125     viewport.sendSelection();
2126   }
2127
2128   /**
2129    * DOCUMENT ME!
2130    *
2131    * @param e
2132    *          DOCUMENT ME!
2133    */
2134   @Override
2135   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2136   {
2137     SequenceGroup sg = viewport.getSelectionGroup();
2138
2139     if (sg == null)
2140     {
2141       selectAllSequenceMenuItem_actionPerformed(null);
2142
2143       return;
2144     }
2145
2146     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2147     {
2148       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2149     }
2150
2151     alignPanel.paintAlignment(true);
2152     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2153     viewport.sendSelection();
2154   }
2155
2156   @Override
2157   public void invertColSel_actionPerformed(ActionEvent e)
2158   {
2159     viewport.invertColumnSelection();
2160     alignPanel.paintAlignment(true);
2161     viewport.sendSelection();
2162   }
2163
2164   /**
2165    * DOCUMENT ME!
2166    *
2167    * @param e
2168    *          DOCUMENT ME!
2169    */
2170   @Override
2171   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2172   {
2173     trimAlignment(true);
2174   }
2175
2176   /**
2177    * DOCUMENT ME!
2178    *
2179    * @param e
2180    *          DOCUMENT ME!
2181    */
2182   @Override
2183   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2184   {
2185     trimAlignment(false);
2186   }
2187
2188   void trimAlignment(boolean trimLeft)
2189   {
2190     ColumnSelection colSel = viewport.getColumnSelection();
2191     int column;
2192
2193     if (colSel.size() > 0)
2194     {
2195       if (trimLeft)
2196       {
2197         column = colSel.getMin();
2198       }
2199       else
2200       {
2201         column = colSel.getMax();
2202       }
2203
2204       SequenceI[] seqs;
2205       if (viewport.getSelectionGroup() != null)
2206       {
2207         seqs = viewport.getSelectionGroup().getSequencesAsArray(
2208                 viewport.getHiddenRepSequences());
2209       }
2210       else
2211       {
2212         seqs = viewport.getAlignment().getSequencesArray();
2213       }
2214
2215       TrimRegionCommand trimRegion;
2216       if (trimLeft)
2217       {
2218         trimRegion = new TrimRegionCommand("Remove Left",
2219                 TrimRegionCommand.TRIM_LEFT, seqs, column,
2220                 viewport.getAlignment(), viewport.getColumnSelection(),
2221                 viewport.getSelectionGroup());
2222         viewport.setStartRes(0);
2223       }
2224       else
2225       {
2226         trimRegion = new TrimRegionCommand("Remove Right",
2227                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2228                 viewport.getAlignment(), viewport.getColumnSelection(),
2229                 viewport.getSelectionGroup());
2230       }
2231
2232       statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2233
2234       addHistoryItem(trimRegion);
2235
2236       for (SequenceGroup sg :viewport.getAlignment().getGroups())
2237       {
2238         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2239                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2240         {
2241           viewport.getAlignment().deleteGroup(sg);
2242         }
2243       }
2244
2245       viewport.firePropertyChange("alignment", null, viewport
2246               .getAlignment().getSequences());
2247     }
2248   }
2249
2250   /**
2251    * DOCUMENT ME!
2252    *
2253    * @param e
2254    *          DOCUMENT ME!
2255    */
2256   @Override
2257   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2258   {
2259     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2260
2261     SequenceI[] seqs;
2262     if (viewport.getSelectionGroup() != null)
2263     {
2264       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2265               viewport.getHiddenRepSequences());
2266       start = viewport.getSelectionGroup().getStartRes();
2267       end = viewport.getSelectionGroup().getEndRes();
2268     }
2269     else
2270     {
2271       seqs = viewport.getAlignment().getSequencesArray();
2272     }
2273
2274     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2275             "Remove Gapped Columns", seqs, start, end,
2276             viewport.getAlignment());
2277
2278     addHistoryItem(removeGapCols);
2279
2280     statusBar.setText("Removed " + removeGapCols.getSize()
2281             + " empty columns.");
2282
2283     // This is to maintain viewport position on first residue
2284     // of first sequence
2285     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2286     int startRes = seq.findPosition(viewport.startRes);
2287     // ShiftList shifts;
2288     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2289     // edit.alColumnChanges=shifts.getInverse();
2290     // if (viewport.hasHiddenColumns)
2291     // viewport.getColumnSelection().compensateForEdits(shifts);
2292     viewport.setStartRes(seq.findIndex(startRes) - 1);
2293     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2294             .getSequences());
2295
2296   }
2297
2298   /**
2299    * DOCUMENT ME!
2300    *
2301    * @param e
2302    *          DOCUMENT ME!
2303    */
2304   @Override
2305   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2306   {
2307     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2308
2309     SequenceI[] seqs;
2310     if (viewport.getSelectionGroup() != null)
2311     {
2312       seqs = viewport.getSelectionGroup().getSequencesAsArray(
2313               viewport.getHiddenRepSequences());
2314       start = viewport.getSelectionGroup().getStartRes();
2315       end = viewport.getSelectionGroup().getEndRes();
2316     }
2317     else
2318     {
2319       seqs = viewport.getAlignment().getSequencesArray();
2320     }
2321
2322     // This is to maintain viewport position on first residue
2323     // of first sequence
2324     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2325     int startRes = seq.findPosition(viewport.startRes);
2326
2327     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2328             viewport.getAlignment()));
2329
2330     viewport.setStartRes(seq.findIndex(startRes) - 1);
2331
2332     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2333             .getSequences());
2334
2335   }
2336
2337   /**
2338    * DOCUMENT ME!
2339    *
2340    * @param e
2341    *          DOCUMENT ME!
2342    */
2343   @Override
2344   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2345   {
2346     viewport.setPadGaps(padGapsMenuitem.isSelected());
2347     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2348             .getSequences());
2349   }
2350
2351   // else
2352   {
2353     // if (justifySeqs>0)
2354     {
2355       // alignment.justify(justifySeqs!=RIGHT_JUSTIFY);
2356     }
2357   }
2358
2359   // }
2360
2361   /**
2362    * DOCUMENT ME!
2363    *
2364    * @param e
2365    *          DOCUMENT ME!
2366    */
2367   @Override
2368   public void findMenuItem_actionPerformed(ActionEvent e)
2369   {
2370     new Finder();
2371   }
2372
2373   @Override
2374   public void newView_actionPerformed(ActionEvent e)
2375   {
2376     newView(true);
2377   }
2378
2379   /**
2380    *
2381    * @param copyAnnotation
2382    *          if true then duplicate all annnotation, groups and settings
2383    * @return new alignment panel, already displayed.
2384    */
2385   public AlignmentPanel newView(boolean copyAnnotation)
2386   {
2387     return newView(null, copyAnnotation);
2388   }
2389
2390   /**
2391    *
2392    * @param viewTitle
2393    *          title of newly created view
2394    * @return new alignment panel, already displayed.
2395    */
2396   public AlignmentPanel newView(String viewTitle)
2397   {
2398     return newView(viewTitle, true);
2399   }
2400
2401   /**
2402    *
2403    * @param viewTitle
2404    *          title of newly created view
2405    * @param copyAnnotation
2406    *          if true then duplicate all annnotation, groups and settings
2407    * @return new alignment panel, already displayed.
2408    */
2409   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2410   {
2411     AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
2412             true);
2413     if (!copyAnnotation)
2414     {
2415       // just remove all the current annotation except for the automatic stuff
2416       newap.av.getAlignment().deleteAllGroups();
2417       for (AlignmentAnnotation alan : newap.av.getAlignment()
2418               .getAlignmentAnnotation())
2419       {
2420         if (!alan.autoCalculated)
2421         {
2422           newap.av.getAlignment().deleteAnnotation(alan);
2423         }
2424         ;
2425       }
2426     }
2427
2428     newap.av.gatherViewsHere = false;
2429
2430     if (viewport.viewName == null)
2431     {
2432       viewport.viewName = "Original";
2433     }
2434
2435     newap.av.historyList = viewport.historyList;
2436     newap.av.redoList = viewport.redoList;
2437
2438     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2439     // make sure the new view has a unique name - this is essential for Jalview
2440     // 2 archives
2441     boolean addFirstIndex = false;
2442     if (viewTitle == null || viewTitle.trim().length() == 0)
2443     {
2444       viewTitle = "View";
2445       addFirstIndex = true;
2446     }
2447     else
2448     {
2449       index = 1;// we count from 1 if given a specific name
2450     }
2451     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2452     Vector comps = (Vector) PaintRefresher.components.get(viewport
2453             .getSequenceSetId());
2454     Vector existingNames = new Vector();
2455     for (int i = 0; i < comps.size(); i++)
2456     {
2457       if (comps.elementAt(i) instanceof AlignmentPanel)
2458       {
2459         AlignmentPanel ap = (AlignmentPanel) comps.elementAt(i);
2460         if (!existingNames.contains(ap.av.viewName))
2461         {
2462           existingNames.addElement(ap.av.viewName);
2463         }
2464       }
2465     }
2466
2467     while (existingNames.contains(newViewName))
2468     {
2469       newViewName = viewTitle + " " + (++index);
2470     }
2471
2472     newap.av.viewName = newViewName;
2473
2474     addAlignmentPanel(newap, true);
2475
2476     if (alignPanels.size() == 2)
2477     {
2478       viewport.gatherViewsHere = true;
2479     }
2480     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2481     return newap;
2482   }
2483
2484   @Override
2485   public void expandViews_actionPerformed(ActionEvent e)
2486   {
2487     Desktop.instance.explodeViews(this);
2488   }
2489
2490   @Override
2491   public void gatherViews_actionPerformed(ActionEvent e)
2492   {
2493     Desktop.instance.gatherViews(this);
2494   }
2495
2496   /**
2497    * DOCUMENT ME!
2498    *
2499    * @param e
2500    *          DOCUMENT ME!
2501    */
2502   @Override
2503   public void font_actionPerformed(ActionEvent e)
2504   {
2505     new FontChooser(alignPanel);
2506   }
2507
2508   /**
2509    * DOCUMENT ME!
2510    *
2511    * @param e
2512    *          DOCUMENT ME!
2513    */
2514   @Override
2515   protected void seqLimit_actionPerformed(ActionEvent e)
2516   {
2517     viewport.setShowJVSuffix(seqLimits.isSelected());
2518
2519     alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel
2520             .calculateIdWidth());
2521     alignPanel.paintAlignment(true);
2522   }
2523
2524   @Override
2525   public void idRightAlign_actionPerformed(ActionEvent e)
2526   {
2527     viewport.rightAlignIds = idRightAlign.isSelected();
2528     alignPanel.paintAlignment(true);
2529   }
2530
2531   @Override
2532   public void centreColumnLabels_actionPerformed(ActionEvent e)
2533   {
2534     viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState();
2535     alignPanel.paintAlignment(true);
2536   }
2537
2538   /*
2539    * (non-Javadoc)
2540    *
2541    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2542    */
2543   @Override
2544   protected void followHighlight_actionPerformed()
2545   {
2546     if (viewport.followHighlight = this.followHighlightMenuItem.getState())
2547     {
2548       alignPanel.scrollToPosition(
2549               alignPanel.seqPanel.seqCanvas.searchResults, false);
2550     }
2551   }
2552
2553   /**
2554    * DOCUMENT ME!
2555    *
2556    * @param e
2557    *          DOCUMENT ME!
2558    */
2559   @Override
2560   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2561   {
2562     viewport.setColourText(colourTextMenuItem.isSelected());
2563     alignPanel.paintAlignment(true);
2564   }
2565
2566   /**
2567    * DOCUMENT ME!
2568    *
2569    * @param e
2570    *          DOCUMENT ME!
2571    */
2572   @Override
2573   public void wrapMenuItem_actionPerformed(ActionEvent e)
2574   {
2575     scaleAbove.setVisible(wrapMenuItem.isSelected());
2576     scaleLeft.setVisible(wrapMenuItem.isSelected());
2577     scaleRight.setVisible(wrapMenuItem.isSelected());
2578     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2579     alignPanel.setWrapAlignment(wrapMenuItem.isSelected());
2580   }
2581
2582   @Override
2583   public void showAllSeqs_actionPerformed(ActionEvent e)
2584   {
2585     viewport.showAllHiddenSeqs();
2586   }
2587
2588   @Override
2589   public void showAllColumns_actionPerformed(ActionEvent e)
2590   {
2591     viewport.showAllHiddenColumns();
2592     repaint();
2593   }
2594
2595   @Override
2596   public void hideSelSequences_actionPerformed(ActionEvent e)
2597   {
2598     viewport.hideAllSelectedSeqs();
2599     alignPanel.paintAlignment(true);
2600   }
2601
2602   /**
2603    * called by key handler and the hide all/show all menu items
2604    *
2605    * @param toggleSeqs
2606    * @param toggleCols
2607    */
2608   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
2609   {
2610
2611     boolean hide = false;
2612     SequenceGroup sg = viewport.getSelectionGroup();
2613     if (!toggleSeqs && !toggleCols)
2614     {
2615       // Hide everything by the current selection - this is a hack - we do the
2616       // invert and then hide
2617       // first check that there will be visible columns after the invert.
2618       if ((viewport.getColumnSelection() != null
2619               && viewport.getColumnSelection().getSelected() != null && viewport
2620               .getColumnSelection().getSelected().size() > 0)
2621               || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
2622                       .getEndRes()))
2623       {
2624         // now invert the sequence set, if required - empty selection implies
2625         // that no hiding is required.
2626         if (sg != null)
2627         {
2628           invertSequenceMenuItem_actionPerformed(null);
2629           sg = viewport.getSelectionGroup();
2630           toggleSeqs = true;
2631
2632         }
2633         viewport.expandColSelection(sg, true);
2634         // finally invert the column selection and get the new sequence
2635         // selection.
2636         invertColSel_actionPerformed(null);
2637         toggleCols = true;
2638       }
2639     }
2640
2641     if (toggleSeqs)
2642     {
2643       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
2644       {
2645         hideSelSequences_actionPerformed(null);
2646         hide = true;
2647       }
2648       else if (!(toggleCols && viewport.getColumnSelection().getSelected()
2649               .size() > 0))
2650       {
2651         showAllSeqs_actionPerformed(null);
2652       }
2653     }
2654
2655     if (toggleCols)
2656     {
2657       if (viewport.getColumnSelection().getSelected().size() > 0)
2658       {
2659         hideSelColumns_actionPerformed(null);
2660         if (!toggleSeqs)
2661         {
2662           viewport.setSelectionGroup(sg);
2663         }
2664       }
2665       else if (!hide)
2666       {
2667         showAllColumns_actionPerformed(null);
2668       }
2669     }
2670   }
2671
2672   /*
2673    * (non-Javadoc)
2674    *
2675    * @see
2676    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
2677    * event.ActionEvent)
2678    */
2679   @Override
2680   public void hideAllButSelection_actionPerformed(ActionEvent e)
2681   {
2682     toggleHiddenRegions(false, false);
2683   }
2684
2685   /*
2686    * (non-Javadoc)
2687    *
2688    * @see
2689    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
2690    * .ActionEvent)
2691    */
2692   @Override
2693   public void hideAllSelection_actionPerformed(ActionEvent e)
2694   {
2695     SequenceGroup sg = viewport.getSelectionGroup();
2696     viewport.expandColSelection(sg, false);
2697     viewport.hideAllSelectedSeqs();
2698     viewport.hideSelectedColumns();
2699     alignPanel.paintAlignment(true);
2700   }
2701
2702   /*
2703    * (non-Javadoc)
2704    *
2705    * @see
2706    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
2707    * ActionEvent)
2708    */
2709   @Override
2710   public void showAllhidden_actionPerformed(ActionEvent e)
2711   {
2712     viewport.showAllHiddenColumns();
2713     viewport.showAllHiddenSeqs();
2714     alignPanel.paintAlignment(true);
2715   }
2716
2717   @Override
2718   public void hideSelColumns_actionPerformed(ActionEvent e)
2719   {
2720     viewport.hideSelectedColumns();
2721     alignPanel.paintAlignment(true);
2722   }
2723
2724   @Override
2725   public void hiddenMarkers_actionPerformed(ActionEvent e)
2726   {
2727     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
2728     repaint();
2729   }
2730
2731   /**
2732    * DOCUMENT ME!
2733    *
2734    * @param e
2735    *          DOCUMENT ME!
2736    */
2737   @Override
2738   protected void scaleAbove_actionPerformed(ActionEvent e)
2739   {
2740     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
2741     alignPanel.paintAlignment(true);
2742   }
2743
2744   /**
2745    * DOCUMENT ME!
2746    *
2747    * @param e
2748    *          DOCUMENT ME!
2749    */
2750   @Override
2751   protected void scaleLeft_actionPerformed(ActionEvent e)
2752   {
2753     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
2754     alignPanel.paintAlignment(true);
2755   }
2756
2757   /**
2758    * DOCUMENT ME!
2759    *
2760    * @param e
2761    *          DOCUMENT ME!
2762    */
2763   @Override
2764   protected void scaleRight_actionPerformed(ActionEvent e)
2765   {
2766     viewport.setScaleRightWrapped(scaleRight.isSelected());
2767     alignPanel.paintAlignment(true);
2768   }
2769
2770   /**
2771    * DOCUMENT ME!
2772    *
2773    * @param e
2774    *          DOCUMENT ME!
2775    */
2776   @Override
2777   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
2778   {
2779     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
2780     alignPanel.paintAlignment(true);
2781   }
2782
2783   /**
2784    * DOCUMENT ME!
2785    *
2786    * @param e
2787    *          DOCUMENT ME!
2788    */
2789   @Override
2790   public void viewTextMenuItem_actionPerformed(ActionEvent e)
2791   {
2792     viewport.setShowText(viewTextMenuItem.isSelected());
2793     alignPanel.paintAlignment(true);
2794   }
2795
2796   /**
2797    * DOCUMENT ME!
2798    *
2799    * @param e
2800    *          DOCUMENT ME!
2801    */
2802   @Override
2803   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
2804   {
2805     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
2806     alignPanel.paintAlignment(true);
2807   }
2808
2809   public FeatureSettings featureSettings;
2810
2811   @Override
2812   public void featureSettings_actionPerformed(ActionEvent e)
2813   {
2814     if (featureSettings != null)
2815     {
2816       featureSettings.close();
2817       featureSettings = null;
2818     }
2819     if (!showSeqFeatures.isSelected())
2820     {
2821       // make sure features are actually displayed
2822       showSeqFeatures.setSelected(true);
2823       showSeqFeatures_actionPerformed(null);
2824     }
2825     featureSettings = new FeatureSettings(this);
2826   }
2827
2828   /**
2829    * Set or clear 'Show Sequence Features'
2830    *
2831    * @param evt
2832    *          DOCUMENT ME!
2833    */
2834   @Override
2835   public void showSeqFeatures_actionPerformed(ActionEvent evt)
2836   {
2837     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
2838     alignPanel.paintAlignment(true);
2839     if (alignPanel.getOverviewPanel() != null)
2840     {
2841       alignPanel.getOverviewPanel().updateOverviewImage();
2842     }
2843   }
2844
2845   /**
2846    * Set or clear 'Show Sequence Features'
2847    *
2848    * @param evt
2849    *          DOCUMENT ME!
2850    */
2851   @Override
2852   public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt)
2853   {
2854     viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
2855             .isSelected());
2856     if (viewport.getShowSequenceFeaturesHeight())
2857     {
2858       // ensure we're actually displaying features
2859       viewport.setShowSequenceFeatures(true);
2860       showSeqFeatures.setSelected(true);
2861     }
2862     alignPanel.paintAlignment(true);
2863     if (alignPanel.getOverviewPanel() != null)
2864     {
2865       alignPanel.getOverviewPanel().updateOverviewImage();
2866     }
2867   }
2868
2869   /**
2870    * DOCUMENT ME!
2871    *
2872    * @param e
2873    *          DOCUMENT ME!
2874    */
2875   @Override
2876   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
2877   {
2878     viewport.setShowAnnotation(annotationPanelMenuItem.isSelected());
2879     alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());
2880   }
2881
2882   @Override
2883   public void alignmentProperties()
2884   {
2885     JEditorPane editPane = new JEditorPane("text/html", "");
2886     editPane.setEditable(false);
2887     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
2888             .formatAsHtml();
2889     editPane.setText("<html>" + contents.toString() + "</html>");
2890     JInternalFrame frame = new JInternalFrame();
2891     frame.getContentPane().add(new JScrollPane(editPane));
2892
2893     Desktop.instance.addInternalFrame(frame, "Alignment Properties: "
2894             + getTitle(), 500, 400);
2895   }
2896
2897   /**
2898    * DOCUMENT ME!
2899    *
2900    * @param e
2901    *          DOCUMENT ME!
2902    */
2903   @Override
2904   public void overviewMenuItem_actionPerformed(ActionEvent e)
2905   {
2906     if (alignPanel.overviewPanel != null)
2907     {
2908       return;
2909     }
2910
2911     JInternalFrame frame = new JInternalFrame();
2912     OverviewPanel overview = new OverviewPanel(alignPanel);
2913     frame.setContentPane(overview);
2914     Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
2915             frame.getWidth(), frame.getHeight());
2916     frame.pack();
2917     frame.setLayer(JLayeredPane.PALETTE_LAYER);
2918     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
2919     {
2920       @Override
2921       public void internalFrameClosed(
2922               javax.swing.event.InternalFrameEvent evt)
2923       {
2924         alignPanel.setOverviewPanel(null);
2925       };
2926     });
2927
2928     alignPanel.setOverviewPanel(overview);
2929   }
2930
2931   @Override
2932   public void textColour_actionPerformed(ActionEvent e)
2933   {
2934     new TextColourChooser().chooseColour(alignPanel, null);
2935   }
2936
2937   /**
2938    * DOCUMENT ME!
2939    *
2940    * @param e
2941    *          DOCUMENT ME!
2942    */
2943   @Override
2944   protected void noColourmenuItem_actionPerformed(ActionEvent e)
2945   {
2946     changeColour(null);
2947   }
2948
2949   /**
2950    * DOCUMENT ME!
2951    *
2952    * @param e
2953    *          DOCUMENT ME!
2954    */
2955   @Override
2956   public void clustalColour_actionPerformed(ActionEvent e)
2957   {
2958     changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
2959   }
2960
2961   /**
2962    * DOCUMENT ME!
2963    *
2964    * @param e
2965    *          DOCUMENT ME!
2966    */
2967   @Override
2968   public void zappoColour_actionPerformed(ActionEvent e)
2969   {
2970     changeColour(new ZappoColourScheme());
2971   }
2972
2973   /**
2974    * DOCUMENT ME!
2975    *
2976    * @param e
2977    *          DOCUMENT ME!
2978    */
2979   @Override
2980   public void taylorColour_actionPerformed(ActionEvent e)
2981   {
2982     changeColour(new TaylorColourScheme());
2983   }
2984
2985   /**
2986    * DOCUMENT ME!
2987    *
2988    * @param e
2989    *          DOCUMENT ME!
2990    */
2991   @Override
2992   public void hydrophobicityColour_actionPerformed(ActionEvent e)
2993   {
2994     changeColour(new HydrophobicColourScheme());
2995   }
2996
2997   /**
2998    * DOCUMENT ME!
2999    *
3000    * @param e
3001    *          DOCUMENT ME!
3002    */
3003   @Override
3004   public void helixColour_actionPerformed(ActionEvent e)
3005   {
3006     changeColour(new HelixColourScheme());
3007   }
3008
3009   /**
3010    * DOCUMENT ME!
3011    *
3012    * @param e
3013    *          DOCUMENT ME!
3014    */
3015   @Override
3016   public void strandColour_actionPerformed(ActionEvent e)
3017   {
3018     changeColour(new StrandColourScheme());
3019   }
3020
3021   /**
3022    * DOCUMENT ME!
3023    *
3024    * @param e
3025    *          DOCUMENT ME!
3026    */
3027   @Override
3028   public void turnColour_actionPerformed(ActionEvent e)
3029   {
3030     changeColour(new TurnColourScheme());
3031   }
3032
3033   /**
3034    * DOCUMENT ME!
3035    *
3036    * @param e
3037    *          DOCUMENT ME!
3038    */
3039   @Override
3040   public void buriedColour_actionPerformed(ActionEvent e)
3041   {
3042     changeColour(new BuriedColourScheme());
3043   }
3044
3045   /**
3046    * DOCUMENT ME!
3047    *
3048    * @param e
3049    *          DOCUMENT ME!
3050    */
3051   @Override
3052   public void nucleotideColour_actionPerformed(ActionEvent e)
3053   {
3054     changeColour(new NucleotideColourScheme());
3055   }
3056
3057   @Override
3058   public void purinePyrimidineColour_actionPerformed(ActionEvent e)
3059   {
3060     changeColour(new PurinePyrimidineColourScheme());
3061   }
3062
3063   /*
3064    * public void covariationColour_actionPerformed(ActionEvent e) {
3065    * changeColour(new
3066    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3067    * ()[0])); }
3068    */
3069   @Override
3070   public void annotationColour_actionPerformed(ActionEvent e)
3071   {
3072     new AnnotationColourChooser(viewport, alignPanel);
3073   }
3074
3075   @Override
3076   public void rnahelicesColour_actionPerformed(ActionEvent e)
3077   {
3078     new RNAHelicesColourChooser(viewport, alignPanel);
3079   }
3080
3081   /**
3082    * DOCUMENT ME!
3083    *
3084    * @param e
3085    *          DOCUMENT ME!
3086    */
3087   @Override
3088   protected void applyToAllGroups_actionPerformed(ActionEvent e)
3089   {
3090     viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
3091   }
3092
3093   /**
3094    * DOCUMENT ME!
3095    *
3096    * @param cs
3097    *          DOCUMENT ME!
3098    */
3099   public void changeColour(ColourSchemeI cs)
3100   {
3101     // TODO: compare with applet and pull up to model method
3102     int threshold = 0;
3103
3104     if (cs != null)
3105     {
3106       if (viewport.getAbovePIDThreshold())
3107       {
3108         threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
3109                 "Background");
3110
3111         cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3112
3113         viewport.setGlobalColourScheme(cs);
3114       }
3115       else
3116       {
3117         cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3118       }
3119
3120       if (viewport.getConservationSelected())
3121       {
3122
3123         Alignment al = (Alignment) viewport.getAlignment();
3124         Conservation c = new Conservation("All",
3125                 ResidueProperties.propHash, 3, al.getSequences(), 0,
3126                 al.getWidth() - 1);
3127
3128         c.calculate();
3129         c.verdict(false, viewport.getConsPercGaps());
3130
3131         cs.setConservation(c);
3132
3133         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
3134                 cs, "Background"));
3135       }
3136       else
3137       {
3138         cs.setConservation(null);
3139       }
3140
3141       cs.setConsensus(viewport.getSequenceConsensusHash());
3142     }
3143
3144     viewport.setGlobalColourScheme(cs);
3145
3146     if (viewport.getColourAppliesToAllGroups())
3147     {
3148
3149
3150       for (SequenceGroup sg:viewport.getAlignment().getGroups())
3151       {
3152         if (cs == null)
3153         {
3154           sg.cs = null;
3155           continue;
3156         }
3157
3158         if (cs instanceof ClustalxColourScheme)
3159         {
3160           sg.cs = new ClustalxColourScheme(sg, viewport
3161                   .getHiddenRepSequences());
3162         }
3163         else if (cs instanceof UserColourScheme)
3164         {
3165           sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
3166         }
3167         else
3168         {
3169           try
3170           {
3171             sg.cs = cs.getClass().newInstance();
3172           } catch (Exception ex)
3173           {
3174           }
3175         }
3176
3177         if (viewport.getAbovePIDThreshold()
3178                 || cs instanceof PIDColourScheme
3179                 || cs instanceof Blosum62ColourScheme)
3180         {
3181           sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
3182
3183           sg.cs.setConsensus(AAFrequency.calculate(
3184                   sg.getSequences(viewport.getHiddenRepSequences()),
3185                   sg.getStartRes(), sg.getEndRes() + 1));
3186         }
3187         else
3188         {
3189           sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
3190         }
3191
3192         if (viewport.getConservationSelected())
3193         {
3194           Conservation c = new Conservation("Group",
3195                   ResidueProperties.propHash, 3, sg.getSequences(viewport
3196                           .getHiddenRepSequences()), sg.getStartRes(),
3197                   sg.getEndRes() + 1);
3198           c.calculate();
3199           c.verdict(false, viewport.getConsPercGaps());
3200           sg.cs.setConservation(c);
3201         }
3202         else
3203         {
3204           sg.cs.setConservation(null);
3205         }
3206       }
3207     }
3208
3209     if (alignPanel.getOverviewPanel() != null)
3210     {
3211       alignPanel.getOverviewPanel().updateOverviewImage();
3212     }
3213
3214     alignPanel.paintAlignment(true);
3215   }
3216
3217   /**
3218    * DOCUMENT ME!
3219    *
3220    * @param e
3221    *          DOCUMENT ME!
3222    */
3223   @Override
3224   protected void modifyPID_actionPerformed(ActionEvent e)
3225   {
3226     if (viewport.getAbovePIDThreshold()
3227             && viewport.getGlobalColourScheme() != null)
3228     {
3229       SliderPanel.setPIDSliderSource(alignPanel,
3230               viewport.getGlobalColourScheme(), "Background");
3231       SliderPanel.showPIDSlider();
3232     }
3233   }
3234
3235   /**
3236    * DOCUMENT ME!
3237    *
3238    * @param e
3239    *          DOCUMENT ME!
3240    */
3241   @Override
3242   protected void modifyConservation_actionPerformed(ActionEvent e)
3243   {
3244     if (viewport.getConservationSelected()
3245             && viewport.getGlobalColourScheme() != null)
3246     {
3247       SliderPanel.setConservationSlider(alignPanel,
3248               viewport.getGlobalColourScheme(), "Background");
3249       SliderPanel.showConservationSlider();
3250     }
3251   }
3252
3253   /**
3254    * DOCUMENT ME!
3255    *
3256    * @param e
3257    *          DOCUMENT ME!
3258    */
3259   @Override
3260   protected void conservationMenuItem_actionPerformed(ActionEvent e)
3261   {
3262     viewport.setConservationSelected(conservationMenuItem.isSelected());
3263
3264     viewport.setAbovePIDThreshold(false);
3265     abovePIDThreshold.setSelected(false);
3266
3267     changeColour(viewport.getGlobalColourScheme());
3268
3269     modifyConservation_actionPerformed(null);
3270   }
3271
3272   /**
3273    * DOCUMENT ME!
3274    *
3275    * @param e
3276    *          DOCUMENT ME!
3277    */
3278   @Override
3279   public void abovePIDThreshold_actionPerformed(ActionEvent e)
3280   {
3281     viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
3282
3283     conservationMenuItem.setSelected(false);
3284     viewport.setConservationSelected(false);
3285
3286     changeColour(viewport.getGlobalColourScheme());
3287
3288     modifyPID_actionPerformed(null);
3289   }
3290
3291   /**
3292    * DOCUMENT ME!
3293    *
3294    * @param e
3295    *          DOCUMENT ME!
3296    */
3297   @Override
3298   public void userDefinedColour_actionPerformed(ActionEvent e)
3299   {
3300     if (e.getActionCommand().equals("User Defined..."))
3301     {
3302       new UserDefinedColours(alignPanel, null);
3303     }
3304     else
3305     {
3306       UserColourScheme udc = (UserColourScheme) UserDefinedColours
3307               .getUserColourSchemes().get(e.getActionCommand());
3308
3309       changeColour(udc);
3310     }
3311   }
3312
3313   public void updateUserColourMenu()
3314   {
3315
3316     Component[] menuItems = colourMenu.getMenuComponents();
3317     int i, iSize = menuItems.length;
3318     for (i = 0; i < iSize; i++)
3319     {
3320       if (menuItems[i].getName() != null
3321               && menuItems[i].getName().equals("USER_DEFINED"))
3322       {
3323         colourMenu.remove(menuItems[i]);
3324         iSize--;
3325       }
3326     }
3327     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
3328     {
3329       java.util.Enumeration userColours = jalview.gui.UserDefinedColours
3330               .getUserColourSchemes().keys();
3331
3332       while (userColours.hasMoreElements())
3333       {
3334         final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
3335                 userColours.nextElement().toString());
3336         radioItem.setName("USER_DEFINED");
3337         radioItem.addMouseListener(new MouseAdapter()
3338         {
3339           @Override
3340           public void mousePressed(MouseEvent evt)
3341           {
3342             if (evt.isControlDown()
3343                     || SwingUtilities.isRightMouseButton(evt))
3344             {
3345               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
3346
3347               int option = JOptionPane.showInternalConfirmDialog(
3348                       jalview.gui.Desktop.desktop,
3349                       "Remove from default list?",
3350                       "Remove user defined colour",
3351                       JOptionPane.YES_NO_OPTION);
3352               if (option == JOptionPane.YES_OPTION)
3353               {
3354                 jalview.gui.UserDefinedColours
3355                         .removeColourFromDefaults(radioItem.getText());
3356                 colourMenu.remove(radioItem);
3357               }
3358               else
3359               {
3360                 radioItem.addActionListener(new ActionListener()
3361                 {
3362                   @Override
3363                   public void actionPerformed(ActionEvent evt)
3364                   {
3365                     userDefinedColour_actionPerformed(evt);
3366                   }
3367                 });
3368               }
3369             }
3370           }
3371         });
3372         radioItem.addActionListener(new ActionListener()
3373         {
3374           @Override
3375           public void actionPerformed(ActionEvent evt)
3376           {
3377             userDefinedColour_actionPerformed(evt);
3378           }
3379         });
3380
3381         colourMenu.insert(radioItem, 15);
3382         colours.add(radioItem);
3383       }
3384     }
3385   }
3386
3387   /**
3388    * DOCUMENT ME!
3389    *
3390    * @param e
3391    *          DOCUMENT ME!
3392    */
3393   @Override
3394   public void PIDColour_actionPerformed(ActionEvent e)
3395   {
3396     changeColour(new PIDColourScheme());
3397   }
3398
3399   /**
3400    * DOCUMENT ME!
3401    *
3402    * @param e
3403    *          DOCUMENT ME!
3404    */
3405   @Override
3406   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
3407   {
3408     changeColour(new Blosum62ColourScheme());
3409   }
3410
3411   /**
3412    * DOCUMENT ME!
3413    *
3414    * @param e
3415    *          DOCUMENT ME!
3416    */
3417   @Override
3418   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3419   {
3420     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3421     AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
3422             .getAlignment().getSequenceAt(0), null);
3423     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3424             viewport.getAlignment()));
3425     alignPanel.paintAlignment(true);
3426   }
3427
3428   /**
3429    * DOCUMENT ME!
3430    *
3431    * @param e
3432    *          DOCUMENT ME!
3433    */
3434   @Override
3435   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3436   {
3437     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3438     AlignmentSorter.sortByID(viewport.getAlignment());
3439     addHistoryItem(new OrderCommand("ID Sort", oldOrder,
3440             viewport.getAlignment()));
3441     alignPanel.paintAlignment(true);
3442   }
3443
3444   /**
3445    * DOCUMENT ME!
3446    *
3447    * @param e
3448    *          DOCUMENT ME!
3449    */
3450   @Override
3451   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3452   {
3453     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3454     AlignmentSorter.sortByLength(viewport.getAlignment());
3455     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3456             viewport.getAlignment()));
3457     alignPanel.paintAlignment(true);
3458   }
3459
3460   /**
3461    * DOCUMENT ME!
3462    *
3463    * @param e
3464    *          DOCUMENT ME!
3465    */
3466   @Override
3467   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3468   {
3469     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3470     AlignmentSorter.sortByGroup(viewport.getAlignment());
3471     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3472             viewport.getAlignment()));
3473
3474     alignPanel.paintAlignment(true);
3475   }
3476
3477   /**
3478    * DOCUMENT ME!
3479    *
3480    * @param e
3481    *          DOCUMENT ME!
3482    */
3483   @Override
3484   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3485   {
3486     new RedundancyPanel(alignPanel, this);
3487   }
3488
3489   /**
3490    * DOCUMENT ME!
3491    *
3492    * @param e
3493    *          DOCUMENT ME!
3494    */
3495   @Override
3496   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3497   {
3498     if ((viewport.getSelectionGroup() == null)
3499             || (viewport.getSelectionGroup().getSize() < 2))
3500     {
3501       JOptionPane.showInternalMessageDialog(this,
3502               "You must select at least 2 sequences.", "Invalid Selection",
3503               JOptionPane.WARNING_MESSAGE);
3504     }
3505     else
3506     {
3507       JInternalFrame frame = new JInternalFrame();
3508       frame.setContentPane(new PairwiseAlignPanel(viewport));
3509       Desktop.addInternalFrame(frame, "Pairwise Alignment", 600, 500);
3510     }
3511   }
3512
3513   /**
3514    * DOCUMENT ME!
3515    *
3516    * @param e
3517    *          DOCUMENT ME!
3518    */
3519   @Override
3520   public void PCAMenuItem_actionPerformed(ActionEvent e)
3521   {
3522     if (((viewport.getSelectionGroup() != null)
3523             && (viewport.getSelectionGroup().getSize() < 4) && (viewport
3524             .getSelectionGroup().getSize() > 0))
3525             || (viewport.getAlignment().getHeight() < 4))
3526     {
3527       JOptionPane.showInternalMessageDialog(this,
3528               "Principal component analysis must take\n"
3529                       + "at least 4 input sequences.",
3530               "Sequence selection insufficient",
3531               JOptionPane.WARNING_MESSAGE);
3532
3533       return;
3534     }
3535
3536     new PCAPanel(alignPanel);
3537   }
3538
3539   @Override
3540   public void autoCalculate_actionPerformed(ActionEvent e)
3541   {
3542     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3543     if (viewport.autoCalculateConsensus)
3544     {
3545       viewport.firePropertyChange("alignment", null, viewport
3546               .getAlignment().getSequences());
3547     }
3548   }
3549
3550   @Override
3551   public void sortByTreeOption_actionPerformed(ActionEvent e)
3552   {
3553     viewport.sortByTree = sortByTree.isSelected();
3554   }
3555
3556   @Override
3557   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3558   {
3559     viewport.followSelection = listenToViewSelections.isSelected();
3560   }
3561
3562   /**
3563    * DOCUMENT ME!
3564    *
3565    * @param e
3566    *          DOCUMENT ME!
3567    */
3568   @Override
3569   public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
3570   {
3571     NewTreePanel("AV", "PID", "Average distance tree using PID");
3572   }
3573
3574   /**
3575    * DOCUMENT ME!
3576    *
3577    * @param e
3578    *          DOCUMENT ME!
3579    */
3580   @Override
3581   public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
3582   {
3583     NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
3584   }
3585
3586   /**
3587    * DOCUMENT ME!
3588    *
3589    * @param e
3590    *          DOCUMENT ME!
3591    */
3592   @Override
3593   protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3594   {
3595     NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
3596   }
3597
3598   /**
3599    * DOCUMENT ME!
3600    *
3601    * @param e
3602    *          DOCUMENT ME!
3603    */
3604   @Override
3605   protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
3606   {
3607     NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
3608   }
3609
3610   /**
3611    * DOCUMENT ME!
3612    *
3613    * @param type
3614    *          DOCUMENT ME!
3615    * @param pwType
3616    *          DOCUMENT ME!
3617    * @param title
3618    *          DOCUMENT ME!
3619    */
3620   void NewTreePanel(String type, String pwType, String title)
3621   {
3622     TreePanel tp;
3623
3624     if (viewport.getSelectionGroup() != null)
3625     {
3626       if (viewport.getSelectionGroup().getSize() < 3)
3627       {
3628         JOptionPane
3629                 .showMessageDialog(
3630                         Desktop.desktop,
3631                         "You need to have more than two sequences selected to build a tree!",
3632                         "Not enough sequences", JOptionPane.WARNING_MESSAGE);
3633         return;
3634       }
3635
3636       SequenceGroup sg = viewport.getSelectionGroup();
3637
3638       /* Decide if the selection is a column region */
3639       for (SequenceI _s:sg.getSequences())
3640       {
3641         if (_s.getLength() < sg
3642                 .getEndRes())
3643         {
3644           JOptionPane
3645                   .showMessageDialog(
3646                           Desktop.desktop,
3647                           "The selected region to create a tree may\nonly contain residues or gaps.\n"
3648                                   + "Try using the Pad function in the edit menu,\n"
3649                                   + "or one of the multiple sequence alignment web services.",
3650                           "Sequences in selection are not aligned",
3651                           JOptionPane.WARNING_MESSAGE);
3652
3653           return;
3654         }
3655       }
3656
3657       title = title + " on region";
3658       tp = new TreePanel(alignPanel, type, pwType);
3659     }
3660     else
3661     {
3662       // are the visible sequences aligned?
3663       if (!viewport.getAlignment().isAligned(false))
3664       {
3665         JOptionPane
3666                 .showMessageDialog(
3667                         Desktop.desktop,
3668                         "The sequences must be aligned before creating a tree.\n"
3669                                 + "Try using the Pad function in the edit menu,\n"
3670                                 + "or one of the multiple sequence alignment web services.",
3671                         "Sequences not aligned",
3672                         JOptionPane.WARNING_MESSAGE);
3673
3674         return;
3675       }
3676
3677       if (viewport.getAlignment().getHeight() < 2)
3678       {
3679         return;
3680       }
3681
3682       tp = new TreePanel(alignPanel, type, pwType);
3683     }
3684
3685     title += " from ";
3686
3687     if (viewport.viewName != null)
3688     {
3689       title += viewport.viewName + " of ";
3690     }
3691
3692     title += this.title;
3693
3694     Desktop.addInternalFrame(tp, title, 600, 500);
3695   }
3696
3697   /**
3698    * DOCUMENT ME!
3699    *
3700    * @param title
3701    *          DOCUMENT ME!
3702    * @param order
3703    *          DOCUMENT ME!
3704    */
3705   public void addSortByOrderMenuItem(String title,
3706           final AlignmentOrder order)
3707   {
3708     final JMenuItem item = new JMenuItem("by " + title);
3709     sort.add(item);
3710     item.addActionListener(new java.awt.event.ActionListener()
3711     {
3712       @Override
3713       public void actionPerformed(ActionEvent e)
3714       {
3715         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3716
3717         // TODO: JBPNote - have to map order entries to curent SequenceI
3718         // pointers
3719         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3720
3721         addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport
3722                 .getAlignment()));
3723
3724         alignPanel.paintAlignment(true);
3725       }
3726     });
3727   }
3728
3729   /**
3730    * Add a new sort by annotation score menu item
3731    *
3732    * @param sort
3733    *          the menu to add the option to
3734    * @param scoreLabel
3735    *          the label used to retrieve scores for each sequence on the
3736    *          alignment
3737    */
3738   public void addSortByAnnotScoreMenuItem(JMenu sort,
3739           final String scoreLabel)
3740   {
3741     final JMenuItem item = new JMenuItem(scoreLabel);
3742     sort.add(item);
3743     item.addActionListener(new java.awt.event.ActionListener()
3744     {
3745       @Override
3746       public void actionPerformed(ActionEvent e)
3747       {
3748         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3749         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3750                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3751         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3752                 viewport.getAlignment()));
3753         alignPanel.paintAlignment(true);
3754       }
3755     });
3756   }
3757
3758   /**
3759    * last hash for alignment's annotation array - used to minimise cost of
3760    * rebuild.
3761    */
3762   protected int _annotationScoreVectorHash;
3763
3764   /**
3765    * search the alignment and rebuild the sort by annotation score submenu the
3766    * last alignment annotation vector hash is stored to minimize cost of
3767    * rebuilding in subsequence calls.
3768    *
3769    */
3770   @Override
3771   public void buildSortByAnnotationScoresMenu()
3772   {
3773     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3774     {
3775       return;
3776     }
3777
3778     if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash)
3779     {
3780       sortByAnnotScore.removeAll();
3781       // almost certainly a quicker way to do this - but we keep it simple
3782       Hashtable scoreSorts = new Hashtable();
3783       AlignmentAnnotation aann[];
3784       for (SequenceI sqa:viewport.getAlignment().getSequences())
3785       {
3786         aann = sqa.getAnnotation();
3787         for (int i = 0; aann != null && i < aann.length; i++)
3788         {
3789           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3790           {
3791             scoreSorts.put(aann[i].label, aann[i].label);
3792           }
3793         }
3794       }
3795       Enumeration labels = scoreSorts.keys();
3796       while (labels.hasMoreElements())
3797       {
3798         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3799                 (String) labels.nextElement());
3800       }
3801       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3802       scoreSorts.clear();
3803
3804       _annotationScoreVectorHash = viewport.getAlignment()
3805               .getAlignmentAnnotation().hashCode();
3806     }
3807   }
3808
3809   /**
3810    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3811    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3812    * call. Listeners are added to remove the menu item when the treePanel is
3813    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3814    * modified.
3815    *
3816    * @param treePanel
3817    *          Displayed tree window.
3818    * @param title
3819    *          SortBy menu item title.
3820    */
3821   @Override
3822   public void buildTreeMenu()
3823   {
3824     sortByTreeMenu.removeAll();
3825
3826     Vector comps = (Vector) PaintRefresher.components.get(viewport
3827             .getSequenceSetId());
3828     Vector treePanels = new Vector();
3829     int i, iSize = comps.size();
3830     for (i = 0; i < iSize; i++)
3831     {
3832       if (comps.elementAt(i) instanceof TreePanel)
3833       {
3834         treePanels.add(comps.elementAt(i));
3835       }
3836     }
3837
3838     iSize = treePanels.size();
3839
3840     if (iSize < 1)
3841     {
3842       sortByTreeMenu.setVisible(false);
3843       return;
3844     }
3845
3846     sortByTreeMenu.setVisible(true);
3847
3848     for (i = 0; i < treePanels.size(); i++)
3849     {
3850       final TreePanel tp = (TreePanel) treePanels.elementAt(i);
3851       final JMenuItem item = new JMenuItem(tp.getTitle());
3852       final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree();
3853       item.addActionListener(new java.awt.event.ActionListener()
3854       {
3855         @Override
3856         public void actionPerformed(ActionEvent e)
3857         {
3858           tp.sortByTree_actionPerformed(null);
3859           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3860
3861         }
3862       });
3863
3864       sortByTreeMenu.add(item);
3865     }
3866   }
3867
3868   public boolean sortBy(AlignmentOrder alorder, String undoname)
3869   {
3870     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3871     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3872     if (undoname != null)
3873     {
3874       addHistoryItem(new OrderCommand(undoname, oldOrder,
3875               viewport.getAlignment()));
3876     }
3877     alignPanel.paintAlignment(true);
3878     return true;
3879   }
3880
3881   /**
3882    * Work out whether the whole set of sequences or just the selected set will
3883    * be submitted for multiple alignment.
3884    *
3885    */
3886   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3887   {
3888     // Now, check we have enough sequences
3889     AlignmentView msa = null;
3890
3891     if ((viewport.getSelectionGroup() != null)
3892             && (viewport.getSelectionGroup().getSize() > 1))
3893     {
3894       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3895       // some common interface!
3896       /*
3897        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3898        * SequenceI[sz = seqs.getSize(false)];
3899        *
3900        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3901        * seqs.getSequenceAt(i); }
3902        */
3903       msa = viewport.getAlignmentView(true);
3904     }
3905     else
3906     {
3907       /*
3908        * Vector seqs = viewport.getAlignment().getSequences();
3909        *
3910        * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
3911        *
3912        * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
3913        * seqs.elementAt(i); } }
3914        */
3915       msa = viewport.getAlignmentView(false);
3916     }
3917     return msa;
3918   }
3919
3920   /**
3921    * Decides what is submitted to a secondary structure prediction service: the
3922    * first sequence in the alignment, or in the current selection, or, if the
3923    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3924    * region or the whole alignment. (where the first sequence in the set is the
3925    * one that the prediction will be for).
3926    */
3927   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3928   {
3929     AlignmentView seqs = null;
3930
3931     if ((viewport.getSelectionGroup() != null)
3932             && (viewport.getSelectionGroup().getSize() > 0))
3933     {
3934       seqs = viewport.getAlignmentView(true);
3935     }
3936     else
3937     {
3938       seqs = viewport.getAlignmentView(false);
3939     }
3940     // limit sequences - JBPNote in future - could spawn multiple prediction
3941     // jobs
3942     // TODO: viewport.getAlignment().isAligned is a global state - the local
3943     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3944     if (!viewport.getAlignment().isAligned(false))
3945     {
3946       seqs.setSequences(new SeqCigar[]
3947       { seqs.getSequences()[0] });
3948       // TODO: if seqs.getSequences().length>1 then should really have warned
3949       // user!
3950
3951     }
3952     return seqs;
3953   }
3954
3955   /**
3956    * DOCUMENT ME!
3957    *
3958    * @param e
3959    *          DOCUMENT ME!
3960    */
3961   @Override
3962   protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
3963   {
3964     // Pick the tree file
3965     JalviewFileChooser chooser = new JalviewFileChooser(
3966             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3967     chooser.setFileView(new JalviewFileView());
3968     chooser.setDialogTitle("Select a newick-like tree file");
3969     chooser.setToolTipText("Load a tree file");
3970
3971     int value = chooser.showOpenDialog(null);
3972
3973     if (value == JalviewFileChooser.APPROVE_OPTION)
3974     {
3975       String choice = chooser.getSelectedFile().getPath();
3976       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
3977       jalview.io.NewickFile fin = null;
3978       try
3979       {
3980         fin = new jalview.io.NewickFile(choice, "File");
3981         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
3982       } catch (Exception ex)
3983       {
3984         JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3985                 "Problem reading tree file", JOptionPane.WARNING_MESSAGE);
3986         ex.printStackTrace();
3987       }
3988       if (fin != null && fin.hasWarningMessage())
3989       {
3990         JOptionPane.showMessageDialog(Desktop.desktop,
3991                 fin.getWarningMessage(), "Possible problem with tree file",
3992                 JOptionPane.WARNING_MESSAGE);
3993       }
3994     }
3995   }
3996
3997   @Override
3998   protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
3999   {
4000     changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4001   }
4002
4003   public TreePanel ShowNewickTree(NewickFile nf, String title)
4004   {
4005     return ShowNewickTree(nf, title, 600, 500, 4, 5);
4006   }
4007
4008   public TreePanel ShowNewickTree(NewickFile nf, String title,
4009           AlignmentView input)
4010   {
4011     return ShowNewickTree(nf, title, input, 600, 500, 4, 5);
4012   }
4013
4014   public TreePanel ShowNewickTree(NewickFile nf, String title, int w,
4015           int h, int x, int y)
4016   {
4017     return ShowNewickTree(nf, title, null, w, h, x, y);
4018   }
4019
4020   /**
4021    * Add a treeviewer for the tree extracted from a newick file object to the
4022    * current alignment view
4023    *
4024    * @param nf
4025    *          the tree
4026    * @param title
4027    *          tree viewer title
4028    * @param input
4029    *          Associated alignment input data (or null)
4030    * @param w
4031    *          width
4032    * @param h
4033    *          height
4034    * @param x
4035    *          position
4036    * @param y
4037    *          position
4038    * @return TreePanel handle
4039    */
4040   public TreePanel ShowNewickTree(NewickFile nf, String title,
4041           AlignmentView input, int w, int h, int x, int y)
4042   {
4043     TreePanel tp = null;
4044
4045     try
4046     {
4047       nf.parse();
4048
4049       if (nf.getTree() != null)
4050       {
4051         tp = new TreePanel(alignPanel, "FromFile", title, nf, input);
4052
4053         tp.setSize(w, h);
4054
4055         if (x > 0 && y > 0)
4056         {
4057           tp.setLocation(x, y);
4058         }
4059
4060         Desktop.addInternalFrame(tp, title, w, h);
4061       }
4062     } catch (Exception ex)
4063     {
4064       ex.printStackTrace();
4065     }
4066
4067     return tp;
4068   }
4069
4070   private boolean buildingMenu = false;
4071
4072   /**
4073    * Generates menu items and listener event actions for web service clients
4074    *
4075    */
4076   public void BuildWebServiceMenu()
4077   {
4078     while (buildingMenu)
4079     {
4080       try
4081       {
4082         System.err.println("Waiting for building menu to finish.");
4083         Thread.sleep(10);
4084       } catch (Exception e)
4085       {
4086       }
4087       ;
4088     }
4089     final AlignFrame me = this;
4090     buildingMenu = true;
4091     new Thread(new Runnable()
4092     {
4093       @Override
4094       public void run()
4095       {
4096         try
4097         {
4098           System.err.println("Building ws menu again "
4099                   + Thread.currentThread());
4100           // TODO: add support for context dependent disabling of services based
4101           // on
4102           // alignment and current selection
4103           // TODO: add additional serviceHandle parameter to specify abstract
4104           // handler
4105           // class independently of AbstractName
4106           // TODO: add in rediscovery GUI function to restart discoverer
4107           // TODO: group services by location as well as function and/or
4108           // introduce
4109           // object broker mechanism.
4110           final Vector<JMenu> wsmenu = new Vector<JMenu>();
4111           final IProgressIndicator af = me;
4112           final JMenu msawsmenu = new JMenu("Alignment");
4113           final JMenu secstrmenu = new JMenu(
4114                   "Secondary Structure Prediction");
4115           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4116           final JMenu analymenu = new JMenu("Analysis");
4117           final JMenu dismenu = new JMenu("Protein Disorder");
4118           // JAL-940 - only show secondary structure prediction services from
4119           // the legacy server
4120           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4121               // &&
4122           Discoverer.services != null && (Discoverer.services.size() > 0))
4123           {
4124             // TODO: refactor to allow list of AbstractName/Handler bindings to
4125             // be
4126             // stored or retrieved from elsewhere
4127             Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS");
4128             Vector secstrpr = (Vector) Discoverer.services
4129                     .get("SecStrPred");
4130             Vector seqsrch = null; // (Vector)
4131                                    // Discoverer.services.get("SeqSearch");
4132             // TODO: move GUI generation code onto service implementation - so a
4133             // client instance attaches itself to the GUI with method call like
4134             // jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance,
4135             // alignframe)
4136             if (msaws != null)
4137             {
4138               // Add any Multiple Sequence Alignment Services
4139               for (int i = 0, j = msaws.size(); i < j; i++)
4140               {
4141                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
4142                         .get(i);
4143                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4144                         .getServiceClient(sh);
4145                 impl.attachWSMenuEntry(msawsmenu, me);
4146
4147               }
4148             }
4149             if (secstrpr != null)
4150             {
4151               // Add any secondary structure prediction services
4152               for (int i = 0, j = secstrpr.size(); i < j; i++)
4153               {
4154                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4155                         .get(i);
4156                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4157                         .getServiceClient(sh);
4158                 impl.attachWSMenuEntry(secstrmenu, me);
4159               }
4160             }
4161             if (seqsrch != null)
4162             {
4163               // Add any sequence search services
4164               for (int i = 0, j = seqsrch.size(); i < j; i++)
4165               {
4166                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
4167                         .elementAt(i);
4168                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4169                         .getServiceClient(sh);
4170                 impl.attachWSMenuEntry(seqsrchmenu, me);
4171               }
4172             }
4173           }
4174
4175           // Add all submenus in the order they should appear on the web
4176           // services menu
4177           wsmenu.add(msawsmenu);
4178           wsmenu.add(secstrmenu);
4179           wsmenu.add(dismenu);
4180           wsmenu.add(analymenu);
4181           // final ArrayList<JMenu> submens=new ArrayList<JMenu>();
4182           // submens.add(msawsmenu);
4183           // submens.add(secstrmenu);
4184           // submens.add(dismenu);
4185           // submens.add(analymenu);
4186
4187           // No search services yet
4188           // wsmenu.add(seqsrchmenu);
4189
4190           javax.swing.SwingUtilities.invokeLater(new Runnable()
4191           {
4192             @Override
4193             public void run()
4194             {
4195               try
4196               {
4197                 webService.removeAll();
4198                 // first, add discovered services onto the webservices menu
4199                 if (wsmenu.size() > 0)
4200                 {
4201                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4202                   {
4203                     webService.add(wsmenu.get(i));
4204                   }
4205                 }
4206                 else
4207                 {
4208                   webService.add(me.webServiceNoServices);
4209                 }
4210                 // TODO: move into separate menu builder class.
4211                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4212                 {
4213                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4214                   if (jws2servs != null)
4215                   {
4216                     if (jws2servs.hasServices())
4217                     {
4218                       jws2servs.attachWSMenuEntry(webService, me);
4219                     }
4220                     if (jws2servs.isRunning())
4221                     {
4222                       JMenuItem tm = new JMenuItem(
4223                               "Still discovering JABA Services");
4224                       tm.setEnabled(false);
4225                       webService.add(tm);
4226                     }
4227                   }
4228                 }
4229
4230                 build_urlServiceMenu(me.webService);
4231                 build_fetchdbmenu(webService);
4232                 for (JMenu item : wsmenu)
4233                 {
4234                   if (item.getItemCount() == 0)
4235                   {
4236                     item.setEnabled(false);
4237                   }
4238                   else
4239                   {
4240                     item.setEnabled(true);
4241                   }
4242                 }
4243               } catch (Exception e)
4244               {
4245               }
4246               ;
4247             }
4248           });
4249         } catch (Exception e)
4250         {
4251         }
4252         ;
4253
4254         buildingMenu = false;
4255       }
4256     }).start();
4257
4258   }
4259
4260   /**
4261    * construct any groupURL type service menu entries.
4262    *
4263    * @param webService
4264    */
4265   private void build_urlServiceMenu(JMenu webService)
4266   {
4267     // TODO: remove this code when 2.7 is released
4268     // DEBUG - alignmentView
4269     /*
4270      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4271      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4272      *
4273      * @Override public void actionPerformed(ActionEvent e) {
4274      * jalview.datamodel.AlignmentView
4275      * .testSelectionViews(af.viewport.getAlignment(),
4276      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4277      *
4278      * }); webService.add(testAlView);
4279      */
4280     // TODO: refactor to RestClient discoverer and merge menu entries for
4281     // rest-style services with other types of analysis/calculation service
4282     // SHmmr test client - still being implemented.
4283     // DEBUG - alignmentView
4284
4285     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4286             .getRestClients())
4287     {
4288       client.attachWSMenuEntry(
4289               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4290               this);
4291     }
4292
4293     if (Cache.getDefault("SHOW_ENFIN_SERVICES", true))
4294     {
4295       jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
4296               webService, this);
4297     }
4298   }
4299
4300   /*
4301    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
4302    * chooser = new JalviewFileChooser(jalview.bin.Cache.
4303    * getProperty("LAST_DIRECTORY"));
4304    *
4305    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
4306    * to Vamsas file"); chooser.setToolTipText("Export");
4307    *
4308    * int value = chooser.showSaveDialog(this);
4309    *
4310    * if (value == JalviewFileChooser.APPROVE_OPTION) {
4311    * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);
4312    * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview(
4313    * chooser.getSelectedFile().getAbsolutePath(), this); } }
4314    */
4315   /**
4316    * prototype of an automatically enabled/disabled analysis function
4317    *
4318    */
4319   protected void setShowProductsEnabled()
4320   {
4321     SequenceI[] selection = viewport.getSequenceSelection();
4322     if (canShowProducts(selection, viewport.getSelectionGroup() != null,
4323             viewport.getAlignment().getDataset()))
4324     {
4325       showProducts.setEnabled(true);
4326
4327     }
4328     else
4329     {
4330       showProducts.setEnabled(false);
4331     }
4332   }
4333
4334   /**
4335    * search selection for sequence xRef products and build the show products
4336    * menu.
4337    *
4338    * @param selection
4339    * @param dataset
4340    * @return true if showProducts menu should be enabled.
4341    */
4342   public boolean canShowProducts(SequenceI[] selection,
4343           boolean isRegionSelection, Alignment dataset)
4344   {
4345     boolean showp = false;
4346     try
4347     {
4348       showProducts.removeAll();
4349       final boolean dna = viewport.getAlignment().isNucleotide();
4350       final Alignment ds = dataset;
4351       String[] ptypes = (selection == null || selection.length == 0) ? null
4352               : CrossRef.findSequenceXrefTypes(dna, selection, dataset);
4353       // Object[] prods =
4354       // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(),
4355       // selection, dataset, true);
4356       final SequenceI[] sel = selection;
4357       for (int t = 0; ptypes != null && t < ptypes.length; t++)
4358       {
4359         showp = true;
4360         final boolean isRegSel = isRegionSelection;
4361         final AlignFrame af = this;
4362         final String source = ptypes[t];
4363         JMenuItem xtype = new JMenuItem(ptypes[t]);
4364         xtype.addActionListener(new ActionListener()
4365         {
4366
4367           @Override
4368           public void actionPerformed(ActionEvent e)
4369           {
4370             // TODO: new thread for this call with vis-delay
4371             af.showProductsFor(af.viewport.getSequenceSelection(), ds,
4372                     isRegSel, dna, source);
4373           }
4374
4375         });
4376         showProducts.add(xtype);
4377       }
4378       showProducts.setVisible(showp);
4379       showProducts.setEnabled(showp);
4380     } catch (Exception e)
4381     {
4382       jalview.bin.Cache.log
4383               .warn("canTranslate threw an exception - please report to help@jalview.org",
4384                       e);
4385       return false;
4386     }
4387     return showp;
4388   }
4389
4390   protected void showProductsFor(SequenceI[] sel, Alignment ds,
4391           boolean isRegSel, boolean dna, String source)
4392   {
4393     final boolean fisRegSel = isRegSel;
4394     final boolean fdna = dna;
4395     final String fsrc = source;
4396     final AlignFrame ths = this;
4397     final SequenceI[] fsel = sel;
4398     Runnable foo = new Runnable()
4399     {
4400
4401       @Override
4402       public void run()
4403       {
4404         final long sttime = System.currentTimeMillis();
4405         ths.setProgressBar("Searching for sequences from " + fsrc, sttime);
4406         try
4407         {
4408           Alignment ds = ths.getViewport().getAlignment().getDataset(); // update
4409           // our local
4410           // dataset
4411           // reference
4412           Alignment prods = CrossRef
4413                   .findXrefSequences(fsel, fdna, fsrc, ds);
4414           if (prods != null)
4415           {
4416             SequenceI[] sprods = new SequenceI[prods.getHeight()];
4417             for (int s = 0; s < sprods.length; s++)
4418             {
4419               sprods[s] = (prods.getSequenceAt(s)).deriveSequence();
4420               if (ds.getSequences() == null
4421                       || !ds.getSequences().contains(
4422                               sprods[s].getDatasetSequence()))
4423                 ds.addSequence(sprods[s].getDatasetSequence());
4424               sprods[s].updatePDBIds();
4425             }
4426             Alignment al = new Alignment(sprods);
4427             AlignedCodonFrame[] cf = prods.getCodonFrames();
4428             al.setDataset(ds);
4429             for (int s = 0; cf != null && s < cf.length; s++)
4430             {
4431               al.addCodonFrame(cf[s]);
4432               cf[s] = null;
4433             }
4434             AlignFrame naf = new AlignFrame(al, DEFAULT_WIDTH,
4435                     DEFAULT_HEIGHT);
4436             String newtitle = "" + ((fdna) ? "Proteins " : "Nucleotides ")
4437                     + " for " + ((fisRegSel) ? "selected region of " : "")
4438                     + getTitle();
4439             Desktop.addInternalFrame(naf, newtitle, DEFAULT_WIDTH,
4440                     DEFAULT_HEIGHT);
4441           }
4442           else
4443           {
4444             System.err.println("No Sequences generated for xRef type "
4445                     + fsrc);
4446           }
4447         } catch (Exception e)
4448         {
4449           jalview.bin.Cache.log.error(
4450                   "Exception when finding crossreferences", e);
4451         } catch (OutOfMemoryError e)
4452         {
4453           new OOMWarning("whilst fetching crossreferences", e);
4454         } catch (Error e)
4455         {
4456           jalview.bin.Cache.log.error("Error when finding crossreferences",
4457                   e);
4458         }
4459         ths.setProgressBar("Finished searching for sequences from " + fsrc,
4460                 sttime);
4461       }
4462
4463     };
4464     Thread frunner = new Thread(foo);
4465     frunner.start();
4466   }
4467
4468   public boolean canShowTranslationProducts(SequenceI[] selection,
4469           AlignmentI alignment)
4470   {
4471     // old way
4472     try
4473     {
4474       return (jalview.analysis.Dna.canTranslate(selection,
4475               viewport.getViewAsVisibleContigs(true)));
4476     } catch (Exception e)
4477     {
4478       jalview.bin.Cache.log
4479               .warn("canTranslate threw an exception - please report to help@jalview.org",
4480                       e);
4481       return false;
4482     }
4483   }
4484
4485   @Override
4486   public void showProducts_actionPerformed(ActionEvent e)
4487   {
4488     // /////////////////////////////
4489     // Collect Data to be translated/transferred
4490
4491     SequenceI[] selection = viewport.getSequenceSelection();
4492     AlignmentI al = null;
4493     try
4494     {
4495       al = jalview.analysis.Dna.CdnaTranslate(selection, viewport
4496               .getViewAsVisibleContigs(true), viewport.getGapCharacter(),
4497               viewport.getAlignment().getDataset());
4498     } catch (Exception ex)
4499     {
4500       al = null;
4501       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4502     }
4503     if (al == null)
4504     {
4505       JOptionPane
4506               .showMessageDialog(
4507                       Desktop.desktop,
4508                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4509                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4510     }
4511     else
4512     {
4513       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4514       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4515               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4516     }
4517   }
4518
4519   @Override
4520   public void showTranslation_actionPerformed(ActionEvent e)
4521   {
4522     // /////////////////////////////
4523     // Collect Data to be translated/transferred
4524
4525     SequenceI[] selection = viewport.getSequenceSelection();
4526     String[] seqstring = viewport.getViewAsString(true);
4527     AlignmentI al = null;
4528     try
4529     {
4530       al = jalview.analysis.Dna.CdnaTranslate(selection, seqstring,
4531               viewport.getViewAsVisibleContigs(true), viewport
4532                       .getGapCharacter(), viewport.getAlignment()
4533                       .getAlignmentAnnotation(), viewport.getAlignment()
4534                       .getWidth(), viewport.getAlignment().getDataset());
4535     } catch (Exception ex)
4536     {
4537       al = null;
4538       jalview.bin.Cache.log.debug("Exception during translation.", ex);
4539     }
4540     if (al == null)
4541     {
4542       JOptionPane
4543               .showMessageDialog(
4544                       Desktop.desktop,
4545                       "Please select at least three bases in at least one sequence in order to perform a cDNA translation.",
4546                       "Translation Failed", JOptionPane.WARNING_MESSAGE);
4547     }
4548     else
4549     {
4550       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4551       Desktop.addInternalFrame(af, "Translation of " + this.getTitle(),
4552               DEFAULT_WIDTH, DEFAULT_HEIGHT);
4553     }
4554   }
4555
4556   /**
4557    * Try to load a features file onto the alignment.
4558    *
4559    * @param file
4560    *          contents or path to retrieve file
4561    * @param type
4562    *          access mode of file (see jalview.io.AlignFile)
4563    * @return true if features file was parsed corectly.
4564    */
4565   public boolean parseFeaturesFile(String file, String type)
4566   {
4567     boolean featuresFile = false;
4568     try
4569     {
4570       featuresFile = new FeaturesFile(file, type).parse(viewport
4571               .getAlignment().getDataset(), alignPanel.seqPanel.seqCanvas
4572               .getFeatureRenderer().featureColours, false,
4573               jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4574     } catch (Exception ex)
4575     {
4576       ex.printStackTrace();
4577     }
4578
4579     if (featuresFile)
4580     {
4581       viewport.showSequenceFeatures = true;
4582       showSeqFeatures.setSelected(true);
4583       if (alignPanel.seqPanel.seqCanvas.fr != null)
4584       {
4585         // update the min/max ranges where necessary
4586         alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
4587       }
4588       if (featureSettings != null)
4589       {
4590         featureSettings.setTableData();
4591       }
4592       alignPanel.paintAlignment(true);
4593     }
4594
4595     return featuresFile;
4596   }
4597
4598   @Override
4599   public void dragEnter(DropTargetDragEvent evt)
4600   {
4601   }
4602
4603   @Override
4604   public void dragExit(DropTargetEvent evt)
4605   {
4606   }
4607
4608   @Override
4609   public void dragOver(DropTargetDragEvent evt)
4610   {
4611   }
4612
4613   @Override
4614   public void dropActionChanged(DropTargetDragEvent evt)
4615   {
4616   }
4617
4618   @Override
4619   public void drop(DropTargetDropEvent evt)
4620   {
4621     Transferable t = evt.getTransferable();
4622     java.util.List files = null;
4623
4624     try
4625     {
4626       DataFlavor uriListFlavor = new DataFlavor(
4627               "text/uri-list;class=java.lang.String");
4628       if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
4629       {
4630         // Works on Windows and MacOSX
4631         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4632         files = (java.util.List) t
4633                 .getTransferData(DataFlavor.javaFileListFlavor);
4634       }
4635       else if (t.isDataFlavorSupported(uriListFlavor))
4636       {
4637         // This is used by Unix drag system
4638         evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4639         String data = (String) t.getTransferData(uriListFlavor);
4640         files = new java.util.ArrayList(1);
4641         for (java.util.StringTokenizer st = new java.util.StringTokenizer(
4642                 data, "\r\n"); st.hasMoreTokens();)
4643         {
4644           String s = st.nextToken();
4645           if (s.startsWith("#"))
4646           {
4647             // the line is a comment (as per the RFC 2483)
4648             continue;
4649           }
4650
4651           java.net.URI uri = new java.net.URI(s);
4652           // check to see if we can handle this kind of URI
4653           if (uri.getScheme().toLowerCase().startsWith("http"))
4654           {
4655             files.add(uri.toString());
4656           }
4657           else
4658           {
4659             // otherwise preserve old behaviour: catch all for file objects
4660             java.io.File file = new java.io.File(uri);
4661             files.add(file.toString());
4662           }
4663         }
4664       }
4665     } catch (Exception e)
4666     {
4667       e.printStackTrace();
4668     }
4669     if (files != null)
4670     {
4671       try
4672       {
4673         // check to see if any of these files have names matching sequences in
4674         // the alignment
4675         SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4676                 .getAlignment().getSequencesArray());
4677         /**
4678          * Object[] { String,SequenceI}
4679          */
4680         ArrayList<Object[]> filesmatched = new ArrayList<Object[]>();
4681         ArrayList<String> filesnotmatched = new ArrayList<String>();
4682         for (int i = 0; i < files.size(); i++)
4683         {
4684           String file = files.get(i).toString();
4685           String pdbfn = "";
4686           String protocol = FormatAdapter.checkProtocol(file);
4687           if (protocol == jalview.io.FormatAdapter.FILE)
4688           {
4689             File fl = new File(file);
4690             pdbfn = fl.getName();
4691           }
4692           else if (protocol == jalview.io.FormatAdapter.URL)
4693           {
4694             URL url = new URL(file);
4695             pdbfn = url.getFile();
4696           }
4697           if (pdbfn.length() > 0)
4698           {
4699             // attempt to find a match in the alignment
4700             SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4701             int l = 0, c = pdbfn.indexOf(".");
4702             while (mtch == null && c != -1)
4703             {
4704               do
4705               {
4706                 l = c;
4707               } while ((c = pdbfn.indexOf(".", l)) > l);
4708               if (l > -1)
4709               {
4710                 pdbfn = pdbfn.substring(0, l);
4711               }
4712               mtch = idm.findAllIdMatches(pdbfn);
4713             }
4714             if (mtch != null)
4715             {
4716               String type = null;
4717               try
4718               {
4719                 type = new IdentifyFile().Identify(file, protocol);
4720               } catch (Exception ex)
4721               {
4722                 type = null;
4723               }
4724               if (type != null)
4725               {
4726                 if (type.equalsIgnoreCase("PDB"))
4727                 {
4728                   filesmatched.add(new Object[]
4729                   { file, protocol, mtch });
4730                   continue;
4731                 }
4732               }
4733             }
4734             // File wasn't named like one of the sequences or wasn't a PDB file.
4735             filesnotmatched.add(file);
4736           }
4737         }
4738         int assocfiles = 0;
4739         if (filesmatched.size() > 0)
4740         {
4741           if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
4742                   || JOptionPane
4743                           .showConfirmDialog(
4744                                   this,
4745                                   "Do you want to automatically associate the "
4746                                           + filesmatched.size()
4747                                           + " PDB files with sequences in the alignment that have the same name ?",
4748                                   "Automatically Associate PDB files by name",
4749                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)
4750
4751           {
4752             for (Object[] fm : filesmatched)
4753             {
4754               // try and associate
4755               // TODO: may want to set a standard ID naming formalism for
4756               // associating PDB files which have no IDs.
4757               for (SequenceI toassoc : (SequenceI[]) fm[2])
4758               {
4759                 PDBEntry pe = new AssociatePdbFileWithSeq()
4760                         .associatePdbWithSeq((String) fm[0],
4761                                 (String) fm[1], toassoc, false);
4762                 if (pe != null)
4763                 {
4764                   System.err.println("Associated file : "
4765                           + ((String) fm[0]) + " with "
4766                           + toassoc.getDisplayId(true));
4767                   assocfiles++;
4768                 }
4769               }
4770               alignPanel.paintAlignment(true);
4771             }
4772           }
4773         }
4774         if (filesnotmatched.size() > 0)
4775         {
4776           if (assocfiles > 0
4777                   && (Cache.getDefault(
4778                           "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane
4779                           .showConfirmDialog(
4780                                   this,
4781                                   "<html>Do you want to <em>ignore</em> the "
4782                                           + filesnotmatched.size()
4783                                           + " files whose names did not match any sequence IDs ?</html>",
4784                                   "Ignore unmatched dropped files ?",
4785                                   JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION))
4786           {
4787             return;
4788           }
4789           for (String fn : filesnotmatched)
4790           {
4791             loadJalviewDataFile(fn, null, null, null);
4792           }
4793
4794         }
4795       } catch (Exception ex)
4796       {
4797         ex.printStackTrace();
4798       }
4799     }
4800   }
4801
4802   /**
4803    * Attempt to load a "dropped" file or URL string: First by testing whether
4804    * it's and Annotation file, then a JNet file, and finally a features file. If
4805    * all are false then the user may have dropped an alignment file onto this
4806    * AlignFrame.
4807    *
4808    * @param file
4809    *          either a filename or a URL string.
4810    */
4811   public void loadJalviewDataFile(String file, String protocol,
4812           String format, SequenceI assocSeq)
4813   {
4814     try
4815     {
4816       if (protocol == null)
4817       {
4818         protocol = jalview.io.FormatAdapter.checkProtocol(file);
4819       }
4820       // if the file isn't identified, or not positively identified as some
4821       // other filetype (PFAM is default unidentified alignment file type) then
4822       // try to parse as annotation.
4823       boolean isAnnotation = (format == null || format
4824               .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
4825               .readAnnotationFile(viewport.getAlignment(), file, protocol)
4826               : false;
4827
4828       if (!isAnnotation)
4829       {
4830         // first see if its a T-COFFEE score file
4831         TCoffeeScoreFile tcf = null;
4832         try
4833         {
4834           tcf = new TCoffeeScoreFile(file, protocol);
4835           if (tcf.isValid())
4836           {
4837             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4838             {
4839               tcoffeeColour.setEnabled(true);
4840               tcoffeeColour.setSelected(true);
4841               changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
4842               isAnnotation = true;
4843               statusBar
4844                       .setText("Successfully pasted T-Coffee scores to alignment.");
4845             }
4846             else
4847             {
4848               // some problem - if no warning its probable that the ID matching process didn't work
4849               JOptionPane.showMessageDialog(Desktop.desktop,
4850                       tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
4851                       "Problem reading T-COFFEE score file",
4852                       JOptionPane.WARNING_MESSAGE);
4853             }
4854           }
4855           else
4856           {
4857             tcf = null;
4858           }
4859         } catch (Exception x)
4860         {
4861           Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
4862           tcf = null;
4863         }
4864         if (tcf == null)
4865         {
4866           // try to see if its a JNet 'concise' style annotation file *before*
4867           // we
4868           // try to parse it as a features file
4869           if (format == null)
4870           {
4871             format = new IdentifyFile().Identify(file, protocol);
4872           }
4873           if (format.equalsIgnoreCase("JnetFile"))
4874           {
4875             jalview.io.JPredFile predictions = new jalview.io.JPredFile(
4876                     file, protocol);
4877             new JnetAnnotationMaker().add_annotation(predictions,
4878                     viewport.getAlignment(), 0, false);
4879             isAnnotation = true;
4880           }
4881           else
4882           {
4883             /*
4884              * if (format.equalsIgnoreCase("PDB")) {
4885              *
4886              * String pdbfn = ""; // try to match up filename with sequence id
4887              * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
4888              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
4889              * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
4890              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
4891              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
4892              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
4893              * // attempt to find a match in the alignment SequenceI mtch =
4894              * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
4895              * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
4896              * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
4897              * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
4898              * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
4899              * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
4900              * { System.err.println("Associated file : " + file + " with " +
4901              * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
4902              * TODO: maybe need to load as normal otherwise return; } }
4903              */
4904             // try to parse it as a features file
4905             boolean isGroupsFile = parseFeaturesFile(file, protocol);
4906             // if it wasn't a features file then we just treat it as a general
4907             // alignment file to load into the current view.
4908             if (!isGroupsFile)
4909             {
4910               new FileLoader().LoadFile(viewport, file, protocol, format);
4911             }
4912             else
4913             {
4914               alignPanel.paintAlignment(true);
4915             }
4916           }
4917         }
4918       }
4919       if (isAnnotation)
4920       {
4921
4922         alignPanel.adjustAnnotationHeight();
4923         viewport.updateSequenceIdColours();
4924         buildSortByAnnotationScoresMenu();
4925         alignPanel.paintAlignment(true);
4926       }
4927     } catch (Exception ex)
4928     {
4929       ex.printStackTrace();
4930     }
4931   }
4932
4933   @Override
4934   public void tabSelectionChanged(int index)
4935   {
4936     if (index > -1)
4937     {
4938       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
4939       viewport = alignPanel.av;
4940       setMenusFromViewport(viewport);
4941     }
4942   }
4943
4944   @Override
4945   public void tabbedPane_mousePressed(MouseEvent e)
4946   {
4947     if (SwingUtilities.isRightMouseButton(e))
4948     {
4949       String reply = JOptionPane.showInternalInputDialog(this,
4950               "Enter View Name", "Edit View Name",
4951               JOptionPane.QUESTION_MESSAGE);
4952
4953       if (reply != null)
4954       {
4955         viewport.viewName = reply;
4956         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4957       }
4958     }
4959   }
4960
4961   public AlignViewport getCurrentView()
4962   {
4963     return viewport;
4964   }
4965
4966   /**
4967    * Open the dialog for regex description parsing.
4968    */
4969   @Override
4970   protected void extractScores_actionPerformed(ActionEvent e)
4971   {
4972     ParseProperties pp = new jalview.analysis.ParseProperties(
4973             viewport.getAlignment());
4974     // TODO: verify regex and introduce GUI dialog for version 2.5
4975     // if (pp.getScoresFromDescription("col", "score column ",
4976     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4977     // true)>0)
4978     if (pp.getScoresFromDescription("description column",
4979             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4980     {
4981       buildSortByAnnotationScoresMenu();
4982     }
4983   }
4984
4985   /*
4986    * (non-Javadoc)
4987    *
4988    * @see
4989    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4990    * )
4991    */
4992   @Override
4993   protected void showDbRefs_actionPerformed(ActionEvent e)
4994   {
4995     viewport.setShowDbRefs(showDbRefsMenuitem.isSelected());
4996   }
4997
4998   /*
4999    * (non-Javadoc)
5000    *
5001    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5002    * ActionEvent)
5003    */
5004   @Override
5005   protected void showNpFeats_actionPerformed(ActionEvent e)
5006   {
5007     viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected());
5008   }
5009
5010   /**
5011    * find the viewport amongst the tabs in this alignment frame and close that
5012    * tab
5013    *
5014    * @param av
5015    */
5016   public boolean closeView(AlignViewport av)
5017   {
5018     if (viewport == av)
5019     {
5020       this.closeMenuItem_actionPerformed(false);
5021       return true;
5022     }
5023     Component[] comp = tabbedPane.getComponents();
5024     for (int i = 0; comp != null && i < comp.length; i++)
5025     {
5026       if (comp[i] instanceof AlignmentPanel)
5027       {
5028         if (((AlignmentPanel) comp[i]).av == av)
5029         {
5030           // close the view.
5031           closeView((AlignmentPanel) comp[i]);
5032           return true;
5033         }
5034       }
5035     }
5036     return false;
5037   }
5038
5039   protected void build_fetchdbmenu(JMenu webService)
5040   {
5041     // Temporary hack - DBRef Fetcher always top level ws entry.
5042     // TODO We probably want to store a sequence database checklist in
5043     // preferences and have checkboxes.. rather than individual sources selected
5044     // here
5045     final JMenu rfetch = new JMenu("Fetch DB References");
5046     rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
5047     webService.add(rfetch);
5048
5049     JMenuItem fetchr = new JMenuItem("Standard Databases");
5050     fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
5051     fetchr.addActionListener(new ActionListener()
5052     {
5053
5054       @Override
5055       public void actionPerformed(ActionEvent e)
5056       {
5057         new Thread(new Runnable()
5058         {
5059
5060           @Override
5061           public void run()
5062           {
5063             new jalview.ws.DBRefFetcher(alignPanel.av
5064                     .getSequenceSelection(), alignPanel.alignFrame)
5065                     .fetchDBRefs(false);
5066           }
5067         }).start();
5068
5069       }
5070
5071     });
5072     rfetch.add(fetchr);
5073     final AlignFrame me = this;
5074     new Thread(new Runnable()
5075     {
5076       @Override
5077       public void run()
5078       {
5079         final jalview.ws.SequenceFetcher sf = SequenceFetcher
5080                 .getSequenceFetcherSingleton(me);
5081         javax.swing.SwingUtilities.invokeLater(new Runnable()
5082         {
5083           @Override
5084           public void run()
5085           {
5086             String[] dbclasses = sf.getOrderedSupportedSources();
5087             // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
5088             // jalview.util.QuickSort.sort(otherdb, otherdb);
5089             List<DbSourceProxy> otherdb;
5090             JMenu dfetch = new JMenu();
5091             JMenu ifetch = new JMenu();
5092             JMenuItem fetchr = null;
5093             int comp = 0, icomp = 0, mcomp = 15;
5094             String mname = null;
5095             int dbi = 0;
5096             for (String dbclass : dbclasses)
5097             {
5098               otherdb = sf.getSourceProxy(dbclass);
5099               // add a single entry for this class, or submenu allowing 'fetch
5100               // all' or pick one
5101               if (otherdb == null || otherdb.size() < 1)
5102               {
5103                 continue;
5104               }
5105               // List<DbSourceProxy> dbs=otherdb;
5106               // otherdb=new ArrayList<DbSourceProxy>();
5107               // for (DbSourceProxy db:dbs)
5108               // {
5109               // if (!db.isA(DBRefSource.ALIGNMENTDB)
5110               // }
5111               if (mname == null)
5112               {
5113                 mname = "From " + dbclass;
5114               }
5115               if (otherdb.size() == 1)
5116               {
5117                 final DbSourceProxy[] dassource = otherdb
5118                         .toArray(new DbSourceProxy[0]);
5119                 DbSourceProxy src = otherdb.get(0);
5120                 fetchr = new JMenuItem(src.getDbSource());
5121                 fetchr.addActionListener(new ActionListener()
5122                 {
5123
5124                   @Override
5125                   public void actionPerformed(ActionEvent e)
5126                   {
5127                     new Thread(new Runnable()
5128                     {
5129
5130                       @Override
5131                       public void run()
5132                       {
5133                         new jalview.ws.DBRefFetcher(alignPanel.av
5134                                 .getSequenceSelection(),
5135                                 alignPanel.alignFrame, dassource)
5136                                 .fetchDBRefs(false);
5137                       }
5138                     }).start();
5139                   }
5140
5141                 });
5142                 fetchr.setToolTipText("<html>"
5143                         + JvSwingUtils.wrapTooltip("Retrieve from "
5144                                 + src.getDbName()) + "<html>");
5145                 dfetch.add(fetchr);
5146                 comp++;
5147               }
5148               else
5149               {
5150                 final DbSourceProxy[] dassource = otherdb
5151                         .toArray(new DbSourceProxy[0]);
5152                 // fetch all entry
5153                 DbSourceProxy src = otherdb.get(0);
5154                 fetchr = new JMenuItem("Fetch All '" + src.getDbSource()
5155                         + "'");
5156                 fetchr.addActionListener(new ActionListener()
5157                 {
5158                   @Override
5159                   public void actionPerformed(ActionEvent e)
5160                   {
5161                     new Thread(new Runnable()
5162                     {
5163
5164                       @Override
5165                       public void run()
5166                       {
5167                         new jalview.ws.DBRefFetcher(alignPanel.av
5168                                 .getSequenceSelection(),
5169                                 alignPanel.alignFrame, dassource)
5170                                 .fetchDBRefs(false);
5171                       }
5172                     }).start();
5173                   }
5174                 });
5175
5176                 fetchr.setToolTipText("<html>"
5177                         + JvSwingUtils.wrapTooltip("Retrieve from all "
5178                                 + otherdb.size() + " sources in "
5179                                 + src.getDbSource() + "<br>First is :"
5180                                 + src.getDbName()) + "<html>");
5181                 dfetch.add(fetchr);
5182                 comp++;
5183                 // and then build the rest of the individual menus
5184                 ifetch = new JMenu("Sources from " + src.getDbSource());
5185                 icomp = 0;
5186                 String imname = null;
5187                 int i = 0;
5188                 for (DbSourceProxy sproxy : otherdb)
5189                 {
5190                   String dbname = sproxy.getDbName();
5191                   String sname = dbname.length() > 5 ? dbname.substring(0,
5192                           5) + "..." : dbname;
5193                   String msname = dbname.length() > 10 ? dbname.substring(
5194                           0, 10) + "..." : dbname;
5195                   if (imname == null)
5196                   {
5197                     imname = "from '" + sname + "'";
5198                   }
5199                   fetchr = new JMenuItem(msname);
5200                   final DbSourceProxy[] dassrc =
5201                   { sproxy };
5202                   fetchr.addActionListener(new ActionListener()
5203                   {
5204
5205                     @Override
5206                     public void actionPerformed(ActionEvent e)
5207                     {
5208                       new Thread(new Runnable()
5209                       {
5210
5211                         @Override
5212                         public void run()
5213                         {
5214                           new jalview.ws.DBRefFetcher(alignPanel.av
5215                                   .getSequenceSelection(),
5216                                   alignPanel.alignFrame, dassrc)
5217                                   .fetchDBRefs(false);
5218                         }
5219                       }).start();
5220                     }
5221
5222                   });
5223                   fetchr.setToolTipText("<html>"
5224                           + JvSwingUtils.wrapTooltip("Retrieve from "
5225                                   + dbname) + "</html>");
5226                   ifetch.add(fetchr);
5227                   ++i;
5228                   if (++icomp >= mcomp || i == (otherdb.size()))
5229                   {
5230                     ifetch.setText(imname + " to '" + sname + "'");
5231                     dfetch.add(ifetch);
5232                     ifetch = new JMenu();
5233                     imname = null;
5234                     icomp = 0;
5235                     comp++;
5236                   }
5237                 }
5238               }
5239               ++dbi;
5240               if (comp >= mcomp || dbi >= (dbclasses.length))
5241               {
5242                 dfetch.setText(mname + " to '" + dbclass + "'");
5243                 rfetch.add(dfetch);
5244                 dfetch = new JMenu();
5245                 mname = null;
5246                 comp = 0;
5247               }
5248             }
5249           }
5250         });
5251       }
5252     }).start();
5253
5254   }
5255
5256   /**
5257    * Left justify the whole alignment.
5258    */
5259   @Override
5260   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5261   {
5262     AlignmentI al = viewport.getAlignment();
5263     al.justify(false);
5264     viewport.firePropertyChange("alignment", null, al);
5265   }
5266
5267   /**
5268    * Right justify the whole alignment.
5269    */
5270   @Override
5271   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5272   {
5273     AlignmentI al = viewport.getAlignment();
5274     al.justify(true);
5275     viewport.firePropertyChange("alignment", null, al);
5276   }
5277
5278   public void setShowSeqFeatures(boolean b)
5279   {
5280     showSeqFeatures.setSelected(true);
5281     viewport.setShowSequenceFeatures(true);
5282   }
5283
5284   /*
5285    * (non-Javadoc)
5286    *
5287    * @see
5288    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5289    * awt.event.ActionEvent)
5290    */
5291   @Override
5292   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5293   {
5294     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5295     alignPanel.paintAlignment(true);
5296   }
5297
5298   /*
5299    * (non-Javadoc)
5300    *
5301    * @see
5302    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5303    * .ActionEvent)
5304    */
5305   @Override
5306   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5307   {
5308     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5309     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310
5311   }
5312
5313   /*
5314    * (non-Javadoc)
5315    *
5316    * @see
5317    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5318    * .event.ActionEvent)
5319    */
5320   @Override
5321   protected void showGroupConservation_actionPerformed(ActionEvent e)
5322   {
5323     viewport.setShowGroupConservation(showGroupConservation.getState());
5324     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5325   }
5326
5327   /*
5328    * (non-Javadoc)
5329    *
5330    * @see
5331    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5332    * .event.ActionEvent)
5333    */
5334   @Override
5335   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5336   {
5337     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5338     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339   }
5340
5341   /*
5342    * (non-Javadoc)
5343    *
5344    * @see
5345    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5346    * .event.ActionEvent)
5347    */
5348   @Override
5349   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5350   {
5351     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5352     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353   }
5354
5355   @Override
5356   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5357   {
5358     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5359     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5360   }
5361
5362   @Override
5363   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5364   {
5365     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5366   }
5367
5368   /*
5369    * (non-Javadoc)
5370    *
5371    * @see
5372    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5373    * .event.ActionEvent)
5374    */
5375   @Override
5376   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5377   {
5378     if (viewport.getSelectionGroup() != null)
5379     {
5380       SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
5381               viewport.getSequenceSelection(),
5382               viewport.getAlignmentView(true).getSequenceStrings(
5383                       viewport.getGapCharacter()), viewport.getAlignment()
5384                       .getGroups());
5385       viewport.getAlignment().deleteAllGroups();
5386       viewport.sequenceColours = null;
5387       viewport.setSelectionGroup(null);
5388       // set view properties for each group
5389       for (int g = 0; g < gps.length; g++)
5390       {
5391         gps[g].setShowNonconserved(viewport.getShowUnconserved());
5392         gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
5393         viewport.getAlignment().addGroup(gps[g]);
5394         Color col = new Color((int) (Math.random() * 255),
5395                 (int) (Math.random() * 255), (int) (Math.random() * 255));
5396         col = col.brighter();
5397         for (SequenceI s:gps[g].getSequences())
5398           viewport.setSequenceColour(
5399                 s, col)
5400           ;
5401       }
5402       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5403       alignPanel.updateAnnotation();
5404       alignPanel.paintAlignment(true);
5405     }
5406   }
5407
5408   /**
5409    * make the given alignmentPanel the currently selected tab
5410    *
5411    * @param alignmentPanel
5412    */
5413   public void setDisplayedView(AlignmentPanel alignmentPanel)
5414   {
5415     if (!viewport.getSequenceSetId().equals(
5416             alignmentPanel.av.getSequenceSetId()))
5417     {
5418       throw new Error(
5419               "Implementation error: cannot show a view from another alignment in an AlignFrame.");
5420     }
5421     if (tabbedPane != null
5422             & alignPanels.indexOf(alignmentPanel) != tabbedPane
5423                     .getSelectedIndex())
5424     {
5425       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5426     }
5427   }
5428 }
5429
5430 class PrintThread extends Thread
5431 {
5432   AlignmentPanel ap;
5433
5434   public PrintThread(AlignmentPanel ap)
5435   {
5436     this.ap = ap;
5437   }
5438
5439   static PageFormat pf;
5440
5441   @Override
5442   public void run()
5443   {
5444     PrinterJob printJob = PrinterJob.getPrinterJob();
5445
5446     if (pf != null)
5447     {
5448       printJob.setPrintable(ap, pf);
5449     }
5450     else
5451     {
5452       printJob.setPrintable(ap);
5453     }
5454
5455     if (printJob.printDialog())
5456     {
5457       try
5458       {
5459         printJob.print();
5460       } catch (Exception PrintException)
5461       {
5462         PrintException.printStackTrace();
5463       }
5464     }
5465   }
5466 }